ncbi-tools6 →
6.1.20120620-12 →
armhf → 2016-08-28 16:43:24
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-03
+==============================================================================+
| ncbi-tools6 6.1.20120620-12 (armhf) 28 Aug 2016 14:02 |
+==============================================================================+
Package: ncbi-tools6
Version: 6.1.20120620-12
Source Version: 6.1.20120620-12
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/ncbi-tools6-tIsQNi/ncbi-tools6-6.1.20120620' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ncbi-tools6-tIsQNi' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-a564a353-61b7-4410-9783-75d6a2f1eaed' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9252 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.2 MB]
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| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
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Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'ncbi-tools6' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/ncbi-tools6.git
Please use:
git clone git://anonscm.debian.org/debian-med/ncbi-tools6.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 69.8 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main ncbi-tools6 6.1.20120620-12 (dsc) [2742 B]
Get:2 http://172.17.0.1/private stretch-staging/main ncbi-tools6 6.1.20120620-12 (tar) [68.4 MB]
Get:3 http://172.17.0.1/private stretch-staging/main ncbi-tools6 6.1.20120620-12 (diff) [1417 kB]
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Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-EuU6Gg/apt_archive/sbuild-build-depends-core-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
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Get:5 file:/<<BUILDDIR>>/resolver-EuU6Gg/apt_archive ./ Packages [525 B]
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+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
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Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 24 not upgraded.
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debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 13920 files and directories currently installed.)
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Merged Build-Depends: debhelper (>= 9), csh | c-shell, libglu1-mesa-dev | libglu-dev, libmotif-dev, libpcre3-dev, libpng-dev, libxmu-dev
Filtered Build-Depends: debhelper (>= 9), csh, libglu1-mesa-dev, libmotif-dev, libpcre3-dev, libpng-dev, libxmu-dev
dpkg-deb: building package 'sbuild-build-depends-ncbi-tools6-dummy' in '/<<BUILDDIR>>/resolver-sO4ayS/apt_archive/sbuild-build-depends-ncbi-tools6-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-sO4ayS/apt_archive ./ InRelease
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Get:3 file:/<<BUILDDIR>>/resolver-sO4ayS/apt_archive ./ Release.gpg [299 B]
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Get:5 file:/<<BUILDDIR>>/resolver-sO4ayS/apt_archive ./ Packages [564 B]
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Reading package lists...
+------------------------------------------------------------------------------+
| Install ncbi-tools6 build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils csh debhelper
dh-autoreconf dh-strip-nondeterminism file fontconfig-config
fonts-dejavu-core gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libbsd0 libcroco3 libdrm-amdgpu1 libdrm-dev
libdrm-exynos1 libdrm-freedreno1 libdrm-nouveau2 libdrm-omap1 libdrm-radeon1
libdrm-tegra0 libexpat1 libexpat1-dev libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev
libfreetype6 libfreetype6-dev libgl1-mesa-dev libgl1-mesa-glx libglapi-mesa
libglib2.0-0 libglu1-mesa libglu1-mesa-dev libice-dev libice6 libicu57
libjpeg62-turbo libmagic-mgc libmagic1 libmotif-common libmotif-dev libmrm4
libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpng-dev
libpng16-16 libpthread-stubs0-dev libsigsegv2 libsm-dev libsm6
libtimedate-perl libtool libuil4 libunistring0 libx11-6 libx11-data
libx11-dev libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0
libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev
libxcb-present-dev libxcb-present0 libxcb-randr0 libxcb-randr0-dev
libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev
libxcb-sync-dev libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1
libxcb1-dev libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev
libxext6 libxfixes-dev libxfixes3 libxft-dev libxft2 libxm4 libxml2
libxmu-dev libxmu-headers libxmu6 libxrender-dev libxrender1
libxshmfence-dev libxshmfence1 libxt-dev libxt6 libxxf86vm-dev libxxf86vm1
m4 man-db mesa-common-dev pkg-config po-debconf ucf uil x11-common
x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev
x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev
x11proto-xext-dev x11proto-xf86vidmode-dev xorg-sgml-doctools xtrans-dev
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libice-doc libsm-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
libxcb-doc libxext-doc libxt-doc less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libgl1-mesa-dri libglib2.0-data shared-mime-info
xdg-user-dirs libpng-tools libltdl-dev libx11-doc xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils csh debhelper
dh-autoreconf dh-strip-nondeterminism file fontconfig-config
fonts-dejavu-core gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libbsd0 libcroco3 libdrm-amdgpu1 libdrm-dev
libdrm-exynos1 libdrm-freedreno1 libdrm-nouveau2 libdrm-omap1 libdrm-radeon1
libdrm-tegra0 libexpat1 libexpat1-dev libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev
libfreetype6 libfreetype6-dev libgl1-mesa-dev libgl1-mesa-glx libglapi-mesa
libglib2.0-0 libglu1-mesa libglu1-mesa-dev libice-dev libice6 libicu57
libjpeg62-turbo libmagic-mgc libmagic1 libmotif-common libmotif-dev libmrm4
libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpng-dev
libpng16-16 libpthread-stubs0-dev libsigsegv2 libsm-dev libsm6
libtimedate-perl libtool libuil4 libunistring0 libx11-6 libx11-data
libx11-dev libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0
libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev
libxcb-present-dev libxcb-present0 libxcb-randr0 libxcb-randr0-dev
libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev
libxcb-sync-dev libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1
libxcb1-dev libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev
libxext6 libxfixes-dev libxfixes3 libxft-dev libxft2 libxm4 libxml2
libxmu-dev libxmu-headers libxmu6 libxrender-dev libxrender1
libxshmfence-dev libxshmfence1 libxt-dev libxt6 libxxf86vm-dev libxxf86vm1
m4 man-db mesa-common-dev pkg-config po-debconf
sbuild-build-depends-ncbi-tools6-dummy ucf uil x11-common x11proto-core-dev
x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev
x11proto-input-dev x11proto-kb-dev x11proto-render-dev x11proto-xext-dev
x11proto-xf86vidmode-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
0 upgraded, 137 newly installed, 0 to remove and 24 not upgraded.
Need to get 40.4 MB/40.5 MB of archives.
After this operation, 120 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-sO4ayS/apt_archive ./ sbuild-build-depends-ncbi-tools6-dummy 0.invalid.0 [802 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+16 [251 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmotif-common all 2.3.4-10 [28.1 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1.1 [41.3 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.24-2 [262 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.5 [271 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.5 [313 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.0-1 [109 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libxft2 armhf 2.3.2-1 [48.3 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libxm4 armhf 2.3.4-10 [813 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libmrm4 armhf 2.3.4-10 [69.5 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libpcrecpp0v5 armhf 2:8.39-1 [149 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libuil4 armhf 2.3.4-10 [125 kB]
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Get:34 http://172.17.0.1/private stretch-staging/main armhf libxxf86vm1 armhf 1:1.1.4-1 [20.2 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-2 [7404 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-1+b1 [803 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf csh armhf 20110502-2.1 [223 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-2 [2546 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.022-1 [13.1 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.022-1 [7902 B]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160814 [800 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libdrm-amdgpu1 armhf 2.4.70-1 [23.9 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libdrm-radeon1 armhf 2.4.70-1 [27.4 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libdrm-nouveau2 armhf 2.4.70-1 [23.3 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libdrm-omap1 armhf 2.4.70-1 [14.9 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libdrm-freedreno1 armhf 2.4.70-1 [23.2 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libdrm-exynos1 armhf 2.4.70-1 [18.0 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libdrm-tegra0 armhf 2.4.70-1 [14.3 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libdrm-dev armhf 2.4.70-1 [185 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libexpat1-dev armhf 2.2.0-1 [117 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libpng-dev armhf 1.6.24-2 [229 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libfreetype6-dev armhf 2.6.3-3+b1 [5757 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1-dev armhf 2.11.0-6.5 [877 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf x11proto-core-dev all 7.0.29-1 [728 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libxau-dev armhf 1:1.0.8-1 [23.0 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libxdmcp-dev armhf 1:1.1.2-1.1 [40.8 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf x11proto-input-dev all 2.3.2-1 [158 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf x11proto-kb-dev all 1.0.7-1 [233 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libxcb1-dev armhf 1.11.1-1.1 [76.2 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf libx11-dev armhf 2:1.6.3-1 [749 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf mesa-common-dev armhf 11.2.2-1 [491 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libglapi-mesa armhf 11.2.2-1 [71.5 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf libxcb-dri2-0 armhf 1.11.1-1.1 [12.7 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf libxcb-dri3-0 armhf 1.11.1-1.1 [11.1 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf libxcb-glx0 armhf 1.11.1-1.1 [25.5 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf libxcb-present0 armhf 1.11.1-1.1 [11.2 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf libxcb-randr0 armhf 1.11.1-1.1 [19.9 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0 armhf 1.11.1-1.1 [17.1 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf libxcb-shape0 armhf 1.11.1-1.1 [11.7 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf libxcb-sync1 armhf 1.11.1-1.1 [14.0 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf libxcb-xfixes0 armhf 1.11.1-1.1 [14.7 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf libxfixes3 armhf 1:5.0.2-1 [20.1 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf libxdamage1 armhf 1:1.1.4-2+b1 [14.1 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf libxshmfence1 armhf 1.2-1 [7642 B]
Get:98 http://172.17.0.1/private stretch-staging/main armhf libgl1-mesa-glx armhf 11.2.2-1 [149 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf libx11-xcb-dev armhf 2:1.6.3-1 [178 kB]
Get:100 http://172.17.0.1/private stretch-staging/main armhf libxcb-dri3-dev armhf 1.11.1-1.1 [11.7 kB]
Get:101 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0-dev armhf 1.11.1-1.1 [21.0 kB]
Get:102 http://172.17.0.1/private stretch-staging/main armhf libxcb-randr0-dev armhf 1.11.1-1.1 [23.7 kB]
Get:103 http://172.17.0.1/private stretch-staging/main armhf libxcb-shape0-dev armhf 1.11.1-1.1 [12.9 kB]
Get:104 http://172.17.0.1/private stretch-staging/main armhf libxcb-xfixes0-dev armhf 1.11.1-1.1 [17.1 kB]
Get:105 http://172.17.0.1/private stretch-staging/main armhf libxcb-sync-dev armhf 1.11.1-1.1 [15.9 kB]
Get:106 http://172.17.0.1/private stretch-staging/main armhf libxcb-present-dev armhf 1.11.1-1.1 [12.7 kB]
Get:107 http://172.17.0.1/private stretch-staging/main armhf libxshmfence-dev armhf 1.2-1 [7152 B]
Get:108 http://172.17.0.1/private stretch-staging/main armhf libxcb-dri2-0-dev armhf 1.11.1-1.1 [14.2 kB]
Get:109 http://172.17.0.1/private stretch-staging/main armhf libxcb-glx0-dev armhf 1.11.1-1.1 [31.4 kB]
Get:110 http://172.17.0.1/private stretch-staging/main armhf x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:111 http://172.17.0.1/private stretch-staging/main armhf x11proto-fixes-dev all 1:5.0-2 [19.2 kB]
Get:112 http://172.17.0.1/private stretch-staging/main armhf libxfixes-dev armhf 1:5.0.2-1 [22.1 kB]
Get:113 http://172.17.0.1/private stretch-staging/main armhf x11proto-damage-dev all 1:1.2.1-2 [11.8 kB]
Get:114 http://172.17.0.1/private stretch-staging/main armhf libxdamage-dev armhf 1:1.1.4-2+b1 [13.9 kB]
Get:115 http://172.17.0.1/private stretch-staging/main armhf libxext-dev armhf 2:1.3.3-1 [102 kB]
Get:116 http://172.17.0.1/private stretch-staging/main armhf x11proto-xf86vidmode-dev all 2.3.1-2 [6114 B]
Get:117 http://172.17.0.1/private stretch-staging/main armhf libxxf86vm-dev armhf 1:1.1.4-1 [24.8 kB]
Get:118 http://172.17.0.1/private stretch-staging/main armhf x11proto-dri2-dev all 2.8-2 [18.2 kB]
Get:119 http://172.17.0.1/private stretch-staging/main armhf x11proto-gl-dev all 1.4.17-1 [28.0 kB]
Get:120 http://172.17.0.1/private stretch-staging/main armhf libgl1-mesa-dev armhf 11.2.2-1 [39.4 kB]
Get:121 http://172.17.0.1/private stretch-staging/main armhf libglu1-mesa armhf 9.0.0-2.1 [130 kB]
Get:122 http://172.17.0.1/private stretch-staging/main armhf libglu1-mesa-dev armhf 9.0.0-2.1 [169 kB]
Get:123 http://172.17.0.1/private stretch-staging/main armhf libice-dev armhf 2:1.0.9-1+b1 [59.0 kB]
Get:124 http://172.17.0.1/private stretch-staging/main armhf x11proto-render-dev all 2:0.11.1-2 [20.8 kB]
Get:125 http://172.17.0.1/private stretch-staging/main armhf libxrender-dev armhf 1:0.9.9-2 [36.5 kB]
Get:126 http://172.17.0.1/private stretch-staging/main armhf libxft-dev armhf 2.3.2-1 [59.1 kB]
Get:127 http://172.17.0.1/private stretch-staging/main armhf libsm-dev armhf 2:1.2.2-1+b1 [33.5 kB]
Get:128 http://172.17.0.1/private stretch-staging/main armhf libxt-dev armhf 1:1.1.5-1 [390 kB]
Get:129 http://172.17.0.1/private stretch-staging/main armhf uil armhf 2.3.4-10 [26.1 kB]
Get:130 http://172.17.0.1/private stretch-staging/main armhf libmotif-dev armhf 2.3.4-10 [2232 kB]
Get:131 http://172.17.0.1/private stretch-staging/main armhf libpcre16-3 armhf 2:8.39-1 [233 kB]
Get:132 http://172.17.0.1/private stretch-staging/main armhf libpcre32-3 armhf 2:8.39-1 [226 kB]
Get:133 http://172.17.0.1/private stretch-staging/main armhf libpcre3-dev armhf 2:8.39-1 [564 kB]
Get:134 http://172.17.0.1/private stretch-staging/main armhf libxmu-headers all 2:1.1.2-2 [51.9 kB]
Get:135 http://172.17.0.1/private stretch-staging/main armhf libxmu-dev armhf 2:1.1.2-2 [56.2 kB]
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Setting up sbuild-build-depends-ncbi-tools6-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.23-4) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.23-4 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3~pre3 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-15 binutils_2.26.1-1 bsdmainutils_9.0.10 bsdutils_1:2.28-6 build-essential_12.2 bzip2_1.0.6-8 console-setup_1.147 console-setup-linux_1.147 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 csh_20110502-2.1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_9.20160814 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.022-1 diffutils_1:3.3-3 dmsetup_2:1.02.130-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fontconfig-config_2.11.0-6.5 fonts-dejavu-core_2.37-1 fuse2fs_1.43.1-1 g++_4:6.1.1-1 g++-6_6.1.1-11+rpi1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.0-4 gcc-6_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 ifupdown_0.8.13 init_1.42 init-system-helpers_1.42 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 iproute2_4.6.0-1 kbd_2.0.3-2 keyboard-configuration_1.147 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg5.0_1.3~pre3 libarchive-zip-perl_1.59-1 libasan3_6.1.1-11+rpi1 libatm1_1:2.5.1-1.6 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.5-1 libaudit1_1:2.6.5-1 libblkid1_2.28-6 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-4 libc-dev-bin_2.23-4 libc6_2.23-4 libc6-dev_2.23-4 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.8-1 libdebconfclient0_0.215 libdevmapper1.02.1_2:1.02.130-1 libdpkg-perl_1.18.10 libdrm-amdgpu1_2.4.70-1 libdrm-dev_2.4.70-1 libdrm-exynos1_2.4.70-1 libdrm-freedreno1_2.4.70-1 libdrm-nouveau2_2.4.70-1 libdrm-omap1_2.4.70-1 libdrm-radeon1_2.4.70-1 libdrm-tegra0_2.4.70-1 libdrm2_2.4.70-1 libexpat1_2.2.0-1 libexpat1-dev_2.2.0-1 libfakeroot_1.21-1 libfdisk1_2.28-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.022-1 libfontconfig1_2.11.0-6.5 libfontconfig1-dev_2.11.0-6.5 libfreetype6_2.6.3-3+b1 libfreetype6-dev_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.2-2 libgdbm3_1.8.3-14 libgl1-mesa-dev_11.2.2-1 libgl1-mesa-glx_11.2.2-1 libglapi-mesa_11.2.2-1 libglib2.0-0_2.48.1-2 libglu1-mesa_9.0.0-2.1 libglu1-mesa-dev_9.0.0-2.1 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libice-dev_2:1.0.9-1+b1 libice6_2:1.0.9-1+b1 libicu57_57.1-2 libidn11_1.33-1 libisl15_0.17.1-1 libjpeg62-turbo_1:1.5.0-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 liblocale-gettext-perl_1.07-3 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmotif-common_2.3.4-10 libmotif-dev_2.3.4-10 libmount1_2.28-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libmrm4_2.3.4-10 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre16-3_2:8.39-1 libpcre3_2:8.39-1 libpcre3-dev_2:8.39-1 libpcre32-3_2:8.39-1 libpcrecpp0v5_2:8.39-1 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng-dev_1.6.24-2 libpng12-0_1.2.54-6 libpng16-16_1.6.24-2 libprocps6_2:3.3.12-2 libpthread-stubs0-dev_0.3-4 libreadline6_6.3-8+b3 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsm-dev_2:1.2.2-1+b1 libsm6_2:1.2.2-1+b1 libsmartcols1_2.28-6 libss2_1.43.1-1 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_230-7+b1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1 libtool_2.4.6-2 libubsan0_6.1.1-11+rpi1 libudev1_230-7+b1 libuil4_2.3.4-10 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-6 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libx11-dev_2:1.6.3-1 libx11-xcb-dev_2:1.6.3-1 libx11-xcb1_2:1.6.3-1 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxcb-dri2-0_1.11.1-1.1 libxcb-dri2-0-dev_1.11.1-1.1 libxcb-dri3-0_1.11.1-1.1 libxcb-dri3-dev_1.11.1-1.1 libxcb-glx0_1.11.1-1.1 libxcb-glx0-dev_1.11.1-1.1 libxcb-present-dev_1.11.1-1.1 libxcb-present0_1.11.1-1.1 libxcb-randr0_1.11.1-1.1 libxcb-randr0-dev_1.11.1-1.1 libxcb-render0_1.11.1-1.1 libxcb-render0-dev_1.11.1-1.1 libxcb-shape0_1.11.1-1.1 libxcb-shape0-dev_1.11.1-1.1 libxcb-sync-dev_1.11.1-1.1 libxcb-sync1_1.11.1-1.1 libxcb-xfixes0_1.11.1-1.1 libxcb-xfixes0-dev_1.11.1-1.1 libxcb1_1.11.1-1.1 libxcb1-dev_1.11.1-1.1 libxdamage-dev_1:1.1.4-2+b1 libxdamage1_1:1.1.4-2+b1 libxdmcp-dev_1:1.1.2-1.1 libxdmcp6_1:1.1.2-1.1 libxext-dev_2:1.3.3-1 libxext6_2:1.3.3-1 libxfixes-dev_1:5.0.2-1 libxfixes3_1:5.0.2-1 libxft-dev_2.3.2-1 libxft2_2.3.2-1 libxm4_2.3.4-10 libxml2_2.9.4+dfsg1-1+b1 libxmu-dev_2:1.1.2-2 libxmu-headers_2:1.1.2-2 libxmu6_2:1.1.2-2 libxrender-dev_1:0.9.9-2 libxrender1_1:0.9.9-2 libxshmfence-dev_1.2-1 libxshmfence1_1.2-1 libxt-dev_1:1.1.5-1 libxt6_1:1.1.5-1 libxxf86vm-dev_1:1.1.4-1 libxxf86vm1_1:1.1.4-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.07-1 mawk_1.3.3-17 mesa-common-dev_11.2.2-1 mount_2.28-6 multiarch-support_2.23-4 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 netbase_5.3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 pkg-config_0.29-4 po-debconf_1.0.19 procps_2:3.3.12-2 psmisc_22.21-2.1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ncbi-tools6-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_230-7+b1 systemd-sysv_230-7+b1 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016f-1 ucf_3.0036 udev_230-7+b1 uil_2.3.4-10 util-linux_2.28-6 x11-common_1:7.7+16 x11proto-core-dev_7.0.29-1 x11proto-damage-dev_1:1.2.1-2 x11proto-dri2-dev_2.8-2 x11proto-fixes-dev_1:5.0-2 x11proto-gl-dev_1.4.17-1 x11proto-input-dev_2.3.2-1 x11proto-kb-dev_1.0.7-1 x11proto-render-dev_2:0.11.1-2 x11proto-xext-dev_7.3.0-1 x11proto-xf86vidmode-dev_2.3.1-2 xkb-data_2.17-1 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Aug 22 12:12:05 2016 UTC using RSA key ID F09F4872
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./ncbi-tools6_6.1.20120620-12.dsc
dpkg-source: info: extracting ncbi-tools6 in ncbi-tools6-6.1.20120620
dpkg-source: info: unpacking ncbi-tools6_6.1.20120620.orig.tar.gz
dpkg-source: info: applying ncbi-tools6_6.1.20120620-12.diff.gz
dpkg-source: info: upstream files that have been modified:
ncbi-tools6-6.1.20120620/.gitignore
ncbi-tools6-6.1.20120620/api/alignmgr2.c
ncbi-tools6-6.1.20120620/api/aliread.c
ncbi-tools6-6.1.20120620/api/pgppop.c
ncbi-tools6-6.1.20120620/api/txalign.c
ncbi-tools6-6.1.20120620/corelib/ncbienv.c
ncbi-tools6-6.1.20120620/corelib/ncbimain.c
ncbi-tools6-6.1.20120620/corelib/ncbimisc.c
ncbi-tools6-6.1.20120620/corelib/ncbitime.c
ncbi-tools6-6.1.20120620/demo/dotmain.c
ncbi-tools6-6.1.20120620/demo/ingenmain.c
ncbi-tools6-6.1.20120620/demo/makeset.c
ncbi-tools6-6.1.20120620/demo/tbl2asn.c
ncbi-tools6-6.1.20120620/desktop/bspview.c
ncbi-tools6-6.1.20120620/desktop/ingenwin.c
ncbi-tools6-6.1.20120620/desktop/seqpanel.c
ncbi-tools6-6.1.20120620/doc/firewall.html
ncbi-tools6-6.1.20120620/doc/fwd_check.sh
ncbi-tools6-6.1.20120620/doc/man/Psequin.1
ncbi-tools6-6.1.20120620/doc/man/asn2all.1
ncbi-tools6-6.1.20120620/doc/man/asn2fsa.1
ncbi-tools6-6.1.20120620/doc/man/asn2gb.1
ncbi-tools6-6.1.20120620/doc/man/asndisc.1
ncbi-tools6-6.1.20120620/doc/man/asnmacro.1
ncbi-tools6-6.1.20120620/doc/man/asntool.1
ncbi-tools6-6.1.20120620/doc/man/asnval.1
ncbi-tools6-6.1.20120620/doc/man/blast.1
ncbi-tools6-6.1.20120620/doc/man/blast2.1
ncbi-tools6-6.1.20120620/doc/man/cleanasn.1
ncbi-tools6-6.1.20120620/doc/man/idfetch.1
ncbi-tools6-6.1.20120620/doc/man/nps2gps.1
ncbi-tools6-6.1.20120620/doc/man/sbtedit.1
ncbi-tools6-6.1.20120620/doc/man/tbl2asn.1
ncbi-tools6-6.1.20120620/make/makeall.unx
ncbi-tools6-6.1.20120620/make/makedemo.unx
ncbi-tools6-6.1.20120620/make/makenet.unx
ncbi-tools6-6.1.20120620/make/makeshlb.unx
ncbi-tools6-6.1.20120620/sequin/sbtedit.c
ncbi-tools6-6.1.20120620/sequin/sequin1.c
ncbi-tools6-6.1.20120620/sequin/sequin7.c
ncbi-tools6-6.1.20120620/sequin/streamer.c
ncbi-tools6-6.1.20120620/tools/readdb.c
ncbi-tools6-6.1.20120620/tools/spidey.c
ncbi-tools6-6.1.20120620/vibrant/netscape.c
ncbi-tools6-6.1.20120620/vibrant/shim3d.c
ncbi-tools6-6.1.20120620/vibrant/vibmain.c
ncbi-tools6-6.1.20120620/vibrant/vibwndws.c
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-a564a353-61b7-4410-9783-75d6a2f1eaed
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=vt102
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package ncbi-tools6
dpkg-buildpackage: info: source version 6.1.20120620-12
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build ncbi-tools6-6.1.20120620
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf build/* bin/* include/* lib/* shlib
mkdir -p build bin include lib
rm -f debian/*.menu debian/asntool.xpm debian/ncbilogo.xpm
chmod -x debian/makemenu debian/installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_auto_configure -a
debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd build && ln -s ../make/*.unx .
ln -s ../make/ln-if-absent build
mv build/makeall.unx build/makefile
/usr/bin/make -C build all LCL=lnx CC="gcc " LDFLAGS1="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"' -fPIE -pie -Wl,-z,relro -Wl,-z,now" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" NCBI_LINKINGLIBDIR="../shlib" \
CFLAGS1="-c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"' -fPIC -D_PNG" \
LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \
LIB30=libncbicn3d.a LIB45=libddvlib.a LIB400=libvibrantOGL.a LIB3000=libncbicn3dOGL.a
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
chmod -R ug+rw,o+r . ../include
./ln-if-absent ../corelib/tsprintf.h ../include
./ln-if-absent ../corelib/gifgen.h ../include
./ln-if-absent ../corelib/ncbi*.h ../include
./ln-if-absent ../corelib/tree*.h ../include
./ln-if-absent ../corelib/regex.h ../include
./ln-if-absent ../corelib/matrix.h ../include
./ln-if-absent ../corelib/binary.h ../include
./ln-if-absent ../corelib/morefile/*.h ../include
./ln-if-absent ../corelib/morefile/*.c .
./ln-if-absent ../link/macmet/MoreCarbonAccessors.h ../include
./ln-if-absent ../corelib/ncbilcl.lnx ../include/ncbilcl.h
./ln-if-absent ../corelib/*.c .
./ln-if-absent ../corelib/core*.h .
./ln-if-absent ../asnlib/*.h .
rm -f ../include/asn.h
mv asn.h ../include
./ln-if-absent ../asnlib/*.c .
./ln-if-absent ../connect/*.c .
./ln-if-absent ../connect/ncbi_ansi_ext.h .
./ln-if-absent ../connect/ncbi_assert.h .
./ln-if-absent ../connect/ncbi_priv.h .
./ln-if-absent ../connect/ncbi_comm.h .
./ln-if-absent ../connect/ncbi_config.h .
./ln-if-absent ../connect/ncbi_connssl.h .
./ln-if-absent ../connect/ncbi_lbsm.h .
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../connect/ncbi_lbsm_ipc.h .
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../connect/ncbi_host_infop.h .
./ln-if-absent ../connect/ncbi_server_infop.h .
./ln-if-absent ../connect/ncbi_servicep.h .
./ln-if-absent ../connect/ncbi_socketp.h .
./ln-if-absent ../connect/ncbi_dispd.h .
./ln-if-absent ../connect/ncbi_lbsmd.h .
./ln-if-absent ../connect/ncbi_local.h .
./ln-if-absent ../connect/ncbi_lb.h .
./ln-if-absent ../connect/ncbi_version.h .
./ln-if-absent ../connect/ncbi_base64.h .
./ln-if-absent ../connect/urlquery.h ../include
mkdir ../include/connect
chmod ug+rw,o+r ../include/connect
cp -fp ../connect/ncbi_*.h ../connect/connect_export.h ../include/connect
./ln-if-absent ../util/tables/*.c .
mkdir -p ../include/util/tables
cp -fp ../util/tables/*.h ../include/util/tables
./ln-if-absent ../util/creaders/*.c .
mkdir -p ../include/util/creaders
cp -fp ../util/creaders/*.h ../include/util/creaders
./ln-if-absent ../ctools/*.c .
./ln-if-absent ../ctools/*.h .
mkdir ../include/ctools
chmod ug+rw,o+r ../include/ctools
cp -fp ../ctools/*.h ../include/ctools
./ln-if-absent ../object/*.c .
./ln-if-absent ../object/*.h ../include
./ln-if-absent ../access/*.c .
./ln-if-absent ../access/*.h ../include
./ln-if-absent ../asnstat/*.h ../include
./ln-if-absent ../api/*.h ../include
./ln-if-absent ../api/*.c .
./ln-if-absent ../api/*.inc .
./ln-if-absent ../cdromlib/*.h ../include
./ln-if-absent ../cdromlib/*.c .
./ln-if-absent ../vibrant/*.h ../include
./ln-if-absent ../vibrant/*.c .
./ln-if-absent ../desktop/*.h ../include
./ln-if-absent ../desktop/*.c .
./ln-if-absent ../biostruc/*.h ../include
./ln-if-absent ../biostruc/*.c .
./ln-if-absent ../biostruc/cdd/*.h ../include
./ln-if-absent ../biostruc/cdd/*.c .
./ln-if-absent ../biostruc/cn3d/*.h ../include
./ln-if-absent ../biostruc/cn3d/*.c .
./ln-if-absent ../tools/*.h ../include
./ln-if-absent ../tools/*.c .
./ln-if-absent ../cn3d/*.h ../include
./ln-if-absent ../cn3d/*.c .
./ln-if-absent ../gif/*.c .
./ln-if-absent ../gif/*.h ../include
./ln-if-absent ../ddv/*.h ../include
./ln-if-absent ../ddv/*.c .
./ln-if-absent ../regexp/*.c .
./ln-if-absent ../regexp/*.h ../include
./ln-if-absent ../internal/compr/*.c .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/compr/*.h ../include
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libindx/*.c .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libindx/*.h ../include
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libpars/*.c .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libpars/*.h ../include
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/*.c .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/*.dat .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideochr*.h ../include
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideoorgs.h .
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.c .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.dat .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.h ../include
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ncbidraw.c ncbidrwg.c
./ln-if-absent ncbithr.c ncbithrs.c
./ln-if-absent ../network/nsclilib/*.h ../include
./ln-if-absent ../network/blast3/client/*.h ../include
./ln-if-absent ../network/id1arch/*.h ../include
./ln-if-absent ../network/id2arch/*.h ../include
mkdir -p ../include/algo/blast/core
./ln-if-absent ../algo/blast/core/*.c .
./ln-if-absent ../algo/blast/core/*.h .
./ln-if-absent ../algo/blast/core/*.inl .
cp -fp ../algo/blast/core/*.h ../include/algo/blast/core
mkdir -p ../include/algo/blast/composition_adjustment
./ln-if-absent ../algo/blast/composition_adjustment/*.c .
cp -fp ../algo/blast/composition_adjustment/*.h \
../include/algo/blast/composition_adjustment
mkdir -p ../include/algo/blast/api
./ln-if-absent ../algo/blast/api/*.c .
cp -fp ../algo/blast/api/*.h ../include/algo/blast/api
chmod -R ug+rw,o+r .
echo Waiting...go
Waiting...go
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbithr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ncbithr.c:289:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbithr.c: In function 's_TlsDestroyAll':
ncbithr.c:2529:11: warning: variable 'err_code' set but not used [-Wunused-but-set-variable]
int err_code = 0;
^~~~~~~~
cp -p ncbithr.o ../lib
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimain.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbimain.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbimain.c:82:1: warning: return type defaults to 'int' [-Wimplicit-int]
main(int argc, char *argv[])
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbibs.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbibs.c:55:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbibs.c: In function 'Nlm_BSSeek':
ncbibs.c:448:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sp == bsp->seekptr) /* already in right position */
^~
ncbibs.c:451:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
bsp->seekptr = sp;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF wwwutils.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbiwww.h:106,
from wwwutils.c:150:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbierr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from corepriv.h:85,
from ncbierr.c:235:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/string.h:635:0,
from ../include/ncbilcl.h:156,
from ../include/ncbi.h:57,
from corepriv.h:85,
from ncbierr.c:235:
In function 'strncat',
inlined from 'ErrMsgRoot_fopen.isra.1' at ncbierr.c:955:13:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbienv.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from corepriv.h:85,
from ncbienv.c:306:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbifile.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbifile.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbiprop.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from corepriv.h:85,
from ncbiprop.c:104:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimath.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbimath.h:69,
from ncbimath.c:90:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimem.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbimem.c:163:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimisc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbimisc.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbimisc.c: In function 'Nlm_MD5Final':
ncbimisc.c:2250:26: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
^
ncbimisc.c: In function 'XmlPathSuffixIs':
ncbimisc.c:2947:58: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (StringHasNoText (parentFilter) || parent != NULL && StringICmp (parent->name, parentFilter) == 0) {
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimsg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from corepriv.h:85,
from ncbimsg.c:167:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbistr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbistr.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbisgml.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbisgml.c:80:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/string.h:635:0,
from ../include/ncbilcl.h:156,
from ../include/ncbi.h:57,
from ncbisgml.c:80:
In function 'strncat',
inlined from 'Nlm_Sgml2Ascii' at ncbisgml.c:284:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'Nlm_Sgml2Ascii' at ncbisgml.c:265:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'Nlm_Sgml2AsciiLen' at ncbisgml.c:354:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'Nlm_Sgml2AsciiLen' at ncbisgml.c:340:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbitime.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbitime.c:77:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbilang.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbilang.c:57:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asnbufo.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asnbufo.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asndebin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asndebin.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asndebin.c: In function 'AsnBinReadVal':
asndebin.c:545:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
asndebin.c:548:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if (atp == NULL)
^~
asndebin.c:614:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* empty sequence written */
^~~~
asndebin.c:616:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
while (atp2 != NULL)
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asnenbin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnenbin.c:88:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asngen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asngen.c:80:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asngen.c: In function 'AsnFindNthPieceOfObject':
asngen.c:540:16: warning: variable 'aeop' set but not used [-Wunused-but-set-variable]
AsnExpOptPtr aeop;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asnio.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnio.c:150:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asnio.c: In function 'AsnIoWriteBlock':
asnio.c:765:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* use alternative write function */
^~~~
asnio.c:768:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if (retval != bytes_to_write)
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asnlex.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnlex.c:104:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asnlex.c: In function 'AsnTxtReadId':
asnlex.c:250:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((token == END_STRUCT) && ((isa == SEQ_TYPE) || (isa == SET_TYPE)))
^~
asnlex.c:253:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (token != IDENT)
^~
asnlex.c: In function 'AsnTxtReadVal':
asnlex.c:397:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* empty sequence written */
^~~~
asnlex.c:399:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
while (atp2 != NULL)
^~~~~
At top level:
asnlex.c:1322:13: warning: 'AsnLexWordUTF8' defined but not used [-Wunused-function]
static Int2 AsnLexWordUTF8 (AsnIoPtr aip)
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asnlext.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnlext.c:57:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asnout.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnout.c:79:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asnout.c: In function 'AsnOutput':
asnout.c:159:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
asnout.c:162:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
for (i = 0; i < 12; i++)
^~~
asnout.c:213:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! loader)
^~
asnout.c:216:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
attvp = p.root_tmpvalue.next;
^~~~~
asnout.c:270:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! loader)
^~
asnout.c:273:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
attp = p.root_tmptype.next;
^~~~
asnout.c:450:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! loader)
^~
asnout.c:453:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
i = 1;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asnprint.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnprint.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asnprint.c: In function 'GetXMLModuleName':
asnprint.c:102:2: warning: statement with no effect [-Wunused-value]
for (currmod; currmod != NULL; currmod = currmod->next)
^~~
asnprint.c: In function 'AsnPrintCloseStruct':
asnprint.c:1771:7: warning: variable 'isa' set but not used [-Wunused-but-set-variable]
Int2 isa;
^~~
asnprint.c: In function 'AsnPrintModuleXMLInc':
asnprint.c:2092:10: warning: variable 'ptr' set but not used [-Wunused-but-set-variable]
CharPtr ptr;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asntypes.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asntypes.c:111:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asntypes.c: In function 'AsnEnumTypeStr':
asntypes.c:1383:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((atp->type->isa != ENUM_TYPE) && (atp->type->isa != INTEGER_TYPE))
^~
asntypes.c:1386:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
avnp = (AsnValxNodePtr) atp->branch;
^~~~
asntypes.c: In function 'AsnTreeLoad':
asntypes.c:1274:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%d %d %d", &numval, &numtype, &nummod);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asntypes.c:1288:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%d %s %ld %lf %d", &isa, name, &intvalue, &realvalue, &next);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asntypes.c:1301:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%d %s %d %d %d %d %d %d %d %d %d %d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&isa, name, &tagclass, &tagnumber, bools, bools+1, bools+2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bools+3, bools+4, &defaultvalue, &type, &branch, &next);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asntypes.c:1333:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%s %s %d %d", name, fname, &type, &next);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asngenob.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asngenob.c:72:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gifgen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from gifgen.c:137:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF togif.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from togif.c:111:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
togif.c: In function 'gdImageCreateFromGif':
togif.c:961:12: warning: variable 'AspectRatio' set but not used [-Wunused-but-set-variable]
int AspectRatio;
^~~~~~~~~~~
togif.c:960:12: warning: variable 'Background' set but not used [-Wunused-but-set-variable]
int Background;
^~~~~~~~~~
togif.c:959:12: warning: variable 'ColorResolution' set but not used [-Wunused-but-set-variable]
int ColorResolution;
^~~~~~~~~~~~~~~
gcc -DNCBI_NOTHREADS_AVAIL -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbithrs.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ncbithrs.c:289:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbithrs.c: In function 's_TlsDestroyAll':
ncbithrs.c:2529:11: warning: unused variable 'err_code' [-Wunused-variable]
int err_code = 0;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -DHAVE_STRING_H -DREGEX_MALLOC regex.c
regex.c: In function 're_match_2':
regex.c:2368:11: warning: unused variable 'destination' [-Wunused-variable]
char *destination; \
^
regex.c:3768:19: note: in expansion of macro 'PUSH_FAILURE_POINT'
PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
^~~~~~~~~~~~~~~~~~
regex.c:2368:11: warning: unused variable 'destination' [-Wunused-variable]
char *destination; \
^
regex.c:3915:11: note: in expansion of macro 'PUSH_FAILURE_POINT'
PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
^~~~~~~~~~~~~~~~~~
regex.c:2368:11: warning: unused variable 'destination' [-Wunused-variable]
char *destination; \
^
regex.c:3968:11: note: in expansion of macro 'PUSH_FAILURE_POINT'
PUSH_FAILURE_POINT (p + mcnt, d, -2);
^~~~~~~~~~~~~~~~~~
regex.c:4071:25: warning: variable 'sdummy' set but not used [-Wunused-but-set-variable]
const char *sdummy;
^~~~~~
regex.c:4070:28: warning: variable 'pdummy' set but not used [-Wunused-but-set-variable]
unsigned char *pdummy;
^~~~~~
regex.c:2368:11: warning: unused variable 'destination' [-Wunused-variable]
char *destination; \
^
regex.c:4107:11: note: in expansion of macro 'PUSH_FAILURE_POINT'
PUSH_FAILURE_POINT (0, 0, -2);
^~~~~~~~~~~~~~~~~~
regex.c:2368:11: warning: unused variable 'destination' [-Wunused-variable]
char *destination; \
^
regex.c:4120:11: note: in expansion of macro 'PUSH_FAILURE_POINT'
PUSH_FAILURE_POINT (0, 0, -2);
^~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF tsprintf.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbiargs.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbiargs.c:82:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF tree.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/treemgr.h:67,
from tree.c:79:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF matrix.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/matrix.h:44,
from matrix.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_socket.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_socket.c:37:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbi_socket.c: In function 's_GetLocalPort':
ncbi_socket.c:386:50: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
if (getsockname(fd, (struct sockaddr*) &sin, &sinlen) == 0
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:127:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getsockname (int __fd, __SOCKADDR_ARG __addr,
^~~~~~~~~~~
ncbi_socket.c: In function 's_IsConnected':
ncbi_socket.c:2435:73: warning: pointer targets in passing argument 5 of 'getsockopt' differ in signedness [-Wpointer-sign]
if (getsockopt(sock->sock, SOL_SOCKET, SO_ERROR, (void*) error, &len)
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:219:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getsockopt (int __fd, int __level, int __optname,
^~~~~~~~~~
ncbi_socket.c: In function 'TRIGGER_Create':
ncbi_socket.c:4002:18: warning: unused variable 'x_id' [-Wunused-variable]
unsigned int x_id = ++s_ID_Counter;
^~~~
ncbi_socket.c: In function 's_CreateListening':
ncbi_socket.c:4454:50: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
x_error = getsockname(x_lsock, &addr.sa, &addrlen) != 0
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:127:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getsockname (int __fd, __SOCKADDR_ARG __addr,
^~~~~~~~~~~
ncbi_socket.c: In function 's_Accept':
ncbi_socket.c:4722:49: warning: pointer targets in passing argument 3 of 'accept' differ in signedness [-Wpointer-sign]
if ((x_sock = accept(lsock->sock, &addr.sa, &addrlen)) == SOCK_INVALID) {
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:243:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int accept (int __fd, __SOCKADDR_ARG __addr,
^~~~~~
ncbi_socket.c: In function 's_CreateOnTop':
ncbi_socket.c:5174:35: warning: pointer targets in passing argument 3 of 'getpeername' differ in signedness [-Wpointer-sign]
if (getpeername(fd, &peer.sa, &peerlen) != 0) {
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:141:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getpeername (int __fd, __SOCKADDR_ARG __addr,
^~~~~~~~~~~
ncbi_socket.c:5210:43: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
if (getsockname(fd, &peer.sa, &peerlen) != 0)
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:127:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getsockname (int __fd, __SOCKADDR_ARG __addr,
^~~~~~~~~~~
ncbi_socket.c: In function 'DSOCK_Bind':
ncbi_socket.c:6609:53: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
x_error = getsockname(sock->sock, &addr.sa, &addrlen) != 0
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:127:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getsockname (int __fd, __SOCKADDR_ARG __addr,
^~~~~~~~~~~
ncbi_socket.c: In function 'DSOCK_RecvMsg':
ncbi_socket.c:7002:52: warning: pointer targets in passing argument 6 of 'recvfrom' differ in signedness [-Wpointer-sign]
(struct sockaddr*) &sin, &sinlen);
^
In file included from /usr/include/arm-linux-gnueabihf/sys/socket.h:280:0,
from ncbi_socketp.h:53,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/bits/socket2.h:64:1: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
recvfrom (int __fd, void *__restrict __buf, size_t __n, int __flags,
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_buffer.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_types.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_core.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_core.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_core_c.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_core_c.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_util.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_util.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_priv.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_assert.h:35,
from ncbi_priv.h:55,
from ncbi_priv.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_ansi_ext.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_ansi_ext.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_connection.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_assert.h:35,
from ncbi_priv.h:55,
from ncbi_connection.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_assert.h:35,
from ncbi_priv.h:55,
from ncbi_connector.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_connutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_connutil.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_file_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_file_connector.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_heapmgr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_assert.h:35,
from ncbi_priv.h:55,
from ncbi_heapmgr.c:114:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_http_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_http_connector.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_memory_connector.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_lbsmd_stub.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_host_info.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_server_info.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_server_info.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_service.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_service.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_version.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_version.h:37,
from ncbi_version.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_service_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_service_connector.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_ftp_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_ftp_connector.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_dispd.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_dispd.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_lb.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_local.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_local.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_socket_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_socket_connector.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urlquery.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from urlquery.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF binary.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/binary.h:60,
from binary.c:59:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_sendmail.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_sendmail.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_base64.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn_connection.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF raw_scoremat.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF drwnflpt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from drwnflpt.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF drwnfspc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from drwnfspc.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF drwnmfls.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from drwnmfls.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rm -f libncbi.a
ar cru libncbi.a ncbimain.o ncbibs.o wwwutils.o ncbierr.o ncbienv.o ncbifile.o ncbiprop.o ncbimath.o ncbimem.o ncbimisc.o ncbimsg.o ncbistr.o ncbisgml.o ncbitime.o ncbilang.o asnbufo.o asndebin.o asnenbin.o asngen.o asnio.o asnlex.o asnlext.o asnout.o asnprint.o asntypes.o asngenob.o gifgen.o togif.o ncbithrs.o regex.o tsprintf.o ncbiargs.o tree.o matrix.o ncbi_socket.o ncbi_buffer.o ncbi_types.o ncbi_core.o ncbi_core_c.o ncbi_util.o ncbi_priv.o ncbi_ansi_ext.o ncbi_connection.o ncbi_connector.o ncbi_connutil.o ncbi_file_connector.o ncbi_heapmgr.o ncbi_http_connector.o ncbi_memory_connector.o ncbi_lbsmd_stub.o ncbi_host_info.o ncbi_server_info.o ncbi_service.o ncbi_version.o ncbi_service_connector.o ncbi_ftp_connector.o ncbi_dispd.o ncbi_lb.o ncbi_local.o ncbi_socket_connector.o urlquery.o binary.o ncbi_sendmail.o ncbi_base64.o asn_connection.o raw_scoremat.o drwnflpt.o drwnfspc.o drwnmfls.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbi.a ../lib
ranlib ../lib/libncbi.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objacces.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asnacces.h:9,
from objacces.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objacces.c: In function 'LinkSetAsnWrite':
objacces.c:137:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:140:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (lsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objacces.c: In function 'LinkSetAsnRead':
objacces.c:211:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:214:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
lsp = LinkSetNew();
^~~
objacces.c:215:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (lsp == NULL)
^~
objacces.c:218:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objacces.c:221:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:223:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* get the num */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objalign.h:103,
from objalign.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objalign.c: In function 'CommonSeqAlignLabelFunc':
objalign.c:135:27: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
CharPtr curr, typelabel, tmp;
^~~
objalign.c: In function 'SeqAlignAsnRead':
objalign.c:595:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:598:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sap = SeqAlignNew();
^~~
objalign.c:599:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sap == NULL)
^~
objalign.c:602:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'DenseDiagAsnWrite':
objalign.c:1018:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1021:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ddp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c: In function 'DenseDiagAsnRead':
objalign.c:1108:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1111:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ddp = DenseDiagNew();
^~~
objalign.c:1112:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ddp == NULL)
^~
objalign.c:1115:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'DenseSegAsnWrite':
objalign.c:1264:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1267:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (dsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c: In function 'DenseSegAsnRead':
objalign.c:1368:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1371:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
dsp = DenseSegNew();
^~~
objalign.c:1372:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dsp == NULL)
^~
objalign.c:1375:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'StdSegAsnWrite':
objalign.c:1553:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1556:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c:1573:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! SeqLocSetAsnWrite(ssp->loc, aip, STD_SEG_loc, STD_SEG_loc_E))
^~
objalign.c:1576:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ssp->scores != NULL)
^~
objalign.c: In function 'StdSegAsnRead':
objalign.c:1618:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1621:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ssp = StdSegNew();
^~~
objalign.c:1622:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ssp == NULL)
^~
objalign.c:1625:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'SeqAlignSetAsnWrite':
objalign.c:1696:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1700:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
oldsap = sap;
^~~~~~
objalign.c: In function 'PackSegAsnWrite':
objalign.c:1884:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1887:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (psp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnCloseStruct(aip, PACKED_SEG_starts, (Pointer)psp->starts))
^~
objalign.c:1919:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
av.ptrvalue = psp->present;
^~
objalign.c: In function 'PackSegAsnRead':
objalign.c:1989:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1992:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
psp = PackSegNew();
^~~
objalign.c:1993:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (psp == NULL)
^~
objalign.c:1996:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'SplicedSegAsnRead':
objalign.c:2169:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseSegAsnRead':
objalign.c:2409:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedExonAsnRead':
objalign.c:2600:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedSegModifierFree':
objalign.c:2858:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'ProductPosFree':
objalign.c:3031:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'SplicedExonChunkFree':
objalign.c:3204:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'SpliceSiteAsnRead':
objalign.c:3446:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'ProtPosAsnRead':
objalign.c:3600:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseAlignAsnRead':
objalign.c:3769:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseSegExtAsnRead':
objalign.c:3988:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedSegModifierAsnRead':
objalign.c:2938:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objalign.c: In function 'SplicedExonChunkAsnRead':
objalign.c:3305:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objall.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/objall.h:64,
from objall.c:63:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objbibli.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asnbibli.h:9,
from objbibli.c:110:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objbibli.c: In function 'AffilAsnRead':
objbibli.c:205:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:208:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
afp = AffilNew();
^~~
objbibli.c: In function 'AffilAsnWrite':
objbibli.c:293:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:296:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (afp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'AuthListFree':
objbibli.c:453:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (alp->affil != NULL)
^~
objbibli.c:455:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return (AuthListPtr)MemFree(alp);
^~~~~~
objbibli.c: In function 'AuthListAsnRead':
objbibli.c:484:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:487:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
alp = AuthListNew();
^~~
objbibli.c: In function 'AuthListAsnWrite':
objbibli.c:578:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:581:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (alp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:583:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)alp)) /* open AuthList SEQUENCE */
^~
objbibli.c:586:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
av.ptrvalue = alp->names;
^~
objbibli.c: In function 'AuthorFree':
objbibli.c:670:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ap->affil != NULL)
^~
objbibli.c:672:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return (AuthorPtr)MemFree(ap);
^~~~~~
objbibli.c: In function 'AuthorAsnRead':
objbibli.c:700:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:703:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ap = AuthorNew();
^~
objbibli.c: In function 'AuthorAsnWrite':
objbibli.c:772:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:775:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ap == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitArtAsnRead':
objbibli.c:916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:919:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cap = CitArtNew();
^~~
objbibli.c: In function 'CitArtAsnWrite':
objbibli.c:1018:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1021:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cap == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1023:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)cap)) /* open the SEQUENCE */
^~
objbibli.c:1026:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cap->title != NULL)
^~
objbibli.c: In function 'ImprintAsnRead':
objbibli.c:1141:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1144:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ip = ImprintNew();
^~
objbibli.c: In function 'ImprintAsnWrite':
objbibli.c:1240:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1243:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitRetractAsnRead':
objbibli.c:1378:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1381:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
crp = CitRetractNew();
^~~
objbibli.c: In function 'CitRetractAsnWrite':
objbibli.c:1432:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1435:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (crp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitJourAsnRead':
objbibli.c:1509:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1512:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cjp = CitJourNew();
^~~
objbibli.c: In function 'CitJourAsnWrite':
objbibli.c:1561:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1564:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cjp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1570:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! ImprintAsnWrite(cjp->imp, aip, CIT_JOUR_imp))
^~
objbibli.c:1572:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cjp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitBookAsnRead':
objbibli.c:1661:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1664:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cbp = CitBookNew();
^~~
objbibli.c: In function 'CitBookAsnWrite':
objbibli.c:1729:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1732:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1745:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! ImprintAsnWrite(cbp->imp, aip, CIT_BOOK_imp))
^~
objbibli.c:1747:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cbp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitProcAsnWrite':
objbibli.c:1864:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1867:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1884:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnCloseStruct(aip, CIT_PROC_meet, (Pointer)cpp->otherdata))
^~
objbibli.c:1886:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cpp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitLetAsnWrite':
objbibli.c:1978:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1981:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (clp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitPatAsnRead':
objbibli.c:2072:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2075:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cpp = CitPatNew();
^~~
objbibli.c: In function 'CitPatAsnWrite':
objbibli.c:2194:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2197:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'IdPatAsnRead':
objbibli.c:2325:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2328:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
idp = IdPatNew();
^~~
objbibli.c: In function 'IdPatAsnWrite':
objbibli.c:2391:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2394:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (idp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitGenAsnRead':
objbibli.c:2523:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2526:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cgp = CitGenNew();
^~~
objbibli.c: In function 'CitGenAsnWrite':
objbibli.c:2604:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2607:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cgp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'TitleAsnWrite':
objbibli.c:2800:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2803:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (tp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitSubFree':
objbibli.c:2882:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (csp == NULL)
^~
objbibli.c:2885:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
AuthListFree(csp->authors);
^~~~~~~~~~~~
objbibli.c: In function 'CitSubAsnRead':
objbibli.c:2916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2919:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
csp = CitSubNew();
^~~
objbibli.c:2931:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2934:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (atp == CIT_SUB_imp)
^~
objbibli.c: In function 'CitSubAsnWrite':
objbibli.c:3002:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3005:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (csp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:3009:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AuthListAsnWrite(csp->authors, aip, CIT_SUB_authors))
^~
objbibli.c:3012:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (csp->imp != NULL)
^~
objbibli.c: In function 'PatPrioritySetAsnRead':
objbibli.c:3665:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ppp == NULL)
^~
objbibli.c:3668:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (head == NULL)
^~
objbibli.c:3686:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3688:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ppp->date = DateAsnRead(aip, atp);
^~~
objbibli.c: In function 'PatPrioritySetAsnWrite':
objbibli.c:3724:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, set, (Pointer)ppp)) /* open the SEQUENCE OF */
^~
objbibli.c:3727:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
for (tmp = ppp; tmp != NULL; tmp = tmp->next)
^~~
objbibli.c: In function 'ArticleIdAsnRead':
objbibli.c:3818:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3821:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
aidp = ArticleIdNew();
^~~~
objbibli.c: In function 'ArticleIdAsnWrite':
objbibli.c:3894:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3897:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (aidp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'PubStatusDateAsnRead':
objbibli.c:4006:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:4009:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
psdp = PubStatusDateNew();
^~~~
objbibli.c: In function 'PubStatusDateAsnWrite':
objbibli.c:4058:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:4061:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (psdp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objfeat.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objfeat.h:48,
from objfeat.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objfeat.c: In function 'ModelEvidenceSupportAsnRead':
objfeat.c:1494:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ExperimentSupportAsnRead':
objfeat.c:1739:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ProgramIdAsnRead':
objfeat.c:1921:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'EvidenceBasisAsnRead':
objfeat.c:2088:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'InferenceSupportAsnRead':
objfeat.c:2252:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ModelEvidenceItemAsnRead':
objfeat.c:2465:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SeqFeatSupportAsnRead':
objfeat.c:2667:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAQualAsnRead':
objfeat.c:4192:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAQualSetAsnRead':
objfeat.c:4341:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAGenAsnRead':
objfeat.c:4469:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'GeneNomenclatureAsnRead':
objfeat.c:4649:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'OrgNameMatch':
objfeat.c:5890:28: warning: self-comparison always evaluates to false [-Wtautological-compare]
|| onp2->mgcode != onp2->mgcode
^~
objfeat.c: In function 'TaxElementAsnWrite':
objfeat.c:7320:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)tep))
^~
objfeat.c:7323:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
av.intvalue = (Int4)(tep->fixed_level);
^~
objfeat.c: In function 'PCRPrimerAsnRead':
objfeat.c:8191:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRPrimerSetAsnRead':
objfeat.c:8333:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRReactionAsnRead':
objfeat.c:8454:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRReactionSetAsnRead':
objfeat.c:8597:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneRefAsnRead':
objfeat.c:8724:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneSeqSetAsnRead':
objfeat.c:8914:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneSeqAsnRead':
objfeat.c:9044:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SomaticOriginAsnRead':
objfeat.c:9393:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SomaticOriginConditionAsnRead':
objfeat.c:9472:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'VariationRefAsnRead':
objfeat.c:9551:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ConsequenceAsnWrite':
objfeat.c:10112:12: warning: variable 'av' set but not used [-Wunused-but-set-variable]
DataVal av;
^~
objfeat.c: In function 'Consequence_loss_of_heterozygosityAsnRead':
objfeat.c:10572:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_frameshiftAsnRead':
objfeat.c:10650:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'VarRefDataFree':
objfeat.c:10750:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'VarRefDataSetAsnRead':
objfeat.c:10803:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_elementFree':
objfeat.c:10997:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'VariationInstAsnRead':
objfeat.c:11126:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: At top level:
objfeat.c:11275:1: warning: "/*" within comment [-Wcomment]
/**************************************************
objfeat.c: In function 'VariantPropertiesAsnRead':
objfeat.c:11304:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PhenotypeAsnRead':
objfeat.c:11625:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PopulationDataAsnRead':
objfeat.c:11821:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ExtLocAsnRead':
objfeat.c:12034:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Seq_seqFree':
objfeat.c:12199:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'DeltaItemAsnRead':
objfeat.c:12232:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_elementAsnRead':
objfeat.c:10539:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objfeat.c: In function 'CodeBreakAsnWrite':
objfeat.c:3647:11: warning: 'tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (! AsnWrite(aip, tmp, &av)) goto erret;
^~~~~~~~~~~~~~~~~~~~~~~
objfeat.c: In function 'VarRefDataAsnRead':
objfeat.c:10965:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objgen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asngen.h:9,
from objgen.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objgen.c: In function 'DateClean':
objgen.c:161:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dp == NULL)
^~
objgen.c:164:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
memset(dp, 0, sizeof(NCBI_Date));
^~~~~~
objgen.c: In function 'DateAsnWrite':
objgen.c:399:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:402:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (dp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'DateAsnRead':
objgen.c:492:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:495:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
dp = DateNew();
^~
objgen.c:496:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dp == NULL)
^~
objgen.c:499:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */
^~
objgen.c: In function 'DbtagFree':
objgen.c:750:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt == NULL)
^~
objgen.c:753:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
dbt->tag = ObjectIdFree(dbt->tag);
^~~
objgen.c: In function 'DbtagAsnRead':
objgen.c:782:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:785:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
dbt = DbtagNew();
^~~
objgen.c:786:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt == NULL)
^~
objgen.c:789:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */
^~
objgen.c:797:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt->tag == NULL)
^~
objgen.c:800:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
atp = AsnReadId(aip, amp, atp); if (atp == NULL) goto erret; /* END_STRUCT */
^~~
objgen.c: In function 'DbtagAsnWrite':
objgen.c:831:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:834:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (dbt == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'ObjectIdAsnRead':
objgen.c:976:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:979:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */
^~
objgen.c:985:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oid == NULL)
^~
objgen.c:987:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (atp == OBJECT_ID_id)
^~
objgen.c: In function 'ObjectIdAsnWrite':
objgen.c:1020:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1023:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (oid == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'NameStdFree':
objgen.c:1153:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (nsp == NULL)
^~
objgen.c:1156:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
for (i = 0; i < 7; i++)
^~~
objgen.c: In function 'NameStdAsnRead':
objgen.c:1187:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1190:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
nsp = NameStdNew();
^~~
objgen.c:1191:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (nsp == NULL)
^~
objgen.c:1194:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */
^~
objgen.c: In function 'NameStdAsnWrite':
objgen.c:1250:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1253:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (nsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'PersonIdFree':
objgen.c:1345:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pid == NULL)
^~
objgen.c:1348:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (pid->choice == 1) /* Dbtag */
^~
objgen.c: In function 'PersonIdAsnWrite':
objgen.c:1441:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1444:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (pid == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'IntFuzzAsnRead':
objgen.c:1657:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1660:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ifp = IntFuzzNew();
^~~
objgen.c:1661:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ifp == NULL)
^~
objgen.c:1664:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE (nothing) */
^~
objgen.c: In function 'UserFieldAsnRead':
objgen.c:1915:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1918:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ufp = UserFieldNew();
^~~
objgen.c: In function 'UserObjectAsnRead':
objgen.c:2395:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:2398:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
uop = UserObjectNew();
^~~
objgen.c:2399:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (uop == NULL)
^~
objgen.c:2402:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objloc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:85,
from objloc.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objloc.c: In function 'SeqIdAsnWrite':
objloc.c:313:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:316:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqIdAsnRead':
objloc.c:441:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:444:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
anp = ValNodeNew(NULL);
^~~
objloc.c: In function 'SeqIdDup':
objloc.c:585:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oldid == NULL)
^~
objloc.c:588:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
newid = ValNodeNew(NULL);
^~~~~
objloc.c: In function 'SeqIdSetAsnRead':
objloc.c:749:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, atp, &av) <= 0) /* end struct */
^~
objloc.c:751:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (first == NULL)
^~
objloc.c: In function 'SeqIdSetAsnWrite':
objloc.c:783:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp2 == NULL)
^~
objloc.c:786:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, settype); goto erret; }
^~
objloc.c: In function 'TextSeqIdAsnWrite':
objloc.c:861:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:864:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (tsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'TextSeqIdAsnRead':
objloc.c:929:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:932:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
tsip = TextSeqIdNew();
^~~~
objloc.c:933:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (tsip == NULL)
^~
objloc.c:936:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PatentSeqIdAsnWrite':
objloc.c:1013:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1016:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (psip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PatentSeqIdAsnRead':
objloc.c:1061:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1064:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
psip = PatentSeqIdNew();
^~~~
objloc.c:1065:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (psip == NULL)
^~
objloc.c:1068:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'GiimAsnWrite':
objloc.c:1144:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1147:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (gip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'GiimAsnRead':
objloc.c:1207:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (gip == NULL)
^~
objloc.c:1210:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PDBSeqIdAsnWrite':
objloc.c:1295:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1298:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (pdbsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PDBSeqIdAsnRead':
objloc.c:1356:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1359:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
pdbsip = PDBSeqIdNew();
^~~~~~
objloc.c:1360:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pdbsip == NULL)
^~
objloc.c:1363:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'SeqLocAsnWrite':
objloc.c:1508:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1511:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocAsnRead':
objloc.c:1602:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1605:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
anp = ValNodeNew(NULL);
^~~
objloc.c:1606:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (anp == NULL)
^~
objloc.c:1609:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the CHOICE value (nothing) */
^~
objloc.c: In function 'SeqLocMixAsnWrite':
objloc.c:1716:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1719:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocEquivAsnWrite':
objloc.c:1783:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1786:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocSetAsnWrite':
objloc.c:1851:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp2 == NULL)
^~
objloc.c:1854:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, set); goto erret; }
^~
objloc.c: In function 'SeqLocSetAsnRead':
objloc.c:1918:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, atp, &av) <= 0) /* read END_STRUCT */
^~
objloc.c:1920:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (first == NULL)
^~
objloc.c: In function 'SeqIntAsnWrite':
objloc.c:2000:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2003:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (sip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqIntAsnRead':
objloc.c:2071:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2074:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sip = SeqIntNew();
^~~
objloc.c:2075:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sip == NULL)
^~
objloc.c:2078:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PackSeqIntAsnWrite':
objloc.c:2155:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2157:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
oldsip = sip;
^~~~~~
objloc.c:2161:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)oldsip))
^~
objloc.c:2163:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
for ( ;sip != NULL; sip = sip->next)
^~~
objloc.c: In function 'SeqPntAsnWrite':
objloc.c:2285:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2288:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (spp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqPntAsnRead':
objloc.c:2348:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2351:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
spp = SeqPntNew();
^~~
objloc.c:2352:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (spp == NULL)
^~
objloc.c:2355:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PackSeqPntAsnWrite':
objloc.c:2453:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2456:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (pspp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PackSeqPntAsnRead':
objloc.c:2525:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2528:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
pspp = PackSeqPntNew();
^~~~
objloc.c:2529:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pspp == NULL)
^~
objloc.c:2532:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'SeqBondAsnWrite':
objloc.c:2696:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2699:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqBondAsnRead':
objloc.c:2748:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2751:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sbp = SeqBondNew();
^~~
objloc.c:2752:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sbp == NULL)
^~
objloc.c:2755:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objmedli.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmedli.h:80,
from objmedli.c:101:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmedli.c: In function 'MedlineMeshAsnRead':
objmedli.c:245:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objmedli.c:248:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
mmp = MedlineMeshNew();
^~~
objmedli.c: In function 'DocRefFree':
objmedli.c:1177:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (drp == NULL)
^~
objmedli.c:1180:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return (DocRefPtr)MemFree(drp);
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objpub.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objpub.h:70,
from objpub.c:122:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objpub.c: In function 'PubSetAsnRead':
objpub.c:824:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, settype, &av) <= 0) /* read START_STRUCT */
^~
objpub.c:827:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (settype == PUB_SET_pub)
^~
objpub.c:894:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, settype, &av) <= 0) /* read END_STRUCT for SET OF */
^~
objpub.c:896:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL)
^~
objpub.c: In function 'PubLabelUnique':
objpub.c:1353:17: warning: unused variable 'pmid' [-Wunused-variable]
Int4 muid = 0, pmid = 0;
^~~~
objpub.c:1353:7: warning: unused variable 'muid' [-Wunused-variable]
Int4 muid = 0, pmid = 0;
^~~~
objpub.c: In function 'PubSetAsnRead':
objpub.c:869:13: warning: 'func' may be used uninitialized in this function [-Wmaybe-uninitialized]
pnt = (* func)(aip, atp);
~~~~^~~~~~~~~~~~~~~~~~~~
objpub.c:880:25: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
cit->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objres.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from objres.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objscoremat.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objscoremat.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objscoremat.c: In function 'PssmAsnRead':
objscoremat.c:93:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmIntermediateDataAsnRead':
objscoremat.c:336:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmFinalDataAsnRead':
objscoremat.c:544:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmParametersAsnRead':
objscoremat.c:759:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmWithParametersAsnRead':
objscoremat.c:936:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'BlockPropertyAsnRead':
objscoremat.c:1102:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'CoreBlockAsnRead':
objscoremat.c:1275:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'LoopConstraintAsnRead':
objscoremat.c:1463:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'CoreDefAsnRead':
objscoremat.c:1626:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'FormatRpsDbParametersAsnRead':
objscoremat.c:1794:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from objseq.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objseq.c: In function 'LinkageEvidenceAsnRead':
objseq.c:1603:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objseq.c: In function 'SeqGapAsnRead':
objseq.c:1755:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objseq.c: In function 'SeqDescrAsnWriteExtra':
objseq.c:2023:48: warning: variable 'had_anp' set but not used [-Wunused-but-set-variable]
Boolean retval = FALSE, had_extra = FALSE, had_anp = FALSE;
^~~~~~~
objseq.c: In function 'AnnotIdAsnWrite':
objseq.c:4806:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:4808:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
break;
^~~~~
objseq.c:4814:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:4816:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
break;
^~~~~
objseq.c: In function 'AnnotDescAsnWrite':
objseq.c:5191:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:5193:12: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
break;
^~~~~
objseq.c: In function 'BioseqAsnRead':
objseq.c:977:21: warning: 'osp' may be used uninitialized in this function [-Wmaybe-uninitialized]
else if (osp->load_by_id) /* don't load it */
~~~^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objblock.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objblock.h:70,
from objblock.c:71:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objblock.c: In function 'EMBLBlockFree':
objblock.c:891:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ebp == NULL)
^~
objblock.c:894:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
DateFree(ebp->creation_date);
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objcode.c
objcode.c:45:51: warning: "/*" within comment [-Wcomment]
* environment variables to allow reading from data/*.val, replaced tabs in source code with spaces
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objcode.h:64,
from objcode.c:102:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objsset.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from objsset.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objsset.c: In function 'BioseqSetFree':
objsset.c:363:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (bsp == NULL)
^~
objsset.c:366:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (bsp->idx.parentptr == NULL || bsp->idx.parenttype == OBJ_SEQSUB) {
^~
objsset.c: In function 'SeqEntryFree':
objsset.c:876:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (sep->choice == 2)
^~
objsset.c:879:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return (SeqEntryPtr)MemFree(sep);
^~~~~~
objsset.c: In function 'SeqEntryFreeComponents':
objsset.c:896:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (sep->choice == 2)
^~
objsset.c:899:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return sep;
^~~~~~
objsset.c: In function 'SeqEntryAsnGet':
objsset.c:1071:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (retcode == 1) /* just after a Bioseq */
^~
objsset.c:1073:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
av.ptrvalue = (Pointer) osp;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objsub.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asnsubmt.h:9,
from objsub.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objsub.c: In function 'SubmitAsnLoad':
objsub.c:338:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (loaded)
^~
objsub.c:341:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! SeqSetAsnLoad ())
^~
objsub.c:344:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnLoad())
^~
objsub.c:347:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ObjMgrTypeLoad(OBJ_SEQSUB, "Seq-submit", seqsubtypename, "Sequence Data Submission",
^~~~~~~~~~~~~~
objsub.c: In function 'SeqSubmitAsnWrite':
objsub.c:452:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:455:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:457:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)ssp))
^~
objsub.c:460:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! SubmitBlockAsnWrite(ssp->sub, aip, SEQ_SUBMIT_sub)) goto erret;
^~
objsub.c: In function 'SeqSubmitAsnRead':
objsub.c:534:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:537:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ssp = SeqSubmitNew();
^~~
objsub.c:538:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ssp == NULL)
^~
objsub.c:541:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objsub.c: In function 'SubmitBlockAsnWrite':
objsub.c:677:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:680:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:682:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)sbp))
^~
objsub.c:685:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! ContactInfoAsnWrite(sbp->contact, aip, SUBMIT_BLOCK_contact))
^~
objsub.c: In function 'SubmitBlockAsnRead':
objsub.c:763:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:766:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
oldatp = atp;
^~~~~~
objsub.c:768:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sbp == NULL)
^~
objsub.c:771:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objsub.c: In function 'ContactInfoAsnWrite':
objsub.c:935:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:938:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:940:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)cip))
^~
objsub.c:943:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cip->name != NULL)
^~
objsub.c: In function 'ContactInfoAsnRead':
objsub.c:1059:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:1061:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
oldatp = atp;
^~~~~~
objsub.c:1064:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (cip == NULL)
^~
objsub.c:1067:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objprt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objprt.h:67,
from objprt.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objprt.c: In function 'PrintFormBooleanAsnRead':
objprt.c:877:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormBooleanFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormEnumAsnRead':
objprt.c:992:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormEnumFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormTextAsnRead':
objprt.c:1100:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormTextFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormAsnRead':
objprt.c:591:6: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp = PrintFormFree(vnp);
~~~~^~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormatAsnRead':
objprt.c:429:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormatFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintTemplateAsnRead':
objprt.c:247:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintTemplateFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormBlockAsnRead':
objprt.c:755:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormBlockFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'UserFormatAsnRead':
objprt.c:1209:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=UserFormatFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objfdef.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objfeat.h:48,
from ../include/objfdef.h:48,
from objfdef.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objalignloc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objalignloc.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objalignloc.c: In function 'AlignLocSetAsnRead':
objalignloc.c:69:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c: In function 'Loc_locFree':
objalignloc.c:196:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalignloc.c: In function 'AlignLocAsnRead':
objalignloc.c:233:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:232:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'Loc_locAsnRead':
objalignloc.c:313:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignIdFree':
objalignloc.c:525:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalignloc.c: In function 'AlignIdAsnRead':
objalignloc.c:557:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignBoxAsnRead':
objalignloc.c:746:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:745:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignRowsAsnRead':
objalignloc.c:925:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:924:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignColumnsAsnRead':
objalignloc.c:1086:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:1085:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignIdAsnRead':
objalignloc.c:613:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objtable.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objtable.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objtable.c: In function 'SeqTableColumnInfoAsnRead':
objtable.c:87:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c:86:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtable.c: In function 'SeqTableColumnAsnRead':
objtable.c:268:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c:267:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtable.c: In function 'SeqTableColumnAsnWrite':
objtable.c:364:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objtable.c: In function 'SeqTableAsnRead':
objtable.c:472:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'CommonStringTableAsnRead':
objtable.c:654:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'CommonStringTableAsnWrite':
objtable.c:729:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objtable.c: In function 'CommonBytesTableAsnRead':
objtable.c:815:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'CommonBytesTableAsnWrite':
objtable.c:890:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objtable.c: In function 'SeqTableSingleDataFree':
objtable.c:1220:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtable.c: In function 'SeqTableSingleDataAsnRead':
objtable.c:1264:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtable.c: In function 'SeqTableMultiDataAsnRead':
objtable.c:1106:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtable.c: In function 'SeqTableSingleDataAsnRead':
objtable.c:1349:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtable.c: In function 'SeqTableSparseIndexAsnRead':
objtable.c:1554:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objpubme.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objpubme.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objpubme.c: In function 'PubmedEntryAsnRead':
objpubme.c:89:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objpubme.c: In function 'PubmedUrlAsnRead':
objpubme.c:285:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objpubme.c:284:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objmdrs.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmdrs.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmdrs.c: In function 'MedlarsEntryAsnRead':
objmdrs.c:85:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmdrs.c: In function 'MedlarsRecordAsnRead':
objmdrs.c:256:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmdrs.c:255:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objproj.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objproj.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objproj.c: In function 'ProjectAsnRead':
objproj.c:116:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objproj.c:115:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objproj.c: In function 'ProjectDescrAsnRead':
objproj.c:718:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objproj.c: In function 'ProjdescFree':
objproj.c:852:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objproj.c: In function 'ProjdescAsnRead':
objproj.c:893:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/mmdbapi.h:92,
from ../include/mapproj.h:45,
from objproj.c:5:
objproj.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/mmdbapi.h:92,
from ../include/mapproj.h:45,
from objproj.c:5:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/mmdbapi.h:92,
from ../include/mapproj.h:45,
from objproj.c:5:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/mmdbapi.h:92,
from ../include/mapproj.h:45,
from objproj.c:5:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
objproj.c: In function 'ProjdescAsnRead':
objproj.c:953:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objproj.c: In function 'ProjectItemAsnRead':
objproj.c:536:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objgbseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objgbseq.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objgbseq.c: In function 'GBSetAsnRead':
objgbseq.c:68:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBSeqAsnRead':
objgbseq.c:229:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBReferenceAsnRead':
objgbseq.c:725:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBCommentAsnRead':
objgbseq.c:963:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBStrucCommentAsnRead':
objgbseq.c:1127:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBFeatureAsnRead':
objgbseq.c:1295:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBFeatureSetAsnRead':
objgbseq.c:1519:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBAltSeqDataAsnRead':
objgbseq.c:1683:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBXrefAsnRead':
objgbseq.c:1846:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBCommentParagraphAsnRead':
objgbseq.c:2012:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBCommentItemAsnRead':
objgbseq.c:2163:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBStrucCommentItemAsnRead':
objgbseq.c:2330:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBIntervalAsnRead':
objgbseq.c:2506:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBQualifierAsnRead':
objgbseq.c:2716:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBAltSeqItemAsnRead':
objgbseq.c:2887:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objtseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objtseq.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objtseq.c: In function 'TSeqAsnRead':
objtseq.c:89:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtseq.c: In function 'TSeqSetAsnRead':
objtseq.c:322:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtseq.c: In function 'BioseqToTSeq':
objtseq.c:448:8: warning: variable 'seqcode' set but not used [-Wunused-but-set-variable]
Uint1 seqcode;
^~~~~~~
objtseq.c: In function 'BioseqToMiniTSeq':
objtseq.c:560:8: warning: variable 'seqcode' set but not used [-Wunused-but-set-variable]
Uint1 seqcode;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objinsdseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objinsdseq.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objinsdseq.c: In function 'INSDSetAsnRead':
objinsdseq.c:68:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDSeqAsnRead':
objinsdseq.c:229:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDReferenceAsnRead':
objinsdseq.c:725:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDCommentAsnRead':
objinsdseq.c:963:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDStrucCommentAsnRead':
objinsdseq.c:1127:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDFeatureAsnRead':
objinsdseq.c:1295:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDFeatureSetAsnRead':
objinsdseq.c:1519:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDAltSeqDataAsnRead':
objinsdseq.c:1683:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDXrefAsnRead':
objinsdseq.c:1846:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDCommentParagraphAsnRead':
objinsdseq.c:2012:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDCommentItemAsnRead':
objinsdseq.c:2163:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDStrucCommentItemAsnRead':
objinsdseq.c:2330:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDIntervalAsnRead':
objinsdseq.c:2506:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDQualifierAsnRead':
objinsdseq.c:2716:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDAltSeqItemAsnRead':
objinsdseq.c:2887:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objmacro.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmacro.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmacro.c: In function 'AECRActionAsnRead':
objmacro.c:87:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:86:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseActionAsnRead':
objmacro.c:269:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:268:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MacroActionListAsnRead':
objmacro.c:472:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:469:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MacroActionListAsnWrite':
objmacro.c:525:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SuspectRuleSetAsnRead':
objmacro.c:586:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:583:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SuspectRuleSetAsnWrite':
objmacro.c:639:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'WordSubstitutionAsnRead':
objmacro.c:719:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c: In function 'WordSubstitutionSetAsnRead':
objmacro.c:884:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:881:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'WordSubstitutionSetAsnWrite':
objmacro.c:937:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'StringConstraintAsnRead':
objmacro.c:1025:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1024:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StringConstraintSetAsnRead':
objmacro.c:1266:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1263:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'StringConstraintSetAsnWrite':
objmacro.c:1319:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'LocationPosConstraintFree':
objmacro.c:1359:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationPosConstraintAsnRead':
objmacro.c:1388:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationConstraintAsnRead':
objmacro.c:1587:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1586:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalValAsnRead':
objmacro.c:1800:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1799:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalValChoiceFree':
objmacro.c:1927:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FeatQualLegalValChoiceAsnRead':
objmacro.c:1959:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalSetAsnRead':
objmacro.c:2111:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2108:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'FeatQualLegalSetAsnWrite':
objmacro.c:2164:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'FeatQualChoiceFree':
objmacro.c:2204:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FeatQualChoiceAsnRead':
objmacro.c:2236:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldAsnRead':
objmacro.c:2415:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2414:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldLegalAsnRead':
objmacro.c:2579:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2578:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldPairAsnRead':
objmacro.c:2742:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2741:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaFeatTypeFree':
objmacro.c:2882:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'RnaFeatTypeAsnRead':
objmacro.c:2914:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaQualAsnRead':
objmacro.c:3162:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3161:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaQualPairAsnRead':
objmacro.c:3327:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3326:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualPairAsnRead':
objmacro.c:3500:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3499:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualChoiceFree':
objmacro.c:3625:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SourceQualChoiceAsnRead':
objmacro.c:3654:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualTextValAsnRead':
objmacro.c:3869:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3868:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualValChoiceFree':
objmacro.c:3996:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SourceQualValChoiceAsnRead':
objmacro.c:4028:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualValSetAsnRead':
objmacro.c:4224:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4221:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SourceQualValSetAsnWrite':
objmacro.c:4277:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'CDSGeneProtFieldPairAsnRead':
objmacro.c:4353:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4352:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldFree':
objmacro.c:4478:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MolinfoFieldAsnRead':
objmacro.c:4507:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoMoleculePairAsnRead':
objmacro.c:4732:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4731:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoTechniquePairAsnRead':
objmacro.c:4893:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4892:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoCompletednessPairAsnRead':
objmacro.c:5054:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5053:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoMolClassPairAsnRead':
objmacro.c:5215:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5214:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoTopologyPairAsnRead':
objmacro.c:5376:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5375:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoStrandPairAsnRead':
objmacro.c:5537:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5536:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldPairFree':
objmacro.c:5662:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MolinfoFieldPairAsnRead':
objmacro.c:5709:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldListAsnRead':
objmacro.c:5901:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5898:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MolinfoFieldListAsnWrite':
objmacro.c:5954:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MolinfoFieldConstraintAsnRead':
objmacro.c:6032:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6031:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StructuredCommentFieldFree':
objmacro.c:6160:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'StructuredCommentFieldAsnRead':
objmacro.c:6192:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StructuredCommentFieldPairAsnRead':
objmacro.c:6386:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6385:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StructuredCommentFieldPairAsnWrite':
objmacro.c:6461:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'DBLinkFieldPairAsnRead':
objmacro.c:6553:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6552:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldConstraintAsnRead':
objmacro.c:6715:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6714:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeFree':
objmacro.c:6843:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeAsnRead':
objmacro.c:6872:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintAsnRead':
objmacro.c:7087:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7086:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PublicationConstraintAsnRead':
objmacro.c:7253:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7252:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceConstraintAsnRead':
objmacro.c:7432:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7431:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtPseudoConstraintAsnRead':
objmacro.c:7621:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7620:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtConstraintFieldFree':
objmacro.c:7746:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'CDSGeneProtConstraintFieldAsnRead':
objmacro.c:7775:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtQualConstraintAsnRead':
objmacro.c:7948:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7947:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtQualConstraintAsnWrite':
objmacro.c:8030:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'FieldConstraintAsnRead':
objmacro.c:8129:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:8128:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldConstraintAsnWrite':
objmacro.c:8204:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'FieldTypeFree':
objmacro.c:8260:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FieldTypeAsnRead':
objmacro.c:8304:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintFree':
objmacro.c:8511:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintAsnRead':
objmacro.c:8540:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'QuantityConstraintFree':
objmacro.c:8718:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'QuantityConstraintAsnRead':
objmacro.c:8747:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceConstraintAsnRead':
objmacro.c:8945:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:8944:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TranslationConstraintAsnRead':
objmacro.c:9170:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9169:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConstraintChoiceFree':
objmacro.c:9322:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConstraintChoiceAsnRead':
objmacro.c:9384:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConstraintChoiceSetAsnRead':
objmacro.c:9616:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9613:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'ConstraintChoiceSetAsnWrite':
objmacro.c:9669:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'TextMarkerFree':
objmacro.c:9709:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TextMarkerAsnRead':
objmacro.c:9741:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TextPortionAsnRead':
objmacro.c:9937:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9936:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldEditAsnRead':
objmacro.c:10153:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10152:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldPairTypeFree':
objmacro.c:10300:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FieldPairTypeAsnRead':
objmacro.c:10350:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyActionAsnRead':
objmacro.c:10567:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10566:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditActionAsnRead':
objmacro.c:10744:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10743:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditActionAsnWrite':
objmacro.c:10819:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'TextTransformFree':
objmacro.c:10875:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TextTransformAsnRead':
objmacro.c:10910:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TextTransformSetAsnRead':
objmacro.c:11081:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11078:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'TextTransformSetAsnWrite':
objmacro.c:11134:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'ConvertActionAsnRead':
objmacro.c:11214:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11213:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CopyActionAsnRead':
objmacro.c:11406:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11405:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SwapActionAsnRead':
objmacro.c:11572:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11571:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SwapActionAsnWrite':
objmacro.c:11647:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'AECRParseActionAsnRead':
objmacro.c:11745:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11744:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveActionAsnRead':
objmacro.c:11961:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11960:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveActionAsnWrite':
objmacro.c:12029:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'RemoveOutsideActionAsnRead':
objmacro.c:12119:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:12118:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ActionChoiceFree':
objmacro.c:12259:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ActionChoiceAsnRead':
objmacro.c:12312:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcOrgChoiceFree':
objmacro.c:12499:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcOrgChoiceAsnRead':
objmacro.c:12528:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcOrgAsnRead':
objmacro.c:12711:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:12710:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcGeneralIdFree':
objmacro.c:12839:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcGeneralIdAsnRead':
objmacro.c:12871:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcFree':
objmacro.c:13027:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcAsnRead':
objmacro.c:13065:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseDstOrgAsnRead':
objmacro.c:13319:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:13318:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseDestFree':
objmacro.c:13447:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseDestAsnRead':
objmacro.c:13485:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationIntervalAsnRead':
objmacro.c:13693:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:13692:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationChoiceFree':
objmacro.c:13818:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationChoiceAsnRead':
objmacro.c:13850:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceListAsnRead':
objmacro.c:14024:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14021:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SequenceListAsnWrite':
objmacro.c:14077:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SequenceListChoiceFree':
objmacro.c:14117:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SequenceListChoiceAsnRead':
objmacro.c:14149:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyFeatureActionAsnRead':
objmacro.c:14338:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14337:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveFeatureActionAsnRead':
objmacro.c:14602:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14601:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFromCDSOptionsAsnRead':
objmacro.c:14766:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14765:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureSrcOptionsFree':
objmacro.c:14900:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConvertFeatureSrcOptionsAsnRead':
objmacro.c:14932:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RegionTypeAsnRead':
objmacro.c:15099:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15098:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureDstOptionsFree':
objmacro.c:15215:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConvertFeatureDstOptionsAsnRead':
objmacro.c:15250:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureActionAsnRead':
objmacro.c:15464:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15463:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditLocationStrandAsnRead':
objmacro.c:15670:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15669:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'Partial5SetActionAsnRead':
objmacro.c:15831:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15830:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'Partial3SetActionAsnRead':
objmacro.c:15992:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15991:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PartialBothSetActionAsnRead':
objmacro.c:16153:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16152:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ExtendToFeatureAsnRead':
objmacro.c:16315:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16314:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationEditTypeFree':
objmacro.c:16452:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationEditTypeAsnRead':
objmacro.c:16499:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditFeatureLocationActionAsnRead':
objmacro.c:16774:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16773:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoBlockAsnRead':
objmacro.c:16971:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16970:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoBlockAsnWrite':
objmacro.c:17053:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'RemoveDescriptorActionAsnRead':
objmacro.c:17151:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17150:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AutodefActionAsnRead':
objmacro.c:17317:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c: In function 'FixPubCapsActionAsnRead':
objmacro.c:17488:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17487:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SortFieldsActionAsnRead':
objmacro.c:17690:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17689:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixAuthorCapsAsnRead':
objmacro.c:17866:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17865:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixCapsActionFree':
objmacro.c:17982:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixCapsActionAsnRead':
objmacro.c:18017:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixFormatActionFree':
objmacro.c:18189:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixFormatActionAsnRead':
objmacro.c:18218:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveDuplicateFeatureActionAsnRead':
objmacro.c:18422:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18421:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'GeneXrefTypeAsnRead':
objmacro.c:18613:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18612:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'XrefTypeFree':
objmacro.c:18747:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'XrefTypeAsnRead':
objmacro.c:18779:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveXrefsActionAsnRead':
objmacro.c:18948:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18947:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveXrefsActionAsnWrite':
objmacro.c:19023:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MakeGeneXrefActionAsnRead':
objmacro.c:19116:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19115:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AuthorFixActionAsnRead':
objmacro.c:19281:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19280:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'UpdateSequencesActionAsnRead':
objmacro.c:19447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19446:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CreateTSAIdsSrcFree':
objmacro.c:19574:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'CreateTSAIdsSrcAsnRead':
objmacro.c:19606:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CreateTSAIdsActionAsnRead':
objmacro.c:19787:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19786:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AutofixActionAsnRead':
objmacro.c:19966:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19965:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixSetsActionFree':
objmacro.c:20084:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixSetsActionAsnRead':
objmacro.c:20113:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TableMatchTypeFree':
objmacro.c:20269:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TableMatchTypeAsnRead':
objmacro.c:20301:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TableMatchAsnRead':
objmacro.c:20547:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:20546:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyTableExtraDataFree':
objmacro.c:20675:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ApplyTableExtraDataAsnRead':
objmacro.c:20704:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyTableActionAsnRead':
objmacro.c:20877:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:20876:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AddFileActionAsnRead':
objmacro.c:21057:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21056:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AddDescriptorListActionAsnRead':
objmacro.c:21225:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21224:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AddDescriptorListActionAsnWrite':
objmacro.c:21300:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'RemoveSequencesActionAsnRead':
objmacro.c:21393:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21392:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveSequencesActionAsnWrite':
objmacro.c:21461:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MacroActionChoiceFree':
objmacro.c:21512:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MacroActionChoiceAsnRead':
objmacro.c:21613:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SearchFuncFree':
objmacro.c:22093:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SearchFuncAsnRead':
objmacro.c:22131:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SimpleReplaceAsnRead':
objmacro.c:22400:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:22399:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ReplaceFuncFree':
objmacro.c:22536:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ReplaceFuncAsnRead':
objmacro.c:22571:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ReplaceRuleAsnRead':
objmacro.c:22751:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:22750:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SuspectRuleAsnRead':
objmacro.c:22921:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:22920:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualChoiceAsnRead':
objmacro.c:3727:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SourceQualValChoiceAsnRead':
objmacro.c:4098:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MolinfoFieldAsnRead':
objmacro.c:4587:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MolinfoFieldPairAsnRead':
objmacro.c:5771:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'StructuredCommentFieldAsnRead':
objmacro.c:6251:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FieldTypeAsnRead':
objmacro.c:8390:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ConstraintChoiceAsnRead':
objmacro.c:9466:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcGeneralIdAsnRead':
objmacro.c:12930:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixCapsActionAsnRead':
objmacro.c:18084:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixFormatActionAsnRead':
objmacro.c:18284:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixSetsActionAsnRead':
objmacro.c:20172:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MacroActionChoiceAsnRead':
objmacro.c:21852:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationPosConstraintAsnRead':
objmacro.c:1447:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'RnaFeatTypeAsnRead':
objmacro.c:3008:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeAsnRead':
objmacro.c:6945:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintAsnRead':
objmacro.c:8613:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'QuantityConstraintAsnRead':
objmacro.c:8806:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'TextMarkerAsnRead':
objmacro.c:9800:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FieldPairTypeAsnRead':
objmacro.c:10416:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ActionChoiceAsnRead':
objmacro.c:12382:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcOrgChoiceAsnRead':
objmacro.c:12580:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcAsnRead':
objmacro.c:13160:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseDestAsnRead':
objmacro.c:13552:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationChoiceAsnRead':
objmacro.c:13906:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ConvertFeatureDstOptionsAsnRead':
objmacro.c:15320:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationEditTypeAsnRead':
objmacro.c:16603:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'TableMatchTypeAsnRead':
objmacro.c:20392:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SearchFuncAsnRead':
objmacro.c:22236:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objent2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objent2.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objent2.c: In function 'Entrez2IdListAsnRead':
objent2.c:87:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:86:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2BooleanExpAsnRead':
objent2.c:276:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2BooleanElementFree':
objent2.c:414:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'Entrez2BooleanElementAsnRead':
objent2.c:455:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LimitsAsnRead':
objent2.c:664:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:663:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2BooleanTermAsnRead':
objent2.c:841:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:840:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2RequestAsnRead':
objent2.c:1037:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1036:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'E2RequestFree':
objent2.c:1198:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'E2RequestAsnRead':
objent2.c:1251:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2EvalBooleanAsnRead':
objent2.c:1488:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1487:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermQueryAsnRead':
objent2.c:1664:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1663:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermPosAsnRead':
objent2.c:1842:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1841:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2HierQueryAsnRead':
objent2.c:2028:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2027:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2GetLinksAsnRead':
objent2.c:2215:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2214:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2IdAsnRead':
objent2.c:2409:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2408:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DtFilterAsnRead':
objent2.c:2573:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2572:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2ReplyAsnRead':
objent2.c:2750:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2749:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'E2ReplyFree':
objent2.c:2922:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'E2ReplyAsnRead':
objent2.c:2978:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2InfoAsnRead':
objent2.c:3224:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2BooleanReplyAsnRead':
objent2.c:3395:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:3394:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumListAsnRead':
objent2.c:3572:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2TermListAsnRead':
objent2.c:3733:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2HierNodeAsnRead':
objent2.c:3905:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2LinkSetAsnRead':
objent2.c:4104:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4103:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkCountListAsnRead':
objent2.c:4280:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2DbInfoAsnRead':
objent2.c:4446:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2FieldInfoAsnRead':
objent2.c:4685:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4684:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkInfoAsnRead':
objent2.c:4928:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4927:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumFieldInfoAsnRead':
objent2.c:5126:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5125:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumAsnRead':
objent2.c:5301:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2DocsumDataAsnRead':
objent2.c:5463:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5462:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermAsnRead':
objent2.c:5629:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5628:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkCountAsnRead':
objent2.c:5811:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5810:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2BooleanElementAsnRead':
objent2.c:522:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objent2.c: In function 'E2ReplyAsnRead':
objent2.c:3062:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ent2api.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ent2api.h:45,
from ent2api.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF pmfapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from pmfapi.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pmfapi.c: In function 'PubMedSynchronousQuery':
pmfapi.c:1224:58: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("PubMedWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'PubSeqSynchronousQueryEx':
pmfapi.c:1458:58: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'PubSeqSynchronousQueryTI':
pmfapi.c:1636:58: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'PubSeqSynchronousQuerySRA':
pmfapi.c:1717:58: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'GiRevHistSynchronousQuery':
pmfapi.c:1790:61: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("GiRevHistWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'GiAccVerSynchronousQuery':
pmfapi.c:1842:60: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("GiAccVerWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'AccnRevHistSynchronousQuery':
pmfapi.c:1893:63: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("AccnRevHistWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'GiSeqIdSetSynchronousQuery':
pmfapi.c:1944:62: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("GiSeqIdSetWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'AccnListSynchronousQuery':
pmfapi.c:1994:60: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("AccnListWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objtax3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objtax3.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objtax3.c: In function 'Taxon3RequestAsnRead':
objtax3.c:86:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'T3RequestFree':
objtax3.c:200:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtax3.c: In function 'SequenceOfIntAsnRead':
objtax3.c:418:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'Taxon3ReplyAsnRead':
objtax3.c:547:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'T3ReplyFree':
objtax3.c:661:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtax3.c: In function 'T3ErrorAsnRead':
objtax3.c:872:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'T3DataAsnRead':
objtax3.c:1071:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'Value_valueFree':
objtax3.c:1252:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtax3.c: In function 'T3StatusFlagsAsnRead':
objtax3.c:1282:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'T3RefreshFlagsAsnRead':
objtax3.c:1606:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
In file included from ../include/strimprt.h:72:0,
from objtax3.c:5:
objtax3.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from objtax3.c:5:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from objtax3.c:5:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from objtax3.c:5:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
objtax3.c: In function 'T3RequestAsnRead':
objtax3.c:297:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax3.c: In function 'T3ReplyAsnRead':
objtax3.c:741:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax3.c: In function 'T3StatusFlagsAsnRead':
objtax3.c:1420:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax3.c:1361:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF tax3api.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from tax3api.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
tax3api.c: In function 'Tax3SynchronousQuery':
tax3api.c:188:27: warning: variable 't3' set but not used [-Wunused-but-set-variable]
time_t t1, t2, t3;
^~
tax3api.c: In function 'CheckSuggestedFixes':
tax3api.c:753:20: warning: variable 'tep' set but not used [-Wunused-but-set-variable]
T3ErrorPtr tep;
^~~
tax3api.c: In function 'TryNewSuggestedFixes':
tax3api.c:865:20: warning: variable 'tep' set but not used [-Wunused-but-set-variable]
T3ErrorPtr tep;
^~~
tax3api.c: In function 'GetSuggestedNamesFromRank':
tax3api.c:1114:20: warning: variable 'tep' set but not used [-Wunused-but-set-variable]
T3ErrorPtr tep;
^~~
tax3api.c: In function 'BioSourceFromBioSample':
tax3api.c:3220:16: warning: unused variable 'max' [-Wunused-variable]
time_t max = 0;
^~~
At top level:
tax3api.c:3003:13: warning: 'AddBioSourcesToChecklist' defined but not used [-Wunused-function]
static void AddBioSourcesToChecklist (ValNodePtr biop_list, ValNodePtr check_list)
^~~~~~~~~~~~~~~~~~~~~~~~
tax3api.c:2345:16: warning: 'StringIsExactMatchForOrgRef' defined but not used [-Wunused-function]
static Boolean StringIsExactMatchForOrgRef (CharPtr str, OrgRefPtr org)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
tax3api.c:1886:16: warning: 'EndsWithSp' defined but not used [-Wunused-function]
static Boolean EndsWithSp (CharPtr str)
^~~~~~~~~~
tax3api.c:616:28: warning: 'TaxFixItemOrigIsOk' defined but not used [-Wunused-function]
static Boolean LIBCALLBACK TaxFixItemOrigIsOk (ValNodePtr vnp)
^~~~~~~~~~~~~~~~~~
tax3api.c:361:16: warning: 'HasMisspellingFlag' defined but not used [-Wunused-function]
static Boolean HasMisspellingFlag (T3DataPtr t)
^~~~~~~~~~~~~~~~~~
tax3api.c:297:13: warning: 'SaveTaxon3Request' defined but not used [-Wunused-function]
static void SaveTaxon3Request (Taxon3RequestPtr t3rp, CharPtr path)
^~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objegkludge.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objegkludge.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objentgene.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objentgene.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objentgene.c: In function 'EntrezgeneAsnRead':
objentgene.c:103:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c: In function 'EntrezgeneSetAsnRead':
objentgene.c:411:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:408:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objentgene.c: In function 'EntrezgeneSetAsnWrite':
objentgene.c:464:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objentgene.c: In function 'GeneTrackAsnRead':
objentgene.c:545:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c: In function 'GeneCommentaryAsnRead':
objentgene.c:764:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c: In function 'Method_methodFree':
objentgene.c:1056:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objentgene.c: In function 'MapsAsnRead':
objentgene.c:1087:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1086:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'Method_methodAsnRead':
objentgene.c:1167:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'GeneSourceAsnRead':
objentgene.c:1408:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1407:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'XtraTermsAsnRead':
objentgene.c:1622:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1621:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'OtherSourceAsnRead':
objentgene.c:1792:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1791:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'MapsAsnRead':
objentgene.c:1219:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objentgene.c:1166:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objmla2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmla2.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmla2.c: In function 'Mla2RequestFree':
objmla2.c:49:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmla2.c: In function 'Mla22RequestAsnRead':
objmla2.c:96:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmla2.c: In function 'TitleMsg2AsnRead':
objmla2.c:447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmla2.c:446:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmla2.c: In function 'TitleMsgList2AsnRead':
objmla2.c:612:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmla2.c: In function 'Mla22RequestAsnRead':
objmla2.c:249:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmla2.c: In function 'Mla2BackAsnRead':
objmla2.c:902:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mla2api.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/mla2api.h:45,
from mla2api.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF qblastapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from qblastapi.c:120:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
qblastapi.c: In function 'SecondQBlastCallback':
qblastapi.c:259:15: warning: variable 'waiting' set but not used [-Wunused-but-set-variable]
Boolean waiting = FALSE;
^~~~~~~
qblastapi.c: In function 'BLASTGetSeqAnnotByRIDEx':
qblastapi.c:823:18: warning: variable 'status' set but not used [-Wunused-but-set-variable]
EIO_Status status;
^~~~~~
qblastapi.c: In function 'BLASTGetQueryBioseqByRIDEx':
qblastapi.c:868:18: warning: variable 'status' set but not used [-Wunused-but-set-variable]
EIO_Status status;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vecscnapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from vecscnapi.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objmim.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmim.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmim.c: In function 'MimSetAsnRead':
objmim.c:86:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimDateAsnRead':
objmim.c:248:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:247:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimEntryAsnRead':
objmim.c:447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimCitAsnRead':
objmim.c:907:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:906:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimTextAsnRead':
objmim.c:1093:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:1092:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimEditItemAsnRead':
objmim.c:1272:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:1271:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimAllelicVariantAsnRead':
objmim.c:1443:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimIndexTermAsnRead':
objmim.c:1634:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimReferenceAsnRead':
objmim.c:1812:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimLinkAsnRead':
objmim.c:2187:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2186:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimAuthorAsnRead':
objmim.c:2360:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2359:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimPageAsnRead':
objmim.c:2525:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2524:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objvalid.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objvalid.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objvalid.c: In function 'FieldRuleAsnRead':
objvalid.c:88:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:87:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objvalid.c: In function 'FieldSetAsnRead':
objvalid.c:256:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:253:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'FieldSetAsnWrite':
objvalid.c:309:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'DependentFieldRuleAsnRead':
objvalid.c:390:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:389:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objvalid.c: In function 'DependentFieldSetAsnRead':
objvalid.c:573:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:570:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'DependentFieldSetAsnWrite':
objvalid.c:626:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'CommentRuleAsnRead':
objvalid.c:708:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:707:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objvalid.c: In function 'CommentSetAsnRead':
objvalid.c:898:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:895:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'CommentSetAsnWrite':
objvalid.c:951:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mimapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mimapi.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cddapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cddapi.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqport.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from seqport.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqport.c: In function 'productLoc_to_locationLoc':
seqport.c:4153:13: warning: variable 'is_cdregion' set but not used [-Wunused-but-set-variable]
Boolean is_cdregion = FALSE;
^~~~~~~~~~~
seqport.c: In function 'NaLocFromNaInterval':
seqport.c:4483:8: warning: variable 'p_end_pos' set but not used [-Wunused-but-set-variable]
Int4 p_end_pos; /*the end of the product sequence in the current loc*/
^~~~~~~~~
seqport.c: In function 'dnaLoc_to_aaLoc':
seqport.c:4599:18: warning: variable 'cds_right' set but not used [-Wunused-but-set-variable]
Int4 cds_left, cds_right;
^~~~~~~~~
seqport.c:4599:8: warning: variable 'cds_left' set but not used [-Wunused-but-set-variable]
Int4 cds_left, cds_right;
^~~~~~~~
seqport.c: In function 'DeltaRevComp':
seqport.c:5281:21: warning: variable 'dspnext' set but not used [-Wunused-but-set-variable]
DeltaSeqPtr dsp, dspnext;
^~~~~~~
seqport.c: In function 'SeqSearchEnterNucWord':
seqport.c:6822:18: warning: variable 'patLen' set but not used [-Wunused-but-set-variable]
Int2 next, patLen, state;
^~~~~~
seqport.c: In function 'ProtSearchEnterProtWord':
seqport.c:7696:18: warning: variable 'patLen' set but not used [-Wunused-but-set-variable]
Int2 next, patLen, state;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from seqport.c:62:
seqport.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF sequtil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from sequtil.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequtil.c: In function 'GetPointsForLeftAndRightOffsets':
sequtil.c:7959:11: warning: variable 'first_strand' set but not used [-Wunused-but-set-variable]
Uint1 first_strand, last_strand;
^~~~~~~~~~~~
sequtil.c: In function 'SeqPointWriteEx':
sequtil.c:8492:15: warning: variable 'fuzzlen' set but not used [-Wunused-but-set-variable]
Int4 fuzzlen, id_len;
^~~~~~~
sequtil.c: In function 'TaxNameFromCommon':
sequtil.c:8647:42: warning: missing braces around initializer [-Wmissing-braces]
static Nlm_TaxCommon taxcommon[40] = {
^
sequtil.c:8647:42: note: (near initialization for 'taxcommon')
sequtil.c: In function 'GetBestScoreAndEvalueFromScorePtr':
sequtil.c:9470:48: warning: variable 'sum_set' set but not used [-Wunused-but-set-variable]
Boolean score_set=FALSE, evalue_set=FALSE, sum_set=FALSE, bit_set=FALSE;
^~~~~~~
sequtil.c: In function 'SeqIdFromAccessionEx':
sequtil.c:10070:38: warning: variable 'sip2' set but not used [-Wunused-but-set-variable]
SeqIdPtr sip2;
^~~~
sequtil.c: In function 'SeqLocCoverage':
sequtil.c:6905:13: warning: 'sip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (SeqIdComp (sip, id_list[j]) == SIC_YES) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~
sequtil.c: In function 'SeqLocCompareEx':
sequtil.c:5792:29: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
for (i = 0; i < num; i++)
^~~
sequtil.c:5792:29: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF prtutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objprt.h:67,
from ../include/prtutil.h:69,
from prtutil.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
prtutil.c: In function 'StdFormatPrint':
prtutil.c:1422:10: warning: unused variable 'ptr' [-Wunused-variable]
CharPtr ptr = NULL;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF simple.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/simple.h:63,
from simple.c:68:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from simple.c:69:0:
../include/all.h:7192:0: warning: "RNA_QUAL" redefined
#define RNA_QUAL &at[2231]
../include/all.h:5745:0: note: this is the location of the previous definition
#define RNA_QUAL &at[1023]
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF tofasta.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from ../include/tofasta.h:47,
from tofasta.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
tofasta.c: In function 'DoSpecialDefline':
tofasta.c:1407:22: warning: variable 'gene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr gene = NULL;
^~~~
tofasta.c: In function 'CreateDefLineExEx':
tofasta.c:4801:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (vnp != NULL)
^~
tofasta.c:4803:15: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (title != NULL) {
^~
tofasta.c: In function 'FastaToSeqEntryInternalExEx':
tofasta.c:2736:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(buffer+1, BuffSize, fd);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tofasta.c:2761:13: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(buffer+i+1, FTSE_BUFF_CHUNK, fd);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
tofasta.c:3479:19: warning: 'GatherGenesForCDS' defined but not used [-Wunused-function]
static ValNodePtr GatherGenesForCDS(SeqLocPtr slp)
^~~~~~~~~~~~~~~~~
tofasta.c:3445:19: warning: 'GatherSeqFeatProt' defined but not used [-Wunused-function]
static SeqFeatPtr GatherSeqFeatProt(BioseqPtr bsp)
^~~~~~~~~~~~~~~~~
tofasta.c:3359:19: warning: 'GetCDSProtUnindexed' defined but not used [-Wunused-function]
static SeqFeatPtr GetCDSProtUnindexed (
^~~~~~~~~~~~~~~~~~~
tofasta.c:3196:19: warning: 'IndexedGatherDescrOnBioseq' defined but not used [-Wunused-function]
static ValNodePtr IndexedGatherDescrOnBioseq (ItemInfoPtr iip, BioseqPtr bsp, Uint1 choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~
tofasta.c:3101:16: warning: 'get_descr' defined but not used [-Wunused-function]
static Boolean get_descr (GatherContextPtr gcp)
^~~~~~~~~
tofasta.c:3072:16: warning: 'get_descr_on_top' defined but not used [-Wunused-function]
static Boolean get_descr_on_top (GatherContextPtr gcp)
^~~~~~~~~~~~~~~~
tofasta.c: In function 'FastaReadSequenceInternalEx':
tofasta.c:2611:27: warning: 'mask_to' may be used uninitialized in this function [-Wmaybe-uninitialized]
mask_sint->to = mask_to;
~~~~~~~~~~~~~~^~~~~~~~~
tofasta.c: In function 'FastaToSeqEntryInternalExEx':
tofasta.c:2852:13: warning: 'fd' may be used uninitialized in this function [-Wmaybe-uninitialized]
ungetc(ch, fd);
^~~~~~~~~~~~~~
tofasta.c:2672:25: warning: 'firstchar' may be used uninitialized in this function [-Wmaybe-uninitialized]
const Char PNTR firstchar;
^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF tofile.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from tofile.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF tomedlin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmedli.h:80,
from tomedlin.c:150:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF valid.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from valid.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
valid.c: In function 'Valid1GatherProc':
valid.c:2238:22: warning: variable 'sc_valid' set but not used [-Wunused-but-set-variable]
EFieldValid sc_valid;
^~~~~~~~
valid.c: In function 'ValidateSeqIdCase':
valid.c:3342:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'ValidateGenProdSet':
valid.c:5551:19: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'CountAdjacentProc':
valid.c:6193:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'ValidateBioseqInst':
valid.c:6584:19: warning: variable 'tech' set but not used [-Wunused-but-set-variable]
Uint1 tech;
^~~~
valid.c:6526:19: warning: variable 'prot' set but not used [-Wunused-but-set-variable]
SeqFeatPtr prot;
^~~~
valid.c: In function 'ValidateBioSource':
valid.c:13688:19: warning: variable 'id' set but not used [-Wunused-but-set-variable]
Int4 id;
^~
valid.c: In function 'ValidateDblink':
valid.c:14737:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'ValidateSeqDescrCommon':
valid.c:14795:19: warning: variable 'pdp' set but not used [-Wunused-but-set-variable]
PubdescPtr pdp;
^~~
valid.c: In function 'ValidateBioseqContextIndexed':
valid.c:17742:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (bvsp->is_mrna || cdscount == 1 && genecount < 2) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
valid.c:17154:41: warning: variable 'utr3gene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr cdsgene, utr5gene, utr3gene;
^~~~~~~~
valid.c: In function 'ValidateBarcodeIndexNumber':
valid.c:18667:21: warning: variable 'bin_len' set but not used [-Wunused-but-set-variable]
Int4 bin_len;
^~~~~~~
valid.c: In function 'ValidateBioseqContext':
valid.c:18775:19: warning: variable 'taxname' set but not used [-Wunused-but-set-variable]
CharPtr taxname = NULL;
^~~~~~~
valid.c: In function 'ValidateRptUnit':
valid.c:20323:32: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean badchars, found, just_nuc_letters, multi_rpt_unit;
^~~~~
valid.c: In function 'CheckForCommonCDSProduct':
valid.c:22238:19: warning: variable 'is_nw' set but not used [-Wunused-but-set-variable]
Boolean is_nw = FALSE;
^~~~~
valid.c:22235:19: warning: variable 'is_nc' set but not used [-Wunused-but-set-variable]
Boolean is_nc = FALSE;
^~~~~
valid.c: In function 'CheckForIllegalDbxref':
valid.c:22617:16: warning: variable 'id' set but not used [-Wunused-but-set-variable]
Int4 id;
^~
valid.c: In function 'ValidateAnticodon':
valid.c:23348:53: warning: variable 'circular' set but not used [-Wunused-but-set-variable]
ordered = TRUE, adjacent = FALSE, circular = FALSE, exception = FALSE;
^~~~~~~~
valid.c:23347:19: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = TRUE, tmpval, mixed_strand = FALSE, unmarked_strand = FALSE,
^~~~~~
valid.c: In function 'IsGeneXrefRedundant':
valid.c:24599:17: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
valid.c: In function 'ValidateSeqFeat':
valid.c:24763:19: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
valid.c:24741:19: warning: variable 'pdp' set but not used [-Wunused-but-set-variable]
PubdescPtr pdp;
^~~
valid.c: In function 'CdTransCheck':
valid.c:26675:19: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'SpliceCheckEx':
valid.c:27477:19: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
valid.c: In function 'CdsProductIdCheck':
valid.c:27823:15: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'ValidateSeqLoc':
valid.c:27887:19: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = TRUE, tmpval, mixed_strand = FALSE, unmarked_strand = FALSE,
^~~~~~
valid.c:27886:24: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
SeqLocPtr tmp, prev;
^~~~
valid.c: In function 'SortSeqGraphProc':
valid.c:28260:26: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (gip2->right < gip2->right) {
^
At top level:
valid.c:24281:16: warning: 'CouldExtendPartial' defined but not used [-Wunused-function]
static Boolean CouldExtendPartial (SeqLocPtr slp, Boolean partial5)
^~~~~~~~~~~~~~~~~~
valid.c:18342:28: warning: 'MultiGeneOverlapFree' defined but not used [-Wunused-function]
static MultiGeneOverlapPtr MultiGeneOverlapFree (MultiGeneOverlapPtr m)
^~~~~~~~~~~~~~~~~~~~
valid.c:18292:19: warning: 'ListFeaturesContainedInLocation' defined but not used [-Wunused-function]
static ValNodePtr ListFeaturesContainedInLocation (BioseqPtr bsp, SeqLocPtr slp, Uint1 seqfeatChoice, Uint1 featdefChoice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
valid.c:13056:16: warning: 'CountryIsClosestToLatLon' defined but not used [-Wunused-function]
static Boolean CountryIsClosestToLatLon (
^~~~~~~~~~~~~~~~~~~~~~~~
valid.c:12959:16: warning: 'LatLonInRange' defined but not used [-Wunused-function]
static Boolean LatLonInRange (
^~~~~~~~~~~~~
valid.c:12157:16: warning: 'LatLonIsValid' defined but not used [-Wunused-function]
static Boolean LatLonIsValid (CharPtr name)
^~~~~~~~~~~~~
valid.c:9394:16: warning: 'ConsistentWithC' defined but not used [-Wunused-function]
static Boolean ConsistentWithC (Char ch)
^~~~~~~~~~~~~~~
valid.c:6450:13: warning: 'ReportLongSeqId' defined but not used [-Wunused-function]
static void ReportLongSeqId (SeqIdPtr sip, ValidStructPtr vsp, Int4 max_len)
^~~~~~~~~~~~~~~
valid.c:5438:13: warning: 'CheckMutSetSources' defined but not used [-Wunused-function]
static void CheckMutSetSources (BioSourcePtr biop, Pointer userdata)
^~~~~~~~~~~~~~~~~~
valid.c:4089:13: warning: 'FindLongIdsThatCollideWhenTruncated' defined but not used [-Wunused-function]
static void FindLongIdsThatCollideWhenTruncated (SeqEntryPtr sep, ValidStructPtr vsp, Int4 trunc_len)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
valid.c:1415:16: warning: 'IsNotUnclassifiedExcept' defined but not used [-Wunused-function]
static Boolean IsNotUnclassifiedExcept (ValidStructPtr vsp)
^~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF valapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from valapi.c:50:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
valapi.c: In function 'DoesStringMatchExpression':
valapi.c:253:15: warning: variable 'errstr' set but not used [-Wunused-but-set-variable]
const char *errstr;
^~~~~~
valapi.c: In function 'ReorderStructuredCommentFields':
valapi.c:777:82: warning: unused variable 'ufp_last' [-Wunused-variable]
UserFieldPtr ufp, ufp_prev = NULL, new_list = NULL, new_prev = NULL, ufp_next, ufp_last = NULL;
^~~~~~~~
valapi.c:777:72: warning: unused variable 'ufp_next' [-Wunused-variable]
UserFieldPtr ufp, ufp_prev = NULL, new_list = NULL, new_prev = NULL, ufp_next, ufp_last = NULL;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF alignmgr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/alignmgr.h:261,
from alignmgr.c:584:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
alignmgr.c: In function 'AlnMgrIndexParentSA':
alignmgr.c:1607:19: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
sap->saip = (Pointer)AMAlignIndexFree(amaip);
^
alignmgr.c: In function 'AlnMgrGetNthBlockRange':
alignmgr.c:4182:21: warning: variable 'amaip' set but not used [-Wunused-but-set-variable]
AMAlignIndexPtr amaip;
^~~~~
alignmgr.c: In function 'AlnMgrMakeFakeMultipleEx':
alignmgr.c:5157:21: warning: variable 'nogap' set but not used [-Wunused-but-set-variable]
Boolean nogap;
^~~~~
alignmgr.c: In function 'AlnMgrMapBioseqToBioseq':
alignmgr.c:10840:19: warning: variable 'gap' set but not used [-Wunused-but-set-variable]
Uint1 gap;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from alignmgr.c:584:
alignmgr.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
alignmgr.c:10572:16: warning: 'am_merge_after_edit' defined but not used [-Wunused-function]
static Boolean am_merge_after_edit (SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~~~
alignmgr.c:6650:16: warning: 'AlnMgrJaggedIndex' defined but not used [-Wunused-function]
static Boolean AlnMgrJaggedIndex(SeqAlignPtr sap, AMmsmsPtr ams_head, AMmsmsPtr *ams_mhead, Int4 numrows)
^~~~~~~~~~~~~~~~~
alignmgr.c:6123:18: warning: 'AlnMgrConstructOverlaps' defined but not used [-Wunused-function]
static AMmsmsPtr AlnMgrConstructOverlaps(AMmsmsPtr ams_head)
^~~~~~~~~~~~~~~~~~~~~~~
alignmgr.c:5405:13: warning: 'AlnMgrMergeNeighbors' defined but not used [-Wunused-function]
static void AlnMgrMergeNeighbors(SeqAlignPtr salp)
^~~~~~~~~~~~~~~~~~~~
alignmgr.c: In function 'AlnMgrUnpackSeqAlign':
alignmgr.c:1149:33: warning: 'sap_segs_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap_segs_prev->next = (SeqAlignPtr)(sap_segs->segs);
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr.c: In function 'am_print_seqalign_indexes':
alignmgr.c:2416:30: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j=0; j<(saip->ssdp[i]->numsect); j++)
~~~~^~~~~~
alignmgr.c:2481:34: warning: 'amaip' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j=0; j<(amaip->amadp[i]->numseg); j++)
~~~~~^~~~~~~
alignmgr.c: In function 'AlnMgrGetNthSeqRangeInSA':
alignmgr.c:4115:19: warning: 'tmp_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
*stop = tmp_end;
~~~~~~^~~~~~~~~
alignmgr.c:4113:20: warning: 'tmp_beg' may be used uninitialized in this function [-Wmaybe-uninitialized]
*start = tmp_beg;
~~~~~~~^~~~~~~~~
alignmgr.c: In function 'AlnMgrDeleteNthRow':
alignmgr.c:9809:31: warning: 'abp_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
abp_prev->next = abp;
~~~~~~~~~~~~~~~^~~~~
alignmgr.c: In function 'AlnMgrGetSubAlign':
alignmgr.c:9097:15: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
salp = am_cleanupsalp(salp);
~~~~~^~~~~~~~~~~~~~~~~~~~~~
alignmgr.c: In function 'AlnMgrMakeMultByIntersectOnMaster':
alignmgr.c:5592:4: warning: 'sip_tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqIdFree(sip_tmp);
^~~~~~~~~~~~~~~~~~
alignmgr.c:5885:21: warning: 'sip_tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
sip_tmp = sip_tmp->next;
~~~~~~~~^~~~~~~~~~~~~~~
alignmgr.c:5846:18: note: 'sip_tmp' was declared here
SeqIdPtr sip_tmp;
^~~~~~~
alignmgr.c:5883:17: warning: 'sip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (SAM_OrderSeqID(sip_tmp, sip) == 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr.c:5844:18: note: 'sip' was declared here
SeqIdPtr sip;
^~~
alignmgr.c: In function 'am_is_consistent':
alignmgr.c:10114:13: warning: 'n' may be used uninitialized in this function [-Wmaybe-uninitialized]
AlnMgrGetNthUnalignedForNthRow(sap, n, i, &u_start, &u_stop);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF aliparse.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/aliparse.h:12,
from aliparse.c:9:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
aliparse.c: In function 's_IsInterleaved':
aliparse.c:929:37: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(s_configInfo.useMaybes == FALSE) &&
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
(seqLinePtr->maybe == FALSE))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aliparse.c:823:20: warning: variable 'isMaybe' set but not used [-Wunused-but-set-variable]
Boolean isMaybe;
^~~~~~~
aliparse.c: In function 's_ProcessInterId':
aliparse.c:1000:15: warning: variable 'errPtr' set but not used [-Wunused-but-set-variable]
ErrInfoPtr errPtr;
^~~~~~
aliparse.c: In function 's_ProcessInterSeq':
aliparse.c:1090:15: warning: variable 'errPtr' set but not used [-Wunused-but-set-variable]
ErrInfoPtr errPtr = NULL;
^~~~~~
aliparse.c: In function 's_AnalyzeInterleaved':
aliparse.c:1193:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aliparse.c: In function 's_ProcessContigId':
aliparse.c:1385:18: warning: variable 'errPtr' set but not used [-Wunused-but-set-variable]
ErrInfoPtr errPtr;
^~~~~~
aliparse.c: In function 's_ProcessContigSeq':
aliparse.c:1476:18: warning: variable 'errPtr' set but not used [-Wunused-but-set-variable]
ErrInfoPtr errPtr;
^~~~~~
aliparse.c: In function 's_AnalyzeContiguous':
aliparse.c:1603:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aliparse.c: In function 's_CheckContext':
aliparse.c:2150:33: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(seqLinePtr->maybe == TRUE) &&
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
(s_configInfo.useMaybes == TRUE))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aliparse.c:2131:20: warning: variable 'errPtr' set but not used [-Wunused-but-set-variable]
ErrInfoPtr errPtr;
^~~~~~
aliparse.c: In function 'PrintOutMultAlign':
aliparse.c:3161:10: warning: statement with no effect [-Wunused-value]
for (d; d<spacer; d++)
^~~
aliparse.c: In function 'ALI_ConvertToNCBIData':
aliparse.c:3227:17: warning: variable 'sdp' set but not used [-Wunused-but-set-variable]
SeqDescrPtr sdp;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/aliparse.h:15,
from aliparse.c:9:
aliparse.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
aliparse.c:57:18: warning: 's_SegCompare' declared 'static' but never defined [-Wunused-function]
static int s_SegCompare(const void *i,
^~~~~~~~~~~~
aliparse.c:3186:13: warning: 'PrintOutSegs' defined but not used [-Wunused-function]
static void PrintOutSegs(SeqAlignPtr sap)
^~~~~~~~~~~~
aliparse.c:3130:13: warning: 'PrintOutMultAlign' defined but not used [-Wunused-function]
static void PrintOutMultAlign(SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~
aliparse.c:449:13: warning: 's_FreeRowList' defined but not used [-Wunused-function]
static void s_FreeRowList (ValNodePtr rowList)
^~~~~~~~~~~~~
aliparse.c: In function 's_GetRowIdString':
aliparse.c:543:20: warning: 'newIdStr' may be used uninitialized in this function [-Wmaybe-uninitialized]
CharPtr newIdStr;
^~~~~~~~
aliparse.c: In function 's_ProcessMaybes':
aliparse.c:696:21: warning: 'lastSeqPart' may be used uninitialized in this function [-Wmaybe-uninitialized]
lastSeqPart->next = newSeqPart;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from ../include/ncbi.h:62:0,
from ../include/aliparse.h:12,
from aliparse.c:9:
../include/ncbistr.h:337:19: warning: 'currentIdStr' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringCmp Nlm_StringCmp
^~~~~~~~~~~~~
aliparse.c:631:18: note: 'currentIdStr' was declared here
CharPtr currentIdStr;
^~~~~~~~~~~~
aliparse.c: In function 'Ali_Read':
aliparse.c:1355:14: warning: 'previousLength' may be used uninitialized in this function [-Wmaybe-uninitialized]
errPtr = Ali_AddError (&(fileInfoPtr->errors),ERR_SEQ_LENGTH_MISMATCH,
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
previousLength,
~~~~~~~~~~~~~~~
s_configInfo.declaredInfo.seqLength);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aliparse.c:1154:20: note: 'previousLength' was declared here
Int4 previousLength;
^~~~~~~~~~~~~~
aliparse.c:927:18: warning: 'seqLinePtr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (seqLinePtr->sequence != NULL)
~~~~~~~~~~^~~~~~~~~~
aliparse.c:820:20: note: 'seqLinePtr' was declared here
SeqLineInfoPtr seqLinePtr;
^~~~~~~~~~
aliparse.c:760:3: warning: 'cLineType' may be used uninitialized in this function [-Wmaybe-uninitialized]
fprintf(stderr,"%04d: MAYBE SEQUENCE[%c] : %s\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqLinePtr->rowNum,
~~~~~~~~~~~~~~~~~~~
cLineType,
~~~~~~~~~~
seqLinePtr->sequence);
~~~~~~~~~~~~~~~~~~~~~
aliparse.c:723:20: note: 'cLineType' was declared here
Char cLineType;
^~~~~~~~~
aliparse.c: In function 'ALI_ConvertToNCBIData':
aliparse.c:3276:4: warning: 'sep_new' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAlignAddInSeqEntry (sep_head, sanp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF aliread.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from aliread.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/aliparse.h:15,
from aliread.c:6:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF alignval.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from alignval.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
alignval.c: In function 'ValidateSeqlengthInDenseSeg':
alignval.c:1214:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if(stptrtemp[j+i*aligndim]+lenptrtemp[i]>bslen)
^
alignval.c: In function 'PercentStringMatch':
alignval.c:1495:32: warning: variable 'max_len' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, min_len, k, max_len;
^~~~~~~
alignval.c: In function 'CheckAlnSeqLens':
alignval.c:1893:12: warning: variable 'aln_len' set but not used [-Wunused-but-set-variable]
Int4 aln_len, start, stop;
^~~~~~~
alignval.c: In function 'ValidateSeqAlign':
alignval.c:1991:16: warning: variable 'ans' set but not used [-Wunused-but-set-variable]
MsgAnswer ans;
^~~
alignval.c: In function 'GetAlignmentColumnPercentIdentities':
alignval.c:2371:14: warning: variable 'num_match' set but not used [-Wunused-but-set-variable]
Int4 num_match;
^~~~~~~~~
alignval.c: In function 'WeightedAlignmentPercentIdentity':
alignval.c:2681:14: warning: variable 'num_match' set but not used [-Wunused-but-set-variable]
Int4 num_match;
^~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from alignval.c:57:
alignval.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
alignval.c:1891:13: warning: 'CheckAlnSeqLens' defined but not used [-Wunused-function]
static void CheckAlnSeqLens (SeqAlignPtr salp)
^~~~~~~~~~~~~~~
alignval.c:1476:16: warning: 'IsSipContainedInStdseg' defined but not used [-Wunused-function]
static Boolean IsSipContainedInStdseg(SeqIdPtr sip, StdSegPtr ssp)
^~~~~~~~~~~~~~~~~~~~~~
alignval.c:568:13: warning: 'delete_bioseqs' defined but not used [-Wunused-function]
static void delete_bioseqs (ValNodePtr ids, Uint2 entityID)
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF sqnutil1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/sqnutils.h:48,
from sqnutil1.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sqnutil1.c: In function 'GeneExtendFunc':
sqnutil1.c:2514:18: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
sqnutil1.c: In function 'ParseAnticodon':
sqnutil1.c:3961:14: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil1.c: In function 'ParseCodeBreak':
sqnutil1.c:4081:17: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil1.c: In function 'CleanOrgModListEx':
sqnutil1.c:6276:48: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
} else if (last->subtype == omp->subtype &&
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
StringICmp (last->subname, omp->subname) == 0 ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil1.c: In function 'CleanUpPubdescAuthors':
sqnutil1.c:9213:20: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
ValNodePtr PNTR prev;
^~~~
sqnutil1.c: In function 'RemoveUnnecessaryGeneXrefs':
sqnutil1.c:14155:24: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil1.c: In function 'LinkTwoFeatures':
sqnutil1.c:18204:25: warning: variable 'prev_xref' set but not used [-Wunused-but-set-variable]
SeqFeatXrefPtr xref, prev_xref, next_xref;
^~~~~~~~~
sqnutil1.c: In function 'RemoveBadCodonRecognizedCallback':
sqnutil1.c:18750:13: warning: variable 'rcodon' set but not used [-Wunused-but-set-variable]
Uint1 rcodon [4];
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from sqnutil1.c:63:
sqnutil1.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
sqnutil1.c:10364:16: warning: 'CleanUpSgml' defined but not used [-Wunused-function]
static CharPtr CleanUpSgml (
^~~~~~~~~~~
sqnutil1.c:10250:13: warning: 'SortGoTermsSfp' defined but not used [-Wunused-function]
static void SortGoTermsSfp (
^~~~~~~~~~~~~~
sqnutil1.c:7645:16: warning: 'IsStringSingleToken' defined but not used [-Wunused-function]
static Boolean IsStringSingleToken (CharPtr str)
^~~~~~~~~~~~~~~~~~~
sqnutil1.c:5290:13: warning: 'CleanupConsSplice' defined but not used [-Wunused-function]
static void CleanupConsSplice (GBQualPtr gbq)
^~~~~~~~~~~~~~~~~
sqnutil1.c:2509:16: warning: 'GeneExtendFunc' defined but not used [-Wunused-function]
static Boolean GeneExtendFunc (GatherContextPtr gcp)
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF sqnutil2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/sqnutils.h:48,
from sqnutil2.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sqnutil2.c: In function 'FindResidueByName':
sqnutil2.c:5197:11: warning: variable 'last' set but not used [-Wunused-but-set-variable]
Uint1 last;
^~~~
sqnutil2.c: In function 'ReadFeatureTableEx':
sqnutil2.c:7202:18: warning: variable 'isnote' set but not used [-Wunused-but-set-variable]
Boolean isnote;
^~~~~~
sqnutil2.c:7194:18: warning: variable 'endsinspace' set but not used [-Wunused-but-set-variable]
Boolean endsinspace;
^~~~~~~~~~~
sqnutil2.c: In function 'SeqEntryCopyReplace':
sqnutil2.c:9199:8: warning: variable 'type' set but not used [-Wunused-but-set-variable]
Uint1 type = 0;
^~~~
sqnutil2.c: In function 'StreamingReadBioseq':
sqnutil2.c:10024:10: warning: variable 'level' set but not used [-Wunused-but-set-variable]
Int2 level;
^~~~~
sqnutil2.c: In function 'StreamAsnForDescriptors':
sqnutil2.c:10257:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (rval = StreamingReadSeqEntry (aip, sp, &sr)) {
^~~~~
sqnutil2.c: In function 'StreamingReadWriteSeqSubmit':
sqnutil2.c:10637:1: warning: label 'ret' defined but not used [-Wunused-label]
ret:
^~~
sqnutil2.c: In function 'WriteAsnWithReplacedDescriptors':
sqnutil2.c:10676:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (rval = StreamingReadWriteSeqEntry(desc_stream_list, aip_in, aip_out, sp)) {
^~~~~
sqnutil2.c: In function 'ReadFeatureTableFile':
sqnutil2.c:11627:18: warning: variable 'begin' set but not used [-Wunused-but-set-variable]
Int4 begin;
^~~~~
sqnutil2.c: In function 'ReadFastaOnly':
sqnutil2.c:11821:18: warning: variable 'seqid' set but not used [-Wunused-but-set-variable]
Char seqid [2048];
^~~~~
sqnutil2.c: In function 'ReadDeltaFastaWithEmptyDefline':
sqnutil2.c:12352:29: warning: variable 'seqid' set but not used [-Wunused-but-set-variable]
Char line [4096], seqid [2048];
^~~~~
sqnutil2.c: In function 'SortSeqGraphProc':
sqnutil2.c:12908:26: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (gip2->right < gip2->right) {
^
sqnutil2.c: In function 'PrintQualityScoresToBuffer':
sqnutil2.c:12958:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil2.c: In function 'GetScoresbySeqId':
sqnutil2.c:13367:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil2.c: In function 'IsStringInSpanInList':
sqnutil2.c:17223:11: warning: variable 'str_val' set but not used [-Wunused-but-set-variable]
Int4 str_val;
^~~~~~~
sqnutil2.c:17221:27: warning: variable 'suffix_len' set but not used [-Wunused-but-set-variable]
Int4 prefix_len = 0, suffix_len;
^~~~~~~~~~
sqnutil2.c: In function 'CreateStructuredCommentsFromFile':
sqnutil2.c:19251:35: warning: variable 'vnp_h' set but not used [-Wunused-but-set-variable]
ValNodePtr table, header, line, vnp_h, vnp_l, tmp;
^~~~~
sqnutil2.c: In function 'AlignmentIntervalToString':
sqnutil2.c:19615:14: warning: variable 'target_strand' set but not used [-Wunused-but-set-variable]
Uint1 target_strand;
^~~~~~~~~~~~~
sqnutil2.c:19614:14: warning: variable 'seq_len' set but not used [-Wunused-but-set-variable]
Int4 seq_len;
^~~~~~~
sqnutil2.c: In function 'AdjustForConsensusSpliceCallback':
sqnutil2.c:20781:33: warning: variable 'partial5_last' set but not used [-Wunused-but-set-variable]
Boolean partial5, partial3, partial5_last, partial3_last, first = TRUE;
^~~~~~~~~~~~~
sqnutil2.c: In function 'RemoveGIProc':
sqnutil2.c:21356:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from sqnutil2.c:58:
sqnutil2.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
sqnutil2.c:16055:13: warning: 'RevCompFeatsOnBioseq' defined but not used [-Wunused-function]
static void RevCompFeatsOnBioseq (BioseqPtr bsp)
^~~~~~~~~~~~~~~~~~~~
sqnutil2.c:8266:16: warning: 'DoesSeqEntryAccessionMatchList' defined but not used [-Wunused-function]
static Boolean DoesSeqEntryAccessionMatchList (SeqEntryPtr sep, ValNodePtr accn_list)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil2.c:4661:16: warning: 'IsNonSeqChar' defined but not used [-Wunused-function]
static Boolean IsNonSeqChar (Char ch, Boolean is_prot)
^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF sqnutil3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/sqnutils.h:48,
from sqnutil3.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sqnutil3.c: In function 'BspLinkCDSmRNAbyOverlap':
sqnutil3.c:526:22: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil3.c: In function 'CautiousSeqEntryCleanup':
sqnutil3.c:2265:16: warning: variable 'taxserver' set but not used [-Wunused-but-set-variable]
Boolean taxserver;
^~~~~~~~~
sqnutil3.c: In function 'ConvertSegSetsToDeltaSequences':
sqnutil3.c:3376:17: warning: variable 'bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr bsp, new_bsp = NULL;
^~~
sqnutil3.c:3370:26: warning: variable 'prev_sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sub_sep, prev_sep, next_sep;
^~~~~~~~
sqnutil3.c: In function 'MakeSequinDataFromAlignmentEx':
sqnutil3.c:5124:32: warning: variable 'num_sets' set but not used [-Wunused-but-set-variable]
Int4 index, curr_seg, num_sets;
^~~~~~~~
sqnutil3.c:5118:26: warning: variable 'salp_last' set but not used [-Wunused-but-set-variable]
SeqAlignPtr salp_list, salp_last;
^~~~~~~~~
sqnutil3.c:5118:15: warning: variable 'salp_list' set but not used [-Wunused-but-set-variable]
SeqAlignPtr salp_list, salp_last;
^~~~~~~~~
sqnutil3.c: In function 'OrgNameMatchExceptOldName':
sqnutil3.c:13089:28: warning: self-comparison always evaluates to false [-Wtautological-compare]
|| onp2->mgcode != onp2->mgcode
^~
sqnutil3.c: In function 'GetCDSformRNA':
sqnutil3.c:19157:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil3.c: In function 'FindTextInFlatfileEx':
sqnutil3.c:20891:19: warning: variable 'okay' set but not used [-Wunused-but-set-variable]
Boolean okay;
^~~~
sqnutil3.c: In function 'CheckForTitleAuthorConflicts':
sqnutil3.c:21972:14: warning: variable 'author_conflict' set but not used [-Wunused-but-set-variable]
Boolean author_conflict = FALSE;
^~~~~~~~~~~~~~~
sqnutil3.c: In function 'SortVnpByBspProjectId':
sqnutil3.c:25733:31: warning: the comparison will always evaluate as 'true' for the address of 'vnp2' will never be NULL [-Waddress]
if (vnp1 != NULL &&& vnp2 != NULL) {
^~
sqnutil3.c: In function 'GetDiscrepancyItemTextEx':
sqnutil3.c:28202:21: warning: variable 'special_flag' set but not used [-Wunused-but-set-variable]
Boolean special_flag = FALSE;
^~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from sqnutil3.c:62:
sqnutil3.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
sqnutil3.c: In function 'FillInMissingTraces':
sqnutil3.c:31968:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
sqnutil3.c:33544:13: warning: 'TestLatLonFormatting' defined but not used [-Wunused-function]
static void TestLatLonFormatting (FILE *fp)
^~~~~~~~~~~~~~~~~~~~
sqnutil3.c:31404:1: warning: 'BarcodeTestForSeqEntry' defined but not used [-Wunused-function]
BarcodeTestForSeqEntry
^~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:31396:13: warning: 'FindBadGPS' defined but not used [-Wunused-function]
static void FindBadGPS (BioseqPtr bsp, Pointer userdata)
^~~~~~~~~~
sqnutil3.c:23725:13: warning: 'FindSuspectrRNAProductsCallback' defined but not used [-Wunused-function]
static void FindSuspectrRNAProductsCallback (SeqFeatPtr sfp, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:19971:16: warning: 'FeatureCountHasNumFeats' defined but not used [-Wunused-function]
static Boolean FeatureCountHasNumFeats (ValNodePtr vnp, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:18676:24: warning: 'SortVnpByHaplotypeThenSequenceAllowNDiff' defined but not used [-Wunused-function]
static int LIBCALLBACK SortVnpByHaplotypeThenSequenceAllowNDiff (VoidPtr ptr1, VoidPtr ptr2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:16581:24: warning: 'IntervalPairFree' defined but not used [-Wunused-function]
static IntervalPairPtr IntervalPairFree (IntervalPairPtr i)
^~~~~~~~~~~~~~~~
sqnutil3.c:13399:16: warning: 'ContainsBracketsOrParentheses' defined but not used [-Wunused-function]
static Boolean ContainsBracketsOrParentheses (CharPtr pattern, CharPtr search)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:10252:13: warning: 'ExtractVnpByStringSearch' defined but not used [-Wunused-function]
static void ExtractVnpByStringSearch (ValNodePtr PNTR list, CharPtr search)
^~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:9755:13: warning: 'GeneLocusTagDiscrepancyCallback' defined but not used [-Wunused-function]
static void GeneLocusTagDiscrepancyCallback (ValNodePtr item_list, Pointer userdata)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:9672:25: warning: 'InconsistentLocusTagPrefix' defined but not used [-Wunused-function]
static ClickableItemPtr InconsistentLocusTagPrefix (PrefixCheckPtr pcp)
^~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:9621:19: warning: 'FreePrefixCheckList' defined but not used [-Wunused-function]
static ValNodePtr FreePrefixCheckList (ValNodePtr prefix_list)
^~~~~~~~~~~~~~~~~~~
sqnutil3.c: In function 'LinkCDSmRNAbyLabelAndLocationCallback':
sqnutil3.c:889:23: warning: 'best_diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (diff < best_diff) {
^
sqnutil3.c: In function 'ValidateInferenceQualifier':
sqnutil3.c:6030:6: warning: 'rest' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (rest == NULL) return BAD_INFERENCE_BODY;
^
sqnutil3.c:6028:6: warning: 'best' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (best < 0 || inferencePrefix [best] == NULL) return BAD_INFERENCE_PREFIX;
^
sqnutil3.c: In function 'tRNASameStrandBioseqCallback':
sqnutil3.c:16126:8: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (strand == Seq_strand_minus) {
^
sqnutil3.c: In function 'CheckForDivConflicts':
sqnutil3.c:7901:11: warning: 'sdp' may be used uninitialized in this function [-Wmaybe-uninitialized]
else ValNodeAddPointer(&(grp_sdp[i]), OBJ_SEQDESC, sdp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c: In function 'FindMismatchedComments':
sqnutil3.c:25390:47: warning: 'sdp' may be used uninitialized in this function [-Wmaybe-uninitialized]
sprintf (fmt, sub_fmt, (CharPtr) sdp->data.ptrvalue);
~~~~~~~~~^~~~~~~~~
sqnutil3.c: In function 'FixCountryColons':
sqnutil3.c:7523:14: warning: 'biop' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
~~~~^~~~~~~~~~~~~~~
sqnutil3.c: In function 'AddmRNAForCDS':
sqnutil3.c:19565:10: warning: 'rna' may be used uninitialized in this function [-Wmaybe-uninitialized]
return rna;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF sqnutil4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/sqnutils.h:48,
from sqnutil4.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sqnutil4.c: In function 'ListClauses':
sqnutil4.c:8272:43: warning: variable 'twobefore' set but not used [-Wunused-but-set-variable]
FeatureClausePtr thisclause, onebefore, twobefore, oneafter, twoafter;
^~~~~~~~~
sqnutil4.c: In function 'SmashOneTallClause':
sqnutil4.c:9576:20: warning: variable 'subclause_featlist' set but not used [-Wunused-but-set-variable]
ValNodePtr subclause_featlist;
^~~~~~~~~~~~~~~~~~
sqnutil4.c: In function 'GetFeatureClauseForSeg':
sqnutil4.c:10448:21: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start, stop;
^~~~~
sqnutil4.c: In function 'IsAmplifiedMiscFeat':
sqnutil4.c:10701:9: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (sfp != NULL && sfp->idx.subtype == FEATDEF_misc_feature
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&& (StringNICmp (sfp->comment, phrase1, StringLen (phrase1)) == 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil4.c: In function 'ConvertProtToImpFunc':
sqnutil4.c:13849:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil4.c: In function 'ExtraCDSCreationActions':
sqnutil4.c:14728:28: warning: variable 'nsep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr psep, nsep;
^~~~
sqnutil4.c: In function 'TESTDisplayQualCombo':
sqnutil4.c:15752:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Int4 val;
^~~
sqnutil4.c: In function 'ConvertCDSToMatPeptideForOverlappingCDS':
sqnutil4.c:17198:15: warning: variable 'crp' set but not used [-Wunused-but-set-variable]
CdRegionPtr crp;
^~~
sqnutil4.c: In function 'AddNewUniqueAnnotations':
sqnutil4.c:17372:39: warning: variable 'sap_tmp_next' set but not used [-Wunused-but-set-variable]
SeqAnnotPtr sap, sap_next, sap_tmp, sap_tmp_next, sap_copy, last_sap;
^~~~~~~~~~~~
sqnutil4.c: In function 'AssignBioseqToLineageGroup':
sqnutil4.c:18024:27: warning: variable 'vnp_last' set but not used [-Wunused-but-set-variable]
ValNodePtr list, vnp, vnp_last = NULL;
^~~~~~~~
sqnutil4.c: In function 'ImportNucleotideFASTASequencesFromFile':
sqnutil4.c:26442:17: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int4 count;
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from sqnutil4.c:58:
sqnutil4.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/tax3api.h:51:0,
from sqnutil4.c:63:
../include/objtax3.h:183:31: warning: 'Value_valueFree' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr ));
^~~~~~~~~~~~~~~
../include/objtax3.h:184:31: warning: 'Value_valueAsnRead' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~
../include/objtax3.h:185:24: warning: 'Value_valueAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~
sqnutil4.c:15901:13: warning: 'TESTDisplayList' defined but not used [-Wunused-function]
static void TESTDisplayList (ValNodePtr new_list)
^~~~~~~~~~~~~~~
sqnutil4.c:15872:19: warning: 'ExpandOneComboListUsingAllPresentQuals' defined but not used [-Wunused-function]
static ValNodePtr ExpandOneComboListUsingAllPresentQuals (QualComboPtr q)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil4.c:15584:16: warning: 'RemoveFieldFromUniqBioSrcGrpList' defined but not used [-Wunused-function]
static Boolean RemoveFieldFromUniqBioSrcGrpList (ValNodePtr list, FieldTypePtr field)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil4.c:9705:19: warning: 'RemoveAllButLastCDS' defined but not used [-Wunused-function]
static ValNodePtr RemoveAllButLastCDS (
^~~~~~~~~~~~~~~~~~~
sqnutil4.c:9674:13: warning: 'SmashTallClauses' defined but not used [-Wunused-function]
static void SmashTallClauses (
^~~~~~~~~~~~~~~~
sqnutil4.c:9510:13: warning: 'RemoveFeats' defined but not used [-Wunused-function]
static void RemoveFeats (
^~~~~~~~~~~
sqnutil4.c:4945:13: warning: 'CountFeatures' defined but not used [-Wunused-function]
static Int4 CountFeatures (
^~~~~~~~~~~~~
sqnutil4.c: In function 'ConvertProtToImpFunc':
sqnutil4.c:14023:13: warning: 'topOfGbqList' may be used uninitialized in this function [-Wmaybe-uninitialized]
sfp->qual = topOfGbqList;
~~~~~~~~~~^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF subutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/objsub.h:76,
from ../include/subutil.h:50,
from subutil.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
subutil.c: In function 'AddSeqLitToBioseq':
subutil.c:769:16: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
subutil.c: In function 'AddReferenceToSegmentedEntry':
subutil.c:1163:22: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
SeqEntryPtr tmp, prev;
^~~~
subutil.c: In function 'GetDNAConv':
subutil.c:1624:15: warning: array subscript has type 'char' [-Wchar-subscripts]
dnaconv[*ptr] = *ptr;
^
subutil.c: In function 'GetProteinConv':
subutil.c:1646:16: warning: array subscript has type 'char' [-Wchar-subscripts]
protconv[*ptr] = *ptr;
^
subutil.c: In function 'AddBasesToByteStore':
subutil.c:1669:26: warning: array subscript has type 'char' [-Wchar-subscripts]
residue = dnaconv[ch];
^
subutil.c: In function 'AddAAsToByteStore':
subutil.c:1700:25: warning: array subscript has type 'char' [-Wchar-subscripts]
residue = aaconv[ch];
^
subutil.c: In function 'CitArtBuild':
subutil.c:2683:21: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp, tmp;
^~~
At top level:
subutil.c:3546:20: warning: 'TranslateCdRegionNew' defined but not used [-Wunused-function]
static SeqEntryPtr TranslateCdRegionNew (
^~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF edutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from ../include/edutil.h:188,
from edutil.c:365:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
edutil.c: In function 'SeqLocsToDeltaSeqs':
edutil.c:795:14: warning: variable 'sip' set but not used [-Wunused-but-set-variable]
SeqIdPtr sip;
^~~
edutil.c: In function 'SeqLocCopyPart':
edutil.c:2243:13: warning: variable 'done' set but not used [-Wunused-but-set-variable]
Boolean done, started, wasa_null, hada_null;
^~~~
edutil.c: In function 'IndexedSeqFeatsCopy':
edutil.c:2400:16: warning: variable 'region' set but not used [-Wunused-but-set-variable]
ValNodePtr region;
^~~~~~
edutil.c: In function 'SeqFeatsCopy':
edutil.c:2504:16: warning: variable 'region' set but not used [-Wunused-but-set-variable]
ValNodePtr region;
^~~~~~
edutil.c: In function 'SeqLocInsert':
edutil.c:3686:10: warning: variable 'diff' set but not used [-Wunused-but-set-variable]
Int4 diff, numpnt, i, tpos;
^~~~
edutil.c: In function 'SeqEdRecreateDeletedFeats':
edutil.c:4212:19: warning: variable 'sfp' set but not used [-Wunused-but-set-variable]
SeqFeatPtr sfp;
^~~
edutil.c: In function 'SeqEdSeqLocInsert':
edutil.c:4512:8: warning: variable 'diff' set but not used [-Wunused-but-set-variable]
Int4 diff, numpnt, i, tpos;
^~~~
edutil.c: In function 'SeqEdSeqLocDelete':
edutil.c:5069:10: warning: variable 'diff' set but not used [-Wunused-but-set-variable]
Int4 diff;
^~~~
edutil.c: In function 'SeqEdInsertAdjustFeat':
edutil.c:5300:7: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
&& sfp->data.choice == SEQFEAT_CDREGION)
edutil.c: In function 'SeqEdDeleteFromBsp':
edutil.c:6485:11: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
&& sfp->data.choice == SEQFEAT_CDREGION)
edutil.c:6548:11: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
&& sfp->data.choice == SEQFEAT_CDREGION)
edutil.c:6437:21: warning: variable 'merge_mode' set but not used [-Wunused-but-set-variable]
Boolean merge_mode;
^~~~~~~~~~
edutil.c:6428:21: warning: variable 'feats_altered' set but not used [-Wunused-but-set-variable]
Boolean feats_altered = FALSE;
^~~~~~~~~~~~~
edutil.c: In function 'BioseqInsert':
cc1: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
edutil.c: In function 'SeqEdInsert':
cc1: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from ../include/seqmgr.h:48,
from asn2ff1.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff1.c: In function 'asn2ff_print':
asn2ff1.c:289:17: warning: unused variable 'dsp' [-Wunused-variable]
DescrStructPtr dsp = NULL;
^~~
asn2ff1.c: In function 'Asn2ffJobCreate':
asn2ff1.c:351:18: warning: unused variable 'itemID' [-Wunused-variable]
Uint4 itemID = 0;
^~~~~~
asn2ff1.c: In function 'SeqEntryToEntrez':
asn2ff1.c:498:15: warning: unused variable 'slp' [-Wunused-variable]
SeqLocPtr slp = NULL;
^~~
asn2ff1.c: In function 'SeqLocToFlat':
asn2ff1.c:1518:19: warning: unused variable 'itemID' [-Wunused-variable]
Uint4 itemID=0;
^~~~~~
asn2ff1.c: In function 'asn2ff_setup':
asn2ff1.c:1579:12: warning: variable 'bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr bsp;
^~~
asn2ff1.c: In function 'PrintStatusLine':
asn2ff1.c:2197:15: warning: unused variable 'ptr' [-Wunused-variable]
CharPtr u, ptr=NULL;
^~~
asn2ff1.c: In function 'asn2gb_setup':
asn2ff1.c:2403:24: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (ajp->genome_view && gbp->map == FALSE || ajp->contig_view) {
At top level:
asn2ff1.c:2189:13: warning: 'PrintStatusLine' defined but not used [-Wunused-function]
static void PrintStatusLine(Asn2ffJobPtr ajp, GBEntryPtr gbp)
^~~~~~~~~~~~~~~
asn2ff1.c:2171:16: warning: 'find_user_object' defined but not used [-Wunused-function]
static Boolean find_user_object(BioseqPtr bsp)
^~~~~~~~~~~~~~~~
asn2ff1.c:816:19: warning: 'SeqEntryToLinkStrEx' defined but not used [-Wunused-function]
static LinkStrPtr SeqEntryToLinkStrEx(Asn2ffJobPtr ajp, SeqEntryPtr sep, LinkStrPtr lsp, Uint1 format)
^~~~~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff1.c:45:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff1.c: In function 'asn2embl_setup':
asn2ff1.c:2754:7: warning: 'max' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (max == index+1) {
^
asn2ff1.c: In function 'asn2gp_setup':
asn2ff1.c:2942:4: warning: 'feat_num' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (index=0; index < feat_num; index++) {
^~~
asn2ff1.c: In function 'SeqEntryToGBFlatNoSeq':
asn2ff1.c:1292:15: warning: 'rsult' may be used uninitialized in this function [-Wmaybe-uninitialized]
Boolean rsult;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/gather.h:166,
from asn2ff2.c:216:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff2.c: In function 'GetStrForBankit':
asn2ff2.c:518:9: warning: unused variable 'i' [-Wunused-variable]
Int2 i=0, ptrlen = 0;
^
asn2ff2.c: In function 'GetCommentByChoice':
asn2ff2.c:769:34: warning: unused variable 'string' [-Wunused-variable]
CharPtr buf = NULL, ptr = NULL, string=NULL, new_string=NULL, str=NULL;
^~~~~~
asn2ff2.c: In function 'GP_GetSeqDescrComms':
asn2ff2.c:1163:10: warning: unused variable 'got_comment' [-Wunused-variable]
Boolean got_comment=FALSE;
^~~~~~~~~~~
asn2ff2.c: At top level:
asn2ff2.c:1358:8: warning: return type defaults to 'int' [-Wimplicit-int]
static ChoicePID(SeqIdPtr sid)
^~~~~~~~~
asn2ff2.c: In function 'GetGibbsqCommentLength':
asn2ff2.c:1600:7: warning: unused variable 'gibbsq' [-Wunused-variable]
Int4 gibbsq=0, total;
^~~~~~
asn2ff2.c: In function 'GatherDescrByChoice':
asn2ff2.c:1864:8: warning: variable 'bspID' set but not used [-Wunused-but-set-variable]
Uint2 bspID;
^~~~~
At top level:
asn2ff2.c:1190:16: warning: 'GetSPBlock' defined but not used [-Wunused-function]
static CharPtr GetSPBlock (Asn2ffJobPtr ajp, GBEntryPtr gbp)
^~~~~~~~~~
asn2ff2.c:680:16: warning: 'GetEvidence' defined but not used [-Wunused-function]
static CharPtr GetEvidence(Asn2ffJobPtr ajp, GBEntryPtr gbp)
^~~~~~~~~~~
asn2ff2.c:232:16: warning: 'has_comment' defined but not used [-Wunused-variable]
static Boolean has_comment;
^~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff2.c:218:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff2.c: In function 'GetCommentByChoice':
asn2ff2.c:829:8: warning: 'is_other' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (is_other == TRUE && mfp->completeness) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:372,
from asn2ff3.c:628:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff3.c: In function 'PutGeneFirst':
asn2ff3.c:1662:26: warning: unused variable 'qual_temp' [-Wunused-variable]
GBQualPtr gbqual, qual, qual_temp=NULL, qual_gene=NULL;
^~~~~~~~~
asn2ff3.c:1661:10: warning: unused variable 'still_looking' [-Wunused-variable]
Boolean still_looking=TRUE;
^~~~~~~~~~~~~
asn2ff3.c: In function 'mRNAEvidenceComment':
asn2ff3.c:1746:9: warning: unused variable 'Locus_id' [-Wunused-variable]
Int4 Locus_id = 0;
^~~~~~~~
asn2ff3.c: In function 'Add_gene_id':
asn2ff3.c:3306:24: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'Nlm_VoidPtr {aka void *}' [-Wformat=]
sprintf(val, "GeneID:%s", vnp->data.ptrvalue);
^
asn2ff3.c: In function 'Add_trid':
asn2ff3.c:3712:7: warning: unused variable 'gi' [-Wunused-variable]
Int4 gi = -1;
^~
At top level:
asn2ff3.c:3291:13: warning: 'Add_gene_id' defined but not used [-Wunused-function]
static void Add_gene_id (GeneStructPtr gsp, SeqFeatPtr sfp_out)
^~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff3.c:628:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
In file included from ../include/ncbi.h:59:0,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:372,
from asn2ff3.c:628:
asn2ff3.c: In function 'Add_dbxref.isra.0':
../include/ncbimem.h:232:23: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
asn2ff3.c:805:10: note: 'val' was declared here
CharPtr val;
^~~
asn2ff3.c: In function 'GettRNAaa':
asn2ff3.c:2208:9: warning: 'seq_code' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr = Get3LetterSymbol(seq_code, table, trna->aa, error_msgs);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:372,
from asn2ff4.c:273:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff4.c: In function 'FlatLocPoint':
asn2ff4.c:437:15: warning: variable 'order' set but not used [-Wunused-but-set-variable]
static Uint1 order[NUM_SEQID];
^~~~~
asn2ff4.c: In function 'do_FlatLoc':
asn2ff4.c:1122:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if ( ! FlatVirtLoc( bsp, slp))
^
asn2ff4.c: At top level:
asn2ff4.c:1347:8: warning: return type defaults to 'int' [-Wimplicit-int]
static CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2)
^~~~~~~~~~
asn2ff4.c: In function 'CreateImpFeatFromProt':
asn2ff4.c:1659:14: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
asn2ff4.c: In function 'MatchNAGeneToFeat':
asn2ff4.c:2196:17: warning: variable 'nsp' set but not used [-Wunused-but-set-variable]
NoteStructPtr nsp; /* UNUSED */
^~~
asn2ff4.c: In function 'MatchAAGeneToFeat':
asn2ff4.c:2367:18: warning: variable 'nsp' set but not used [-Wunused-but-set-variable]
NoteStructPtr nsp; /* UNUSED */
^~~
asn2ff4.c: In function 'SortOrganizeFeat':
asn2ff4.c:2457:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ofp == NULL)
^~
asn2ff4.c:2459:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ofp->sfpListsize > 0 && ofp->sortListsize < ofp->sfpListsize) {
^~
asn2ff4.c: In function 'OrganizeSeqFeat':
asn2ff4.c:2578:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ajp->ignore_top)
^~
asn2ff4.c:2580:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
gsc.seglevels = 1;
^~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff4.c:273:
At top level:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff4.c: In function 'CheckNewSfpLoc.isra.0':
asn2ff4.c:1767:7: warning: 'slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (SeqLocLen(slp) <= BioseqGetLen(bsp)) {
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff5.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:372,
from asn2ff5.c:177:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff5.c: In function 'format_cit_sub':
asn2ff5.c:1023:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
format == EMBLPEPT_FMT && afp->choice == 1)
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
asn2ff5.c:926:41: warning: variable 'need_space' set but not used [-Wunused-but-set-variable]
Boolean need_comma = FALSE, /*UNUSED*/need_space = TRUE;
^~~~~~~~~~
asn2ff5.c: In function 'format_thesis':
asn2ff5.c:1213:20: warning: variable 'embl_format' set but not used [-Wunused-but-set-variable]
Boolean /*UNUSED*/embl_format = FALSE;
^~~~~~~~~~~
asn2ff5.c: In function 'format_book':
asn2ff5.c:1296:10: warning: variable 'embl_format' set but not used [-Wunused-but-set-variable]
Boolean embl_format = FALSE;
^~~~~~~~~~~
asn2ff5.c: In function 'format_jourarticle':
asn2ff5.c:1680:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (ip->pages != NULL)
^
asn2ff5.c: In function 'StripParanthesis':
asn2ff5.c:2124:12: warning: value computed is not used [-Wunused-value]
temp++; *ptr_in++;
^~~~~~~~~
asn2ff5.c: In function 'PostARefErrMessage':
asn2ff5.c:3005:20: warning: variable 'ignore_this' set but not used [-Wunused-but-set-variable]
Boolean /*UNUSED*/ignore_this, submit=FALSE, error;
^~~~~~~~~~~
asn2ff5.c: At top level:
asn2ff5.c:188:26: warning: 'GetSubmitterName' declared 'static' but never defined [-Wunused-function]
static CharPtr /*UNUSED*/GetSubmitterName PROTO ((Uint1 format, ValNodePtr pub));
^~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff5.c:177:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff5.c: In function 'FlatJournal':
asn2ff5.c:1051:11: warning: 'afp' may be used uninitialized in this function [-Wmaybe-uninitialized]
AffilPtr afp;
^~~
asn2ff5.c:2073:10: warning: 'temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
temp = StringMove (temp," ");
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
asn2ff5.c:1946:23: note: 'temp' was declared here
CharPtr affil=NULL, temp, dup_pages=NULL, retval=NULL;
^~~~
asn2ff5.c: In function 'CheckPubs':
asn2ff5.c:2772:5: warning: 'status' may be used uninitialized in this function [-Wmaybe-uninitialized]
PostARefErrMessage (ajp, bsp, psp, NULL, status, NULL);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff6.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ff6.h:134,
from asn2ff6.c:347:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff6.c: In function 'AddGBQual':
asn2ff6.c:1327:18: warning: variable 'note' set but not used [-Wunused-but-set-variable]
GBQualPtr curq, note = NULL;
^~~~
asn2ff6.c: In function 'FlatOrganelle':
asn2ff6.c:1483:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! retval )
^~
asn2ff6.c:1486:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
break;
^~~~~
asn2ff6.c: In function 'BioseqGetGBDivCodeEx':
asn2ff6.c:1700:23: warning: variable 'diff' set but not used [-Wunused-but-set-variable]
Int2 tech, /*UNUSED*/diff, retval = 0;
^~~~
asn2ff6.c: In function 'GR_PrintPubs':
asn2ff6.c:2297:41: warning: unused variable 'stop' [-Wunused-variable]
Int4 muid, pmid, pat_seqid=0, start=0, stop=0;
^~~~
asn2ff6.c:2297:32: warning: unused variable 'start' [-Wunused-variable]
Int4 muid, pmid, pat_seqid=0, start=0, stop=0;
^~~~~
asn2ff6.c:2297:13: warning: variable 'pmid' set but not used [-Wunused-but-set-variable]
Int4 muid, pmid, pat_seqid=0, start=0, stop=0;
^~~~
asn2ff6.c:2296:10: warning: unused variable 'descr' [-Wunused-variable]
CharPtr descr = NULL;
^~~~~
asn2ff6.c: In function 'ValidateLocus':
asn2ff6.c:2786:17: warning: variable 'base_locus_max' set but not used [-Wunused-but-set-variable]
Int2 /*UNUSED*/base_locus_max, buf_index, exp, length, num_of_digits;
^~~~~~~~~~~~~~
asn2ff6.c: In function 'ValidateOtherAccession':
asn2ff6.c:2886:29: warning: unused variable 'FiveNum' [-Wunused-variable]
Boolean FirstLetter=FALSE, FiveNum = FALSE;
^~~~~~~
asn2ff6.c:2886:10: warning: unused variable 'FirstLetter' [-Wunused-variable]
Boolean FirstLetter=FALSE, FiveNum = FALSE;
^~~~~~~~~~~
asn2ff6.c: In function 'AddExtraAccessions':
asn2ff6.c:3498:20: warning: variable 'ncbi' set but not used [-Wunused-but-set-variable]
Boolean /*UNUSED*/ncbi = FALSE;
^~~~
At top level:
asn2ff6.c:2883:13: warning: 'ValidateOtherAccession' defined but not used [-Wunused-function]
static Int2 ValidateOtherAccession(CharPtr new_buf, CharPtr orig_buf)
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from asn2ff6.c:347:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff6.c: In function 'ValidateLocus':
asn2ff6.c:2786:44: warning: 'exp' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 /*UNUSED*/base_locus_max, buf_index, exp, length, num_of_digits;
^~~
asn2ff6.c: In function 'MakeBaseLocusAwp':
asn2ff6.c:3070:49: warning: 'num_of_digits' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 index, length, base_locus_max, name_len, num_of_digits, num_seg;
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb1.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb1.c: In function 'IsWholeWordSubstr':
asn2gnb1.c:2092:19: warning: variable 'right' set but not used [-Wunused-but-set-variable]
Boolean left, right;
^~~~~
asn2gnb1.c: In function 's_LocusGetBaseName':
asn2gnb1.c:2240:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
asn2gnb1.c:2242:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
newLength = segNameLen - deleteChars;
^~~~~~~~~
asn2gnb1.c: In function 'DoOneSection':
asn2gnb1.c:2363:24: warning: variable 'iasp' set but not used [-Wunused-but-set-variable]
IntAsn2gbSectPtr iasp;
^~~~
asn2gnb1.c:2357:24: warning: variable 'bkmask' set but not used [-Wunused-but-set-variable]
BlockMask bkmask;
^~~~~~
asn2gnb1.c: In function 'Count2Seg':
asn2gnb1.c:3215:18: warning: variable 'to' set but not used [-Wunused-but-set-variable]
Int4 to;
^~
asn2gnb1.c:3213:18: warning: variable 'parent' set but not used [-Wunused-but-set-variable]
BioseqPtr parent;
^~~~~~
asn2gnb1.c: At top level:
asn2gnb1.c:3492:3: warning: missing braces around initializer [-Wmissing-braces]
{TRUE, TRUE, TRUE, TRUE, TRUE,
^
asn2gnb1.c:3492:3: note: (near initialization for 'flagTable[0]')
asn2gnb1.c:3500:3: warning: missing braces around initializer [-Wmissing-braces]
{FALSE, TRUE, TRUE, TRUE, TRUE,
^
asn2gnb1.c:3500:3: note: (near initialization for 'flagTable[1]')
asn2gnb1.c:3508:3: warning: missing braces around initializer [-Wmissing-braces]
{FALSE, FALSE, FALSE, FALSE, FALSE,
^
asn2gnb1.c:3508:3: note: (near initialization for 'flagTable[2]')
asn2gnb1.c:3516:3: warning: missing braces around initializer [-Wmissing-braces]
{FALSE, FALSE, FALSE, FALSE, FALSE,
^
asn2gnb1.c:3516:3: note: (near initialization for 'flagTable[3]')
asn2gnb1.c:3489:33: warning: missing braces around initializer [-Wmissing-braces]
static ModeFlags flagTable [] = {
^
asn2gnb1.c:3489:33: note: (near initialization for 'flagTable')
asn2gnb1.c: In function 'SeqIdWriteForTable':
asn2gnb1.c:5571:13: warning: variable 'pdb' set but not used [-Wunused-but-set-variable]
pdb = NULL, general = NULL, gi = NULL;
^~~
asn2gnb1.c:5570:40: warning: variable 'patent' set but not used [-Wunused-but-set-variable]
SeqIdPtr accn = NULL, local = NULL, patent = NULL,
^~~~~~
In file included from ../include/ncbi.h:58:0,
from asn2gnb1.c:43:
asn2gnb1.c: In function 'DoImmediateFormat':
../include/ncbistd.h:286:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb1.c:6704:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb1.c:6683:20: warning: variable 'is_www' set but not used [-Wunused-but-set-variable]
Boolean is_www;
^~~~~~
In file included from ../include/ncbi.h:58:0,
from asn2gnb1.c:43:
asn2gnb1.c: In function 'asn2gnbk_format':
../include/ncbistd.h:286:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb1.c:6825:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb1.c: In function 'asn2gnbk_cleanup':
asn2gnb1.c:6871:21: warning: variable 'iasp' set but not used [-Wunused-but-set-variable]
IntAsn2gbSectPtr iasp;
^~~~
asn2gnb1.c: In function 'SeqEntryToGnbk':
asn2gnb1.c:7057:22: warning: variable 'userdata' set but not used [-Wunused-but-set-variable]
Pointer userdata = NULL;
^~~~~~~~
asn2gnb1.c:7052:22: warning: variable 'gbseq' set but not used [-Wunused-but-set-variable]
GBSeqPtr gbseq = NULL;
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb1.c:58:
asn2gnb1.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb2.c: In function 's_LocusAddSuffix':
asn2gnb2.c:206:11: warning: variable 'ch' set but not used [-Wunused-but-set-variable]
Char ch;
^~
asn2gnb2.c: In function 'AddLocusBlock':
asn2gnb2.c:1323:66: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
} else if ((moltype >= 2 && moltype <= 8) || moltype >= 10 && moltype <= 11) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
asn2gnb2.c: In function 'AddDblinkBlock':
asn2gnb2.c:2756:22: warning: variable 'parentID' set but not used [-Wunused-but-set-variable]
Int4 parentID;
^~~~~~~~
asn2gnb2.c: In function 'GetRefsOnBioseq':
asn2gnb2.c:5448:22: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
asn2gnb2.c:5445:22: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb2.c:5439:22: warning: variable 'right' set but not used [-Wunused-but-set-variable]
Int4 right;
^~~~~
asn2gnb2.c:5433:22: warning: variable 'left' set but not used [-Wunused-but-set-variable]
Int4 left;
^~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb2.c:57:
asn2gnb2.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb3.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb3.c: In function 'GetStatusForRefTrack':
asn2gnb3.c:601:22: warning: variable 'urf' set but not used [-Wunused-but-set-variable]
UserFieldPtr ufp, urf = NULL;
^~~
asn2gnb3.c: In function 'GetSourcesOnBioseq':
asn2gnb3.c:4151:22: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
asn2gnb3.c:4149:22: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start;
^~~~~
asn2gnb3.c:4148:22: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb3.c: In function 'GetFeatsOnCdsProduct':
asn2gnb3.c:5007:22: warning: variable 'isRefSeq' set but not used [-Wunused-but-set-variable]
Boolean isRefSeq;
^~~~~~~~
asn2gnb3.c: In function 'GetRemoteFeatsOnCdsProduct':
asn2gnb3.c:5155:20: warning: variable 'lastsfp' set but not used [-Wunused-but-set-variable]
SeqFeatPtr lastsfp;
^~~~~~~
asn2gnb3.c:5154:20: warning: variable 'lastsap' set but not used [-Wunused-but-set-variable]
SeqAnnotPtr lastsap;
^~~~~~~
asn2gnb3.c:5153:20: warning: variable 'lastright' set but not used [-Wunused-but-set-variable]
Int4 lastright;
^~~~~~~~~
asn2gnb3.c:5152:20: warning: variable 'lastleft' set but not used [-Wunused-but-set-variable]
Int4 lastleft;
^~~~~~~~
asn2gnb3.c:5151:20: warning: variable 'isRefSeq' set but not used [-Wunused-but-set-variable]
Boolean isRefSeq;
^~~~~~~~
asn2gnb3.c: In function 'GetFeatsOnBioseq':
asn2gnb3.c:5376:22: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start;
^~~~~
asn2gnb3.c:5349:22: warning: variable 'icp' set but not used [-Wunused-but-set-variable]
IntCdsBlockPtr icp;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb3.c:57:
asn2gnb3.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb4.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb4.c: In function 'FormatFeatureBlockQuals':
asn2gnb4.c:3591:50: warning: "/*" within comment [-Wcomment]
StringChr (str + 1, '(') == NULL /* && StringChr (str, ',') != NULL */) {
asn2gnb4.c:2969:24: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb4.c:2910:24: warning: variable 'at_end' set but not used [-Wunused-but-set-variable]
Boolean at_end = FALSE;
^~~~~~
asn2gnb4.c: In function 'FF_asn2gb_www_featkey':
asn2gnb4.c:5180:16: warning: variable 'prefix' set but not used [-Wunused-but-set-variable]
CharPtr prefix = "?";
^~~~~~
asn2gnb4.c: In function 'FormatFeatureBlockEx':
asn2gnb4.c:6354:22: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
In file included from ../include/ncbi.h:58:0,
from asn2gnb4.c:42:
asn2gnb4.c: In function 'DoImmediateRemoteFeatureFormat':
../include/ncbistd.h:286:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb4.c:8448:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb4.c: In function 'FormatFeatureQuals':
../include/ncbistd.h:286:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb4.c:8521:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb4.c:57:
asn2gnb4.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
asn2gnb4.c: In function 'FormatFeatureBlockEx':
asn2gnb4.c:7398:24: warning: 'sep' may be used uninitialized in this function [-Wmaybe-uninitialized]
oldscope = SeqEntrySetScope (sep);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb5.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb5.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb5.c: In function 'FormatCitBookArt':
asn2gnb5.c:1874:16: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb5.c:57:
asn2gnb5.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb6.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb6.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb6.c: In function 'FlatLocElement':
asn2gnb6.c:2386:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (sintp->to > 0 &&
~~~~~~~~~~~~~~^~
(sintp->to != sintp->from ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sintp->if_from != NULL ||
~~~~~~~~~~~~~~~~~~~~~~~~~
sintp->if_to != NULL) ||
~~~~~~~~~~~~~~~~~~~~~
asn2gnb6.c: In function 'FormatContigBlock':
asn2gnb6.c:5401:20: warning: variable 'dspnext' set but not used [-Wunused-but-set-variable]
DeltaSeqPtr dspnext;
^~~~~~~
asn2gnb6.c: In function 'FormatSequenceBlock':
asn2gnb6.c:5855:21: warning: variable 'iasp' set but not used [-Wunused-but-set-variable]
IntAsn2gbSectPtr iasp;
^~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb6.c:57:
asn2gnb6.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ftusrstr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ftusrstr.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gbfeat.c
gbfeat.c: In function 'CkLabelType':
gbfeat.c:1529:33: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
for (str = bptr; *str != '\0' && IS_ALPHA(*str) || IS_DIGIT(*str)
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gbftglob.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gbparint.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/parsegb.h:57,
from gbparint.c:99:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gbparint.c: In function 'Nlm_gbparselex':
gbparint.c:2128:24: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (*current_col != '\0')
^
gbparint.c: In function 'Nlm_gbparselex_ver':
gbparint.c:2514:24: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (*current_col != '\0')
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF utilpars.c
utilpars.c:112:39: warning: missing braces around initializer [-Wmissing-braces]
ParFlat_AA_array[ParFlat_TOTAL_AA] = {
^
utilpars.c:112:39: note: (near initialization for 'ParFlat_AA_array')
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF utilpub.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from utilpub.c:13:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
utilpub.c: In function 'FindCit':
utilpub.c:998:24: warning: variable 'ifp' set but not used [-Wunused-but-set-variable]
ImpFeatPtr /*UNUSED*/ifp;
^~~
utilpub.c: In function 'ChangeCitQual':
utilpub.c:1053:53: warning: variable 'pub' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp, pubset = NULL, pub_min, /*UNUSED*/pub;
^~~
utilpub.c:1052:34: warning: variable 'descr' set but not used [-Wunused-but-set-variable]
ValNodePtr PNTR vnpp, /*UNUSED*/descr;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ffprint.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:372,
from ffprint.c:127:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ffprint.c: In function 'FFBSPrint':
ffprint.c:347:19: warning: unused variable 'byte_sp' [-Wunused-variable]
ByteStorePtr byte_sp = NULL;
^~~~~~~
At top level:
ffprint.c:420:16: warning: 'ff_print_insert' defined but not used [-Wunused-function]
static CharPtr ff_print_insert(CharPtr str, CharPtr ins)
^~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from ffprint.c:127:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF wprint.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from wprint.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
wprint.c: In function 'LocPrintGenome':
wprint.c:1696:14: warning: unused variable 'sep' [-Wunused-variable]
SeqEntryPtr sep = NULL;
^~~
wprint.c:1695:25: warning: unused variable 'b' [-Wunused-variable]
BioseqPtr bsp = NULL, b = NULL;
^
wprint.c:1695:13: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp = NULL, b = NULL;
^~~
wprint.c:1692:34: warning: unused variable 'temp' [-Wunused-variable]
static Char buf[14], val[166], temp[166];
^~~~
At top level:
wprint.c:1692:34: warning: 'temp' defined but not used [-Wunused-variable]
wprint.c:79:13: warning: 'link_gdb_map' defined but not used [-Wunused-variable]
static Char link_gdb_map[MAX_WWWBUF];
^~~~~~~~~~~~
wprint.c:77:13: warning: 'link_pir' defined but not used [-Wunused-variable]
static Char link_pir[MAX_WWWBUF];
^~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from wprint.c:51:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
In file included from ../include/ncbi.h:62:0,
from wprint.c:46:
wprint.c: In function 'www_xref':
../include/ncbistr.h:331:19: warning: 'prefix' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringLen Nlm_StringLen
^~~~~~~~~~~~~
wprint.c:1358:19: note: 'prefix' was declared here
CharPtr s, link, prefix, ss;
^~~~~~
In file included from ../include/ncbi.h:62:0,
from wprint.c:46:
../include/ncbistr.h:331:19: warning: 'link' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringLen Nlm_StringLen
^~~~~~~~~~~~~
wprint.c:1358:13: note: 'link' was declared here
CharPtr s, link, prefix, ss;
^~~~
wprint.c: In function 'PrintSPBlock':
wprint.c:1570:6: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
AddLink(s);
^~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF satutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/satutil.h:12,
from satutil.c:87:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
satutil.c: In function 'CopyFeatureFromAlign':
satutil.c:1011:10: warning: variable 'check_gap' set but not used [-Wunused-but-set-variable]
Boolean check_gap;
^~~~~~~~~
At top level:
satutil.c:168:16: warning: 'bk_map_one_location' defined but not used [-Wunused-function]
static Boolean bk_map_one_location(SeqLocPtr source_loc, SeqAlignPtr align, SeqIdPtr target_sip, Boolean check_gap, Int4Ptr r_start, Int4Ptr r_stop, SeqLocPtr PNTR head_slp)
^~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqmgr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from seqmgr.c:55:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqmgr.c: In function 'SeqEntrySetScope':
seqmgr.c:313:13: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
seqmgr.c: In function 'ClearBioseqFindCache':
seqmgr.c:899:14: warning: variable 'smp' set but not used [-Wunused-but-set-variable]
SeqMgrPtr smp;
^~~
seqmgr.c: In function 'GetUniGeneIDForSeqId':
seqmgr.c:3676:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(StringCmp(db_tag->db, "BSNR") == 0)
^~
seqmgr.c:3678:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if(StringCmp(db_tag->db, "HUMGEN") == 0)
^~
seqmgr.c: In function 'SeqMgrGetExtraDataForOmdp':
seqmgr.c:3736:14: warning: variable 'omp' set but not used [-Wunused-but-set-variable]
ObjMgrPtr omp;
^~~
seqmgr.c: In function 'CheckForTransSplice':
seqmgr.c:5644:14: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
SeqLocPtr prev, tmp;
^~~~
seqmgr.c: In function 'SeqEntryAsnOut':
seqmgr.c:11692:41: warning: variable 'aopp_desc' set but not used [-Wunused-but-set-variable]
AsnOptionPtr aopp_feat = NULL, aopp_desc = NULL;
^~~~~~~~~
seqmgr.c:11692:23: warning: variable 'aopp_feat' set but not used [-Wunused-but-set-variable]
AsnOptionPtr aopp_feat = NULL, aopp_desc = NULL;
^~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from seqmgr.c:65:
seqmgr.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
seqmgr.c: In function 'SeqMgrGetNextDescriptor':
seqmgr.c:9580:71: warning: 'bssp' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (omdp->datatype == OBJ_BIOSEQSET && bssp != NULL && bssp->seqentry != NULL) {
~~~~^~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objmgr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from objmgr.c:51:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmgr.c: In function 'ObjMgrReapOne':
objmgr.c:2727:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (omp->reaping) /* protect against recursion caused by ObjMgrSendMsg */
^~
objmgr.c:2730:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
lowest = UINT4_MAX;
^~~~~~
objmgr.c: In function 'ObjMgrDeSelectStructFunc':
objmgr.c:3767:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (next != NULL)
^~
objmgr.c:3770:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ObjMgrSendDeSelMsg (omp, ssp->entityID, ssp->itemID, ssp->itemtype, ssp->regiontype, ssp->region);
^~~~~~~~~~~~~~~~~~
objmgr.c: In function 'ObjMgrSelectFunc2':
objmgr.c:4031:22: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = FALSE;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gather.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/gather.h:166,
from gather.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gather.c: In function 'AttachDataProc':
gather.c:4825:30: warning: variable 'into_seqentry' set but not used [-Wunused-but-set-variable]
Boolean no_good = FALSE, into_seqentry = FALSE;
^~~~~~~~~~~~~
gather.c: In function 'GatherSeqFeat':
gather.c:1570:42: warning: 'newid' may be used uninitialized in this function [-Wmaybe-uninitialized]
tslp = SeqLocReMap(newid, slp, cbp->loc, offset, rev);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gather.c:1530:86: warning: 'max_interval' may be used uninitialized in this function [-Wmaybe-uninitialized]
lrdp = (GatherRangePtr)MemNew((size_t)((max_interval + 20) * sizeof(GatherRange)));
^
gather.c:1537:33: warning: 'offset' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (SeqLocOffset(slp, tslp, &(lrdp[ctr]), offset))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/ncbi.h:59:0,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/gather.h:166,
from gather.c:44:
../include/ncbimem.h:232:23: warning: 'lrdp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
gather.c:1404:38: note: 'lrdp' was declared here
GatherRangePtr rdp = NULL, trdp, lrdp;
^~~~
gather.c: In function 'gather_align_data':
gather.c:2278:11: warning: 'h_stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(!(h_stop < m_start || h_start > m_stop)) /*it is within the range*/
^
gather.c:2278:12: warning: 'h_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(!(h_stop < m_start || h_start > m_stop)) /*it is within the range*/
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gather.c:2468:58: warning: 'master_loc' may be used uninitialized in this function [-Wmaybe-uninitialized]
stop = inverse ? SeqLocLen(master_loc) * mag_val : SeqLocLen(master_loc)/mag_val;
^~~~~~~~~~~~~~~~~~~~~
gather.c:2466:73: warning: 'mag_val' may be used uninitialized in this function [-Wmaybe-uninitialized]
stop = inverse ? (len /mag_val) : (len * mag_val);
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
gather.c: In function 'GatherBioseqFunc':
gather.c:3305:53: warning: 'tlen' may be used uninitialized in this function [-Wmaybe-uninitialized]
rdp->right = offset + tlen - 1;
~~~~~~~^~~~~~
gather.c:3296:40: warning: 'trunc_r' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (trunc_r)
^
gather.c:3291:39: warning: 'trunc_l' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (trunc_l)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF accmmdbs.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from accmmdbs.c:120:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF acccn3ds.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from acccn3ds.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF lsqfetch.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from ../include/seqmgr.h:48,
from ../include/lsqfetch.h:110,
from lsqfetch.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF findrepl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from findrepl.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF codon.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/codon.h:61,
from codon.c:2:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
codon.c: In function 'make_cds_paragraph':
codon.c:262:7: warning: variable 'space_len' set but not used [-Wunused-but-set-variable]
Int4 space_len, i;
^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF jzcoll.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/maputil.h:113,
from ../include/jzcoll.h:123,
from jzcoll.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
jzcoll.c: In function 'load_default_matrix':
jzcoll.c:99:6: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]][pchars[j]] = webb_blosum62[i][j];
^
jzcoll.c:99:17: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]][pchars[j]] = webb_blosum62[i][j];
^
jzcoll.c:101:5: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]]['*'] = ss['*'][pchars[i]] = -4;
^
jzcoll.c:101:31: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]]['*'] = ss['*'][pchars[i]] = -4;
^
jzcoll.c: In function 'GetUseThisGi':
jzcoll.c:143:10: warning: unused variable 'retval' [-Wunused-variable]
Boolean retval=FALSE;
^~~~~~
jzcoll.c: In function 'buffer_for_feature':
jzcoll.c:514:7: warning: unused variable 'i' [-Wunused-variable]
Int2 i=0;
^
jzcoll.c: In function 'ProcessTextInsertion':
jzcoll.c:878:7: warning: variable 'last_ins' set but not used [-Wunused-but-set-variable]
Int4 last_ins;
^~~~~~~~
jzcoll.c: In function 'satcollfunc':
jzcoll.c:1723:12: warning: variable 'head' set but not used [-Wunused-but-set-variable]
SeqLocPtr head;
^~~~
jzcoll.c:1721:8: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
jzcoll.c:1720:7: warning: variable 'current_pos' set but not used [-Wunused-but-set-variable]
Int4 current_pos;
^~~~~~~~~~~
jzcoll.c:1714:12: warning: unused variable 'slp' [-Wunused-variable]
SeqLocPtr slp = NULL;
^~~
jzcoll.c: In function 'collect_anpnode_with_option':
jzcoll.c:3053:13: warning: unused variable 'prev' [-Wunused-variable]
ValNodePtr prev = NULL;
^~~~
jzcoll.c: In function 'ck_seqfeat_extra':
jzcoll.c:3414:10: warning: unused variable 'has_gb' [-Wunused-variable]
Boolean has_gb = FALSE, has_med = FALSE;
^~~~~~
jzcoll.c: In function 'collseqfunc':
jzcoll.c:3768:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(omtp->labelfunc !=NULL)
^~
jzcoll.c:3770:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
fnp->landmark = check_feature_for_landmark(chp->thislabel, chp->gdata, sfp, gcp, chp->priority);
^~~
jzcoll.c: In function 'load_open_close_sts_mark':
jzcoll.c:4010:10: warning: variable 'collected' set but not used [-Wunused-but-set-variable]
Boolean collected = FALSE;
^~~~~~~~~
jzcoll.c: In function 'FeatNodeCompProc':
jzcoll.c:4225:20: warning: variable 'gr2' set but not used [-Wunused-but-set-variable]
GatherRange gr1, gr2;
^~~
jzcoll.c:4225:15: warning: variable 'gr1' set but not used [-Wunused-but-set-variable]
GatherRange gr1, gr2;
^~~
At top level:
jzcoll.c:2316:16: warning: 'stop_collecting_alignment' defined but not used [-Wunused-function]
static Boolean stop_collecting_alignment(ValNodePtr anp_list, Int4 max_num)
^~~~~~~~~~~~~~~~~~~~~~~~~
jzcoll.c:1654:16: warning: 'collect_sequence_label' defined but not used [-Wunused-function]
static Boolean collect_sequence_label(Uint1 format)
^~~~~~~~~~~~~~~~~~~~~~
jzcoll.c: In function 'load_text':
jzcoll.c:421:39: warning: 'smtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
stdaa_res = SeqMapTableConvert(smtp, m_res);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF jzmisc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/jzmisc.h:86,
from jzmisc.c:23:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF maputil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/maputil.h:113,
from maputil.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
maputil.c: In function 'load_gene_list':
maputil.c:690:8: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Uint1 val;
^~~
maputil.c: In function 'gmarkfunc':
maputil.c:985:13: warning: variable 'syn' set but not used [-Wunused-but-set-variable]
ValNodePtr syn = NULL;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mconsist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/mconsist.h:4,
from mconsist.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF macroapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from macroapi.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
macroapi.c: In function 'AdvancedStringCompare':
macroapi.c:4416:23: warning: variable 'init_target_match_len' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, init_target_match_len = 0, target_match_len = 0;
^~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'RemoveGBQualMatch':
macroapi.c:6919:27: warning: variable 'does_match' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE, does_match, do_remove;
^~~~~~~~~~
macroapi.c: In function 'SetNameInPrimerList':
macroapi.c:10517:21: warning: variable 'prev_pp' set but not used [-Wunused-but-set-variable]
PCRPrimerPtr pp, prev_pp = NULL;
^~~~~~~
macroapi.c: In function 'SetSeqInPrimerList':
macroapi.c:10538:21: warning: variable 'prev_pp' set but not used [-Wunused-but-set-variable]
PCRPrimerPtr pp, prev_pp = NULL;
^~~~~~~
macroapi.c: In function 'GetCitListsForSeqEntry':
macroapi.c:15443:19: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
macroapi.c:15441:19: warning: variable 'okay' set but not used [-Wunused-but-set-variable]
Boolean okay;
^~~~
macroapi.c: In function 'GetPubMLStatus':
macroapi.c:17914:14: warning: variable 'csp' set but not used [-Wunused-but-set-variable]
CitSubPtr csp;
^~~
macroapi.c: In function 'ApplyPartial5SetActionToSeqFeat':
macroapi.c:24814:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'ApplyPartial3SetActionToSeqFeat':
macroapi.c:24937:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'ApplyPartialBothSetActionToSeqFeat':
macroapi.c:25004:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'FindPosBeforeFeat':
macroapi.c:25301:15: warning: variable 'regulator' set but not used [-Wunused-but-set-variable]
SeqFeatPtr regulator = NULL, candidate;
^~~~~~~~~
macroapi.c: In function 'PerformAutofixInSeqEntry':
macroapi.c:28058:8: warning: unused variable 'num_created' [-Wunused-variable]
Int4 num_created = 0;
^~~~~~~~~~~
macroapi.c: In function 'AddFileDescriptors':
macroapi.c:28453:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (sdp = SeqDescAsnRead (aip, NULL)) {
^~~~~
macroapi.c: In function 'PreprocessAddDescriptorListMacro':
macroapi.c:30069:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (sdp = SeqDescAsnRead (aip, NULL)) {
^~~~~
macroapi.c: In function 'SummarizeRemoveOutsideAction':
macroapi.c:30940:11: warning: unused variable 'case_insensitive' [-Wunused-variable]
CharPtr case_insensitive = " (case insensitive)";
^~~~~~~~~~~~~~~~
macroapi.c: In function 'GetObjectTableForTabTable':
macroapi.c:35366:63: warning: variable 'last' set but not used [-Wunused-but-set-variable]
ValNodePtr obj_table = NULL, obj_row, last_obj = NULL, tmp, last = NULL;
^~~~
macroapi.c: In function 'CheckObjTableForExistingText':
macroapi.c:35930:14: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
macroapi.c: In function 'FixSuspectProductNamesInEntrezGene':
macroapi.c:38178:18: warning: variable 'prefix' set but not used [-Wunused-but-set-variable]
CharPtr prefix = NULL;
^~~~~~
At top level:
macroapi.c:35102:16: warning: 'IsFieldTypeProteinDesc' defined but not used [-Wunused-function]
static Boolean IsFieldTypeProteinDesc (FieldTypePtr ft)
^~~~~~~~~~~~~~~~~~~~~~
macroapi.c:26150:13: warning: 'GetDescriptorTypeFromDescriptorChoice' defined but not used [-Wunused-function]
static Int4 GetDescriptorTypeFromDescriptorChoice (Uint1 descriptor_choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:20392:13: warning: 'GetFieldsFromAECR' defined but not used [-Wunused-function]
static void GetFieldsFromAECR (AECRActionPtr act, FieldTypePtr PNTR pField, ValNodePtr PNTR pFieldPair)
^~~~~~~~~~~~~~~~~
macroapi.c:15632:13: warning: 'InitBatchExtraForAECRActionAndObjectList' defined but not used [-Wunused-function]
static void InitBatchExtraForAECRActionAndObjectList (BatchExtraPtr batch_extra, AECRActionPtr action, ValNodePtr object_list)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:10224:16: warning: 'HasMultiplePrimerSets' defined but not used [-Wunused-function]
static Boolean HasMultiplePrimerSets (CharPtr value)
^~~~~~~~~~~~~~~~~~~~~
macroapi.c:5435:16: warning: 'DoesLocationMatchConstraint' defined but not used [-Wunused-function]
static Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:4543:13: warning: 'TestAdvancedStringMatch' defined but not used [-Wunused-function]
static void TestAdvancedStringMatch (void)
^~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:2760:13: warning: 'OriginFromOriginName' defined but not used [-Wunused-function]
static Int4 OriginFromOriginName (CharPtr origin_name)
^~~~~~~~~~~~~~~~~~~~
macroapi.c:1189:16: warning: 'IsObjectAppropriateForFieldPair' defined but not used [-Wunused-function]
static Boolean IsObjectAppropriateForFieldPair (Uint1 choice, Pointer data, FieldPairTypePtr fieldpair)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'GetFeatureListForProteinBioseq':
macroapi.c:34248:10: warning: 'sfp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (sfp != NULL)
^
macroapi.c: In function 'ConvertToBond':
macroapi.c:24176:7: warning: 'slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
bsp = GetBioseqGivenSeqLoc (slp, sfp->idx.entityID);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'ConvertToSite':
macroapi.c:24223:7: warning: 'slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
bsp = GetBioseqGivenSeqLoc (slp, sfp->idx.entityID);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'SetAuthorListFromString':
macroapi.c:14074:17: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
name_list = FreeNameList (1, vnp);
^~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'CaptureRefBlockSerialNumbers':
macroapi.c:15424:26: warning: 'ppr' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp->data.ptrvalue = ppr;
~~~~~~~~~~~~~~~~~~~^~~~~
macroapi.c: In function 'SetFieldValueForObjectEx':
macroapi.c:13405:29: warning: 'ipp' may be used uninitialized in this function [-Wmaybe-uninitialized]
new_ipp[i] = ipp[i];
~~~^~~
macroapi.c:13352:21: note: 'ipp' was declared here
Int4Ptr ipp, new_ipp;
^~~
macroapi.c:13350:21: warning: 'cpp' may be used uninitialized in this function [-Wmaybe-uninitialized]
CharPtr PNTR cpp;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salpedit.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from salpedit.c:2:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salpedit.c: In function 'SeqAlignInsert':
salpedit.c:162:12: warning: variable 'ssp' set but not used [-Wunused-but-set-variable]
StdSegPtr ssp;
^~~
salpedit.c:161:22: warning: variable 'ddp' set but not used [-Wunused-but-set-variable]
DenseDiagPtr ddp;
^~~
At top level:
salpedit.c:4120:18: warning: 'build_slp_for_gcontig' defined but not used [-Wunused-function]
static SeqLocPtr build_slp_for_gcontig (BioseqPtr gcontig_bsp, SeqIdPtr gcontig_sip)
^~~~~~~~~~~~~~~~~~~~~
salpedit.c:4073:17: warning: 'get_best_id' defined but not used [-Wunused-function]
static SeqIdPtr get_best_id(BioseqPtr bsp)
^~~~~~~~~~~
salpedit.c:4046:16: warning: 'second_seq_has_gap' defined but not used [-Wunused-function]
static Boolean second_seq_has_gap(BioseqPtr s_bsp)
^~~~~~~~~~~~~~~~~~
salpedit.c:4016:18: warning: 'dup_mul_locs' defined but not used [-Wunused-function]
static SeqLocPtr dup_mul_locs(SeqLocPtr slp)
^~~~~~~~~~~~
salpedit.c:3968:18: warning: 'create_fake_bioseq' defined but not used [-Wunused-function]
static BioseqPtr create_fake_bioseq(SeqLocPtr seq_loc, CharPtr fake_name)
^~~~~~~~~~~~~~~~~~
salpedit.c:3937:13: warning: 'reverse_seqloc' defined but not used [-Wunused-function]
static void reverse_seqloc (SeqLocPtr s_loc)
^~~~~~~~~~~~~~
salpedit.c:3850:13: warning: 'save_output' defined but not used [-Wunused-function]
static void save_output (SeqIdPtr sip, CharPtr f_name, SeqAlignPtr align)
^~~~~~~~~~~
salpedit.c:3836:13: warning: 'get_align_list_len' defined but not used [-Wunused-function]
static Int4 get_align_list_len(SeqAlignPtr align)
^~~~~~~~~~~~~~~~~~
salpedit.c:2939:20: warning: 'open_annot' defined but not used [-Wunused-function]
static SeqAnnotPtr open_annot(CharPtr f_name)
^~~~~~~~~~
salpedit.c:2835:13: warning: 'SeqAnnotWrite' defined but not used [-Wunused-function]
static void SeqAnnotWrite(SeqAlignPtr align)
^~~~~~~~~~~~~
salpedit.c:2653:16: warning: 'FigureAlignRange' defined but not used [-Wunused-function]
static Boolean FigureAlignRange(SeqAlignPtr align, SeqLocPtr m_loc, SeqLocPtr s_loc)
^~~~~~~~~~~~~~~~
salpedit.c:1665:16: warning: 'free_diag_in_list' defined but not used [-Wunused-function]
static Boolean free_diag_in_list(ValNodePtr ddp_list, DenseDiagPtr ddp)
^~~~~~~~~~~~~~~~~
salpedit.c:1605:16: warning: 'is_overlap' defined but not used [-Wunused-function]
static Boolean is_overlap(BoolPtr status, Int4 from, Int4 len)
^~~~~~~~~~
salpedit.c:1560:13: warning: 'filter_wrong_orientation' defined but not used [-Wunused-function]
static void filter_wrong_orientation (SeqAlignPtr align, Boolean same_orient)
^~~~~~~~~~~~~~~~~~~~~~~~
salpedit.c:1479:16: warning: 'filter_this_seg' defined but not used [-Wunused-function]
static Boolean filter_this_seg (DenseDiagPtr curr, DenseDiagPtr PNTR h_list, Int2 order)
^~~~~~~~~~~~~~~
salpedit.c:1422:16: warning: 'convert_ddp_to_array' defined but not used [-Wunused-function]
static Int4Ptr convert_ddp_to_array (ValNodePtr ddp_list, Uint1 strand, Int2 s_order, Int4Ptr p_num)
^~~~~~~~~~~~~~~~~~~~
salpedit.c:1387:14: warning: 'has_too_much_overlap' defined but not used [-Wunused-function]
static Uint1 has_too_much_overlap (Int4 start_1, Int4 stop_1, Int4 start_2, Int4 stop_2)
^~~~~~~~~~~~~~~~~~~~
salpedit.c:1281:13: warning: 'attach_new_align' defined but not used [-Wunused-function]
static void attach_new_align(SeqAlignPtr new_salp, SeqAlignPtr PNTR old) {
^~~~~~~~~~~~~~~~
salpedit.c:1169:20: warning: 'JZSeqAlignMerge' defined but not used [-Wunused-function]
static SeqAlignPtr JZSeqAlignMerge(SeqAlignPtr f_align, SeqIdPtr from_id, Int4 from, Int4 to, Uint1 strand, SeqIdPtr to_id, Int4 pos, SeqAlignPtr t_align)
^~~~~~~~~~~~~~~
salpedit.c:254:16: warning: 'is_gap_segment' defined but not used [-Wunused-function]
static Boolean is_gap_segment(Int4Ptr c_starts, Int2 dim)
^~~~~~~~~~~~~~
salpedit.c:158:20: warning: 'SeqAlignInsert' defined but not used [-Wunused-function]
static SeqAlignPtr SeqAlignInsert(SeqIdPtr from_id, Int4 from, Int4 to, Uint1 strand, SeqIdPtr to_id, Int4 pos, SeqAlignPtr head, Boolean merge, Boolean add_insertion)
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salpstat.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from salpstat.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salpstat.c: In function 'DenseSegStats':
salpstat.c:310:10: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if(dsp && (((mmatches || mmismatches) && bsp_1 && bsp_2)) || !(mmatches || mmismatches)) {
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salpstat.c: In function 'SeqAlignScoreFix':
salpstat.c:162:20: warning: 'sp_last' may be used uninitialized in this function [-Wmaybe-uninitialized]
sp_last->next = (ScorePtr) MemNew(sizeof(Score));
salpstat.c: In function 'DenseSegStats':
salpstat.c:382:7: warning: 'spp_2' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqPortFree(spp_2);
^~~~~~~~~~~~~~~~~~
salpstat.c:381:7: warning: 'spp_1' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqPortFree(spp_1);
^~~~~~~~~~~~~~~~~~
salpstat.c: In function 'SeqAlignWindowScoreFN':
salpstat.c:2038:45: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
residue_score[pos]=score;
~~~~~~~~~~~~~~~~~~^~~~~~
salpstat.c:2020:34: warning: 'pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
qgaps_score[last_pos]=-(g_open+len*g_ext);
^
salpstat.c: In function 'SeqAlignWindowScore':
salpstat.c:2214:12: warning: 'scoreptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
return scoreptr;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salpacc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salpacc.h:33,
from salpacc.c:40:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salpacc.c: In function 'SeqAlignStrand':
salpacc.c:334:20: warning: unused variable 'this_strand' [-Wunused-variable]
Uint1Ptr this_strand=Seq_strand_unknown;
^~~~~~~~~~~
salpacc.c: In function 'SeqAlignStop':
salpacc.c:561:13: warning: 'this_stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(this_stop!=-1)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salprop.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from ../include/salprop.h:46,
from salprop.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salprop.c: In function 'CopySeqLocFromSeqAlign':
salprop.c:398:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
salprop.c:401:16: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if(crp != NULL) /*for coding region features*/
^~
salprop.c:291:12: warning: variable 'check_gap' set but not used [-Wunused-but-set-variable]
Boolean check_gap;
^~~~~~~~~
salprop.c: In function 'FeatListToProp':
salprop.c:1336:20: warning: variable 'feat_itemID' set but not used [-Wunused-but-set-variable]
Uint4 feat_itemID;
^~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from salprop.c:46:
salprop.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from salprop.c:42:0:
../include/salprop.h:50:16: warning: 'GBFeat' defined but not used [-Wunused-variable]
static CharPtr GBFeat[number_GBFeat] = {
^~~~~~
salprop.c: In function 'ApplyNewSeqFeat':
salprop.c:620:11: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
j = stop - SeqLocStop(sfp_location);
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salprop.c:514:17: note: 'stop' was declared here
stop,
^~~~
salprop.c:674:17: warning: 'sfp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqFeatPtr sfp;
^~~
salprop.c:733:24: warning: 'ppp.p5' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (!sfp_p5 && ppp.p5)
~~~~~~~~^~~~~~~~~
salprop.c:679:17: note: 'ppp.p5' was declared here
ParTials ppp;
^~~
salprop.c:737:12: warning: 'ppp.p3' may be used uninitialized in this function [-Wmaybe-uninitialized]
SetSeqLocPartial (sfp->location, afp->noLeft, afp->noRight);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salprop.c:679:17: note: 'ppp.p3' was declared here
ParTials ppp;
^~~
salprop.c:861:33: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((val2=is_id_unique (entityID, SeqLocId(sfp->product))))
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salsap.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from ../include/salsap.h:57,
from salsap.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salsap.c: In function 'DenseDiagToDenseSegFunc':
salsap.c:2912:30: warning: variable 'slpstop2' set but not used [-Wunused-but-set-variable]
slpstop1 = 0, slpstop2 = 0;
^~~~~~~~
salsap.c:2912:16: warning: variable 'slpstop1' set but not used [-Wunused-but-set-variable]
slpstop1 = 0, slpstop2 = 0;
^~~~~~~~
salsap.c:2911:31: warning: variable 'slpstart2' set but not used [-Wunused-but-set-variable]
Int4 slpstart1 = 0, slpstart2 = 0,
^~~~~~~~~
salsap.c:2911:16: warning: variable 'slpstart1' set but not used [-Wunused-but-set-variable]
Int4 slpstart1 = 0, slpstart2 = 0,
^~~~~~~~~
salsap.c:2909:28: warning: variable 'start2' set but not used [-Wunused-but-set-variable]
Int4 start1 = 0, start2 = 0,
^~~~~~
salsap.c:2909:16: warning: variable 'start1' set but not used [-Wunused-but-set-variable]
Int4 start1 = 0, start2 = 0,
^~~~~~
In file included from ../include/sqnutils.h:51:0,
from salsap.c:47:
salsap.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
salsap.c:3631:13: warning: 'FindSeqAlignCallback' defined but not used [-Wunused-function]
static void FindSeqAlignCallback (SeqEntryPtr sep, Pointer mydata,
^~~~~~~~~~~~~~~~~~~~
salsap.c:2157:16: warning: 'AreDenseSegSegmentsValid' defined but not used [-Wunused-function]
static Boolean AreDenseSegSegmentsValid (DenseSegPtr dsp, Int4 start, Int4 num)
^~~~~~~~~~~~~~~~~~~~~~~~
salsap.c: In function 'SeqAlignEndExtend':
salsap.c:986:18: warning: 'n_strands' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint1Ptr n_strands;
^~~~~~~~~
salsap.c: In function 'CleanStrandsSeqAlign':
salsap.c:1614:15: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 dim;
^~~
salsap.c:1613:15: warning: 'numseg' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 numseg;
^~~~~~
salsap.c:1611:15: warning: 'startp' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4Ptr startp;
^~~~~~
salsap.c:1610:15: warning: 'lenp' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4Ptr lenp;
^~~~
salsap.c: In function 'LocalAlignToSeqAnnotDimn':
salsap.c:1851:9: warning: 'the_lens' may be used uninitialized in this function [-Wmaybe-uninitialized]
while ( j < lens )
^
salsap.c: In function 'multseqalign_from_pairseqalign':
salsap.c:4394:19: warning: 'strandp' may be used uninitialized in this function [-Wmaybe-uninitialized]
strandp++;
~~~~~~~^~
salsap.c:4245:6: warning: 'ok' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (!ok)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salstruc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from ../include/salstruc.h:56,
from salstruc.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salstruc.c: In function 'data_collect_arrange':
salstruc.c:1338:22: warning: variable 'maxscroll' set but not used [-Wunused-but-set-variable]
Int4 maxscroll;
^~~~~~~~~
salstruc.c: In function 'ShowAlignmentText':
salstruc.c:2203:29: warning: variable 'itemtype' set but not used [-Wunused-but-set-variable]
Uint2 entityID, itemtype;
^~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from salstruc.c:40:
salstruc.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from salstruc.c:41:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
salstruc.c: In function 'prot_to_rputprot':
salstruc.c:707:11: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 j, k;
^
salstruc.c: In function 'data_collect_arrange':
salstruc.c:967:29: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
drawfeat = is_feature_to_buffer(vnpfeat, itemID, entityID, fromseq, length, salp, adp->input_format, adp->sqloc_list);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salstruc.c:872:19: note: 'entityID' was declared here
Uint2 entityID;
^~~~~~~~
salstruc.c:1093:44: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
seq_info->entityID=entityID;
~~~~~~~~~~~~~~~~~~^~~~~~~~~
salstruc.c:1005:17: note: 'entityID' was declared here
Uint2 entityID;
^~~~~~~~
salstruc.c: In function 'ShowAlignmentText':
salstruc.c:2194:19: warning: 'bspsip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqIdPtr bspsip;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from salutil.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salutil.c: In function 'ReadBufferFromSap':
salutil.c:128:24: warning: variable 'buffstart' set but not used [-Wunused-but-set-variable]
Int4 bufflen, buffstart;
^~~~~~~~~
salutil.c:127:15: warning: variable 'sumstart' set but not used [-Wunused-but-set-variable]
Int4 sumstart;
^~~~~~~~
salutil.c: In function 'IS_protSeqLoc':
salutil.c:594:11: warning: variable 'seq' set but not used [-Wunused-but-set-variable]
CharPtr seq;
^~~
salutil.c: In function 'ReplaceSeqIdWithSeqId':
salutil.c:1236:20: warning: variable 'oldscope' set but not used [-Wunused-but-set-variable]
SeqEntryPtr oldscope;
^~~~~~~~
salutil.c: In function 'del_ssp_fromid':
salutil.c:1722:24: warning: variable 'pressp' set but not used [-Wunused-but-set-variable]
SelEdStructPtr ssp, pressp = NULL;
^~~~~~
salutil.c: In function 'checkCDSselect_forprotein':
salutil.c:2510:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (feat != NULL)
^
salutil.c: In function 'NoMoreSegGapForOneAlignment':
salutil.c:3647:8: warning: implicit declaration of function 'AlnMgr2IndexSingleChildSeqAlign' [-Wimplicit-function-declaration]
AlnMgr2IndexSingleChildSeqAlign(salp); /* make sure it's dense-seg */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from salutil.c:53:
salutil.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
salutil.c: In function 'sesp_to_slp':
salutil.c:1976:9: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (k=1; k<j; k++) sesp=sesp->next;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF udvseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from ../include/udvseq.h:100,
from udvseq.c:112:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
udvseq.c: In function 'UDV_EncodeIdxFeat':
udvseq.c:448:2: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return *((Int4Ptr) index_g);
^~~~~~
udvseq.c: In function 'UDV_BigEncodeIdxFeat':
udvseq.c:473:2: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return *((Uint8Ptr) index_g);
^~~~~~
udvseq.c: In function 'UDV_ParaGFTableFeatures':
udvseq.c:947:22: warning: 'nFeatLines' may be used uninitialized in this function [-Wmaybe-uninitialized]
pgp->nFeatLines=nFeatLines/*-decal*/;
~~~~~~~~~~~~~~~^~~~~~~~~~~
udvseq.c:990:9: warning: 'PosFeat' may be used uninitialized in this function [-Wmaybe-uninitialized]
(Uint2)PosFeat-decal,(Uint2)0));
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blocks.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/blocks.h:88,
from blocks.c:93:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blocks.c: In function 'IndexBlocks':
blocks.c:928:19: warning: operation on 'segp_align->to' may be undefined [-Wsequence-point]
segp_align->to = segp_align->to = -1;
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
blocks.c: In function 'IndexNewBlocks':
blocks.c:1084:19: warning: operation on 'segp_align->to' may be undefined [-Wsequence-point]
segp_align->to = segp_align->to = -1;
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
blocks.c: In function 'GetBlockOrientation':
blocks.c:2383:11: warning: 'orient' may be used uninitialized in this function [-Wmaybe-uninitialized]
return orient;
^~~~~~
blocks.c: In function 'SAMergeBlocks':
blocks.c:2165:21: warning: 'tmp2' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp2 = tmp2->next;
~~~~~^~~~~~~~~~~~
blocks.c:1572:28: warning: 'tmp_head' may be used uninitialized in this function [-Wmaybe-uninitialized]
merged->segp_head = tmp_head;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~
blocks.c:1470:27: warning: 'tmp_curr' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp1->prev = tmp_curr;
~~~~~~~~~~~^~~~~~~~~~
blocks.c:1709:27: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp1->prev = prev;
~~~~~~~~~~~^~~~~~
blocks.c:1670:34: warning: 'new_sabp1' may be used uninitialized in this function [-Wmaybe-uninitialized]
new_sabp1->segp_head = tmp_head;
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
blocks.c: In function 'SASplitBlock':
blocks.c:2796:25: warning: 'segp2_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
segp2->prev = segp2_prev;
~~~~~~~~~~~~^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF pgppop.c
pgppop.c:307:2: warning: missing braces around initializer [-Wmissing-braces]
{
^
pgppop.c:307:2: note: (near initialization for 'DDV_PaletteRGB')
pgppop.c: In function 'DDV_WWW_get_CDS_minus':
pgppop.c:578:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
pgppop.c:576:5: warning: variable 'numivals2' set but not used [-Wunused-but-set-variable]
numivals2=0;
^~~~~~~~~
pgppop.c: In function 'DDV_WWW_get_CDS_plus':
pgppop.c:700:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
pgppop.c: In function 'GetClrFromClrGlobal':
pgppop.c:1326:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
if (*((Uint4Ptr)rgb1 )== *((Uint4Ptr)rgb2)){
^~
pgppop.c:1326:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pgppop.c: In function 'DDV_DisplayTopScale':
pgppop.c:1549:7: warning: unused variable 'szBlank' [-Wunused-variable]
Char szBlank[TABLE_LEFT_MARGIN+5]={""};
^~~~~~~
pgppop.c: In function 'DDV_GetBLASTCompLine_1':
pgppop.c:1985:31: warning: array subscript has type 'char' [-Wchar-subscripts]
if (matrix[s][q]>0){
^
pgppop.c:1985:34: warning: array subscript has type 'char' [-Wchar-subscripts]
if (matrix[s][q]>0){
^
pgppop.c: In function 'DDV_DisplayDefaultAlign':
pgppop.c:3417:13: warning: unused variable 'sabp' [-Wunused-variable]
SABlockPtr sabp=NULL;/*indexed SeqAlign*/
^~~~
pgppop.c: In function 'DDV_ShowSeqAlign':
pgppop.c:3760:10: warning: unused variable 'szPopSetAuth' [-Wunused-variable]
Char szPopSetAuth[INFO_SIZE+1]={""};
^~~~~~~~~~~~
pgppop.c:3758:10: warning: unused variable 'szPopSetName' [-Wunused-variable]
Char szPopSetName[INFO_SIZE+1]={""};/*article title of the Pop-Set*/
^~~~~~~~~~~~
pgppop.c: In function 'DDV_PrintPopSetSummary':
pgppop.c:3931:9: warning: variable 'bPairwise' set but not used [-Wunused-but-set-variable]
Boolean bPairwise=TRUE,bPrintTax,bPrintCom;
^~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from pgppop.c:298:
pgppop.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/ddvcreate.h:143,
from pgppop.c:303:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
pgppop.c:2912:13: warning: 'DDV_PrintFastaGappedSequence' defined but not used [-Wunused-function]
static void DDV_PrintFastaGappedSequence(CharPtr szSequence,FILE *fp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pgppop.c:2865:13: warning: 'DDV_GetGappedSequence' defined but not used [-Wunused-function]
static void DDV_GetGappedSequence(SegmentPtr segp,CharPtr szSequence,
^~~~~~~~~~~~~~~~~~~~~
pgppop.c:2090:13: warning: 'DDV_HideMaskedLetters' defined but not used [-Wunused-function]
static void DDV_HideMaskedLetters(CharPtr szSeqMaster,ParaGPtr pgp,ValNodePtr mask)
^~~~~~~~~~~~~~~~~~~~~
pgppop.c:563:13: warning: 'DDV_WWW_get_CDS_minus' defined but not used [-Wunused-function]
static void DDV_WWW_get_CDS_minus(SeqMgrFeatContextPtr context,Int4 start,
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from pgppop.c:300:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
pgppop.c: In function 'DDV_PopDisplay2':
pgppop.c:1246:23: warning: 'pgp2' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (pgp2 && ((pgp2->StopLetter-pgp2->StartLetter+1)>=AbsLengthAli)) {
~~~~^~~~~~~~~~~~
pgppop.c:1253:14: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp->next=NULL;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF samutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/samutil.h:230,
from samutil.c:280:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
samutil.c: In function 'SAM_AlignIdComp':
samutil.c:1034:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((a == NULL) || (b == NULL))
^~
samutil.c:1037:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
choice = a->choice;
^~~~~~
samutil.c: In function 'SAM_AlignIdDup':
samutil.c:1090:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oldid == NULL)
^~
samutil.c:1093:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
newid = ValNodeNew(NULL);
^~~~~
samutil.c: In function 'DDE_FreeStack':
samutil.c:1794:11: warning: operation on 'Index' may be undefined [-Wsequence-point]
Index = ++Index % DDE_STACK_SIZE;
samutil.c: In function 'DDE_Add':
samutil.c:1849:22: warning: operation on 'pStack->StackMin' may be undefined [-Wsequence-point]
pStack->StackMin = ++pStack->StackMin % DDE_STACK_SIZE;
samutil.c:1860:22: warning: operation on 'pStack->StackIndex' may be undefined [-Wsequence-point]
pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE;
samutil.c: In function 'DDE_Prev':
samutil.c:1924:22: warning: operation on 'pStack->StackIndex' may be undefined [-Wsequence-point]
pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE;
samutil.c: In function 'DDE_Next':
samutil.c:1955:22: warning: operation on 'pStack->StackIndex' may be undefined [-Wsequence-point]
pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE;
samutil.c: In function 'DDE_ShowRow':
samutil.c:2222:26: warning: variable 'NumRows' set but not used [-Wunused-but-set-variable]
Int4 i, NumRows, HiRow, LowRow, tmp1, tmp2;
^~~~~~~
samutil.c: In function 'DDE_AddGapToEndOfAllRows':
samutil.c:3344:41: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr ptxtList, last_vnp, vnp;
^~~
samutil.c: In function 'DDE_RightAddNode':
samutil.c:3945:33: warning: variable 'new_vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp, next_vnp, new_vnp;
^~~~~~~
samutil.c: In function 'DDE_LeftMergeAndAddNodeList':
samutil.c:3995:24: warning: variable 'RetVal2' set but not used [-Wunused-but-set-variable]
Boolean RetVal1, RetVal2, IsLeftAlignedGap, NodeDeleted;
^~~~~~~
samutil.c: In function 'DDE_RightMergeAndAddNodeList':
samutil.c:4051:38: warning: variable 'RetVal2' set but not used [-Wunused-but-set-variable]
Boolean RetVal=FALSE, RetVal1, RetVal2, HeadChanged;
^~~~~~~
samutil.c: In function 'DDE_ShiftRightBoundaryLeft1':
samutil.c:4830:41: warning: variable 'Index' set but not used [-Wunused-but-set-variable]
Int4 NumBlocks, i, NumRows, Index, BlockCount=0;
^~~~~
samutil.c: In function 'DDE_CreateArraysForDenseSeg':
samutil.c:5266:22: warning: variable 'NumSegs' set but not used [-Wunused-but-set-variable]
Int4 NumRows, NumSegs, i, StartIndex, StopIndex, ArrayIndex=0;
^~~~~~~
samutil.c: In function 'DDE_GetLastVNP':
samutil.c:3381:9: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return(last_vnp);
^
samutil.c: In function 'DDE_GetNumResidues':
samutil.c:3404:13: warning: 'to' may be used uninitialized in this function [-Wmaybe-uninitialized]
return((to-from) + 1);
~~~^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ddvcolor.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvcolor.c:160:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvcolor.c: In function 'DDV_GetColor':
ddvcolor.c:1422:10: warning: unused variable 'retval' [-Wunused-variable]
Int4 retval = 0;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ddvcolor.c:165:
ddvcolor.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF viewmgr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/viewmgr.h:111,
from viewmgr.c:165:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from viewmgr.c:167:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from viewmgr.c:168:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
viewmgr.c:683:13: warning: 'ViewMgr_Swap' defined but not used [-Wunused-function]
static void ViewMgr_Swap(SeqAlign *salp1, SeqAlign *salp2)
^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ddvcreate.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ddvcreate.h:142,
from ddvcreate.c:245:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvcreate.c:290:2: warning: missing braces around initializer [-Wmissing-braces]
{
^
ddvcreate.c:290:2: note: (near initialization for 'DDV_PaletteRGB')
ddvcreate.c: In function 'DDV_CreateDisplayFromIndex_1':
ddvcreate.c:493:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp))
^~~~~
ddvcreate.c: In function 'DDV_CreateDisplayFromIndex_2':
ddvcreate.c:529:21: warning: variable 'more' set but not used [-Wunused-but-set-variable]
Boolean more;
^~~~
ddvcreate.c: In function 'DDV_CreateDisplayFromIndex_EX2':
ddvcreate.c:779:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp))
^~~~~
ddvcreate.c:690:21: warning: variable 'last' set but not used [-Wunused-but-set-variable]
Boolean last;
^~~~
ddvcreate.c:686:21: warning: variable 'PopulateTo' set but not used [-Wunused-but-set-variable]
Int4 PopulateTo;
^~~~~~~~~~
ddvcreate.c: In function 'DDV_DisplayNewBLAST':
ddvcreate.c:1942:16: warning: variable 'what' set but not used [-Wunused-but-set-variable]
Uint1 what;
^~~~
ddvcreate.c: In function 'UDV_BigEncodeIdxFeat4':
ddvcreate.c:2878:2: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return *((Uint8Ptr) index_g);
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/ddvcreate.h:143,
from ddvcreate.c:245:
ddvcreate.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ddvcreate.c:249:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ddvcreate.c:2362:16: warning: 'DDV_DisplayBlastSAP' defined but not used [-Wunused-function]
static Boolean DDV_DisplayBlastSAP(SeqAlignPtr sap, ValNodePtr mask,
^~~~~~~~~~~~~~~~~~~
ddvcreate.c:525:16: warning: 'DDV_CreateDisplayFromIndex_2' defined but not used [-Wunused-function]
static Boolean DDV_CreateDisplayFromIndex_2(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, Int2 LineSize)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvcreate.c: In function 'UAMgrIntUAMsg':
ddvcreate.c:1141:11: warning: 'stop_middle' may be used uninitialized in this function [-Wmaybe-uninitialized]
ubd->from=Start;
~~~~~~~~~^~~~~~
ddvcreate.c:1158:73: note: 'stop_middle' was declared here
Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
^~~~~~~~~~~
ddvcreate.c:1195:4: warning: 'start_middle' may be used uninitialized in this function [-Wmaybe-uninitialized]
UABitDescrInit(&uamp->ubd[0],0,start_middle-1,TRUE);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvcreate.c:1158:60: note: 'start_middle' was declared here
Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
^~~~~~~~~~~~
ddvcreate.c:1201:60: warning: 'halfBspLengthSeqR' may be used uninitialized in this function [-Wmaybe-uninitialized]
UABitDescrInit(&uamp->ubd[1],halfBspLengthSeqL,MaxLength-halfBspLengthSeqR-1,TRUE);
~~~~~~~~~^~~~~~~~~~~~~~~~~~
ddvcreate.c:1158:24: note: 'halfBspLengthSeqR' was declared here
Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
^~~~~~~~~~~~~~~~~
ddvcreate.c:1200:50: warning: 'halfBspLengthSeqL' may be used uninitialized in this function [-Wmaybe-uninitialized]
UABitDescrInit(&uamp->ubd[0],BspStart,BspStart+halfBspLengthSeqL-1,FALSE);
~~~~~~~~^~~~~~~~~~~~~~~~~~
ddvcreate.c:1158:6: note: 'halfBspLengthSeqL' was declared here
Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
^~~~~~~~~~~~~~~~~
ddvcreate.c: In function 'DDV_PopulateDisplayForDisc':
ddvcreate.c:1048:16: warning: 'vnp_para' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp_list[n-1]=vnp_para;
~~~~~~~~~~~~~^~~~~~~~~
ddvcreate.c: In function 'UABuildDescriptor2':
ddvcreate.c:1541:13: warning: 'stopcopy' may be used uninitialized in this function [-Wmaybe-uninitialized]
*TotLength+=(stopcopy-startcopy);/*to be used for the display coord. system*/
^~
ddvcreate.c: In function 'DDV_DumpSAPInAFile':
ddvcreate.c:1798:2: warning: 'matrix' may be used uninitialized in this function [-Wmaybe-uninitialized]
DDV_AffichageParaG(mpplp,0,0,mpplp->LengthAli-1,mpplp->LengthAli,0,option,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LineSize,hFile,byteSpp,matrix,gclr,NULL);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvcreate.c: In function 'DDV_ReadSeqBin':
ddvcreate.c:2593:9: warning: 'btr' may be used uninitialized in this function [-Wmaybe-uninitialized]
return btr;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF jsavlt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/jsavlt.h:4,
from jsavlt.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF needleman.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/needleman.h:40,
from needleman.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
needleman.c: In function 'NeedlemanWunschQuadraticByLoc':
needleman.c:281:24: warning: variable 'bestDbPos' set but not used [-Wunused-but-set-variable]
Int4 bestQueryPos, bestDbPos; /*position ending best score in
^~~~~~~~~
needleman.c:281:10: warning: variable 'bestQueryPos' set but not used [-Wunused-but-set-variable]
Int4 bestQueryPos, bestDbPos; /*position ending best score in
^~~~~~~~~~~~
needleman.c: In function 'FetchSequenceByLoc':
needleman.c:243:12: warning: 'query' may be used uninitialized in this function [-Wmaybe-uninitialized]
return query;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF txalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/maputil.h:113,
from ../include/jzcoll.h:123,
from ../include/txalign.h:228,
from txalign.c:559:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
txalign.c: In function 'addLinkoutForDefline':
txalign.c:706:13: warning: variable 'hasLinkout' set but not used [-Wunused-but-set-variable]
Boolean hasLinkout=FALSE;
^~~~~~~~~~
txalign.c: In function 'addLinkoutForBioseq':
txalign.c:774:13: warning: variable 'hasLinkout' set but not used [-Wunused-but-set-variable]
Boolean hasLinkout=FALSE;
^~~~~~~~~~
txalign.c: In function 'load_align_sum_for_StdSeg':
txalign.c:2748:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (bsp = BioseqLockById(SeqLocId(ssp->loc->next))) {
^~
txalign.c: In function 'ShowAlignNodeText2Ex':
txalign.c:3548:13: warning: variable 'is_end' set but not used [-Wunused-but-set-variable]
Boolean is_end, strip_semicolon=TRUE;
^~~~~~
txalign.c: In function 'Tx_PrintDefLine':
txalign.c:4597:7: warning: unused variable 'seqid_length' [-Wunused-variable]
Int4 seqid_length = 0, total_length = 0;
^~~~~~~~~~~~
txalign.c: In function 'PrintDefLinesFromSeqAlignWithPath':
txalign.c:5012:39: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
} else if (bestid != NULL && !(options & TXALIGN_NO_DUMPGNL) || (options & TXALIGN_NO_ENTREZ))
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
txalign.c:5016:29: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (bsp = BioseqLockById(bestid)) {
^~
txalign.c:4718:10: warning: unused variable 'ColumnDistance' [-Wunused-variable]
Int2 ColumnDistance=2, extraSpace=0, extraSpace2=0, strLen=0, maxEvalWidth=5, maxNWidth=2;
^~~~~~~~~~~~~~
txalign.c:4710:43: warning: unused variable 'sip_list' [-Wunused-variable]
SeqIdPtr bestid, gi_list, subject_id, sip_list=NULL, last_id;
^~~~~~~~
txalign.c:4706:17: warning: variable 'ptr_start' set but not used [-Wunused-but-set-variable]
Char *ptr, *ptr_start, *eval_buff_ptr, *bit_score_buff_ptr;
^~~~~~~~~
txalign.c: In function 'FormatScoreFromSeqAlignEx':
txalign.c:5335:25: warning: unused variable 't_adj' [-Wunused-variable]
Int4 m_adj = 0, t_adj = 0;
^~~~~
txalign.c:5334:29: warning: unused variable 'last_t_to' [-Wunused-variable]
Int4 last_m_to = 0, last_t_to = 0;
^~~~~~~~~
txalign.c: In function 'FSFPrintOneDefline':
txalign.c:5443:14: warning: variable 'seqid_len' set but not used [-Wunused-but-set-variable]
Int4 gi, seqid_len = 0;
^~~~~~~~~
txalign.c: In function 'FormatScoreFunc':
txalign.c:5660:13: warning: variable 'allocated' set but not used [-Wunused-but-set-variable]
Boolean allocated, first;
^~~~~~~~~
txalign.c: In function 'OOFShowSingleAlignment':
txalign.c:6326:27: warning: array subscript has type 'char' [-Wchar-subscripts]
else if(matrix[line1[line_index]][line2[line_index]] > 0)
^
txalign.c:6326:46: warning: array subscript has type 'char' [-Wchar-subscripts]
else if(matrix[line1[line_index]][line2[line_index]] > 0)
^
txalign.c:6093:13: warning: variable 'lines' set but not used [-Wunused-but-set-variable]
Int4 i, lines, k, shift_info = 0;
^~~~~
txalign.c: In function 'OOFDisplayTraceBack1':
txalign.c:6581:33: warning: unused variable 'st' [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:6581:9: warning: unused variable 'tmp' [-Wunused-variable]
tmp[10] = " ", *st;
^~~
txalign.c: In function 'OOFDisplayTraceBack2':
txalign.c:6655:33: warning: unused variable 'st' [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c: In function 'FDGetTaxNamesFromBioseq':
txalign.c:6757:21: warning: variable 'bdsp' set but not used [-Wunused-but-set-variable]
BlastDefLinePtr bdsp;
^~~~
txalign.c: At top level:
txalign.c:828:19: warning: 'ProcessTextInsertion' declared 'static' but never defined [-Wunused-function]
static ValNodePtr ProcessTextInsertion PROTO((AlignNodePtr anp, Int4 m_left, Int4 m_right, BioseqPtr bsp, Int4 line_len, Int1 frame));
^~~~~~~~~~~~~~~~~~~~
txalign.c:6655:33: warning: 'st' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:6581:9: warning: 'tmp' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~~
txalign.c:6581:33: warning: 'st' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:3433:1: warning: 'get_seq_id' defined but not used [-Wunused-function]
get_seq_id(SeqAlignPtr sap, Int2 index)
^~~~~~~~~~
txalign.c:2338:16: warning: 'has_hit_in_region' defined but not used [-Wunused-function]
static Boolean has_hit_in_region(Uint1Ptr all_frame)
^~~~~~~~~~~~~~~~~
txalign.c:630:16: warning: 'getNameInitials' defined but not used [-Wunused-function]
static CharPtr getNameInitials(CharPtr name){
^~~~~~~~~~~~~~~
In file included from ../include/ncbi.h:62:0,
from ../include/maputil.h:113,
from ../include/jzcoll.h:123,
from ../include/txalign.h:228,
from txalign.c:559:
txalign.c: In function 'DrawTextToBuffer':
../include/ncbistr.h:331:19: warning: 'HTML_buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringLen Nlm_StringLen
^~~~~~~~~~~~~
txalign.c:1612:10: note: 'HTML_buffer' was declared here
CharPtr HTML_buffer;
^~~~~~~~~~~
txalign.c: In function 'OOFShowSingleAlignment.isra.11':
txalign.c:6049:16: warning: 'number' may be used uninitialized in this function [-Wmaybe-uninitialized]
number = number/10;
~~~~~~~^~~~~~~~~~~
txalign.c:6078:16: note: 'number' was declared here
static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
^~~~~~~~~~~~~~~~~~~~~~
txalign.c:6049:16: warning: 'number' may be used uninitialized in this function [-Wmaybe-uninitialized]
number = number/10;
~~~~~~~^~~~~~~~~~~
txalign.c:6078:16: note: 'number' was declared here
static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
^~~~~~~~~~~~~~~~~~~~~~
txalign.c:6049:16: warning: 'number' may be used uninitialized in this function [-Wmaybe-uninitialized]
number = number/10;
~~~~~~~^~~~~~~~~~~
txalign.c:6078:16: note: 'number' was declared here
static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
^~~~~~~~~~~~~~~~~~~~~~
txalign.c:6049:16: warning: 'number' may be used uninitialized in this function [-Wmaybe-uninitialized]
number = number/10;
~~~~~~~^~~~~~~~~~~
txalign.c:6078:16: note: 'number' was declared here
static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
^~~~~~~~~~~~~~~~~~~~~~
txalign.c:6237:12: warning: 'dna_line_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (dna_line_start == 0)
^
txalign.c:6240:11: warning: 'pro_line_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(pro_line_start == 0)
^
txalign.c: In function 'find_score_in_align':
txalign.c:2598:33: warning: 'smtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
stdaa_res = SeqMapTableConvert(smtp, t_res);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
txalign.c:2498:20: note: 'smtp' was declared here
SeqMapTablePtr smtp;
^~~~
txalign.c:2463:13: warning: 't_spp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqPortFree(t_spp);
^~~~~~~~~~~~~~~~~~
txalign.c:2394:23: note: 't_spp' was declared here
SeqPortPtr m_spp, t_spp;
^~~~~
txalign.c:2460:11: warning: 'm_spp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(m_spp == NULL)
^
txalign.c:2394:16: note: 'm_spp' was declared here
SeqPortPtr m_spp, t_spp;
^~~~~
txalign.c: In function 'ShowAlignNodeText2Ex.isra.12':
txalign.c:2284:25: warning: 'm_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
to = MIN(master_len-1, to + 3);
^
txalign.c:3543:10: note: 'm_len' was declared here
Int4 m_len; /*length of the master sequence*/
^~~~~
txalign.c: In function 'ShowTextAlignFromAnnot3':
txalign.c:1467:12: warning: 'retval' may be used uninitialized in this function [-Wmaybe-uninitialized]
return retval;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF fdlobj.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from fdlobj.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
fdlobj.c: In function 'BlastDefLineSetAsnRead':
fdlobj.c:69:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
fdlobj.c: In function 'BlastDefLineAsnRead':
fdlobj.c:202:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF alignmgr2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/alignmgr2.h:110,
from alignmgr2.c:232:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
alignmgr2.c: In function 'AlnMgr2IndexSingleDenseSegSA':
alignmgr2.c:875:13: warning: statement with no effect [-Wunused-value]
for (j; j<dsp->numseg && next == -1; j++)
^~~
alignmgr2.c: In function 'AlnMgr2CopySeg':
alignmgr2.c:2967:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (ldelta = ABS(s->beg - beg)) {
^~
alignmgr2.c: In function 'AlnMgr2AddInNewPairwiseSA':
alignmgr2.c:3204:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (a = AlnMgr2GetNextSeqPiece(a)) {
^~~~~
alignmgr2.c:3206:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (b = AlnMgr2GetNextLimitedSeqPiece(b, a)) {
^~~~~
alignmgr2.c:3216:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (A = AlnMgr2GetNextSeqPiece(A)) {
^~~~~
alignmgr2.c:3220:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (B = AlnMgr2GetNextLimitedSeqPiece(B, A)) {};
^~~~~
alignmgr2.c: In function 'AlnMgr2SetUnaln':
alignmgr2.c:5393:22: warning: variable 'dsp' set but not used [-Wunused-but-set-variable]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2PrintSeqAlign':
alignmgr2.c:5606:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (more = AlnMgr2GetNextAlnBit(sap, amp))
^~~~~
alignmgr2.c: In function 'AlnMgr2GetNextAlnBit':
alignmgr2.c:5702:21: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
alignmgr2.c: In function 'AlnMgr2GetUnalignedInfo':
alignmgr2.c:6068:22: warning: variable 'saip' set but not used [-Wunused-but-set-variable]
SAIndex2Ptr saip;
^~~~
alignmgr2.c: In function 'AlnMgr2GetInterruptInfo':
alignmgr2.c:6314:7: warning: statement with no effect [-Wunused-value]
for (i; i<interrupt->segnum; i++)
^~~
alignmgr2.c: In function 'AlnMgr2ComputeScoreForSeqAlign':
alignmgr2.c:8324:17: warning: variable 'numseqs' set but not used [-Wunused-but-set-variable]
Int4 numseqs;
^~~~~~~
alignmgr2.c:8322:17: warning: variable 'mismatch' set but not used [-Wunused-but-set-variable]
Int4 mismatch;
^~~~~~~~
alignmgr2.c:8321:17: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from alignmgr2.c:232:
alignmgr2.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
alignmgr2.c:3540:13: warning: 'AlnMgr2AddInNewSA' defined but not used [-Wunused-function]
static void AlnMgr2AddInNewSA(SeqAlignPtr parent, SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~
alignmgr2.c:2351:18: warning: 'AlnMgr2GetEdgeList' defined but not used [-Wunused-function]
static AMEdgePtr AlnMgr2GetEdgeList(Int4 vertexnum, AMEdgePtr edge_head, AMEdgePtr already_used)
^~~~~~~~~~~~~~~~~~
alignmgr2.c:2123:13: warning: 'AlnMgr2SortVerticesByNumEdges' defined but not used [-Wunused-function]
static void AlnMgr2SortVerticesByNumEdges(AMVertexPtr PNTR vertexarray, Int4 numvertices)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:1051:13: warning: 'AlnMgr2UnpackSeqAlignChain' defined but not used [-Wunused-function]
static void AlnMgr2UnpackSeqAlignChain(SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetLongestSeqLoc':
alignmgr2.c:10114:15: warning: 'slp_longest' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqLocPtr slp_longest;
^~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2IndexLite':
alignmgr2.c:991:33: warning: 'sap_segs_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap_segs_prev->next = (SeqAlignPtr)(sap_segs->segs);
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:958:17: note: 'sap_segs_prev' was declared here
SeqAlignPtr sap_segs_prev;
^~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetUnalignedInfo':
alignmgr2.c:6105:54: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
*from = dsp->starts[dsp->dim*i+row-1]+dsp->lens[i];
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetMaxUnalignedLength':
alignmgr2.c:7031:22: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAIndex2Ptr saip;
^~~~
alignmgr2.c:7060:19: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (i=0; i<dsp->dim; i++)
~~~^~~~~
alignmgr2.c: In function 'AlnMgr2GetInterruptInfo':
alignmgr2.c:6336:16: warning: 'iip' may be used uninitialized in this function [-Wmaybe-uninitialized]
iip->strand = strand;
~~~~~~~~~~~~^~~~~~~~
alignmgr2.c:6165:19: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
trans = saip->srdp[saip->anchor-1]->sect;
~~~~^~~~~~
alignmgr2.c:6320:48: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
iip->starts[k] = dsp->starts[dsp->dim*i + interrupt->row-1];
~~~^~~~~
alignmgr2.c: In function 'AlnMgr2GetNthSeqRangeInSA':
alignmgr2.c:6461:15: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
srdp = saip->srdp[n-1];
~~~~^~~~~~
alignmgr2.c:6472:57: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
beg = dsp->starts[srdp->sect[srdp->numsect-1]*(dsp->dim) + n-1];
~~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetNthRowSpanInSA':
alignmgr2.c:6533:20: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
*start = saip->aligncoords[i];
~~~~^~~~~~~~~~~~~
alignmgr2.c:6541:41: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
*stop = saip->aligncoords[i] + dsp->lens[srdp->sect[srdp->numsect-1]] - 1;
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetAlnLength':
alignmgr2.c:6772:17: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
len += AlnMgr2GetMaxUnalignedLength(salp, i);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:6764:22: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (saip->aligncoords[saip->numseg-1]+dsp->lens[lastseg]);
~~~~^~~~~~~~~~~~~
alignmgr2.c:6771:20: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
len += dsp->lens[i];
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetNextAlnBit':
alignmgr2.c:6008:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->anchor <= 0)
~~~~^~~~~~~~
alignmgr2.c:6004:59: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
amp->from_row = dsp->starts[trans[start_sect]*dsp->dim+amp->row_num-1] + offset;
~~~^~~~~
alignmgr2.c: In function 'AlnMgr2IsSAPDiscAli':
alignmgr2.c:6796:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->numunaln > 0)
~~~~^~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetNumAlnBlocks':
alignmgr2.c:6819:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->numunaln >= 0)
~~~~^~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetNthBlockRange':
alignmgr2.c:6853:20: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
*start = saip->aligncoords[saip->unaln[n-1]+1];
~~~~^~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetNthUnalignedForNthRow':
alignmgr2.c:6872:22: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAIndex2Ptr saip;
^~~~
alignmgr2.c:6919:65: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
*start = dsp->starts[(saip->srdp[row-1]->unaligned[i])*dsp->dim+row-1] + dsp->lens[(saip->srdp[row-1]->unaligned[i])];
~~~^~~~~
alignmgr2.c: In function 'AlnMgr2GetNextLengthBit':
alignmgr2.c:7002:26: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxseg = saip->unaln[*seg];
~~~~^~~~~~~
alignmgr2.c:6937:22: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2GetNumSegsInRange':
alignmgr2.c:7168:62: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
start = binary_search_on_uint4_list(aligncoords, from, dsp->numseg);
~~~^~~~~~~~
alignmgr2.c:7133:21: warning: 'aligncoords' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint4Ptr aligncoords;
^~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2MapBioseqToSeqAlign':
alignmgr2.c:7635:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->anchor > 0)
~~~~^~~~~~~~
alignmgr2.c:7573:21: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2MapSeqAlignToBioseq':
alignmgr2.c:7671:21: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAIndex2Ptr saip;
^~~~
alignmgr2.c:7713:36: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (dsp->starts[sect*(dsp->dim)+row-1] + dsp->lens[sect] - 1 - offset);
~~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetSubAlign':
alignmgr2.c:8022:12: warning: 'sap_real' may be used uninitialized in this function [-Wmaybe-uninitialized]
salp = SeqAlignDup(sap_real);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2FillInUnaligned':
alignmgr2.c:9852:12: warning: 'offset' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr = curr + 1 + offset;
~~~~~^~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF alnread.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF acerdapi.c
acerdapi.c: In function 'DoesSeqStringMatchBsp':
acerdapi.c:201:30: warning: variable 'seq_len' set but not used [-Wunused-but-set-variable]
Int4 ctr, pos = 0, i, len, seq_len;
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from acerdapi.c:40:
acerdapi.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF aceread.c
aceread.c:3308:12: warning: 's_GetUngappedPosition' defined but not used [-Wunused-function]
static int s_GetUngappedPosition (int gapped_pos, char *seq)
^~~~~~~~~~~~~~~~~~~~~
aceread.c:276:13: warning: 'AdjustGapInfoFor3Trim' defined but not used [-Wunused-function]
static void AdjustGapInfoFor3Trim (TGapInfoPtr gap_info, int new_len)
^~~~~~~~~~~~~~~~~~~~~
aceread.c:247:13: warning: 'AdjustGapInfoFor5Trim' defined but not used [-Wunused-function]
static void AdjustGapInfoFor5Trim (TGapInfoPtr gap_info, int trim)
^~~~~~~~~~~~~~~~~~~~~
aceread.c:134:12: warning: 's_IsGapChar' defined but not used [-Wunused-function]
static int s_IsGapChar (char ch, char *gap_chars)
^~~~~~~~~~~
aceread.c: In function 's_ReadContig':
aceread.c:1477:33: warning: 'linestring' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (linestring != NULL) free (linestring);
^~~~~~~~~~~~~~~~~
rm -f libncbiobj.a
ar cru libncbiobj.a objacces.o objalign.o objall.o objbibli.o objfeat.o objgen.o objloc.o objmedli.o objpub.o objres.o objscoremat.o objseq.o objblock.o objcode.o objsset.o objsub.o objprt.o objfdef.o objalignloc.o objtable.o objpubme.o objmdrs.o objproj.o objgbseq.o objtseq.o objinsdseq.o objmacro.o objent2.o ent2api.o pmfapi.o objtax3.o tax3api.o objegkludge.o objentgene.o objmla2.o mla2api.o qblastapi.o vecscnapi.o objmim.o objvalid.o mimapi.o cddapi.o seqport.o sequtil.o prtutil.o simple.o tofasta.o tofile.o tomedlin.o valid.o valapi.o alignmgr.o aliparse.o aliread.o alignval.o sqnutil1.o sqnutil2.o sqnutil3.o sqnutil4.o subutil.o edutil.o asn2ff1.o asn2ff2.o asn2ff3.o asn2ff4.o asn2ff5.o asn2ff6.o asn2gnb1.o asn2gnb2.o asn2gnb3.o asn2gnb4.o asn2gnb5.o asn2gnb6.o ftusrstr.o gbfeat.o gbftglob.o gbparint.o utilpars.o utilpub.o ffprint.o wprint.o satutil.o seqmgr.o objmgr.o gather.o accmmdbs.o acccn3ds.o lsqfetch.o findrepl.o codon.o jzcoll.o jzmisc.o maputil.o mconsist.o macroapi.o salpedit.o salpstat.o salpacc.o salprop.o salsap.o salstruc.o salutil.o udvseq.o blocks.o pgppop.o samutil.o ddvcolor.o viewmgr.o ddvcreate.o jsavlt.o needleman.o txalign.o fdlobj.o alignmgr2.o alnread.o acerdapi.o aceread.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbiobj.a ../lib
ranlib ../lib/libncbiobj.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cdentrez.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from cdentrez.c:162:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cdentrez.c:283:23: warning: 'CdEntMlSumGet' declared 'static' but never defined [-Wunused-function]
static DocSumPtr NEAR CdEntMlSumGet PROTO((Int4 uid));
^~~~~~~~~~~~~
cdentrez.c:310:23: warning: 'CdEntSeqSumGet' declared 'static' but never defined [-Wunused-function]
static DocSumPtr NEAR CdEntSeqSumGet PROTO((Int4 uid, DocType type));
^~~~~~~~~~~~~~
cdentrez.c:2935:23: warning: 'MedSumAsnRead' defined but not used [-Wunused-function]
static DocSumPtr NEAR MedSumAsnRead (AsnIoPtr aip, DocUid uid)
^~~~~~~~~~~~~
cdentrez.c:1616:26: warning: 'FreePostingList' defined but not used [-Wunused-function]
static ByteStorePtr NEAR FreePostingList (ByteStorePtr lst)
^~~~~~~~~~~~~~~
cdentrez.c:307:20: warning: 'BIOSEQ_id_E' defined but not used [-Wunused-variable]
static AsnTypePtr BIOSEQ_id_E = NULL;
^~~~~~~~~~~
cdentrez.c: In function 'CdEntrezMergeTerm':
cdentrez.c:2675:17: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized]
*totl = total;
~~~~~~^~~~~~~
cdentrez.c:2672:17: warning: 'special' may be used uninitialized in this function [-Wmaybe-uninitialized]
*spcl = special;
~~~~~~^~~~~~~~~
cdentrez.c:2640:5: warning: 'termpage' may be used uninitialized in this function [-Wmaybe-uninitialized]
cd3_CdTermScan (db, fld, termpage, (Int4)0, ScanAndFreeProc);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdentrez.c: In function 'CdLinkUidList':
cdentrez.c:938:9: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
return count;
^~~~~
cdentrez.c: In function 'CdTermListByTerm':
cdentrez.c:1036:10: warning: 'first' may be used uninitialized in this function [-Wmaybe-uninitialized]
rsult = cd3_CdTermScan(type,field,first,0,TermListTermScanProc);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdentrez.c: In function 'CdEntTLAddTerm':
cdentrez.c:1895:24: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (scanOk && total > 0) {
~~~~~~~^~~~~~~~~~~~
cdentrez.c:1787:13: note: 'total' was declared here
Int4 total;
^~~~~
cdentrez.c: In function 'CdEntrezFindTerm':
cdentrez.c:1123:3: warning: 'ctp' may be used uninitialized in this function [-Wmaybe-uninitialized]
CdTermFree(ctp);
^~~~~~~~~~~~~~~
cdentrez.c: In function 'CdEntMedlineEntryListGet':
cdentrez.c:2720:6: warning: 'aip' may be used uninitialized in this function [-Wmaybe-uninitialized]
cd3_CdDocAsnClose(aip);
^~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cdromlib.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objacces.h:64,
from ../include/cdromlib.h:71,
from cdromlib.c:73:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cdnewlib.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objacces.h:64,
from ../include/cdromlib.h:71,
from cdnewlib.c:208:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cdnewlib.c:600:27: warning: missing braces around initializer [-Wmissing-braces]
struct CdFInfo _finfo[] = {
^
cdnewlib.c:600:27: note: (near initialization for '_finfo')
cdnewlib.c:614:27: warning: missing braces around initializer [-Wmissing-braces]
struct CdDirInfo _dir[] = {
^
cdnewlib.c:614:27: note: (near initialization for '_dir')
cdnewlib.c: In function 'cd3_CdDocAsnOpen':
cdnewlib.c:1327:9: warning: unused variable 'fdir' [-Wunused-variable]
char *fdir = NULL;
^~~~
cdnewlib.c: In function 'CdDevice_Init':
cdnewlib.c:2739:6: warning: variable 'cd_num' set but not used [-Wunused-but-set-variable]
int cd_num;
^~~~~~
At top level:
cdnewlib.c:3605:13: warning: 'Cache_Purge' defined but not used [-Wunused-function]
static void Cache_Purge (Cache *cache)
^~~~~~~~~~~
cdnewlib.c:3592:14: warning: 'Cache_Peek' defined but not used [-Wunused-function]
static void* Cache_Peek (Cache *cache, long id)
^~~~~~~~~~
cdnewlib.c:3569:12: warning: 'Cache_Touch' defined but not used [-Wunused-function]
static int Cache_Touch (Cache *cache, long id)
^~~~~~~~~~~
cdnewlib.c:3506:12: warning: 'Cache_Delete' defined but not used [-Wunused-function]
static int Cache_Delete (Cache *cache, long id)
^~~~~~~~~~~~
cdnewlib.c:638:18: warning: '_div' defined but not used [-Wunused-variable]
static DivInfo * _div;
^~~~
cdnewlib.c:582:15: warning: '_empty_string' defined but not used [-Wunused-variable]
static char * _empty_string = "";
^~~~~~~~~~~~~
cdnewlib.c: In function 'UnixFileGets':
cdnewlib.c:1509:6: warning: 'ch' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ch == '\0') {
^
cdnewlib.c: In function 'trmncmp':
cdnewlib.c:2379:13: warning: 'c2' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (c1 - c2);
~~~~^~~~~
cdnewlib.c:2379:13: warning: 'c1' may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /usr/include/string.h:635:0,
from ../include/ncbilcl.h:156,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objacces.h:64,
from ../include/cdromlib.h:71,
from cdnewlib.c:208:
In function 'strncat',
inlined from 'CdDevice_FileBuildPath.part.17' at cdnewlib.c:2679:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'CdDevice_Init' at cdnewlib.c:2751:3:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'CdDevice_Init' at cdnewlib.c:2769:6:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdnewlib.c: In function 'TrmIndex_Lookup':
cdnewlib.c:2136:24: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
int lo, hi, mid, len, d;
^
cdnewlib.c:2168:27: warning: 'term' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (d==0 && len == (int)strlen(term))
^~~~~~~~~~~~
cdnewlib.c:2136:14: warning: 'mid' may be used uninitialized in this function [-Wmaybe-uninitialized]
int lo, hi, mid, len, d;
^~~
cdnewlib.c: In function 'UidIndex_Lookup':
cdnewlib.c:1986:20: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
page_num = (uid < *p && mid >0) ? mid-1 : mid;
^~
cdnewlib.c:1986:42: warning: 'mid' may be used uninitialized in this function [-Wmaybe-uninitialized]
page_num = (uid < *p && mid >0) ? mid-1 : mid;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF casn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from casn.c:84:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cdconfig.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cdconfig.c:75:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/ncbi.h:58:0,
from cdconfig.c:75:
cdconfig.c: In function 'ChangeMedia':
../include/ncbistd.h:278:15: warning: statement with no effect [-Wunused-value]
#define FALSE ((Nlm_Boolean)0)
^
../include/ncbifile.h:169:76: note: in expansion of macro 'FALSE'
#define EjectCd(sVolume, deviceName, rawDeviceName, mountPoint, mountCmd) FALSE
^~~~~
cdconfig.c:941:29: note: in expansion of macro 'EjectCd'
EjectCd(toBeEjected->entrez_info->volume_label,
^~~~~~~
../include/ncbistd.h:278:15: warning: statement with no effect [-Wunused-value]
#define FALSE ((Nlm_Boolean)0)
^
../include/ncbifile.h:170:76: note: in expansion of macro 'FALSE'
#define MountCd(sVolume, deviceName, mountPoint, mountCmd) FALSE
^~~~~
cdconfig.c:960:17: note: in expansion of macro 'MountCd'
MountCd(newMedia->entrez_info->volume_label, cdm->device_name,
^~~~~~~
cdconfig.c: At top level:
cdconfig.c:191:17: warning: 'UnMarkLRUineligible' declared 'static' but never defined [-Wunused-function]
static void UnMarkLRUineligible PROTO((void));
^~~~~~~~~~~~~~~~~~~
cdconfig.c: In function 'EntrezInfoMerge':
cdconfig.c:1141:23: warning: 'besttype' may be used uninitialized in this function [-Wmaybe-uninitialized]
EntrezTypeDataPtr besttype;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/cdrom.h:9,
from objentr.c:102:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objentr.c: In function 'CdRomAsnLoad':
objentr.c:170:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (loaded)
^~
objentr.c:172:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
loaded = TRUE;
^~~~~~
objentr.c: In function 'DocSumAsnRead':
objentr.c:970:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentr.c:969:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
At top level:
objentr.c:806:23: warning: 'EntrezDivInfo_Destruct' defined but not used [-Wunused-function]
static EntrezDivInfo* EntrezDivInfo_Destruct (EntrezDivInfo *div)
^~~~~~~~~~~~~~~~~~~~~~
objentr.c:771:16: warning: 'EntrezLinkInfo_AsnWrite' defined but not used [-Wunused-function]
static Boolean EntrezLinkInfo_AsnWrite (const EntrezLinkInfo *link, AsnIo *stream, AsnType *type)
^~~~~~~~~~~~~~~~~~~~~~~
objentr.c: In function 'EntrezInfoAsnRead':
objentr.c:818:5: warning: 'div' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (div == NULL)
^
objentr.c:241:17: note: 'div' was declared here
EntrezDivInfo *div;
^~~
objentr.c:763:17: warning: 'link' may be used uninitialized in this function [-Wmaybe-uninitialized]
link->datasize = (int) val.intvalue;
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
objentr.c:240:18: note: 'link' was declared here
EntrezLinkInfo *link;
^~~~
objentr.c:704:19: warning: 'fld' may be used uninitialized in this function [-Wmaybe-uninitialized]
fld->post_type = (PostType) val.intvalue;
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
objentr.c:239:19: note: 'fld' was declared here
EntrezFieldInfo *fld;
^~~
objentr.c:649:18: warning: 'tinf' may be used uninitialized in this function [-Wmaybe-uninitialized]
tinf->asntype = (char*) val.ptrvalue;
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
objentr.c:238:18: note: 'tinf' was declared here
EntrezTypeInfo *tinf;
^~~~
objentr.c:856:16: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
div->docs[i++] = val.intvalue;
~^~
objentr.c:824:7: note: 'i' was declared here
int i;
^
rm -f libncbicdr.a
ar cru libncbicdr.a cdentrez.o cdromlib.o cdnewlib.o casn.o cdconfig.o objentr.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbicdr.a ../lib
ranlib ../lib/libncbicdr.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibbutns.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibbutns.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibbutns.c: In function 'Nlm_CheckCallback':
vibbutns.c:328:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_RadioCallback':
vibbutns.c:347:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_SetButtonStatus':
vibbutns.c:668:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Nlm_Int2 val;
^~~
vibbutns.c: In function 'Nlm_NewButton.isra.1':
vibbutns.c:1133:3: warning: 'call' may be used uninitialized in this function [-Wmaybe-uninitialized]
XtAddCallback (c, call, Nlm_ButtonCallback, (XtPointer) b);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibextra.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibextra.c:87:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibextra.c: In function 'Nlm_RGB2HSL.constprop':
vibextra.c:1219:13: warning: 'min' may be used uninitialized in this function [-Wmaybe-uninitialized]
i++; if ( i > 2 ) i=0;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibfiles.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibforms.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from vibforms.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibgroup.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibgroup.c:84:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF viblists.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from viblists.c:161:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
viblists.c: In function 'Nlm_SetListPosition':
viblists.c:1118:15: warning: variable 'is_realized' set but not used [-Wunused-but-set-variable]
Nlm_Boolean is_realized;
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibmenus.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibmenus.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibmenus.c: In function 'Nlm_IsMenuItemChecked':
vibmenus.c:563:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CheckMenuItem':
vibmenus.c:591:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableMenuItem':
vibmenus.c:1986:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:1985:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoice':
vibmenus.c:2052:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceGroup':
vibmenus.c:2102:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceItem':
vibmenus.c:2146:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2144:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableMenuItem':
vibmenus.c:2309:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2308:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoice':
vibmenus.c:2375:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoiceItem':
vibmenus.c:2469:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2467:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_RemoveSubMenu':
vibmenus.c:2607:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CountMenuItems':
vibmenus.c:3036:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetMenuItem':
vibmenus.c:3219:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetPopListTitle':
vibmenus.c:3329:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
Nlm_MenU m;
^
vibmenus.c: In function 'Nlm_AppendItems':
vibmenus.c:3948:17: warning: unused variable 'accel' [-Wunused-variable]
Nlm_Char accel;
^~~~~
vibmenus.c: In function 'Nlm_NewPopupList':
vibmenus.c:4939:19: warning: unused variable 'lbl' [-Wunused-variable]
Widget lbl;
^~~
vibmenus.c:4937:19: warning: unused variable 'color' [-Wunused-variable]
Pixel color;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibprmpt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibprmpt.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibsbars.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibsbars.c:128:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibslate.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibslate.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibslate.c: In function 'Nlm_EnableSlate':
vibslate.c:1199:18: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_DisableSlate':
vibslate.c:1254:18: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_SelectSlate':
vibslate.c:1515:5: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:1517:5: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SelectPanel':
vibslate.c:1544:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:1546:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateClick':
vibslate.c:2026:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_SlateClickCallback':
vibslate.c:2157:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2159:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateInputCallback':
vibslate.c:2313:7: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues(w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2315:7: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues(w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateDrawCallback':
vibslate.c:2359:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2361:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibtexts.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibtexts.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibtexts.c: In function 'Nlm_TextCallback':
vibtexts.c:2982:24: warning: unused variable 'cbs' [-Wunused-variable]
XmAnyCallbackStruct *cbs = (XmAnyCallbackStruct *)call_data;
^~~
vibtexts.c: In function 'Nlm_LoseFocusCallback':
vibtexts.c:2999:25: warning: variable 'cbs' set but not used [-Wunused-but-set-variable]
XmAnyCallbackStruct *cbs;
^~~
vibtexts.c: In function 'Nlm_TabCallback':
vibtexts.c:3109:15: warning: variable 'event' set but not used [-Wunused-but-set-variable]
XKeyEvent *event;
^~~~~
vibtexts.c: In function 'Nlm_HiddenReturnCallback':
vibtexts.c:3122:15: warning: variable 'event' set but not used [-Wunused-but-set-variable]
XKeyEvent *event;
^~~~~
vibtexts.c: In function 'Nlm_HiddenActivateCallback':
vibtexts.c:3135:25: warning: variable 'cbs' set but not used [-Wunused-but-set-variable]
XmAnyCallbackStruct *cbs;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibutils.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from vibutils.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibwndws.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibwndws.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibwndws.c: In function 'Nlm_SetColorMap':
vibwndws.c:1060:13: warning: variable 'defaultdepth' set but not used [-Wunused-but-set-variable]
int defaultdepth;
^~~~~~~~~~~~
vibwndws.c: In function 'Nlm_SetWindowTitle':
vibwndws.c:1567:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_GetWindowTitle':
vibwndws.c:1610:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_NewWindow':
vibwndws.c:2155:19: warning: variable 'screen_num' set but not used [-Wunused-but-set-variable]
int screen_num;
^~~~~~~~~~
vibwndws.c: In function 'Nlm_HideWindow':
vibwndws.c:2526:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowNormal':
vibwndws.c:2969:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowModal':
vibwndws.c:3014:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowDocument':
vibwndws.c:3060:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_VibMainPrelude':
vibwndws.c:6771:13: warning: unused variable 'retval' [-Wunused-variable]
Nlm_Int2 retval;
^~~~~~
vibwndws.c: In function 'Nlm_RemoveDyingWindows':
vibwndws.c:6893:20: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibmain.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibmain.c:40:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibmain.c:121:1: warning: return type defaults to 'int' [-Wimplicit-int]
main (int argc, char *argv[])
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbidraw.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ncbidraw.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF drawing.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from drawing.c:128:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mapping.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from mapping.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mapping.c: In function 'Nlm_MapRectToWorldBox':
mapping.c:139:8: warning: variable 'curScale' set but not used [-Wunused-but-set-variable]
Int4 curScale;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF picture.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from picture.c:100:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF viewer.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from viewer.c:120:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF document.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from document.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
document.c: In function 'Nlm_PrintDocument':
document.c:4413:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
document.c:4417:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF table.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/panels.h:68,
from table.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF palette.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/panels.h:68,
from palette.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF diagnost.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from diagnost.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF image.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from image.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
image.c: In function 'ShiftXMask':
image.c:840:26: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
if(!((mask >> hi + low) & (unsigned long)1)) break;
~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF pictur3d.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/pictur3d.h:49,
from ../include/ppict3d.h:49,
from pictur3d.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pictur3d.c: In function 'Nlm_DeleteFromSeg':
pictur3d.c:114:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else seg->first = b->next;
^~~~
pictur3d.c:115:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if ( seg->last == b ) seg->last = bprev;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF prim3d1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d1.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF prim3d2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d2.c:65:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF prim3d3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d3.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF prim3d4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d4.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF prim3d5.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d5.c:66:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF viewer3d.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vibmouse.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from vibmouse.c:67:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF netscape.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from netscape.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netscape.c: In function 'NS_Obtain_lock':
netscape.c:236:10: warning: variable 'waited' set but not used [-Wunused-but-set-variable]
Bool waited = False;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF imagelst.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/imagelst.h:52,
from imagelst.c:61:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF treeview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/treemgr.h:67,
from treeview.c:91:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF shim3d.c
shim3d.c: In function 'Nlm_AddHalfWorm3D':
shim3d.c:3461:46: warning: unused variable 'tmp' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:40: warning: unused variable 'pCz' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:34: warning: unused variable 'pCy' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:28: warning: unused variable 'pCx' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:22: warning: unused variable 'pNz' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:16: warning: unused variable 'pNy' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:10: warning: unused variable 'pNx' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3460:47: warning: unused variable 'Cz' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3460:42: warning: unused variable 'Cy' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3460:37: warning: unused variable 'Cx' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3460:32: warning: unused variable 'Nz' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3460:27: warning: unused variable 'Ny' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3460:15: warning: unused variable 'Nx' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3459:21: warning: unused variable 'pi' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~
shim3d.c:3459:15: warning: unused variable 'sinj' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~~~
shim3d.c:3459:9: warning: unused variable 'cosj' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~~~
shim3d.c:3458:33: warning: unused variable 'prevlen' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~~~~~~
shim3d.c:3458:29: warning: unused variable 'Vz' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3458:25: warning: unused variable 'Vy' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3458:21: warning: unused variable 'Vx' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3458:17: warning: unused variable 'Hz' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3458:13: warning: unused variable 'Hy' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3458:9: warning: unused variable 'Hx' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3457:21: warning: unused variable 'dQtz' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3457:15: warning: unused variable 'dQty' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3457:9: warning: unused variable 'dQtx' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3455:14: warning: unused variable 'len' [-Wunused-variable]
GLdouble len, R1x, R1y, R1z, R2x, R2y, R2z, MG[4][3],
^~~
shim3d.c:3454:26: warning: unused variable 'offset' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^~~~~~
shim3d.c:3454:23: warning: unused variable 'm' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^
shim3d.c:3454:20: warning: unused variable 'k' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^
shim3d.c:3454:17: warning: unused variable 'j' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF odlbox.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from odlbox.c:50:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
odlbox.c: In function 'LB_onVScroll':
odlbox.c:424:12: warning: variable 'IsGoUp' set but not used [-Wunused-but-set-variable]
Boolean IsGoUp=FALSE;
^~~~~~
rm -f libvibrant.a
ar cru libvibrant.a vibbutns.o vibextra.o vibfiles.o vibforms.o vibgroup.o viblists.o vibmenus.o vibprmpt.o vibsbars.o vibslate.o vibtexts.o vibutils.o vibwndws.o vibmain.o ncbidraw.o drawing.o mapping.o picture.o viewer.o document.o table.o palette.o diagnost.o image.o pictur3d.o prim3d1.o prim3d2.o prim3d3.o prim3d4.o prim3d5.o viewer3d.o vibmouse.o netscape.o imagelst.o treeview.o shim3d.o odlbox.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libvibrant.a ../lib
ranlib ../lib/libvibrant.a
mv vibbutns.o vibbutns.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibbutns.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibbutns.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibbutns.c: In function 'Nlm_CheckCallback':
vibbutns.c:328:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_RadioCallback':
vibbutns.c:347:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_SetButtonStatus':
vibbutns.c:668:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Nlm_Int2 val;
^~~
vibbutns.c: In function 'Nlm_NewButton.isra.1':
vibbutns.c:1133:3: warning: 'call' may be used uninitialized in this function [-Wmaybe-uninitialized]
XtAddCallback (c, call, Nlm_ButtonCallback, (XtPointer) b);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv vibbutns.o vibbutns.glo
mv vibbutns.tmp vibbutns.o
mv vibextra.o vibextra.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibextra.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibextra.c:87:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibextra.c: In function 'Nlm_RGB2HSL.constprop':
vibextra.c:1219:13: warning: 'min' may be used uninitialized in this function [-Wmaybe-uninitialized]
i++; if ( i > 2 ) i=0;
^
mv vibextra.o vibextra.glo
mv vibextra.tmp vibextra.o
mv vibfiles.o vibfiles.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibfiles.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibfiles.o vibfiles.glo
mv vibfiles.tmp vibfiles.o
mv vibforms.o vibforms.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibforms.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from vibforms.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibforms.o vibforms.glo
mv vibforms.tmp vibforms.o
mv vibgroup.o vibgroup.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibgroup.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibgroup.c:84:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibgroup.o vibgroup.glo
mv vibgroup.tmp vibgroup.o
mv viblists.o viblists.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viblists.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from viblists.c:161:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
viblists.c: In function 'Nlm_SetListPosition':
viblists.c:1118:15: warning: variable 'is_realized' set but not used [-Wunused-but-set-variable]
Nlm_Boolean is_realized;
^~~~~~~~~~~
mv viblists.o viblists.glo
mv viblists.tmp viblists.o
mv vibmenus.o vibmenus.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmenus.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibmenus.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibmenus.c: In function 'Nlm_IsMenuItemChecked':
vibmenus.c:563:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CheckMenuItem':
vibmenus.c:591:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableMenuItem':
vibmenus.c:1986:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:1985:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoice':
vibmenus.c:2052:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceGroup':
vibmenus.c:2102:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceItem':
vibmenus.c:2146:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2144:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableMenuItem':
vibmenus.c:2309:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2308:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoice':
vibmenus.c:2375:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoiceItem':
vibmenus.c:2469:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2467:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_RemoveSubMenu':
vibmenus.c:2607:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CountMenuItems':
vibmenus.c:3036:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetMenuItem':
vibmenus.c:3219:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetPopListTitle':
vibmenus.c:3329:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
Nlm_MenU m;
^
vibmenus.c: In function 'Nlm_AppendItems':
vibmenus.c:3948:17: warning: unused variable 'accel' [-Wunused-variable]
Nlm_Char accel;
^~~~~
vibmenus.c: In function 'Nlm_NewPopupList':
vibmenus.c:4939:19: warning: unused variable 'lbl' [-Wunused-variable]
Widget lbl;
^~~
vibmenus.c:4937:19: warning: unused variable 'color' [-Wunused-variable]
Pixel color;
^~~~~
mv vibmenus.o vibmenus.glo
mv vibmenus.tmp vibmenus.o
mv vibprmpt.o vibprmpt.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibprmpt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibprmpt.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibprmpt.o vibprmpt.glo
mv vibprmpt.tmp vibprmpt.o
mv vibsbars.o vibsbars.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibsbars.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibsbars.c:128:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibsbars.o vibsbars.glo
mv vibsbars.tmp vibsbars.o
mv vibslate.o vibslate.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibslate.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibslate.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibslate.c: In function 'Nlm_EnableSlate':
vibslate.c:1199:18: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_DisableSlate':
vibslate.c:1254:18: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_SelectSlate':
vibslate.c:1515:5: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:1517:5: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SelectPanel':
vibslate.c:1544:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:1546:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateClick':
vibslate.c:2026:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_SlateClickCallback':
vibslate.c:2157:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2159:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateInputCallback':
vibslate.c:2313:7: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues(w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2315:7: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues(w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateDrawCallback':
vibslate.c:2359:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2361:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_Set3DColorMap':
vibslate.c:2686:17: warning: unused variable 'testvisual' [-Wunused-variable]
Boolean testvisual;
^~~~~~~~~~
vibslate.c:2685:13: warning: variable 'defaultdepth' set but not used [-Wunused-but-set-variable]
int defaultdepth;
^~~~~~~~~~~~
mv vibslate.o vibslate.glo
mv vibslate.tmp vibslate.o
mv vibtexts.o vibtexts.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibtexts.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibtexts.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibtexts.c: In function 'Nlm_TextCallback':
vibtexts.c:2982:24: warning: unused variable 'cbs' [-Wunused-variable]
XmAnyCallbackStruct *cbs = (XmAnyCallbackStruct *)call_data;
^~~
vibtexts.c: In function 'Nlm_LoseFocusCallback':
vibtexts.c:2999:25: warning: variable 'cbs' set but not used [-Wunused-but-set-variable]
XmAnyCallbackStruct *cbs;
^~~
vibtexts.c: In function 'Nlm_TabCallback':
vibtexts.c:3109:15: warning: variable 'event' set but not used [-Wunused-but-set-variable]
XKeyEvent *event;
^~~~~
vibtexts.c: In function 'Nlm_HiddenReturnCallback':
vibtexts.c:3122:15: warning: variable 'event' set but not used [-Wunused-but-set-variable]
XKeyEvent *event;
^~~~~
vibtexts.c: In function 'Nlm_HiddenActivateCallback':
vibtexts.c:3135:25: warning: variable 'cbs' set but not used [-Wunused-but-set-variable]
XmAnyCallbackStruct *cbs;
^~~
mv vibtexts.o vibtexts.glo
mv vibtexts.tmp vibtexts.o
mv vibutils.o vibutils.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibutils.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from vibutils.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibutils.o vibutils.glo
mv vibutils.tmp vibutils.o
mv vibwndws.o vibwndws.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibwndws.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibwndws.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibwndws.c: In function 'Nlm_SetColorMap':
vibwndws.c:1060:13: warning: variable 'defaultdepth' set but not used [-Wunused-but-set-variable]
int defaultdepth;
^~~~~~~~~~~~
vibwndws.c: In function 'Nlm_SetWindowTitle':
vibwndws.c:1567:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_GetWindowTitle':
vibwndws.c:1610:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_NewWindow':
vibwndws.c:2155:19: warning: variable 'screen_num' set but not used [-Wunused-but-set-variable]
int screen_num;
^~~~~~~~~~
vibwndws.c: In function 'Nlm_HideWindow':
vibwndws.c:2526:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowNormal':
vibwndws.c:2969:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowModal':
vibwndws.c:3014:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowDocument':
vibwndws.c:3060:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_VibMainPrelude':
vibwndws.c:6771:13: warning: unused variable 'retval' [-Wunused-variable]
Nlm_Int2 retval;
^~~~~~
vibwndws.c: In function 'Nlm_RemoveDyingWindows':
vibwndws.c:6893:20: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
At top level:
vibwndws.c:1318:16: warning: 'Nlm_StandardColormap' defined but not used [-Wunused-function]
static Boolean Nlm_StandardColormap(Colormap *cMap,
^~~~~~~~~~~~~~~~~~~~
mv vibwndws.o vibwndws.glo
mv vibwndws.tmp vibwndws.o
mv vibmain.o vibmain.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmain.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibmain.c:40:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibmain.c:121:1: warning: return type defaults to 'int' [-Wimplicit-int]
main (int argc, char *argv[])
^~~~
mv vibmain.o vibmain.glo
mv vibmain.tmp vibmain.o
mv ncbidraw.o ncbidraw.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL ncbidraw.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ncbidraw.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv ncbidraw.o ncbidraw.glo
mv ncbidraw.tmp ncbidraw.o
mv drawing.o drawing.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL drawing.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from drawing.c:128:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv drawing.o drawing.glo
mv drawing.tmp drawing.o
mv mapping.o mapping.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL mapping.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from mapping.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mapping.c: In function 'Nlm_MapRectToWorldBox':
mapping.c:139:8: warning: variable 'curScale' set but not used [-Wunused-but-set-variable]
Int4 curScale;
^~~~~~~~
mv mapping.o mapping.glo
mv mapping.tmp mapping.o
mv picture.o picture.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL picture.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from picture.c:100:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv picture.o picture.glo
mv picture.tmp picture.o
mv viewer.o viewer.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viewer.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from viewer.c:120:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv viewer.o viewer.glo
mv viewer.tmp viewer.o
mv document.o document.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL document.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from document.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
document.c: In function 'Nlm_PrintDocument':
document.c:4413:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
document.c:4417:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
mv document.o document.glo
mv document.tmp document.o
mv table.o table.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL table.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/panels.h:68,
from table.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv table.o table.glo
mv table.tmp table.o
mv palette.o palette.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL palette.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/panels.h:68,
from palette.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv palette.o palette.glo
mv palette.tmp palette.o
mv diagnost.o diagnost.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL diagnost.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from diagnost.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv diagnost.o diagnost.glo
mv diagnost.tmp diagnost.o
mv image.o image.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL image.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from image.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
image.c: In function 'ShiftXMask':
image.c:840:26: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
if(!((mask >> hi + low) & (unsigned long)1)) break;
~~~^~~~~
mv image.o image.glo
mv image.tmp image.o
mv pictur3d.o pictur3d.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL pictur3d.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/pictur3d.h:49,
from ../include/ppict3d.h:49,
from pictur3d.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pictur3d.c: In function 'Nlm_DeleteFromSeg':
pictur3d.c:114:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else seg->first = b->next;
^~~~
pictur3d.c:115:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if ( seg->last == b ) seg->last = bprev;
^~
mv pictur3d.o pictur3d.glo
mv pictur3d.tmp pictur3d.o
mv prim3d1.o prim3d1.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d1.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv prim3d1.o prim3d1.glo
mv prim3d1.tmp prim3d1.o
mv prim3d2.o prim3d2.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d2.c:65:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv prim3d2.o prim3d2.glo
mv prim3d2.tmp prim3d2.o
mv prim3d3.o prim3d3.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d3.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv prim3d3.o prim3d3.glo
mv prim3d3.tmp prim3d3.o
mv prim3d4.o prim3d4.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d4.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv prim3d4.o prim3d4.glo
mv prim3d4.tmp prim3d4.o
mv prim3d5.o prim3d5.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d5.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d5.c:66:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv prim3d5.o prim3d5.glo
mv prim3d5.tmp prim3d5.o
mv viewer3d.o viewer3d.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viewer3d.c
mv viewer3d.o viewer3d.glo
mv viewer3d.tmp viewer3d.o
mv vibmouse.o vibmouse.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmouse.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from vibmouse.c:67:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibmouse.o vibmouse.glo
mv vibmouse.tmp vibmouse.o
mv netscape.o netscape.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL netscape.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from netscape.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netscape.c: In function 'NS_Obtain_lock':
netscape.c:236:10: warning: variable 'waited' set but not used [-Wunused-but-set-variable]
Bool waited = False;
^~~~~~
mv netscape.o netscape.glo
mv netscape.tmp netscape.o
mv imagelst.o imagelst.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL imagelst.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/imagelst.h:52,
from imagelst.c:61:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv imagelst.o imagelst.glo
mv imagelst.tmp imagelst.o
mv treeview.o treeview.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL treeview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/treemgr.h:67,
from treeview.c:91:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv treeview.o treeview.glo
mv treeview.tmp treeview.o
mv shim3d.o shim3d.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL shim3d.c
shim3d.c: In function 'OGL_AddCylinder3D':
shim3d.c:906:14: warning: unused variable 'iCount' [-Wunused-variable]
Nlm_Int4 iCount;
^~~~~~
shim3d.c: In function 'OGL_AddText3D':
shim3d.c:1198:22: warning: unused variable 'i' [-Wunused-variable]
Nlm_Int4 Length, i;
^
shim3d.c: In function 'OGL_Zoom_DragMA':
shim3d.c:1758:16: warning: unused variable 'OGL_Data' [-Wunused-variable]
TOGL_Data *OGL_Data = MAToOGL(ma);
^~~~~~~~
shim3d.c: In function 'OGL_Hit':
shim3d.c:2053:37: warning: left shift count >= width of type [-Wshift-count-overflow]
ZMinName = ZMinName << (sizeof(GLuint) * 8);
^~
shim3d.c: In function 'write_row_callback':
shim3d.c:2899:15: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
float start, end;
^~~~~
shim3d.c:2899:22: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
float start, end;
^~~
shim3d.c: In function 'SetOGLFont':
shim3d.c:2369:64: warning: 'closest' may be used uninitialized in this function [-Wmaybe-uninitialized]
fontInfo = XLoadQueryFont(Nlm_currentXDisplay, list[closest]);
^
shim3d.c:2364:37: warning: 'mindiff' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ii == 0 || diff < mindiff) {
~~~~~^~~~~~~~~
shim3d.c:2369:64: warning: 'list' may be used uninitialized in this function [-Wmaybe-uninitialized]
fontInfo = XLoadQueryFont(Nlm_currentXDisplay, list[closest]);
^
shim3d.c: In function 'Nlm_AddHalfWorm3D':
shim3d.c:3454:26: warning: 'offset' may be used uninitialized in this function [-Wmaybe-uninitialized]
Nlm_Int4 i, j, k, m, offset;
^~~~~~
mv shim3d.o shim3d.glo
mv shim3d.tmp shim3d.o
mv odlbox.o odlbox.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL odlbox.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from odlbox.c:50:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
odlbox.c: In function 'LB_onVScroll':
odlbox.c:424:12: warning: variable 'IsGoUp' set but not used [-Wunused-but-set-variable]
Boolean IsGoUp=FALSE;
^~~~~~
mv odlbox.o odlbox.glo
mv odlbox.tmp odlbox.o
rm -f libvibrantOGL.a
ar cru libvibrantOGL.a vibbutns.glo vibextra.glo vibfiles.glo vibforms.glo vibgroup.glo viblists.glo vibmenus.glo vibprmpt.glo vibsbars.glo vibslate.glo vibtexts.glo vibutils.glo vibwndws.glo vibmain.glo ncbidraw.glo drawing.glo mapping.glo picture.glo viewer.glo document.glo table.glo palette.glo diagnost.glo image.glo pictur3d.glo prim3d1.glo prim3d2.glo prim3d3.glo prim3d4.glo prim3d5.glo viewer3d.glo vibmouse.glo netscape.glo imagelst.glo treeview.glo shim3d.glo odlbox.glo
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libvibrantOGL.a ../lib
ranlib ../lib/libvibrantOGL.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF accentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from accentr.c:297:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
accentr.c: In function 'EntrezBiostrucGet':
accentr.c:2113:17: warning: unused variable 'retval' [-Wunused-variable]
BiostrucPtr retval = NULL;
^~~~~~
accentr.c: In function 'EntrezGIForSeqIdFunc':
accentr.c:3283:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! gi) return OM_MSG_RET_OK;
^~
accentr.c:3285:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sip2 = ValNodeNew(NULL);
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF accutils.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from ../include/accutils.h:119,
from accutils.c:149:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rm -f libncbiacc.a
ar cru libncbiacc.a accentr.o accutils.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbiacc.a ../lib
ranlib ../lib/libncbiacc.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF drawseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from drawseq.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
drawseq.c: In function 'AddFlatNodeSymbol':
drawseq.c:811:7: warning: unused variable 'symbol_height' [-Wunused-variable]
Int4 symbol_height = 8;
^~~~~~~~~~~~~
drawseq.c: In function 'AddAlignBlocks':
drawseq.c:970:7: warning: variable 'c_num' set but not used [-Wunused-but-set-variable]
Int2 c_num;
^~~~~
drawseq.c: In function 'AddAlignFeature':
drawseq.c:1369:8: warning: unused variable 'ptype' [-Wunused-variable]
Uint1 ptype = 0;
^~~~~
drawseq.c: In function 'AddAlignmentMismatch':
drawseq.c:1523:7: warning: variable 'i_right' set but not used [-Wunused-but-set-variable]
Int4 i_right;
^~~~~~~
drawseq.c: In function 'DrawRestrictionMap':
drawseq.c:1811:10: warning: unused variable 'retval' [-Wunused-variable]
Boolean retval = FALSE;
^~~~~~
drawseq.c:1802:15: warning: variable 'center' set but not used [-Wunused-but-set-variable]
Int4 x1, x2, center;
^~~~~~
drawseq.c: In function 'DrawFeatures':
drawseq.c:2563:7: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Int2 entityID;
^~~~~~~~
drawseq.c: In function 'DrawOneSeqLoc':
drawseq.c:3020:10: warning: variable 'show_seq_label' set but not used [-Wunused-but-set-variable]
Boolean show_seq_label = TRUE; /*show the label of a sequence*/
^~~~~~~~~~~~~~
drawseq.c:3009:10: warning: variable 'ends' set but not used [-Wunused-but-set-variable]
Boolean ends;
^~~~
drawseq.c: In function 'Label_GData':
drawseq.c:3439:10: warning: variable 'success' set but not used [-Wunused-but-set-variable]
Boolean success = FALSE;
^~~~~~~
drawseq.c: In function 'DrawEquivAlign':
drawseq.c:3594:8: warning: unused variable 'my_gray_color' [-Wunused-variable]
Uint1 my_gray_color[]={63, 63, 63};
^~~~~~~~~~~~~
drawseq.c: In function 'load_align_label_rectangle':
drawseq.c:4352:10: warning: variable 'found_it' set but not used [-Wunused-but-set-variable]
Boolean found_it;
^~~~~~~~
drawseq.c: In function 'PicForAlignNode':
drawseq.c:4558:18: warning: variable 'min_scale' set but not used [-Wunused-but-set-variable]
Int4 max_width, min_scale;
^~~~~~~~~
At top level:
drawseq.c:3525:22: warning: 'get_ith_arp' defined but not used [-Wunused-function]
static AlignRangePtr get_ith_arp(AlignRangePtr arp, Int2 i)
^~~~~~~~~~~
drawseq.c:3511:18: warning: 'get_map_pos' defined but not used [-Wunused-function]
static MapPosPtr get_map_pos(MapLayoutPtr mlp, SeqIdPtr sip)
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF dotmatrx.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dotmatrx.h:47,
from dotmatrx.c:32:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF fea2seg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from fea2seg.c:74:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF fstyle.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from fstyle.c:55:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF smdlg1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from smdlg1.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF smdlg2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from smdlg2.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
smdlg2.c: In function 'Nlm_CreateDlgGroup':
smdlg2.c:631:12: warning: variable 'toAlign' set but not used [-Wunused-but-set-variable]
Handle toAlign[3];
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF smdlg3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from smdlg3.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF smtools.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from smtools.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF styleman.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from styleman.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF stylemui.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from stylemui.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF glbpic.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from glbpic.c:22:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
glbpic.c: In function 'label_linear_mark':
glbpic.c:1295:7: warning: unused variable 'tick_len' [-Wunused-variable]
Int4 tick_len = TICK_LEN;
^~~~~~~~
glbpic.c: In function 'add_alignment_to_global':
glbpic.c:1552:8: warning: variable 'p_val' set but not used [-Wunused-but-set-variable]
Uint1 p_val;
^~~~~
At top level:
glbpic.c:1748:16: warning: 'get_print_score' defined but not used [-Wunused-function]
static Boolean get_print_score(FloatHi min_score, FloatHi max_score, CharPtr label, Uint1 status)
^~~~~~~~~~~~~~~
glbpic.c:584:19: warning: 'extract_align_range' defined but not used [-Wunused-function]
static ValNodePtr extract_align_range(ValNodePtr PNTR arp_list, Uint1 displayOrder)
^~~~~~~~~~~~~~~~~~~
glbpic.c: In function 'get_circle_label_align':
glbpic.c:2349:9: warning: 'align' may be used uninitialized in this function [-Wmaybe-uninitialized]
return align;
^~~~~
glbpic.c: In function 'label_circle_mark':
glbpic.c:2479:6: warning: 'first_align' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(label_align)
^~~~~~
glbpic.c:2450:5: warning: 'p_align' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(label_align)
^~~~~~
glbpic.c:2474:26: warning: 'first_left' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(ABS(first_left - left) < (t_width +3))
^
glbpic.c:2469:28: warning: 'first_width' may be used uninitialized in this function [-Wmaybe-uninitialized]
t_width = (first_width + width)/2;
~~~~~~~~~~~~~^~~~~~~~
glbpic.c:2473:24: warning: 'first_top' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(ABS(first_top - top )< (font_height+3))
^
In file included from ../include/glbpic.h:7:0,
from glbpic.c:23:
glbpic.c: In function 'add_alignment_to_global':
../include/picture.h:520:22: warning: 'g_top' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddTextLabel Nlm_AddTextLabel
^~~~~~~~~~~~~~~~
glbpic.c:1560:7: note: 'g_top' was declared here
Int4 g_top, g_bottom;
^~~~~
glbpic.c: In function 'Draw_Global':
glbpic.c:2177:12: warning: 'seglen' may be used uninitialized in this function [-Wmaybe-uninitialized]
m_stop += seglen;
~~~~~~~^~~~~~~~~
glbpic.c:1943:8: note: 'seglen' was declared here
Int4 seglen;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF layout.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/maputil.h:113,
from ../include/jzcoll.h:123,
from ../include/layout.h:3,
from layout.c:2:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
layout.c: In function 'LayoutNodeFlat':
layout.c:326:24: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp, next, prev;
^~~~
layout.c: In function 'layout_uncompressed_group':
layout.c:1244:20: warning: variable 'group_stop' set but not used [-Wunused-but-set-variable]
Int2 group_start, group_stop;
^~~~~~~~~~
layout.c: In function 'LayoutFeatNode':
layout.c:1365:17: warning: variable 'y_next' set but not used [-Wunused-but-set-variable]
Int4 cur_line, y_next;
^~~~~~
layout.c:1364:17: warning: variable 'labelstyle' set but not used [-Wunused-but-set-variable]
Int4 segstyle, labelstyle;
^~~~~~~~~~
layout.c:1363:10: warning: variable 'show_trunc' set but not used [-Wunused-but-set-variable]
Boolean show_trunc = FALSE;
^~~~~~~~~~
layout.c:1350:10: warning: variable 'k' set but not used [-Wunused-but-set-variable]
Int2 i, k;
^
layout.c: In function 'LayoutAlignNode':
layout.c:2208:7: warning: unused variable 'num' [-Wunused-variable]
Int4 num = 0;
^~~
At top level:
layout.c:1779:16: warning: 'modify_master_line' defined but not used [-Wunused-function]
static Boolean modify_master_line(ValNodePtr vnp, Int4Ptr m_left, Int4Ptr m_right, Int4 maxScale, Uint1 label_align)
^~~~~~~~~~~~~~~~~~
layout.c: In function 'GroupFeatNode':
layout.c:636:14: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
prev->next = new;
~~~~~~~~~~~^~~~~
layout.c:594:35: note: 'prev' was declared here
ValNodePtr my_node = NULL, curr, prev, next;
^~~~
layout.c: In function 'OrderCdsmRNA':
layout.c:963:9: warning: 'm_missed' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(missed < m_missed)
^
layout.c:940:15: note: 'm_missed' was declared here
Int2 missed, m_missed; /*number of exons missed at both end*/
^~~~~~~~
layout.c: In function 'LayoutFeatNode':
layout.c:1503:12: warning: 'p_right' may be used uninitialized in this function [-Wmaybe-uninitialized]
p_right = MAX(right, p_right);
layout.c:1502:11: warning: 'p_left' may be used uninitialized in this function [-Wmaybe-uninitialized]
p_left = MIN(left, p_left);
layout.c:1504:14: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxHeight = MAX(height, maxHeight);
layout.c: In function 'LayoutAlignNode':
layout.c:2215:17: warning: 'next_line' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 cur_line, next_line;
^~~~~~~~~
layout.c:2251:7: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
i = find_align_line_number(anp, vnp->next,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
label_align, &next, &line_status_list, m_right, maxScale);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF saldist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from ../include/saldist.h:48,
from saldist.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
saldist.c: In function 'AAcode':
saldist.c:1003:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='A') return(1); if (car=='B') return(2);
^~
saldist.c:1003:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='A') return(1); if (car=='B') return(2);
^~
saldist.c:1004:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='C') return(3); if (car=='D') return(4);
^~
saldist.c:1004:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='C') return(3); if (car=='D') return(4);
^~
saldist.c:1005:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='E') return(5); if (car=='F') return(6);
^~
saldist.c:1005:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='E') return(5); if (car=='F') return(6);
^~
saldist.c:1006:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='G') return(7); if (car=='H') return(8);
^~
saldist.c:1006:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='G') return(7); if (car=='H') return(8);
^~
saldist.c:1007:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='I') return(9); if (car=='K') return(10);
^~
saldist.c:1007:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='I') return(9); if (car=='K') return(10);
^~
saldist.c:1008:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='L') return(11); if (car=='M') return(12);
^~
saldist.c:1008:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='L') return(11); if (car=='M') return(12);
^~
saldist.c:1009:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='N') return(13); if (car=='P') return(14);
^~
saldist.c:1009:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='N') return(13); if (car=='P') return(14);
^~
saldist.c:1010:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='Q') return(15); if (car=='R') return(16);
^~
saldist.c:1010:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='Q') return(15); if (car=='R') return(16);
^~
saldist.c:1011:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='S') return(17); if (car=='T') return(18);
^~
saldist.c:1011:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='S') return(17); if (car=='T') return(18);
^~
saldist.c:1012:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='V') return(19); if (car=='W') return(20);
^~
saldist.c:1012:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='V') return(19); if (car=='W') return(20);
^~
saldist.c:1013:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='X') return(21); if (car=='Y') return(22);
^~
saldist.c:1013:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='X') return(21); if (car=='Y') return(22);
^~
saldist.c:1014:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='Z') return(23); if (car=='U') return(24);
^~
saldist.c:1014:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='Z') return(23); if (car=='U') return(24);
^~
saldist.c: In function 'copy_string':
saldist.c:1289:12: warning: value computed is not used [-Wunused-value]
*from++;
^~~~~~~
saldist.c:1302:11: warning: value computed is not used [-Wunused-value]
*from++;
^~~~~~~
saldist.c: In function 'nss_ref_complength':
saldist.c:1479:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-')
^
saldist.c:1455:16: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c:1455:12: warning: variable 'c1' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c: In function 'nss_pw_complength':
saldist.c:1572:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-')
^
saldist.c:1547:16: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c:1547:12: warning: variable 'c1' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c: In function 'nss_gp_complength':
saldist.c:1675:21: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-')
^
saldist.c:1640:16: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c:1640:12: warning: variable 'c1' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c: In function 'SortbySimProc':
saldist.c:2139:31: warning: variable 'newsalpd' set but not used [-Wunused-but-set-variable]
SeqAlignPtr newsalp, newsalpd;
^~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from saldist.c:49:
saldist.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
saldist.c:1853:22: warning: 'scangp_calcul' defined but not used [-Wunused-function]
static Int4Ptr PNTR scangp_calcul (EditAlignDataPtr adp, Int2 seq1, Int2 seq2, Int4 from, Int4 to, Int2 group, Int2 choice, Int2 win_width)
^~~~~~~~~~~~~
saldist.c:1080:24: warning: 'FloatLomatrix' defined but not used [-Wunused-function]
static FloatLoPtr PNTR FloatLomatrix (Int2 nrows, Int2 ncol)
^~~~~~~~~~~~~
saldist.c:999:13: warning: 'AAcode' defined but not used [-Wunused-function]
static Int2 AAcode(Char car)
^~~~~~
saldist.c:928:16: warning: 'new_matrice' defined but not used [-Wunused-function]
static Boolean new_matrice (Int2 simmatrix, CharPtr path)
^~~~~~~~~~~
saldist.c:910:14: warning: 'matrixlst' defined but not used [-Wunused-variable]
static Char *matrixlst [] = {"", "idmat",
^~~~~~~~~
saldist.c: In function 'writematrixhalf.constprop':
saldist.c:1225:18: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp=vnp->next;
~~~^~~~~~~~~~
saldist.c: In function 'PwDistanceLongItem':
saldist.c:1151:18: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp=vnp->next;
~~~^~~~~~~~~~
saldist.c:1104:19: note: 'vnp' was declared here
ValNodePtr vnp,
^~~
saldist.c: In function 'SortbyLenItem':
saldist.c:2192:11: warning: 'mink' may be used uninitialized in this function [-Wmaybe-uninitialized]
lens [mink] = maxlens + 10;
^
saldist.c:2172:28: note: 'mink' was declared here
Int2 j, k, mink;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF saled.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/saledit.h:48,
from saled.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
saled.c: In function 'ReadAlignmentForSeqEntry':
saled.c:3325:21: warning: unused variable 'dirty' [-Wunused-variable]
dirty = FALSE;
^~~~~
saled.c:3321:21: warning: unused variable 'salp' [-Wunused-variable]
SeqAlignPtr salp=NULL,
^~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from saled.c:49:
saled.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from saled.c:55:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salfiles.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/saledit.h:48,
from ../include/salfiles.h:48,
from salfiles.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salfiles.c: In function 'NewFastaRead':
salfiles.c:315:30: warning: variable 'lastsegsip' set but not used [-Wunused-but-set-variable]
SeqIdPtr segsip=NULL, lastsegsip=NULL;
^~~~~~~~~~
salfiles.c: In function 'ReadAlignmentToStrings':
salfiles.c:664:16: warning: unused variable 'nseq' [-Wunused-variable]
Int2 nseq = 0;
^~~~
salfiles.c: In function 'MacawRead':
salfiles.c:1257:15: warning: unused variable 'vnp' [-Wunused-variable]
vnp = NULL;
^~~
salfiles.c: In function 'ReadLocalAlign':
salfiles.c:1370:14: warning: variable 'tmp1' set but not used [-Wunused-but-set-variable]
tmp1;
^~~~
salfiles.c: In function 'ImportFromFile':
salfiles.c:2072:20: warning: unused variable 'sep' [-Wunused-variable]
SeqEntryPtr sep = NULL;
^~~
salfiles.c:2071:20: warning: unused variable 'sap' [-Wunused-variable]
SeqAnnotPtr sap = NULL;
^~~
salfiles.c: In function 'FindSeqEntryForSeqIdCallback':
salfiles.c:2672:12: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (SeqIdForSameBioseq(cip->sip, sip))
^~
salfiles.c:2674:15: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cip->bsp = bsp;
^~~
salfiles.c: In function 'sesp_to_pept':
salfiles.c:2713:18: warning: unused variable 'bufferPtr' [-Wunused-variable]
bufferPtr = NULL;
^~~~~~~~~
salfiles.c: In function 'SaveFeatProc':
salfiles.c:3387:22: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salfiles.c: In function 'CCReadAnythingLoop':
salfiles.c:3685:16: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from salfiles.c:48:
salfiles.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
salfiles.c:501:19: warning: 'get_lens_fromseqalign' defined but not used [-Wunused-function]
static ValNodePtr get_lens_fromseqalign (SeqAlignPtr salp)
^~~~~~~~~~~~~~~~~~~~~
salfiles.c: In function 'CCDownloadProc':
salfiles.c:2218:7: warning: 'new_sep' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp = SeqEntryToSeqLoc (sep, &n, adp->mol_type);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salfiles.c:2286:15: note: 'new_sep' was declared here
SeqEntryPtr new_sep;
^~~~~~~
salfiles.c: In function 'NewFastaRead.constprop':
salfiles.c:460:6: warning: 'sip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (sip!=NULL)
^
salfiles.c: In function 'GapFastaRead':
salfiles.c:751:19: warning: 'seqstr' may be used uninitialized in this function [-Wmaybe-uninitialized]
seqstr [lgseq] = '\0';
^
salfiles.c:654:16: note: 'seqstr' was declared here
seqstr;
^~~~~~
salfiles.c:724:15: warning: 'startp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (!startp) {
^
salfiles.c:660:16: note: 'startp' was declared here
Boolean startp;
^~~~~~
salfiles.c: In function 'ReadLocalAlignment':
salfiles.c:1287:3: warning: 'seqvnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
ValNodeFree (seqvnp);
^~~~~~~~~~~~~~~~~~~~
salfiles.c:1113:19: note: 'seqvnp' was declared here
ValNodePtr vnp, seqvnp;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salpanel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/saledit.h:48,
from salpanel.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salpanel.c: In function 'go_to_next_to_draw':
salpanel.c:331:17: warning: statement with no effect [-Wunused-value]
offsettmp;
^~~~~~~~~
salpanel.c: In function 'next_to_draw':
salpanel.c:471:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if ( curstr != NULL )
^
salpanel.c: In function 'AssociatePropagatedSubloc':
salpanel.c:3131:16: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
salpanel.c: In function 'FeaturePropagateForm':
salpanel.c:4670:15: warning: variable 'ppt' set but not used [-Wunused-but-set-variable]
PrompT ppt;
^~~
salpanel.c:4665:15: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
salpanel.c: In function 'OkToContinueWithFeatureApply':
salpanel.c:6099:14: warning: unused variable 'num_missing' [-Wunused-variable]
Int4 num_missing = 0, seq_num, start_num;
^~~~~~~~~~~
salpanel.c: In function 'DoApplyFeatureToAlignment':
salpanel.c:6215:31: warning: unused variable 'found_null' [-Wunused-variable]
Boolean found_null = FALSE;
^~~~~~~~~~
salpanel.c: In function 'ApplyFeatureToAlignment':
salpanel.c:6417:31: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from salpanel.c:45:
salpanel.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from salpanel.c:52:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
salpanel.c:5055:13: warning: 'BatchApplyFeatureDetailsMessage' defined but not used [-Wunused-function]
static void BatchApplyFeatureDetailsMessage (DialoG d, Int2 mssg)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salpanel.c:224:13: warning: 'get_client_rectxy' defined but not used [-Wunused-function]
static void get_client_rectxy (PaneL p, RectPtr prc, Int2 x, Int2 y)
^~~~~~~~~~~~~~~~~
salpanel.c:113:14: warning: 'leftOvalFillSym' defined but not used [-Wunused-variable]
static Uint1 leftOvalFillSym [] = {
^~~~~~~~~~~~~~~
salpanel.c:110:14: warning: 'rightOvalFillSym' defined but not used [-Wunused-variable]
static Uint1 rightOvalFillSym [] = {
^~~~~~~~~~~~~~~~
salpanel.c:107:14: warning: 'leftOvalSym' defined but not used [-Wunused-variable]
static Uint1 leftOvalSym [] = {
^~~~~~~~~~~
salpanel.c:104:14: warning: 'rightOvalSym' defined but not used [-Wunused-variable]
static Uint1 rightOvalSym [] = {
^~~~~~~~~~~~
salpanel.c:101:14: warning: 'downTriFillSym' defined but not used [-Wunused-variable]
static Uint1 downTriFillSym [] = {
^~~~~~~~~~~~~~
salpanel.c:98:14: warning: 'upTriFillSym' defined but not used [-Wunused-variable]
static Uint1 upTriFillSym [] = {
^~~~~~~~~~~~
salpanel.c:89:14: warning: 'ovalFillSym' defined but not used [-Wunused-variable]
static Uint1 ovalFillSym [] = {
^~~~~~~~~~~
salpanel.c:86:14: warning: 'diamondFillSym' defined but not used [-Wunused-variable]
static Uint1 diamondFillSym [] = {
^~~~~~~~~~~~~~
salpanel.c:80:14: warning: 'downTriSym' defined but not used [-Wunused-variable]
static Uint1 downTriSym [] = {
^~~~~~~~~~
salpanel.c:77:14: warning: 'upTriSym' defined but not used [-Wunused-variable]
static Uint1 upTriSym [] = {
^~~~~~~~
salpanel.c:68:14: warning: 'ovalSym' defined but not used [-Wunused-variable]
static Uint1 ovalSym [] = {
^~~~~~~
salpanel.c:65:14: warning: 'diamondSym' defined but not used [-Wunused-variable]
static Uint1 diamondSym [] = {
^~~~~~~~~~
salpanel.c: In function 'draw_feat.isra.14.part.15':
salpanel.c:1939:17: warning: 'col1' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 col1;
^~~~
salpanel.c: In function 'on_draw':
salpanel.c:2527:23: warning: 'draw_diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
draw_seq (adp, curssp, from_inseq, drw_width, ptlh, curstr, draw_diff, masterstr, TRUE, itemsubtype, FALSE);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salparam.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from ../include/salparam.h:48,
from salparam.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salparam.c: In function 'mergelst':
salparam.c:1325:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Boolean val;
^~~
salparam.c: In function 'unmergelst':
salparam.c:1340:20: warning: variable 'dbdp' set but not used [-Wunused-but-set-variable]
DialogBoxDataPtr dbdp;
^~~~
salparam.c: In function 'FormulaDialog':
salparam.c:1398:36: warning: variable 'b5' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3, b4, b5;
^~
salparam.c: In function 'JK_NTPattern2Ex':
salparam.c:1596:19: warning: variable 'debug_str' set but not used [-Wunused-but-set-variable]
CharPtr debug_str;
^~~~~~~~~
salparam.c: In function 'DotPlotBtn':
salparam.c:1936:22: warning: variable 'status' set but not used [-Wunused-but-set-variable]
Int2 status;
^~~~~~
salparam.c: In function 'DotPlotDialog':
salparam.c:1973:20: warning: variable 'bt1' set but not used [-Wunused-but-set-variable]
ButtoN bt1, bt2;
^~~
salparam.c: In function 'DotPlotItem':
salparam.c:2004:22: warning: variable 'status' set but not used [-Wunused-but-set-variable]
Int2 status;
^~~~~~
salparam.c: In function 'SelectSeqFunc':
salparam.c:2308:20: warning: variable 'str' set but not used [-Wunused-but-set-variable]
CharPtr str;
^~~
salparam.c: In function 'HighlightSelectionFunc':
salparam.c:2344:22: warning: variable 'wdp' set but not used [-Wunused-but-set-variable]
SeqEditViewFormPtr wdp;
^~~
salparam.c: In function 'PropagateFeatureProc':
salparam.c:2623:25: warning: variable 'iID' set but not used [-Wunused-but-set-variable]
Uint2 eID, iID,
^~~
salparam.c:2614:20: warning: variable 'salp' set but not used [-Wunused-but-set-variable]
SeqAlignPtr salp;
^~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from salparam.c:49:
salparam.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from salparam.c:58:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
salparam.c: In function 'FileInProc':
salparam.c:782:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%d %ld", &n, &lens);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salparam.c: In function 'DotPlotBtn':
salparam.c:1951:13: warning: 'sep' may be used uninitialized in this function [-Wmaybe-uninitialized]
bsp = (BioseqPtr) sep->data.ptrvalue;
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salsa.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from salsa.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salsa.c: In function 'SelectSubsProc':
salsa.c:2140:23: warning: variable 'svpp' set but not used [-Wunused-but-set-variable]
SeqEditViewProcsPtr svpp=NULL;
^~~~
salsa.c: In function 'SetSeqInfo':
salsa.c:3195:17: warning: unused variable 'vnp' [-Wunused-variable]
ValNodePtr vnp = NULL;
^~~
salsa.c: In function 'SetupAlignDataSap':
salsa.c:3410:16: warning: variable 'entityID_sap' set but not used [-Wunused-but-set-variable]
Uint2 entityID_sap;
^~~~~~~~~~~~
salsa.c: In function 'get_bestpos_formerge':
salsa.c:4304:17: warning: variable 'insert_after' set but not used [-Wunused-but-set-variable]
insert_after=FALSE;
^~~~~~~~~~~~
salsa.c:4303:17: warning: variable 'insert_before' set but not used [-Wunused-but-set-variable]
Boolean insert_before=FALSE,
^~~~~~~~~~~~~
salsa.c: In function 'CreateSeqAlignViewForm':
salsa.c:4689:22: warning: variable 'mergebtn' set but not used [-Wunused-but-set-variable]
ButtoN mergebtn;
^~~~~~~~
salsa.c: In function 'AlgEditFunc':
salsa.c:4988:23: warning: unused variable 'wdp' [-Wunused-variable]
SeqEditViewFormPtr wdp = NULL;
^~~
salsa.c:4986:23: warning: unused variable 'w' [-Wunused-variable]
WindoW w = NULL;
^
salsa.c: In function 'OldAlignmentEditor':
salsa.c:5118:16: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Int2 rval;
^~~~
salsa.c: In function 'LaunchAnnotAlignEditor':
salsa.c:5305:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignEditor':
salsa.c:5322:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignViewer':
salsa.c:5339:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop':
salsa.c:5354:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop2':
salsa.c:5371:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop3':
salsa.c:5390:20: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop4':
salsa.c:5417:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
salsa.c: In function 'InsertSeqProc':
salsa.c:5587:17: warning: variable 'cnclbt' set but not used [-Wunused-but-set-variable]
ButtoN insbt, cnclbt;
^~~~~~
salsa.c:5585:10: warning: variable 'insprt' set but not used [-Wunused-but-set-variable]
PrompT insprt;
^~~~~~
salsa.c: In function 'SeqAlignBestHit':
salsa.c:5654:22: warning: variable 'last' set but not used [-Wunused-but-set-variable]
Int4 last;
^~~~
salsa.c: In function 'SeqAlignStartUpdate':
salsa.c:5839:22: warning: variable 'k' set but not used [-Wunused-but-set-variable]
Int2 index, k, j;
^
salsa.c:5838:15: warning: variable 'start' set but not used [-Wunused-but-set-variable]
start;
^~~~~
salsa.c:5837:15: warning: variable 'len_sum' set but not used [-Wunused-but-set-variable]
Int4 len_sum,
^~~~~~~
salsa.c:5834:15: warning: variable 'lenp' set but not used [-Wunused-but-set-variable]
Int4Ptr lenp,
^~~~
salsa.c:5833:15: warning: variable 'pre' set but not used [-Wunused-but-set-variable]
SeqIdPtr pre, sip, next;
^~~
salsa.c: In function 'CCNormalizeSeqAlignId':
salsa.c:6788:23: warning: unused variable 'gi' [-Wunused-variable]
Int4 gi = 0;
^~
salsa.c:6787:17: warning: unused variable 'missing_fmt' [-Wunused-variable]
CharPtr missing_fmt = "The alignment contains %s that can not be found in GenBank.\nPlease check the accession number.\n";
^~~~~~~~~~~
salsa.c:6786:17: warning: unused variable 'missing_cont_fmt' [-Wunused-variable]
CharPtr missing_cont_fmt = "The alignment contains %s that can not be found in GenBank.\nPlease check the accession number.\nContinue anyway?\n";
^~~~~~~~~~~~~~~~
salsa.c: In function 'ValidateSeqAlignandACCEx':
salsa.c:7145:16: warning: variable 'ans' set but not used [-Wunused-but-set-variable]
MsgAnswer ans;
^~~
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from salsa.c:48:
salsa.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from salsa.c:68:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
salsa.c:87:13: warning: 'InsertSequenceDlg' declared 'static' but never defined [-Wunused-function]
static void InsertSequenceDlg (ButtoN b);
^~~~~~~~~~~~~~~~~
salsa.c:6021:13: warning: 'SWPrintFarpointerAln' defined but not used [-Wunused-function]
static void SWPrintFarpointerAln(SeqAlignPtr sap, FILE *fp)
^~~~~~~~~~~~~~~~~~~~
salsa.c:4884:16: warning: 'DeltaLitOnly' defined but not used [-Wunused-function]
static Boolean DeltaLitOnly (BioseqPtr bsp)
^~~~~~~~~~~~
salsa.c:2360:13: warning: 'MakeCdRgnrProc' defined but not used [-Wunused-function]
static void MakeCdRgnrProc (IteM i) {
^~~~~~~~~~~~~~
salsa.c:2356:13: warning: 'MakeCdRgnProc' defined but not used [-Wunused-function]
static void MakeCdRgnProc (IteM i) {
^~~~~~~~~~~~~
salsa.c:1760:13: warning: 'AcceptCloseWindowButton' defined but not used [-Wunused-function]
static void AcceptCloseWindowButton (ButtoN b)
^~~~~~~~~~~~~~~~~~~~~~~
In file included from salsa.c:52:0:
../include/salprop.h:50:16: warning: 'GBFeat' defined but not used [-Wunused-variable]
static CharPtr GBFeat[number_GBFeat] = {
^~~~~~
In file included from ../include/ncbi.h:65:0,
from ../include/salsa.h:48,
from salsa.c:43:
salsa.c: In function 'ExportFASTAForUnselectedUpdates':
../include/ncbifile.h:138:19: warning: 'fp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define FileClose Nlm_FileClose
^~~~~~~~~~~~~
salsa.c:6398:23: note: 'fp' was declared here
FILE *fp;
^~
In file included from ../include/ncbi.h:65:0,
from ../include/salsa.h:48,
from salsa.c:43:
salsa.c: In function 'ExportBadAlignments':
../include/ncbifile.h:138:19: warning: 'fp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define FileClose Nlm_FileClose
^~~~~~~~~~~~~
salsa.c:6366:23: note: 'fp' was declared here
FILE *fp;
^~
salsa.c: In function 'SeqAlignBestHit.isra.13':
salsa.c:5795:23: warning: 'nctr' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = nctr+beg+end;
~~~~^~~~
salsa.c:5795:27: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = nctr+beg+end;
~~~~~~~~^~~~
salsa.c:5795:23: warning: 'beg' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = nctr+beg+end;
~~~~^~~~
salsa.c: In function 'BioseqEditMsgFunc':
salsa.c:912:51: warning: 'anp' may be used uninitialized in this function [-Wmaybe-uninitialized]
ssp = SelStructNew (anp->seq_entityID, anp->bsp_itemID, OBJ_BIOSEQ, from, to, anp->sip, Seq_strand_plus, FALSE);
~~~^~~~~~~~~~~~
salsa.c:890:20: note: 'anp' was declared here
AlignNodePtr anp;
^~~
salsa.c: In function 'DeleteProc':
salsa.c:1955:165: warning: 'sap' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((adp->sap1_original && (FindSeqIdinSeqAlign ((SeqAlignPtr)adp->sap1_original->data, SeqLocId(slp))) > 0) || (FindSeqIdinSeqAlign ((SeqAlignPtr)sap->data, SeqLocId(slp))) > 0)
~~~^~~~~~
salsa.c: In function 'SkipThisWindowProc':
salsa.c:4591:6: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
LaunchAlignViewer(salp);
^~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqfltr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from seqfltr.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqfltr.c: In function 'FilterSeq':
seqfltr.c:259:21: warning: 'fptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
sgp->values = (Pointer) fptr;
~~~~~~~~~~~~^~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqgraph.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from seqgraph.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqgraph.c: In function 'EndPointDialogToEndPointValNode':
seqgraph.c:140:10: warning: 'eplist' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (Pointer) eplist;
^~~~~~~~~~~~~~~~
seqgraph.c: In function 'SeqLocGraphViewProc':
seqgraph.c:1155:17: warning: 'eplist' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (eplist->next == NULL)
~~~~~~^~~~~~
seqgraph.c: In function 'CutOffProc':
seqgraph.c:911:11: warning: 'fval' may be used uninitialized in this function [-Wmaybe-uninitialized]
val = fval/2;
~~~~^~~~~~~~
seqgraph.c:841:14: note: 'fval' was declared here
FloatHi fval;
^~~~
seqgraph.c:1050:20: warning: 'eplist' may be used uninitialized in this function [-Wmaybe-uninitialized]
eplist->next = NULL;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqgrphx.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from seqgrphx.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqgrphx.c:28:25: warning: 'MatrixMsgFunc' defined but not used [-Wunused-function]
static Int2 LIBCALLBACK MatrixMsgFunc (OMMsgStructPtr ommsp)
^~~~~~~~~~~~~
seqgrphx.c: In function 'FilterMsgFunc':
seqgrphx.c:224:12: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (s == NULL)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqmtrx.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from seqmtrx.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqpcc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from seqpcc.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqpcc.c: In function 'PCCProc':
seqpcc.c:229:6: warning: 'pbsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((spp = SeqPortNew (pbsp, start, end, 0, Seq_code_iupacaa)) != NULL)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqanal.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from seqanal.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF aacomp.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from aacomp.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
aacomp.c:86:20: warning: 'AACGraph' defined but not used [-Wunused-function]
static SeqGraphPtr AACGraph (SeqPortPtr spp, Int4 start, Int4 end, Int4 window,
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqscrl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from ../include/seqscrl.h:4,
from seqscrl.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF valdlg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/vibforms.h:46,
from valdlg.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
valdlg.c: In function 'ClickRulesDoc':
valdlg.c:373:22: warning: unused variable 'scroll_pos' [-Wunused-variable]
Int2 scroll_pos = 0;
^~~~~~~~~~
valdlg.c:372:22: warning: unused variable 'sb_vert' [-Wunused-variable]
BaR sb_vert = NULL;
^~~~~~~
valdlg.c: In function 'UpdateRuleList':
valdlg.c:479:26: warning: unused variable 'last_cr' [-Wunused-variable]
CommentRulePtr new_cr, last_cr = NULL;
^~~~~~~
valdlg.c: In function 'SaveRuleChanges':
valdlg.c:540:23: warning: variable 'dlg' set but not used [-Wunused-but-set-variable]
CommentSetDlgPtr dlg;
^~~
valdlg.c: In function 'LaunchCommentRulesEditor':
valdlg.c:553:23: warning: unused variable 'm' [-Wunused-variable]
MenU m;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vsm.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/vsmpriv.h:48,
from vsm.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vsm.c: In function 'VSMDrawAbout':
vsm.c:1462:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (vsmp->title != NULL)
^~
vsm.c:1464:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (vsmp->aboutinfo != NULL)
^~
vsm.c: In function 'VSMAboutProc':
vsm.c:1492:8: warning: variable 'p' set but not used [-Wunused-but-set-variable]
PaneL p;
^
vsm.c: In function 'VSeqMgrCreateMainWindow':
vsm.c:1601:12: warning: variable 'omp' set but not used [-Wunused-but-set-variable]
ObjMgrPtr omp;
^~~
vsm.c: In function 'VSeqMgrPopulateMain':
vsm.c:1742:13: warning: variable 'atp' set but not used [-Wunused-but-set-variable]
AsnTypePtr atp;
^~~
vsm.c: In function 'VSMGatherPictProc':
vsm.c:2225:15: warning: variable 'bssp' set but not used [-Wunused-but-set-variable]
BioseqSetPtr bssp;
^~~~
vsm.c:2220:30: warning: variable 'bottom' set but not used [-Wunused-but-set-variable]
Int4 top, lineheight, left, bottom, width, maxwidth;
^~~~~~
vsm.c: In function 'VSMAddPictureToEntity':
vsm.c:2853:10: warning: variable 'ptr' set but not used [-Wunused-but-set-variable]
Pointer ptr;
^~~
vsm.c:2852:13: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vsmfile.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/vsmpriv.h:48,
from vsmfile.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vsmfile.c: In function 'VSMGenericBinAsnOpen':
vsmfile.c:259:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
vsmfile.c: In function 'VSMGenericFastaSave':
vsmfile.c:395:11: warning: variable 'code' set but not used [-Wunused-but-set-variable]
Uint1 code;
^~~~
vsmfile.c: In function 'VSMFastaProtSaveWithProduct':
vsmfile.c:527:11: warning: variable 'code' set but not used [-Wunused-but-set-variable]
Uint1 code;
^~~~
vsmfile.c: In function 'VSMSaveSetsAsFiles':
vsmfile.c:1365:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vsmutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from vsmutil.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vsmutil.c: In function 'GetDocPosForError':
vsmutil.c:1657:18: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Int2 val;
^~~
At top level:
vsmutil.c:1542:16: warning: 'MakeFieldReports' defined but not used [-Wunused-function]
static Boolean MakeFieldReports (ValNodePtr report_list, ValNodePtr field_list, FILE *fp)
^~~~~~~~~~~~~~~~
vsmutil.c:387:20: warning: 'GetSeqDescGivenIDs' defined but not used [-Wunused-function]
static SeqDescrPtr GetSeqDescGivenIDs (Uint2 entityID, Uint4 itemID, Uint2 itemtype)
^~~~~~~~~~~~~~~~~~
vsmutil.c: In function 'ContinueProc':
vsmutil.c:2157:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2156:5: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'RevalidateProc':
vsmutil.c:2124:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2123:5: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'SetVerbosityAndRepopulate':
vsmutil.c:2198:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2197:5: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'ClearValidateWindow':
vsmutil.c:613:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [sev] = 0;
~~~~~~~~~~~~~~~~~~^~~
vsmutil.c:612:7: note: within this loop
for (sev = SEV_NONE; sev <= SEV_MAX; sev++) {
^~~
vsmutil.c: In function 'CreateValidateWindowExExEx':
vsmutil.c:2521:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2520:9: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF udvgraph.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from ../include/udviewer.h:209,
from udvgraph.c:177:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
udvgraph.c: In function 'UDV_click_item':
udvgraph.c:877:9: warning: unused variable 'IsTransNeeded' [-Wunused-variable]
Boolean IsTransNeeded=FALSE;
^~~~~~~~~~~~~
udvgraph.c: In function 'UDV_SendBSPSelectMsg':
udvgraph.c:1230:13: warning: variable 'bDeselectAll' set but not used [-Wunused-but-set-variable]
Boolean bDeselectAll=TRUE;
^~~~~~~~~~~~
udvgraph.c:1226:30: warning: variable 'bsp_coord_old' set but not used [-Wunused-but-set-variable]
Int4 first_bsp_coord, bsp_coord_old,old_pos;
^~~~~~~~~~~~~
udvgraph.c: In function 'UDV_draw_helixDNA':
udvgraph.c:1827:15: warning: variable 'cyChar_2' set but not used [-Wunused-but-set-variable]
Int2 cxChar_2,cyChar_2;
^~~~~~~~
udvgraph.c: In function 'draw_logo':
udvgraph.c:1940:38: warning: variable 'cyGlobal' set but not used [-Wunused-but-set-variable]
Int2 pos,cxChar=7,cyChar=13,cxGlobal,cyGlobal;
^~~~~~~~
udvgraph.c: In function 'UDV_draw_CDS_minus':
udvgraph.c:2337:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
udvgraph.c:2332:5: warning: variable 'numivals2' set but not used [-Wunused-but-set-variable]
numivals2=0,
^~~~~~~~~
udvgraph.c: In function 'UDV_draw_CDS_plus':
udvgraph.c:2461:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
udvgraph.c: In function 'UDV_draw_panel':
udvgraph.c:4111:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(vdp->vgp->MasterViewer == SAMVIEWDDV)
^~
udvgraph.c:4113:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
Row = ViewMgr_GetRow(svpp, vdp->userkey);
^~~
udvgraph.c:4041:21: warning: unused variable 'vnp_seqinfo' [-Wunused-variable]
ValNodePtr vnp_seqinfo=NULL;
^~~~~~~~~~~
udvgraph.c:4035:45: warning: variable 'nLinesDraw' set but not used [-Wunused-but-set-variable]
Int4 decal_haut,from_row,to_row,nTotRow,nLinesDraw;
^~~~~~~~~~
udvgraph.c:4035:37: warning: variable 'nTotRow' set but not used [-Wunused-but-set-variable]
Int4 decal_haut,from_row,to_row,nTotRow,nLinesDraw;
^~~~~~~
At top level:
udvgraph.c:3921:14: warning: 'UDV_calc_decalRC' defined but not used [-Wunused-function]
static Int4 UDV_calc_decalRC(ValNodePtr ParaG,Int4 ScrollPos,
^~~~~~~~~~~~~~~~
udvgraph.c:3433:14: warning: 'UDV_Draw_features_label' defined but not used [-Wunused-function]
static void UDV_Draw_features_label(UnDViewerGraphDataPtr GrData,
^~~~~~~~~~~~~~~~~~~~~~~
udvgraph.c:1298:13: warning: 'UDV_AutoSelectAllSeq' defined but not used [-Wunused-function]
static void UDV_AutoSelectAllSeq(ViewerDialogDataPtr vdp,Boolean bSelect)
^~~~~~~~~~~~~~~~~~~~
udvgraph.c:971:14: warning: 'UDV_draw_horz_cursor' defined but not used [-Wunused-function]
static void UDV_draw_horz_cursor(UnDViewerGraphDataPtr GrData,
^~~~~~~~~~~~~~~~~~~~
udvgraph.c:948:13: warning: 'UDV_draw_vert_cursor' defined but not used [-Wunused-function]
static void UDV_draw_vert_cursor(RecT rcClip,PoinT pos)
^~~~~~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from udvgraph.c:180:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
udvgraph.c: In function 'UDV_GetCurrentDispRange':
udvgraph.c:638:15: warning: 'pgp' may be used uninitialized in this function [-Wmaybe-uninitialized]
*from_bsp=pgp->StartLetter;
~~~^~~~~~~~~~~~~
udvgraph.c: In function 'UDV_Draw_features':
udvgraph.c:3203:58: warning: 'idx6' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_draw_thin_line((Int2)(start_x+idx5),(Int2)(stop_x+idx6),y,
~~~~~~~^~~~~~
udvgraph.c:3203:38: warning: 'idx5' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_draw_thin_line((Int2)(start_x+idx5),(Int2)(stop_x+idx6),y,
~~~~~~~~^~~~~~
udvgraph.c:3196:47: warning: 'idx4' may be used uninitialized in this function [-Wmaybe-uninitialized]
stop2=_min_(pgp->StopLetter,context->ivals[idx4]);
^
udvgraph.c:3189:58: warning: 'idx3' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_draw_thin_line((Int2)(start_x+idx2),(Int2)(stop_x+idx3),y,
~~~~~~~^~~~~~
udvgraph.c:3189:38: warning: 'idx2' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_draw_thin_line((Int2)(start_x+idx2),(Int2)(stop_x+idx3),y,
~~~~~~~~^~~~~~
udvgraph.c:3182:49: warning: 'idx1' may be used uninitialized in this function [-Wmaybe-uninitialized]
start2=_max_(pgp->StartLetter,context->ivals[idx1]);
^
In file included from ../include/udviewer.h:225:0,
from udvgraph.c:177:
../include/udvdef.h:187:40: warning: 'stop_x2' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define _max_(a,b) ((a)>=(b)?(a):(b))
^
udvgraph.c:2803:21: note: 'stop_x2' was declared here
Int2 start_x,stop_x,stop_x2, /*id. but in pixels*/
^~~~~~~
udvgraph.c: In function 'UDV_ClickProc':
udvgraph.c:1461:8: warning: 'vmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_SelectFeatInFeatDlg(vmp,entityID,itemID);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF udvopen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from ../include/udviewer.h:209,
from udvopen.c:101:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
udvopen.c: In function 'UDV_FileOpen':
udvopen.c:875:16: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b,b1,b2;
^~
udvopen.c:875:11: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b,b1,b2;
^
udvopen.c: In function 'UDV_CreateListBioseqDlg':
udvopen.c:1180:9: warning: the address of 'szName' will always evaluate as 'true' [-Waddress]
if (szName){
^~~~~~
udvopen.c: In function 'UDV_FOpenCancelProc':
udvopen.c:792:23: warning: 'vmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_set_PullMenus(&vmp->MainMenu,TRUE);
^~~~~~~~~~~~~~
udvopen.c: In function 'UDV_analyze_SEP_for_open':
udvopen.c:325:15: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
vmp->entityID=entityID;
~~~~~~~~~~~~~^~~~~~~~~
udvopen.c:327:14: warning: 'dataptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
vmp->dataptr=dataptr;
~~~~~~~~~~~~^~~~~~~~
udvopen.c: In function 'UDV_FOpenAcceptProc':
udvopen.c:855:23: warning: 'vmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_set_PullMenus(&vmp->MainMenu,TRUE);
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF udvpanel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from ../include/udviewer.h:209,
from udvpanel.c:197:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
udvpanel.c: In function 'UDV_GotoBtnProc':
udvpanel.c:2080:22: warning: variable 'old_ivalue' set but not used [-Wunused-but-set-variable]
Int4 iValue,old_ivalue,line_num,from_bsp,to_bsp,
^~~~~~~~~~
udvpanel.c:2079:15: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
udvpanel.c: In function 'CreateMainControls':
udvpanel.c:2165:8: warning: variable 'cxChar' set but not used [-Wunused-but-set-variable]
Int2 cxChar,cyChar,Margins;
^~~~~~
udvpanel.c: In function 'UDV_SearchFeatForKey':
udvpanel.c:3478:14: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1,b2;
^~
At top level:
udvpanel.c:2773:28: warning: 'FeaturesListBoxScan' defined but not used [-Wunused-function]
static Boolean LIBCALLBACK FeaturesListBoxScan (SeqFeatPtr sfp,
^~~~~~~~~~~~~~~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/udviewer.h:220,
from udvpanel.c:197:
udvpanel.c: In function 'InitFeaturesListDlg':
../include/vibdefns.h:315:19: warning: 'pop' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PopupItem Nlm_PopupItem
^~~~~~~~~~~~~
udvpanel.c:3194:7: note: 'pop' was declared here
PopuP pop;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF dotvibrant.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/dotviewer.h:15,
from dotvibrant.c:84:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dotvibrant.c: In function 'DOT_DisplayHits':
dotvibrant.c:564:18: warning: variable 'ycomp' set but not used [-Wunused-but-set-variable]
Int4 ycomp, xcomp;
^~~~~
dotvibrant.c: In function 'DOT_VscrlProc':
dotvibrant.c:918:16: warning: variable 'visLines' set but not used [-Wunused-but-set-variable]
Int2 visLines, vmargin, hmargin;
^~~~~~~~
dotvibrant.c: In function 'DOT_HscrlProc':
dotvibrant.c:972:20: warning: variable 'visLines' set but not used [-Wunused-but-set-variable]
Int2 dx, visLines, offset, hmargin, vmargin;
^~~~~~~~
dotvibrant.c: In function 'DOT_VCrossHairs':
dotvibrant.c:1402:10: warning: unused variable 'cursor_size' [-Wunused-variable]
Int4 cursor_size =15;
^~~~~~~~~~~
dotvibrant.c: In function 'DOT_HCrossHairs':
dotvibrant.c:1427:9: warning: unused variable 'cursor_size' [-Wunused-variable]
Int4 cursor_size = 15;
^~~~~~~~~~~
dotvibrant.c: In function 'DOT_MoveCrossHairs':
dotvibrant.c:1453:18: warning: variable 'data' set but not used [-Wunused-but-set-variable]
DOTSelDataPtr data;
^~~~
dotvibrant.c:1452:10: warning: unused variable 'cursor_size' [-Wunused-variable]
Int4 cursor_size = 15;
^~~~~~~~~~~
dotvibrant.c: In function 'DOT_DrawXAxis':
dotvibrant.c:1532:38: warning: unused variable 'title' [-Wunused-variable]
Char scale_buf[15] = {""}, title[50]={""}; /*scale value*/
^~~~~
dotvibrant.c: In function 'DOT_DrawYAxis':
dotvibrant.c:1642:38: warning: unused variable 'title' [-Wunused-variable]
Char scale_buf[15] = {""}, title[50]={""}; /*scale value*/
^~~~~
dotvibrant.c:1641:55: warning: variable 'Fh_4' set but not used [-Wunused-but-set-variable]
Int4 pos, ylen, x, y, scale_pos, i, j, Fh_2,Fh_4;
^~~~
dotvibrant.c: In function 'DOT_SVDisplayDiags':
dotvibrant.c:1770:28: warning: variable 'aln_diag' set but not used [-Wunused-but-set-variable]
Int4 diag, aln_diag;
^~~~~~~~
dotvibrant.c:1770:22: warning: variable 'diag' set but not used [-Wunused-but-set-variable]
Int4 diag, aln_diag;
^~~~
dotvibrant.c:1766:22: warning: variable 'width' set but not used [-Wunused-but-set-variable]
Int4 width, height;
^~~~~
dotvibrant.c:1765:31: warning: variable 'p_HFrom' set but not used [-Wunused-but-set-variable]
Int4 p_VFrom, p_HFrom;
^~~~~~~
dotvibrant.c:1765:22: warning: variable 'p_VFrom' set but not used [-Wunused-but-set-variable]
Int4 p_VFrom, p_HFrom;
^~~~~~~
dotvibrant.c:1762:28: warning: unused variable 'cutoff' [-Wunused-variable]
Int4 stop, cutoff=0, q_start, s_start, length;
^~~~~~
dotvibrant.c:1760:34: warning: variable 'seg3' set but not used [-Wunused-but-set-variable]
SegmenT seg1, seg2, seg3, seg4;
^~~~
dotvibrant.c: In function 'DOT_FillNewSeqBufs':
dotvibrant.c:2197:19: warning: unused variable 'alp' [-Wunused-variable]
DOTAlignInfoPtr alp=NULL;
^~~
dotvibrant.c: In function 'DOT_InitCInfo':
dotvibrant.c:2258:14: warning: unused variable 'colBuf' [-Wunused-variable]
Char colBuf[12]={""};
^~~~~~
dotvibrant.c: In function 'DOT_SVDisplaySequence':
dotvibrant.c:2379:16: warning: variable 'matrix' set but not used [-Wunused-but-set-variable]
Int4Ptr PNTR matrix;
^~~~~~
dotvibrant.c:2367:14: warning: variable 'vis_2' set but not used [-Wunused-but-set-variable]
Int4 vis_2, buf_len;
^~~~~
dotvibrant.c:2364:14: warning: unused variable 'prot_threshold' [-Wunused-variable]
Int4 prot_threshold=0, bloc_cntr;
^~~~~~~~~~~~~~
dotvibrant.c:2350:24: warning: variable 'mip2' set but not used [-Wunused-but-set-variable]
DOTMainDataPtr mip1, mip2;
^~~~
dotvibrant.c: In function 'DOT_SVClickProc':
dotvibrant.c:2807:17: warning: unused variable 'handled' [-Wunused-variable]
Int2 handled=0;
^~~~~~~
dotvibrant.c: In function 'DOT_ResizeFeatWindow':
dotvibrant.c:3016:63: warning: variable 'SubjectHeight' set but not used [-Wunused-but-set-variable]
Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw;
^~~~~~~~~~~~~
dotvibrant.c:3016:51: warning: variable 'QueryHeight' set but not used [-Wunused-but-set-variable]
Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw;
^~~~~~~~~~~
dotvibrant.c:3016:37: warning: variable 'gap' set but not used [-Wunused-but-set-variable]
Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw;
^~~
dotvibrant.c: In function 'DOT_ResizeSequenceWindow':
dotvibrant.c:3098:25: warning: variable 'is_visible2' set but not used [-Wunused-but-set-variable]
Boolean is_visible1, is_visible2;
^~~~~~~~~~~
dotvibrant.c:3098:12: warning: variable 'is_visible1' set but not used [-Wunused-but-set-variable]
Boolean is_visible1, is_visible2;
^~~~~~~~~~~
dotvibrant.c:3095:51: warning: variable 'V1Height' set but not used [-Wunused-but-set-variable]
Int2 height,width,gap,vsbWidth,in,hsbHeight,V1Height,V2Height, goHeight;
^~~~~~~~
dotvibrant.c: In function 'DOT_HideFeatDlg':
dotvibrant.c:3745:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
dotvibrant.c: In function 'DOT_SVBuildDiagViewer':
dotvibrant.c:4031:18: warning: variable 'mip' set but not used [-Wunused-but-set-variable]
DOTMainDataPtr mip;
^~~
dotvibrant.c:4029:28: warning: unused variable 'str2' [-Wunused-variable]
Char str1[41]={""}, str2[41]={""};
^~~~
dotvibrant.c:4029:13: warning: unused variable 'str1' [-Wunused-variable]
Char str1[41]={""}, str2[41]={""};
^~~~
dotvibrant.c:4022:18: warning: variable 'pr2' set but not used [-Wunused-but-set-variable]
PrompT pr1, pr2;
^~~
dotvibrant.c:4022:13: warning: variable 'pr1' set but not used [-Wunused-but-set-variable]
PrompT pr1, pr2;
^~~
dotvibrant.c: In function 'DOT_UpdateDataRects':
dotvibrant.c:4166:19: warning: variable 'dy' set but not used [-Wunused-but-set-variable]
Int4 comp, dx, dy, xstart, ystart;
^~
dotvibrant.c:4166:15: warning: variable 'dx' set but not used [-Wunused-but-set-variable]
Int4 comp, dx, dy, xstart, ystart;
^~
dotvibrant.c: In function 'DOT_MsgFunc':
dotvibrant.c:4215:17: warning: variable 'vdp2' set but not used [-Wunused-but-set-variable]
DOTVibDataPtr vdp2 = NULL;
^~~~
dotvibrant.c: In function 'DOT_ReleaseProc':
dotvibrant.c:4373:32: warning: unused variable 'yaxis_incr' [-Wunused-variable]
Boolean xaxis_incr=TRUE, yaxis_incr=TRUE;
^~~~~~~~~~
dotvibrant.c:4373:15: warning: unused variable 'xaxis_incr' [-Wunused-variable]
Boolean xaxis_incr=TRUE, yaxis_incr=TRUE;
^~~~~~~~~~
dotvibrant.c:4371:19: warning: variable 'alp' set but not used [-Wunused-but-set-variable]
DOTAlignInfoPtr alp=NULL;
^~~
dotvibrant.c:4370:18: warning: variable 'mip1' set but not used [-Wunused-but-set-variable]
DOTMainDataPtr mip1=NULL;
^~~~
dotvibrant.c: In function 'DOT_StartDOTPLOT':
dotvibrant.c:4891:23: warning: variable 'vdp' set but not used [-Wunused-but-set-variable]
DOTVibDataPtr vdp;
^~~
dotvibrant.c: In function 'DOT_DoZoom':
dotvibrant.c:5106:18: warning: variable 'data' set but not used [-Wunused-but-set-variable]
DOTSelDataPtr data;
^~~~
dotvibrant.c: In function 'DOT_ZoomProc':
dotvibrant.c:5204:23: warning: variable 'temport' set but not used [-Wunused-but-set-variable]
WindoW temport, w;
^~~~~~~
dotvibrant.c: In function 'AlnMgr2GetNextLine':
dotvibrant.c:5315:3: warning: value computed is not used [-Wunused-value]
*n++;
^~~~
dotvibrant.c: In function 'DOT_GetAlign':
dotvibrant.c:5332:44: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Int4 x1, y1, x2, y2, numlines=0, n=0, i=0;
^
dotvibrant.c: In function 'DOT_FillAlignInfoPointer':
dotvibrant.c:5565:16: warning: unused variable 'i' [-Wunused-variable]
Int4 i=0, n=0;
^
dotvibrant.c: In function 'DOT_Prob_FillAlignInfoPointer':
dotvibrant.c:5681:16: warning: unused variable 'i' [-Wunused-variable]
Int4 i=0, n=0;
^
dotvibrant.c:5680:16: warning: unused variable 'numsaps' [-Wunused-variable]
Int4 numsaps = 0, numlines = 0;
^~~~~~~
dotvibrant.c:5678:37: warning: unused variable 'sap_tmp' [-Wunused-variable]
SeqAlignPtr sap=NULL, salp=NULL, sap_tmp=NULL;
^~~~~~~
dotvibrant.c: In function 'DOT_DoBlast':
dotvibrant.c:5918:23: warning: unused variable 'eval' [-Wunused-variable]
Char eval[11]={""};
^~~~
dotvibrant.c:5917:23: warning: variable 'is_local' set but not used [-Wunused-but-set-variable]
Boolean is_local;
^~~~~~~~
dotvibrant.c:5915:23: warning: unused variable 'entityID' [-Wunused-variable]
Uint2 entityID=0;
^~~~~~~~
dotvibrant.c: In function 'DOT_CreateWindowDetails':
dotvibrant.c:6214:27: warning: variable 'pr2' set but not used [-Wunused-but-set-variable]
PrompT pr1, pr2;
^~~
dotvibrant.c:6214:22: warning: variable 'pr1' set but not used [-Wunused-but-set-variable]
PrompT pr1, pr2;
^~~
dotvibrant.c:6207:21: warning: variable 'g1' set but not used [-Wunused-but-set-variable]
GrouP g, g1, g2;
^~
dotvibrant.c: In function 'DOT_ResizeMainWindow':
dotvibrant.c:6273:35: warning: variable 'gap' set but not used [-Wunused-but-set-variable]
Int2 height, width, in , gap;
^~~
dotvibrant.c: In function 'DOT_FindAlignment':
dotvibrant.c:6662:29: warning: unused variable 'rb_fixed' [-Wunused-variable]
Boolean lt_fixed=FALSE, rb_fixed=FALSE;
^~~~~~~~
dotvibrant.c:6662:13: warning: unused variable 'lt_fixed' [-Wunused-variable]
Boolean lt_fixed=FALSE, rb_fixed=FALSE;
^~~~~~~~
dotvibrant.c:6661:17: warning: variable 'data' set but not used [-Wunused-but-set-variable]
DOTSelDataPtr data;
^~~~
dotvibrant.c: In function 'SCP_CompareOrderOrganizeBioseqs':
dotvibrant.c:6792:25: warning: variable 'itemID' set but not used [-Wunused-but-set-variable]
Uint4 itemID=0;
^~~~~~
dotvibrant.c: In function 'SCP_OrganizeAlnsInSet':
dotvibrant.c:6873:21: warning: variable 'indextype' set but not used [-Wunused-but-set-variable]
Int4 indextype;
^~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/alignmgr2.h:111,
from ../include/actutils.h:105,
from ../include/dotviewer.h:32,
from dotvibrant.c:84:
dotvibrant.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from ../include/dotviewer.h:32,
from dotvibrant.c:84:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
dotvibrant.c:6642:16: warning: 'DOT_DeselectPrim' defined but not used [-Wunused-function]
static Boolean DOT_DeselectPrim (SegmenT seg, PrimitivE prim, Uint2 segID,Uint2 primID, Uint2 primCt, VoidPtr userdata)
^~~~~~~~~~~~~~~~
dotvibrant.c:6346:13: warning: 'DOT_NewAnalysis' defined but not used [-Wunused-function]
static void DOT_NewAnalysis (ButtoN b)
^~~~~~~~~~~~~~~
dotvibrant.c:5894:16: warning: 'DOT_get_eval' defined but not used [-Wunused-function]
static FloatHi DOT_get_eval(Int4 exp)
^~~~~~~~~~~~
dotvibrant.c:5325:16: warning: 'DOT_GetAlign' defined but not used [-Wunused-function]
static Boolean DOT_GetAlign (DOTAlignInfoPtr alp)
^~~~~~~~~~~~
dotvibrant.c:5281:16: warning: 'AlnMgr2GetNextLine' defined but not used [-Wunused-function]
static Boolean AlnMgr2GetNextLine(SeqAlignPtr sap, AlnMsg2Ptr amp1, AlnMsg2Ptr amp2, Int4Ptr x1, Int4Ptr y1, Int4Ptr x2, Int4Ptr y2, Int4Ptr n)
^~~~~~~~~~~~~~~~~~
dotvibrant.c:4767:13: warning: 'DOT_FeatAnalysisProc' defined but not used [-Wunused-function]
static void DOT_FeatAnalysisProc(ButtoN b)
^~~~~~~~~~~~~~~~~~~~
dotvibrant.c:4749:13: warning: 'DOT_GetInfoProc' defined but not used [-Wunused-function]
static void DOT_GetInfoProc (IteM i)
^~~~~~~~~~~~~~~
dotvibrant.c:4213:25: warning: 'DOT_MsgFunc' defined but not used [-Wunused-function]
static Int2 LIBCALLBACK DOT_MsgFunc (OMMsgStructPtr ommsp)
^~~~~~~~~~~
dotvibrant.c:3688:13: warning: 'DOT_HideAcceptProc' defined but not used [-Wunused-function]
static void DOT_HideAcceptProc(ButtoN b)
^~~~~~~~~~~~~~~~~~
dotvibrant.c:3318:13: warning: 'DOT_AddFeatureToSegment' defined but not used [-Wunused-function]
static void DOT_AddFeatureToSegment(SeqMgrFeatContextPtr context,
^~~~~~~~~~~~~~~~~~~~~~~
dotvibrant.c:2954:13: warning: 'DOT_SVChangeLabels' defined but not used [-Wunused-function]
static void DOT_SVChangeLabels (GrouP g)
^~~~~~~~~~~~~~~~~~
dotvibrant.c:2760:16: warning: 'DOT_SVGetDiag' defined but not used [-Wunused-function]
static Boolean DOT_SVGetDiag (Uint2 segID, Uint2 primID, VoidPtr userdata)
^~~~~~~~~~~~~
dotvibrant.c: In function 'DOT_GetNthSeqFromAlign':
dotvibrant.c:5087:3: warning: 'spp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqPortFree(spp);
^~~~~~~~~~~~~~~~
dotvibrant.c: In function 'DOT_SVPopulateSequenceViewer':
dotvibrant.c:2611:19: warning: 'strand2' may be used uninitialized in this function [-Wmaybe-uninitialized]
DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dotvibrant.c:2380:23: note: 'strand2' was declared here
Uint1 strand1, strand2;
^~~~~~~
dotvibrant.c:2611:19: warning: 'strand1' may be used uninitialized in this function [-Wmaybe-uninitialized]
DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dotvibrant.c:2380:14: note: 'strand1' was declared here
Uint1 strand1, strand2;
^~~~~~~
dotvibrant.c:2560:45: warning: 'residue_names' may be used uninitialized in this function [-Wmaybe-uninitialized]
qBuf[c]=*residue_names[(int)*q];
^
dotvibrant.c:2378:16: note: 'residue_names' was declared here
CharPtr PNTR residue_names;
^~~~~~~~~~~~~
dotvibrant.c:2611:19: warning: 's_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dotvibrant.c:2370:42: note: 's_pos' was declared here
Int4 hit_start, hit_stop, q_pos, s_pos;
^~~~~
dotvibrant.c:2611:19: warning: 'q_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dotvibrant.c:2370:35: note: 'q_pos' was declared here
Int4 hit_start, hit_stop, q_pos, s_pos;
^~~~~
dotvibrant.c:2504:11: warning: 'hit_stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
hit_stop+=hit_stop/10;
~~~~~~~~^~~~~~~~~~~~~
dotvibrant.c:2370:25: note: 'hit_stop' was declared here
Int4 hit_start, hit_stop, q_pos, s_pos;
^~~~~~~~
dotvibrant.c:2570:26: warning: 'hit_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (hit_start<=i && i<=(hit_stop+bloc_size))
^
dotvibrant.c:2370:14: note: 'hit_start' was declared here
Int4 hit_start, hit_stop, q_pos, s_pos;
^~~~~~~~~
dotvibrant.c:2503:16: warning: 'buf_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
end=s+buf_len-1;
^
dotvibrant.c:2367:21: note: 'buf_len' was declared here
Int4 vis_2, buf_len;
^~~~~~~
dotvibrant.c:2545:18: warning: 'is_na' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (is_na)
^
dotvibrant.c:2361:27: note: 'is_na' was declared here
Boolean ambig=FALSE, is_na;
^~~~~
dotvibrant.c:2503:6: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
end=s+buf_len-1;
~~~^~~~~~~~~~~~
dotvibrant.c:2357:14: note: 's' was declared here
Uint1Ptr s;
^
dotvibrant.c:2626:16: warning: 'q' may be used uninitialized in this function [-Wmaybe-uninitialized]
q++;
~^~
dotvibrant.c:2356:14: note: 'q' was declared here
Uint1Ptr q;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF dlgutil1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from dlgutil1.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dlgutil1.c: In function 'IsAuthList':
dlgutil1.c:3008:8: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
dlgutil1.c: In function 'TestAuthorDialog':
dlgutil1.c:3357:20: warning: unused variable 'cp' [-Wunused-variable]
CharPtr cp;
^~
dlgutil1.c: In function 'TestIntervalEditor':
dlgutil1.c:5318:20: warning: variable 'fuzz_to' set but not used [-Wunused-but-set-variable]
Int2 fuzz_to;
^~~~~~~
dlgutil1.c:5317:20: warning: variable 'fuzz_from' set but not used [-Wunused-but-set-variable]
Int2 fuzz_from;
^~~~~~~~~
dlgutil1.c:5316:41: warning: variable 'fuzz_before' set but not used [-Wunused-but-set-variable]
Boolean isInterval, isPoint, fuzz_before, fuzz_after;
^~~~~~~~~~~
dlgutil1.c: In function 'CreateStandardEditMenu':
dlgutil1.c:9189:8: warning: variable 'i' set but not used [-Wunused-but-set-variable]
IteM i;
^
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from dlgutil1.c:55:
dlgutil1.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
dlgutil1.c:8378:25: warning: 'GetNthNameValuePair' defined but not used [-Wunused-function]
static NameValuePairPtr GetNthNameValuePair (Int4 n, ValNodePtr list)
^~~~~~~~~~~~~~~~~~~
dlgutil1.c:8061:16: warning: 'ParseSpecimenVoucherOk' defined but not used [-Wunused-function]
static Boolean ParseSpecimenVoucherOk (CharPtr str)
^~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF dlgutil2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from dlgutil2.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dlgutil2.c: In function 'CreateImportFields':
dlgutil2.c:1401:19: warning: variable 'is_gap' set but not used [-Wunused-but-set-variable]
Boolean is_gap = FALSE;
^~~~~~
dlgutil2.c: In function 'UpdateTableDisplayDialogScrollBars':
dlgutil2.c:3532:11: warning: variable 'y' set but not used [-Wunused-but-set-variable]
Int4 x, y;
^
dlgutil2.c:3532:8: warning: variable 'x' set but not used [-Wunused-but-set-variable]
Int4 x, y;
^
dlgutil2.c: In function 'GetTableDisplayCell':
dlgutil2.c:3931:8: warning: variable 'start_row' set but not used [-Wunused-but-set-variable]
Int4 start_row, start_col;
^~~~~~~~~
dlgutil2.c: In function 'NewCreateInferenceDialog':
dlgutil2.c:7600:19: warning: variable 'fnt' set but not used [-Wunused-but-set-variable]
FonT fnt;
^~~
dlgutil2.c: In function 'ClickableListOnKey':
dlgutil2.c:10202:20: warning: variable 'clp' set but not used [-Wunused-but-set-variable]
ClickableListPtr clp;
^~~
dlgutil2.c: In function 'GetSelectedClickableListText':
dlgutil2.c:10874:36: warning: variable 'char_offset' set but not used [-Wunused-but-set-variable]
Int2 item, row, col, char_offset;
^~~~~~~~~~~
dlgutil2.c: In function 'AutomatchFeatures':
dlgutil2.c:13840:36: warning: variable 's3' set but not used [-Wunused-but-set-variable]
SeqIntPtr s1, s2, s3;
^~
At top level:
dlgutil2.c:11993:16: warning: 'ParseMultiListQualOk' defined but not used [-Wunused-function]
static Boolean ParseMultiListQualOk (CharPtr val)
^~~~~~~~~~~~~~~~~~~~
dlgutil2.c:10059:13: warning: 'ClickClickableListItem' defined but not used [-Wunused-function]
static void ClickClickableListItem (DoC d, PoinT pt)
^~~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:10039:13: warning: 'DrawClickableListItem' defined but not used [-Wunused-function]
static void DrawClickableListItem (DoC d, RectPtr r, Int2 item, Int2 firstLine)
^~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:8577:13: warning: 'GetCategoryNumFromName' defined but not used [-Wunused-function]
static Int4 GetCategoryNumFromName (CharPtr category)
^~~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:1672:16: warning: 'GetNameForFeature' defined but not used [-Wunused-function]
static CharPtr GetNameForFeature (SeqFeatPtr sfp)
^~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF e2trmlst.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from e2trmlst.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
e2trmlst.c: In function 'ReadAFew':
e2trmlst.c:2230:61: warning: left-hand operand of comma expression has no effect [-Wunused-value]
for (row = 1, termPtr = e2TermListPtr->list; row <= *count, termPtr != NULL; row++, termPtr = termPtr->next) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF e2docsum.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from e2docsum.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
e2docsum.c: In function 'FormatCdsSeq':
e2docsum.c:1523:22: warning: variable 'gene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr gene = NULL;
^~~~
e2docsum.c: In function 'FetchSequence':
e2docsum.c:1591:16: warning: variable 'currDbName' set but not used [-Wunused-but-set-variable]
CharPtr currDbName;
^~~~~~~~~~
e2docsum.c:1580:16: warning: variable 'group_segs' set but not used [-Wunused-but-set-variable]
Uint1 group_segs = 0;
^~~~~~~~~~
e2docsum.c: In function 'SaveDocsumProject':
e2docsum.c:3606:16: warning: variable 'sfp' set but not used [-Wunused-but-set-variable]
SummFormPtr sfp;
^~~
e2docsum.c: In function 'RetrieveGeneration':
e2docsum.c:4135:19: warning: variable 'e2ip' set but not used [-Wunused-but-set-variable]
Entrez2InfoPtr e2ip;
^~~~
e2docsum.c: In function 'SetupMenus':
e2docsum.c:4849:16: warning: variable 'c' set but not used [-Wunused-but-set-variable]
ChoicE c;
^
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/bspview.h:48,
from e2docsum.c:53:
e2docsum.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strucapi.h:52:0,
from e2docsum.c:62:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
e2docsum.c: In function 'LaunchStructureViewer':
e2docsum.c:2981:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
e2docsum.c: In function 'LaunchSequin':
e2docsum.c:2838:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
e2docsum.c:2883:13: warning: 'GetBiostrucMaxModels' defined but not used [-Wunused-function]
static Int4 GetBiostrucMaxModels (void)
^~~~~~~~~~~~~~~~~~~~
e2docsum.c:2850:13: warning: 'GetBiostrucComplexity' defined but not used [-Wunused-function]
static Int4 GetBiostrucComplexity (void)
^~~~~~~~~~~~~~~~~~~~~
e2docsum.c:2154:20: warning: 'cddDocProcs' defined but not used [-Wunused-variable]
static DocPrntProc cddDocProcs [] = { Query_FetchDocSum, Query_FetchFields, FetchUid, NULL };
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF asn2graphic.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn2graphic.h:45,
from ../include/asn2graphicp.h:45,
from asn2graphic.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2graphic.c: In function 'ParseFilterItem':
asn2graphic.c:1191:21: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int2 i, j;
^
asn2graphic.c: In function 'GeneProductsLayoutInternal':
asn2graphic.c:3730:36: warning: variable 'featureStart' set but not used [-Wunused-but-set-variable]
Int4 newLeft, featureStart, rowMaxRight;
^~~~~~~~~~~~
asn2graphic.c: In function 'ScaleSntDrawProc':
asn2graphic.c:4401:28: warning: variable 'r' set but not used [-Wunused-but-set-variable]
RecT r;
^
asn2graphic.c: In function 'GphSentProc':
asn2graphic.c:4996:16: warning: variable 'scaleY' set but not used [-Wunused-but-set-variable]
Int4 scaleY;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2graphic.c:46:
asn2graphic.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
asn2graphic.c: In function 'ProcessRows':
asn2graphic.c:4361:13: warning: 'SegmentTreeBot' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (! EnsureFeatureHasSegment (FPSP, featdeftype, SegmentTreeBot)) return 0;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2graphic.c:4353:24: warning: 'SegmentTreeMid' may be used uninitialized in this function [-Wmaybe-uninitialized]
SegmentTreeBot = CreateSegment (SegmentTreeMid, 0, 0);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2graphic.c:4349:24: warning: 'SegmentTreeTop' may be used uninitialized in this function [-Wmaybe-uninitialized]
SegmentTreeMid = CreateSegment (SegmentTreeTop , 0, 0);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF medview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/medview.h:48,
from medview.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
medview.c: In function 'PrintMedlineViewForm':
medview.c:588:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF bspview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from bspview.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from bspview.c:61:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from bspview.c:61:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from bspview.c:61:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from bspview.c:61:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gbfview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from gbfview.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gbfview.c: In function 'RelModeFailText':
gbfview.c:1004:22: warning: variable 'hasPubs' set but not used [-Wunused-but-set-variable]
Boolean hasPubs;
^~~~~~~
gbfview.c: In function 'PopulateFlatFile':
gbfview.c:1289:22: warning: variable 'doColors' set but not used [-Wunused-but-set-variable]
Boolean doColors;
^~~~~~~~
gbfview.c: In function 'PopulateFasta':
gbfview.c:1714:33: warning: left-hand operand of comma expression has no effect [-Wunused-value]
if (ISA_na (bsp->mol)) {TRUE,
^
gbfview.c:1646:20: warning: variable 'group_segs' set but not used [-Wunused-but-set-variable]
Uint1 group_segs;
^~~~~~~~~~
gbfview.c: In function 'PopulateAsnOrXML':
gbfview.c:1969:16: warning: variable 'lookupFar' set but not used [-Wunused-but-set-variable]
Boolean lookupFar = FALSE;
^~~~~~~~~
gbfview.c:1968:16: warning: variable 'lockFar' set but not used [-Wunused-but-set-variable]
Boolean lockFar = FALSE;
^~~~~~~
gbfview.c: In function 'PrintFlatFileFastaOrAsn':
gbfview.c:2491:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
gbfview.c: In function 'ReleaseIcon':
gbfview.c:667:21: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
gbfview.c:1231:13: warning: 'LookForFarProds' defined but not used [-Wunused-function]
static void LookForFarProds (
^~~~~~~~~~~~~~~
gbfview.c:1212:13: warning: 'LookForFarBsp' defined but not used [-Wunused-function]
static void LookForFarBsp (
^~~~~~~~~~~~~
gbfview.c:944:13: warning: 'LookForPubs' defined but not used [-Wunused-function]
static void LookForPubs (BioseqPtr bsp, Pointer userdata)
^~~~~~~~~~~
gbfview.c:289:16: warning: 'ColorIcon' defined but not used [-Wunused-function]
static Boolean ColorIcon (
^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gphview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from gphview.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gphview.c: In function 'ReleaseAlignment':
gphview.c:1306:18: warning: variable 'slp' set but not used [-Wunused-but-set-variable]
SeqLocPtr slp;
^~~
gphview.c: In function 'DrawAlignOnAllSequences':
gphview.c:1391:10: warning: variable 'vn' set but not used [-Wunused-but-set-variable]
ValNode vn;
^~
gphview.c: In function 'ReleaseDesktop':
gphview.c:1836:18: warning: variable 'seg' set but not used [-Wunused-but-set-variable]
SegmenT seg;
^~~
gphview.c: In function 'AutoScrollGeneName':
gphview.c:2100:21: warning: variable 'num' set but not used [-Wunused-but-set-variable]
Int2 num;
^~~
gphview.c: In function 'DisplayGeneChoiceWindow':
gphview.c:2426:22: warning: variable 'p' set but not used [-Wunused-but-set-variable]
PrompT p;
^
gphview.c: In function 'PrintGraphical':
gphview.c:3268:14: warning: unused variable 'ans' [-Wunused-variable]
MsgAnswer ans;
^~~
gphview.c: In function 'PopulateAsn2GphGraphic':
gphview.c:3868:16: warning: variable 'min' set but not used [-Wunused-but-set-variable]
Int4 min;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gphdraw.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from gphdraw.c:59:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gphdraw.c: In function 'GraphSentProc':
gphdraw.c:195:18: warning: variable 'scaleY' set but not used [-Wunused-but-set-variable]
Int4 scaleY;
^~~~~~
gphdraw.c: In function 'DrawGraphToPanel':
gphdraw.c:453:27: warning: variable 'xp' set but not used [-Wunused-but-set-variable]
Int4Ptr xpoints, xp;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gxydraw.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from gxydraw.c:50:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gxydraw.c: In function 'DotXYPlot':
gxydraw.c:259:19: warning: 'xaxiscount' may be used uninitialized in this function [-Wmaybe-uninitialized]
gsp->xaxiscount = xaxiscount;
~~~~~~~~~~~~~~~~^~~~~~~~~~~~
gxydraw.c:182:19: note: 'xaxiscount' was declared here
Int4 xaxiscount, yaxiscount;
^~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gtrdraw.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from gtrdraw.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/vibrant.h:130:0,
from gtrdraw.c:53:
gtrdraw.c: In function 'TreeSentProc':
../include/vibdefns.h:655:20: warning: 'f' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define DeleteFont Nlm_DeleteFont
^~~~~~~~~~~~~~
gtrdraw.c:82:11: note: 'f' was declared here
FonT f, fx;
^
In file included from ../include/vibrant.h:130:0,
from gtrdraw.c:53:
../include/vibdefns.h:643:20: warning: 'fx' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SelectFont Nlm_SelectFont
^~~~~~~~~~~~~~
gtrdraw.c:82:14: note: 'fx' was declared here
FonT f, fx;
^~
In file included from ../include/vibrant.h:130:0,
from gtrdraw.c:53:
../include/vibdefns.h:623:21: warning: 'curB' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SelectColor Nlm_SelectColor
^~~~~~~~~~~~~~~
gtrdraw.c:83:23: note: 'curB' was declared here
Uint1 curR, curG, curB;
^~~~
In file included from ../include/vibrant.h:130:0,
from gtrdraw.c:53:
../include/vibdefns.h:623:21: warning: 'curG' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SelectColor Nlm_SelectColor
^~~~~~~~~~~~~~~
gtrdraw.c:83:17: note: 'curG' was declared here
Uint1 curR, curG, curB;
^~~~
In file included from ../include/vibrant.h:130:0,
from gtrdraw.c:53:
../include/vibdefns.h:623:21: warning: 'curR' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SelectColor Nlm_SelectColor
^~~~~~~~~~~~~~~
gtrdraw.c:83:11: note: 'curR' was declared here
Uint1 curR, curG, curB;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqpanel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqpanel.c: In function 'FillFeatureInfo':
seqpanel.c:427:18: warning: variable 'stop' set but not used [-Wunused-but-set-variable]
Int4 j, start, stop;
^~~~
seqpanel.c:427:11: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 j, start, stop;
^~~~~
seqpanel.c: In function 'DrawFeatureCodonLines':
seqpanel.c:1897:21: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
Char tmp[2];
^~~
seqpanel.c: In function 'DrawFeature':
seqpanel.c:2127:21: warning: variable 'prot_len' set but not used [-Wunused-but-set-variable]
Int4 prot_len;
^~~~~~~~
seqpanel.c: In function 'GetSeqChapterFeatureInfo':
seqpanel.c:3136:18: warning: variable 'stop' set but not used [-Wunused-but-set-variable]
Int4 j, start, stop;
^~~~
seqpanel.c:3136:11: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 j, start, stop;
^~~~~
seqpanel.c: In function 'onSeqEdVScrollBarSeqPanel':
seqpanel.c:3406:17: warning: variable 'totallines' set but not used [-Wunused-but-set-variable]
Int4 totallines;
^~~~~~~~~~
seqpanel.c: In function 'PrintFeature':
seqpanel.c:3812:28: warning: variable 'fRight' set but not used [-Wunused-but-set-variable]
Int4 fLeft, fRight, swap;
^~~~~~
seqpanel.c:3812:21: warning: variable 'fLeft' set but not used [-Wunused-but-set-variable]
Int4 fLeft, fRight, swap;
^~~~~
seqpanel.c: In function 'PrintTranslatedFrame':
seqpanel.c:3966:17: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
Char tmp[2];
^~~
seqpanel.c: In function 'ExportSequenceText':
seqpanel.c:4372:34: warning: pointer targets in passing argument 1 of 'complement_string' differ in signedness [-Wpointer-sign]
complement_string (file_line + SEQ_ED_PRINT_SEQ_OFFSET);
^~~~~~~~~
In file included from ../include/alignmgr2.h:112:0,
from seqpanel.c:39:
../include/salutil.h:78:20: note: expected 'Nlm_CharPtr {aka char *}' but argument is of type 'Nlm_Uint1Ptr {aka unsigned char *}'
NLM_EXTERN CharPtr complement_string (CharPtr str);
^~~~~~~~~~~~~~~~~
seqpanel.c:4236:17: warning: variable 'curr_para_strings' set but not used [-Wunused-but-set-variable]
ValNodePtr curr_para_strings = NULL;
^~~~~~~~~~~~~~~~~
seqpanel.c:4229:17: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
Uint1Ptr buf;
^~~
seqpanel.c: In function 'SeqEdOnClick':
seqpanel.c:4946:21: warning: variable 'direction' set but not used [-Wunused-but-set-variable]
Int4 direction;
^~~~~~~~~
seqpanel.c: In function 'SeqAlnOnDrag':
seqpanel.c:5685:34: warning: variable 'is_ctrl' set but not used [-Wunused-but-set-variable]
Boolean is_double_click, is_ctrl;
^~~~~~~
seqpanel.c:5685:17: warning: variable 'is_double_click' set but not used [-Wunused-but-set-variable]
Boolean is_double_click, is_ctrl;
^~~~~~~~~~~~~~~
seqpanel.c: In function 'ResizeSeqEdView':
seqpanel.c:5760:8: warning: variable 'sequence_pos' set but not used [-Wunused-but-set-variable]
Int4 sequence_pos = 0;
^~~~~~~~~~~~
seqpanel.c:5755:8: warning: variable 'height' set but not used [-Wunused-but-set-variable]
Int4 height, width;
^~~~~~
seqpanel.c: In function 'WriteAlignmentInterleaveToFileEx':
seqpanel.c:8664:22: warning: passing argument 1 of 'fputs' from incompatible pointer type [-Wincompatible-pointer-types]
fputs (fp, printed_line);
^~
In file included from ../include/ncbilcl.h:154:0,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
/usr/include/stdio.h:689:12: note: expected 'const char * restrict' but argument is of type 'FILE * {aka struct _IO_FILE *}'
extern int fputs (const char *__restrict __s, FILE *__restrict __stream);
^~~~~
seqpanel.c:8664:26: warning: passing argument 2 of 'fputs' from incompatible pointer type [-Wincompatible-pointer-types]
fputs (fp, printed_line);
^~~~~~~~~~~~
In file included from ../include/ncbilcl.h:154:0,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
/usr/include/stdio.h:689:12: note: expected 'FILE * restrict {aka struct _IO_FILE * restrict}' but argument is of type 'Nlm_CharPtr {aka char *}'
extern int fputs (const char *__restrict __s, FILE *__restrict __stream);
^~~~~
seqpanel.c: In function 'WriteAlignmentContiguousToFile':
seqpanel.c:8760:20: warning: passing argument 1 of 'fputs' from incompatible pointer type [-Wincompatible-pointer-types]
fputs (fp, printed_line);
^~
In file included from ../include/ncbilcl.h:154:0,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
/usr/include/stdio.h:689:12: note: expected 'const char * restrict' but argument is of type 'FILE * {aka struct _IO_FILE *}'
extern int fputs (const char *__restrict __s, FILE *__restrict __stream);
^~~~~
seqpanel.c:8760:24: warning: passing argument 2 of 'fputs' from incompatible pointer type [-Wincompatible-pointer-types]
fputs (fp, printed_line);
^~~~~~~~~~~~
In file included from ../include/ncbilcl.h:154:0,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
/usr/include/stdio.h:689:12: note: expected 'FILE * restrict {aka struct _IO_FILE * restrict}' but argument is of type 'Nlm_CharPtr {aka char *}'
extern int fputs (const char *__restrict __s, FILE *__restrict __stream);
^~~~~
seqpanel.c: In function 'ReverseSequenceStrandsInAlignment':
seqpanel.c:9007:17: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from seqpanel.c:39:
seqpanel.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
seqpanel.c:1171:16: warning: 'GetAlignmentColumnPercentIDsForAlignmentSection' defined but not used [-Wunused-function]
static double *GetAlignmentColumnPercentIDsForAlignmentSection (BioseqViewPtr bvp, Int4 line, Int4 aln_idx)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
seqpanel.c: In function 'SeqEdFindPatternDialog':
../include/vibdefns.h:505:22: warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AlignObjects Nlm_AlignObjects
^~~~~~~~~~~~~~~~
seqpanel.c:7632:25: note: 'g1' was declared here
GrouP h, g1, g2;
^~
In file included from ../include/ncbi.h:62:0,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
seqpanel.c: In function 'PrintFeature':
../include/ncbistr.h:331:19: warning: 'str_prot' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringLen Nlm_StringLen
^~~~~~~~~~~~~
seqpanel.c:3810:21: note: 'str_prot' was declared here
CharPtr str_prot;
^~~~~~~~
seqpanel.c: In function 'SeqEdOnClick':
seqpanel.c:5026:10: warning: 'is_left_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (is_left_end)
^
seqpanel.c: In function 'SeqEdExportProc':
seqpanel.c:4353:13: warning: 'seq_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqEdPrintTextLineToFile ((CharPtr)file_line, from, to, seq_pos, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqpanel.c:4233:17: note: 'seq_pos' was declared here
Int4 seq_pos;
^~~~~~~
seqpanel.c: In function 'onDrawSeqPanel':
seqpanel.c:1301:24: warning: 'alnbuf' may be used uninitialized in this function [-Wmaybe-uninitialized]
MemCpy(buf, alnbuf + from, len);
~~~~~~~^~~~~~
seqpanel.c:2466:33: note: 'alnbuf' was declared here
Uint1Ptr buf, seqbuf, alnbuf;
^~~~~~
seqpanel.c:1252:3: warning: 'seqbuf' may be used uninitialized in this function [-Wmaybe-uninitialized]
AlignmentIntervalToString (tmp_salp, row, start, stop, bvp->TargetRow,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bvp->viewWholeEntity, seqbuf, alnbuf, &alnbuf_len,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bvp->showAlnSubstitutions);
~~~~~~~~~~~~~~~~~~~~~~~~~~
seqpanel.c:2466:25: note: 'seqbuf' was declared here
Uint1Ptr buf, seqbuf, alnbuf;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ingengraph.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from ../include/seqmgr.h:48,
from ../include/ingengraph.h:52,
from ingengraph.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ingengraph.c: In function 'Ing_BigEncodeIdxFeat':
ingengraph.c:262:2: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return *((Uint8Ptr) index_g);
^~~~~~
ingengraph.c: In function 'Ing_AddOneAlignToOverviewPage':
ingengraph.c:355:3: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
ingengraph.c:357:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
prim = AddRectangle(seg, start, (row)*(-20), stop, (row)*(-20)+j, NO_ARROW, FALSE,0);
^~~~
ingengraph.c:347:13: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp=NULL;
^~~
ingengraph.c: In function 'Ing_AddAlignsToOverviewPage':
ingengraph.c:372:18: warning: unused variable 'buf' [-Wunused-variable]
Char buf[41]={""};
^~~
ingengraph.c:367:18: warning: variable 'NewLine' set but not used [-Wunused-but-set-variable]
Boolean NewLine=FALSE;
^~~~~~~
ingengraph.c: In function 'Ing_DrawOverviewPage':
ingengraph.c:492:14: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
Int4 offset;
^~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/ingengraph.h:54,
from ingengraph.c:45:
../include/vibdefns.h:438:17: warning: unused variable 'Nlm_Visible' [-Wunused-variable]
#define Visible Nlm_Visible
^
ingengraph.c:488:14: note: in expansion of macro 'Visible'
Boolean Visible=FALSE;
^~~~~~~
ingengraph.c: In function 'Ing_PopOverviewPage':
ingengraph.c:715:16: warning: variable 'margin' set but not used [-Wunused-but-set-variable]
Int4 margin, len;
^~~~~~
ingengraph.c:714:16: warning: unused variable 'buf' [-Wunused-variable]
Char buf[50]={""};
^~~
ingengraph.c:708:16: warning: unused variable 'sanp' [-Wunused-variable]
SeqAnnotPtr sanp=NULL;
^~~~
ingengraph.c: In function 'Ing_AddAlignsToDetailedPage':
ingengraph.c:1097:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((start - offset - (label_len - feat_len)/2)<0)
^~
ingengraph.c:1099:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (bOver_the_edge)
^~
ingengraph.c: In function 'Ing_PopDetailedPage':
ingengraph.c:1437:16: warning: variable 'CurrentSeg' set but not used [-Wunused-but-set-variable]
SegmenT CurrentSeg=NULL;
^~~~~~~~~~
ingengraph.c: In function 'Ing_ExploreSegments':
ingengraph.c:1829:22: warning: unused variable 'isDraft' [-Wunused-variable]
Boolean isDraft = FALSE;
^~~~~~~
ingengraph.c:1827:22: warning: unused variable 'vnp' [-Wunused-variable]
ValNodePtr vnp = NULL;
^~~
ingengraph.c:1826:22: warning: unused variable 'gbp' [-Wunused-variable]
GBBlockPtr gbp = NULL;
^~~
ingengraph.c:1824:33: warning: variable 'black' set but not used [-Wunused-but-set-variable]
Uint1 orange[3], black[3];
^~~~~
ingengraph.c:1823:33: warning: variable 'lime' set but not used [-Wunused-but-set-variable]
Uint1 indigo[3], lime[3];
^~~~
ingengraph.c:1823:22: warning: variable 'indigo' set but not used [-Wunused-but-set-variable]
Uint1 indigo[3], lime[3];
^~~~~~
ingengraph.c: In function 'Ing_AddGCRect':
ingengraph.c:1933:17: warning: variable 'comp2' set but not used [-Wunused-but-set-variable]
FloatHi comp2, comp_prev;
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/ingengraph.h:63,
from ingengraph.c:45:
ingengraph.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
ingengraph.c:71:13: warning: 'Ing_GetNamesZoomedVal' declared 'static' but never defined [-Wunused-function]
static void Ing_GetNamesZoomedVal(VieweR vNames,Int4Ptr from, Int4Ptr to,
^~~~~~~~~~~~~~~~~~~~~
ingengraph.c:602:28: warning: 'Ing_CollectFeatures1' defined but not used [-Wunused-function]
static Boolean LIBCALLBACK Ing_CollectFeatures1(SeqFeatPtr sfp, SeqMgrFeatContextPtr sfc)
^~~~~~~~~~~~~~~~~~~~
ingengraph.c:583:24: warning: 'Ing_SortByChoice' defined but not used [-Wunused-function]
static int LIBCALLBACK Ing_SortByChoice (VoidPtr ptr1, VoidPtr ptr2)
^~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ingenext.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn2ff.h:113,
from ../include/ingenwin.h:58,
from ../include/ingenext.h:53,
from ingenext.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ingenext.c: In function 'Ing_KeepTheBestAlignments':
ingenext.c:167:20: warning: variable 'amaip' set but not used [-Wunused-but-set-variable]
AMAlignIndex2Ptr amaip = NULL;
^~~~~
ingenext.c: In function 'Ing_HandleQBlastResults':
ingenext.c:272:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, TRUE, TRUE, TRUE)){
^~~~~
ingenext.c: In function 'Ing_HandleResults':
ingenext.c:535:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, TRUE, TRUE, TRUE)){
^~~~~
ingenext.c: In function 'Ing_AccepttRNAargsProc':
ingenext.c:739:18: warning: unused variable 'paramlist' [-Wunused-variable]
ValNodePtr paramlist = NULL;
^~~~~~~~~
ingenext.c: In function 'Ing_tRNAscanProc':
ingenext.c:915:22: warning: unused variable 'moveMe' [-Wunused-variable]
ValNodePtr moveMe = NULL;
^~~~~~
ingenext.c:906:22: warning: unused variable 'first' [-Wunused-variable]
TexT first = NULL;
^~~~~
ingenext.c:902:22: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
ingenext.c:896:17: warning: unused variable 'args' [-Wunused-variable]
CharPtr args = NULL;
^~~~
ingenext.c: In function 'Ing_ReadtRNAConfigFile':
ingenext.c:1125:15: warning: variable 'demomode' set but not used [-Wunused-but-set-variable]
Boolean demomode = FALSE;
^~~~~~~~
ingenext.c: In function 'Ing_DoBlast2Seqs':
ingenext.c:1312:23: warning: variable 'is_local' set but not used [-Wunused-but-set-variable]
Boolean is_local, first_bsp=TRUE;
^~~~~~~~
ingenext.c: In function 'Ing_CreateDotMatrixForm':
ingenext.c:1834:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE))
^~~~~
ingenext.c: In function 'Ing_RunSpidey':
ingenext.c:1994:20: warning: unused variable 'sanp' [-Wunused-variable]
SeqAnnotPtr sanp = NULL;
^~~~
ingenext.c:1993:20: warning: unused variable 'spidp_next' [-Wunused-variable]
SPI_mRNAPtr spidp_next = NULL;
^~~~~~~~~~
ingenext.c:1992:20: warning: unused variable 'spidp_head' [-Wunused-variable]
SPI_mRNAPtr spidp_head = NULL;
^~~~~~~~~~
ingenext.c: In function 'Ing_ReadmRNAs_ext':
ingenext.c:2025:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE))
^~~~~
ingenext.c: In function 'Ing_DeleteInsertInGenomic':
ingenext.c:2522:16: warning: unused variable 'newsegs' [-Wunused-variable]
Int2 newsegs = 0, offset = 0;
^~~~~~~
ingenext.c: In function 'Ing_ReplaceAllMismatchedInLocation':
ingenext.c:2777:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (!All)
^~
ingenext.c:2781:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
SeqLocReplace(msip, mmis, mmis, mstrand, gsip, gmis, gmis, gstrand);
^~~~~~~~~~~~~
ingenext.c:2615:21: warning: unused variable 'str' [-Wunused-variable]
Char str[200] = {""};
^~~
ingenext.c:2612:22: warning: unused variable 'amaip' [-Wunused-variable]
AMAlignIndex2Ptr amaip = NULL;
^~~~~
ingenext.c: In function 'Ing_MismatchProc':
ingenext.c:3025:15: warning: unused variable 'sip' [-Wunused-variable]
SeqIdPtr sip = NULL;
^~~
ingenext.c: In function 'Ing_PrintSpideyReport':
ingenext.c:3471:27: warning: variable 'gmis' set but not used [-Wunused-but-set-variable]
Int4 mmis, gmis, miscount = 0;
^~~~
ingenext.c: In function 'Ing_PrintBlastReport':
ingenext.c:3853:18: warning: unused variable 'more' [-Wunused-variable]
Boolean more = FALSE;
^~~~
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/vibdefns.h:622:16: warning: variable 'Nlm_DkGray' set but not used [-Wunused-but-set-variable]
#define DkGray Nlm_DkGray
^
ingenext.c:3850:18: note: in expansion of macro 'DkGray'
Uint1 DkGray[3];
^~~~~~
ingenext.c: In function 'Ing_PopulateReport':
ingenext.c:4328:20: warning: unused variable 'sip' [-Wunused-variable]
SeqIdPtr sip=NULL;
^~~
ingenext.c:4324:20: warning: unused variable 'temp' [-Wunused-variable]
CharPtr temp = NULL;
^~~~
ingenext.c: In function 'Ing_ResizeReportWindow':
ingenext.c:4484:12: warning: variable 'hsb' set but not used [-Wunused-but-set-variable]
BaR hsb;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from ../include/ingenwin.h:60,
from ../include/ingenext.h:53,
from ingenext.c:46:
ingenext.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:135:0,
from ../include/ingenwin.h:62,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/objblst3.h:180:35: warning: 'Cutoff2_cutoff2Free' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr ));
^~~~~~~~~~~~~~~~~~~
../include/objblst3.h:181:35: warning: 'Cutoff2_cutoff2AsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:182:24: warning: 'Cutoff2_cutoff2AsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:199:33: warning: 'Cutoff_cutoffFree' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr ));
^~~~~~~~~~~~~~~~~
../include/objblst3.h:200:33: warning: 'Cutoff_cutoffAsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:201:24: warning: 'Cutoff_cutoffAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ingenext.c:130:13: warning: 'querytimercount' defined but not used [-Wunused-variable]
static Int4 querytimercount = 0;
^~~~~~~~~~~~~~~
ingenext.c:129:13: warning: 'querytimerlimit' defined but not used [-Wunused-variable]
static Int4 querytimerlimit = 100;
^~~~~~~~~~~~~~~
ingenext.c:59:28: warning: 'Ing_BlastCallback' defined but not used [-Wunused-function]
static Boolean LIBCALLBACK Ing_BlastCallback (BlastResponse *brp,
^~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:134:0,
from ../include/ingenwin.h:62,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/blstspc.h:229:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/blstspc.h:228:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/blstspc.h:227:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/blstspc.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "blstspc.h23";
^~~~~~~~~~~
ingenext.c: In function 'Ing_DoBlast2Seqs':
ingenext.c:1457:17: warning: 'e_head' may be used uninitialized in this function [-Wmaybe-uninitialized]
e_tmp->next=e_head;
~~~~~~~~~~~^~~~~~~
ingenext.c: In function 'Ing_MismatchProc':
ingenext.c:3170:32: warning: 'gstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
gstart = start + (stop - gstart);
~~~~~~^~~~~~~~~
ingenext.c:3206:23: warning: 'mstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
else if (mstart == R1 || mstart == R2 || mstart == R3){
~~~~~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ingenwin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn2ff.h:113,
from ../include/ingenwin.h:58,
from ingenwin.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ingenwin.c: In function 'Ing_PopulateDetailedPage':
ingenwin.c:134:22: warning: unused variable 'bSelected' [-Wunused-variable]
Boolean bSelected = FALSE;
^~~~~~~~~
ingenwin.c: In function 'Ing_DoRange':
ingenwin.c:394:22: warning: variable 'bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr bsp;
^~~
ingenwin.c: In function 'Ing_PopulateCpG':
ingenwin.c:576:19: warning: variable 'nchars' set but not used [-Wunused-but-set-variable]
Int2 cxChar, nchars;
^~~~~~
ingenwin.c: In function 'Ing_ResizeCpGWindow':
ingenwin.c:642:12: warning: variable 'hsb' set but not used [-Wunused-but-set-variable]
BaR hsb;
^~~
ingenwin.c: In function 'Ing_PopulateMotif':
ingenwin.c:718:26: warning: variable 'nchars' set but not used [-Wunused-but-set-variable]
Int2 cxChar, nchars;
^~~~~~
ingenwin.c:717:24: warning: variable 'swidth' set but not used [-Wunused-but-set-variable]
Int4 slen, swidth;
^~~~~~
ingenwin.c:717:18: warning: variable 'slen' set but not used [-Wunused-but-set-variable]
Int4 slen, swidth;
^~~~
ingenwin.c: In function 'Ing_ResizeMotifWindow':
ingenwin.c:785:12: warning: unused variable 'name' [-Wunused-variable]
CharPtr name = NULL;
^~~~
ingenwin.c:783:12: warning: variable 'hsb' set but not used [-Wunused-but-set-variable]
BaR hsb;
^~~
ingenwin.c: In function 'Ing_ShowComplexity':
ingenwin.c:1270:10: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
while ((Boolean)(slp_feat=SeqLocFindNext(slp_dust,slp_feat))){
^
ingenwin.c: In function 'Ing_CreateNewFeature':
ingenwin.c:1301:22: warning: unused variable 'rnatype' [-Wunused-variable]
Uint1 rnatype=0;
^~~~~~~
ingenwin.c: In function 'Ing_GetAlignmentIntervals':
ingenwin.c:1418:20: warning: unused variable 'master' [-Wunused-variable]
SeqIdPtr master = NULL;
^~~~~~
ingenwin.c: In function 'Ing_OldGetAlignmentIntervals':
ingenwin.c:1494:20: warning: unused variable 'master' [-Wunused-variable]
SeqIdPtr master = NULL;
^~~~~~
ingenwin.c: In function 'Ing_OldMakeLocListFromSAP':
ingenwin.c:1613:26: warning: unused variable 'slp2' [-Wunused-variable]
SeqLocPtr slp1 = NULL, slp2 = NULL;
^~~~
ingenwin.c:1613:13: warning: unused variable 'slp1' [-Wunused-variable]
SeqLocPtr slp1 = NULL, slp2 = NULL;
^~~~
ingenwin.c: In function 'Ing_OM_MsgFunc':
ingenwin.c:2380:15: warning: the address of 'sfc' will always evaluate as 'true' [-Waddress]
if (&sfc)
^
ingenwin.c:2284:22: warning: unused variable 'segID' [-Wunused-variable]
Uint2 segID=0;
^~~~~
ingenwin.c:2280:22: warning: unused variable 'sep' [-Wunused-variable]
SeqEntryPtr sep=NULL;
^~~
ingenwin.c:2271:31: warning: unused variable 'number' [-Wunused-variable]
Int4 score=0, number=0;
^~~~~~
ingenwin.c:2271:22: warning: unused variable 'score' [-Wunused-variable]
Int4 score=0, number=0;
^~~~~
ingenwin.c:2270:34: warning: unused variable 'n' [-Wunused-variable]
Int4 s1=0, s2=0, n=1;
^
ingenwin.c:2270:28: warning: unused variable 's2' [-Wunused-variable]
Int4 s1=0, s2=0, n=1;
^~
ingenwin.c:2270:22: warning: unused variable 's1' [-Wunused-variable]
Int4 s1=0, s2=0, n=1;
^~
ingenwin.c: In function 'Ing_MoveCursor':
ingenwin.c:2631:9: warning: variable 'grayClr2' set but not used [-Wunused-but-set-variable]
Uint1 grayClr2[3];
^~~~~~~~
ingenwin.c: In function 'Ing_FeatViewerClickProc':
ingenwin.c:2814:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (subSeg=FindSegPrim(v, pt, NULL, NULL, &prim)){
^~
ingenwin.c:2804:14: warning: unused variable 'slp' [-Wunused-variable]
SeqLocPtr slp=NULL;
^~~
ingenwin.c: In function 'Ing_SequenceClickProc':
ingenwin.c:2908:22: warning: variable 'ssp' set but not used [-Wunused-but-set-variable]
SelStructPtr ssp=NULL;
^~~
ingenwin.c: In function 'Ing_ReadInBlastAsn':
ingenwin.c:3077:19: warning: unused variable 'Report' [-Wunused-variable]
IngReportPtr Report=NULL;
^~~~~~
ingenwin.c:3075:19: warning: unused variable 'sip' [-Wunused-variable]
SeqIdPtr sip=NULL;
^~~
ingenwin.c:3074:19: warning: unused variable 'salp' [-Wunused-variable]
SeqAlignPtr salp=NULL;
^~~~
ingenwin.c:3073:19: warning: unused variable 'n_sap' [-Wunused-variable]
SeqAlignPtr n_sap=NULL;
^~~~~
ingenwin.c: In function 'Ing_ParseSeqIdFile':
ingenwin.c:3142:20: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp=NULL;
^~~
ingenwin.c: In function 'Ing_ReadInFeatureTable':
ingenwin.c:3194:20: warning: variable 'sanp' set but not used [-Wunused-but-set-variable]
SeqAnnotPtr sanp;
^~~~
ingenwin.c: In function 'Ing_AssembleGenscanInfo':
ingenwin.c:3258:17: warning: unused variable 'slp' [-Wunused-variable]
SeqLocPtr slp=NULL;
^~~
ingenwin.c: In function 'Ing_ReadInGenscan':
ingenwin.c:3300:33: warning: unused variable 'str' [-Wunused-variable]
CharPtr letter=NULL, str=NULL;
^~~
ingenwin.c:3300:20: warning: unused variable 'letter' [-Wunused-variable]
CharPtr letter=NULL, str=NULL;
^~~~~~
ingenwin.c:3298:33: warning: unused variable 'first_pass' [-Wunused-variable]
Boolean found=FALSE, first_pass=FALSE;
^~~~~~~~~~
ingenwin.c: In function 'Ing_AssembleTabDelimited':
ingenwin.c:3519:17: warning: variable 'score' set but not used [-Wunused-but-set-variable]
Int4 score;
^~~~~
ingenwin.c:3516:17: warning: unused variable 'tmp' [-Wunused-variable]
CharPtr tmp=NULL;
^~~
ingenwin.c: In function 'Ing_ReadInTabDelimited':
ingenwin.c:3659:40: warning: variable 'label_str' set but not used [-Wunused-but-set-variable]
CharPtr tmp=NULL, str=NULL, label_str=NULL;
^~~~~~~~~
ingenwin.c:3659:20: warning: unused variable 'tmp' [-Wunused-variable]
CharPtr tmp=NULL, str=NULL, label_str=NULL;
^~~
ingenwin.c:3653:20: warning: unused variable 'lip_tmp' [-Wunused-variable]
IngInfoPtr lip_tmp=NULL;
^~~~~~~
ingenwin.c:3650:20: warning: unused variable 'letter' [-Wunused-variable]
CharPtr letter=NULL;
^~~~~~
ingenwin.c: In function 'Ing_FileOpenSpecial':
ingenwin.c:3984:16: warning: unused variable 'Report' [-Wunused-variable]
IngReportPtr Report=NULL;
^~~~~~
ingenwin.c: In function 'Ing_FileOpenMain':
ingenwin.c:4078:21: warning: unused variable 'sep_orig' [-Wunused-variable]
SeqEntryPtr sep_orig=NULL, sep=NULL;
^~~~~~~~
ingenwin.c: In function 'Ing_ResizeMainWindow':
ingenwin.c:4187:25: warning: variable 'InfoHeight' set but not used [-Wunused-but-set-variable]
Int2 RulerHeight, InfoHeight;
^~~~~~~~~~
ingenwin.c: In function 'Ing_OpenFromFileORNetwork':
ingenwin.c:4491:25: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b,b2;
^~
ingenwin.c: In function 'Ing_EditFeature':
ingenwin.c:4640:22: warning: variable 'igvp' set but not used [-Wunused-but-set-variable]
IngGenomeViewerPtr igvp=NULL;
^~~~
ingenwin.c: In function 'Ing_MarkSeqAnnot':
ingenwin.c:4713:16: warning: unused variable 'bNoParent' [-Wunused-variable]
Boolean bNoParent = FALSE;
^~~~~~~~~
ingenwin.c: In function 'Ing_CreateMismatchedDialog':
ingenwin.c:4924:31: warning: 'main' is usually a function [-Wmain]
GrouP g, g1, g2, main;
^~~~
ingenwin.c: In function 'Ing_PropagateClickProc':
ingenwin.c:5064:22: warning: unused variable 'primID' [-Wunused-variable]
Uint2 primID=0;
^~~~~~
ingenwin.c:5063:22: warning: unused variable 'itemtype' [-Wunused-variable]
Uint2 itemtype=0;
^~~~~~~~
ingenwin.c:5062:22: warning: unused variable 'itemID' [-Wunused-variable]
Uint4 itemID=0;
^~~~~~
ingenwin.c:5061:22: warning: unused variable 'entityID' [-Wunused-variable]
Uint2 entityID=0;
^~~~~~~~
ingenwin.c:5060:22: warning: unused variable 'ssp' [-Wunused-variable]
SelStructPtr ssp=NULL;
^~~
ingenwin.c:5059:22: warning: unused variable 'igvp' [-Wunused-variable]
IngGenomeViewerPtr igvp=NULL;
^~~~
ingenwin.c: In function 'Ing_PrintCompProteins':
ingenwin.c:5146:32: warning: unused variable 'str2' [-Wunused-variable]
Char str1[200] = {""}, str2[10] = {""};
^~~~
ingenwin.c: In function 'Ing_PropagateReport':
ingenwin.c:5282:14: warning: variable 'ARROW' set but not used [-Wunused-but-set-variable]
Uint1 ARROW=NO_ARROW;
^~~~~
ingenwin.c:5279:14: warning: unused variable 'stringwidth' [-Wunused-variable]
Int4 stringwidth = 0;
^~~~~~~~~~~
ingenwin.c:5277:14: warning: unused variable 'left' [-Wunused-variable]
Int4 left = 10;
^~~~
ingenwin.c:5276:14: warning: variable 'prim' set but not used [-Wunused-but-set-variable]
PrimitivE prim;
^~~~
ingenwin.c: In function 'Ing_DoPropagate':
ingenwin.c:5596:14: warning: unused variable 'strErr' [-Wunused-variable]
Char strErr[50]={""};
^~~~~~
ingenwin.c: In function 'Ing_GetFromNetwork':
ingenwin.c:7518:11: warning: unused variable 'szAppName' [-Wunused-variable]
Char szAppName [10]={"Ingenue"};
^~~~~~~~~
ingenwin.c: In function 'Ing_SetupMainWindow':
ingenwin.c:7761:16: warning: unused variable 'szAppName' [-Wunused-variable]
Char szAppName [10]={"Ingenue"};
^~~~~~~~~
ingenwin.c:7760:48: warning: unused variable 'str2' [-Wunused-variable]
Char title[100]={""}, str1[20]={""}, str2[20]={""};
^~~~
ingenwin.c:7760:33: warning: unused variable 'str1' [-Wunused-variable]
Char title[100]={""}, str1[20]={""}, str2[20]={""};
^~~~
ingenwin.c:7760:16: warning: unused variable 'title' [-Wunused-variable]
Char title[100]={""}, str1[20]={""}, str2[20]={""};
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from ../include/ingenwin.h:60,
from ingenwin.c:45:
ingenwin.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ingenwin.c:45:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ingenwin.c:45:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ingenwin.c:45:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ingenwin.c:45:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:135:0,
from ../include/ingenwin.h:62,
from ingenwin.c:45:
../include/objblst3.h:180:35: warning: 'Cutoff2_cutoff2Free' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr ));
^~~~~~~~~~~~~~~~~~~
../include/objblst3.h:181:35: warning: 'Cutoff2_cutoff2AsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:182:24: warning: 'Cutoff2_cutoff2AsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:199:33: warning: 'Cutoff_cutoffFree' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr ));
^~~~~~~~~~~~~~~~~
../include/objblst3.h:200:33: warning: 'Cutoff_cutoffAsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:201:24: warning: 'Cutoff_cutoffAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ingenwin.c:7552:13: warning: 'Ing_ItemtoNetwork' defined but not used [-Wunused-function]
static void Ing_ItemtoNetwork(IteM i){
^~~~~~~~~~~~~~~~~
ingenwin.c:6717:13: warning: 'Ing_BspListProc' defined but not used [-Wunused-function]
static void Ing_BspListProc(IteM i)
^~~~~~~~~~~~~~~
ingenwin.c:5535:16: warning: 'Ing_KeywordAlreadyInList' defined but not used [-Wunused-function]
static Boolean Ing_KeywordAlreadyInList (ValNodePtr head, CharPtr kwd)
^~~~~~~~~~~~~~~~~~~~~~~~
ingenwin.c:1869:16: warning: 'Ing_DeSelectPrim' defined but not used [-Wunused-function]
static Boolean Ing_DeSelectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata)
^~~~~~~~~~~~~~~~
ingenwin.c:1610:18: warning: 'Ing_OldMakeLocListFromSAP' defined but not used [-Wunused-function]
static SeqLocPtr Ing_OldMakeLocListFromSAP(SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~~~~~~~~~
ingenwin.c:1487:23: warning: 'Ing_OldGetAlignmentIntervals' defined but not used [-Wunused-function]
static IngIvalInfoPtr Ing_OldGetAlignmentIntervals (SeqAlignPtr sap, Int4 from_row, Int4 to_row, Int4 from, Int4 to, Uint1 strand)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:134:0,
from ../include/ingenwin.h:62,
from ingenwin.c:45:
../include/blstspc.h:229:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/blstspc.h:228:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/blstspc.h:227:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/blstspc.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "blstspc.h23";
^~~~~~~~~~~
ingenwin.c: In function 'Ing_ReplaceMismatchedProc':
ingenwin.c:4902:3: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
Ing_ReplaceAllMismatchedInLocation(igvp, rmp->sap, start, stop, GetStatus(rmp->all), GetStatus(rmp->gaps), GetStatus(rmp->inserts));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ingenwin.c:4902:3: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
ingenwin.c: In function 'Ing_PropagateReport':
ingenwin.c:5224:12: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
last_pos = j;
~~~~~~~~~^~~
ingenwin.c:5137:17: note: 'j' was declared here
Int4 i, j, k, row;
^
ingenwin.c: In function 'Ing_FileOpenSpecial':
ingenwin.c:3290:12: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
slp_list=Ing_MakeSlpList(NULL, n/2, ivals, strand, igvp->bsp->id);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ingenwin.c:3255:17: note: 'strand' was declared here
Uint1 strand;
^~~~~~
ingenwin.c: In function 'Ing_KozakProc':
ingenwin.c:1048:6: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ans == ANS_NO)
^
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ingenwin.c:45:
../include/vibdefns.h:446:16: warning: 'ReportW' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Select Nlm_Select
^~~~~~~~~~
ingenwin.c:1006:22: note: 'ReportW' was declared here
WindoW ReportW;
^~~~~~~
ingenwin.c: In function 'Ing_SignalPeptideProc':
ingenwin.c:1099:6: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ans == ANS_NO)
^
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ingenwin.c:45:
../include/vibdefns.h:446:16: warning: 'ReportW' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Select Nlm_Select
^~~~~~~~~~
ingenwin.c:1057:22: note: 'ReportW' was declared here
WindoW ReportW;
^~~~~~~
ingenwin.c: In function 'Ing_RepeatsProc':
ingenwin.c:997:6: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ans == ANS_NO)
^
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ingenwin.c:45:
../include/vibdefns.h:446:16: warning: 'ReportW' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Select Nlm_Select
^~~~~~~~~~
ingenwin.c:955:22: note: 'ReportW' was declared here
WindoW ReportW;
^~~~~~~
ingenwin.c: In function 'Ing_PolyAProc':
ingenwin.c:946:6: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ans == ANS_NO)
^
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ingenwin.c:45:
../include/vibdefns.h:446:16: warning: 'ReportW' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Select Nlm_Select
^~~~~~~~~~
ingenwin.c:904:22: note: 'ReportW' was declared here
WindoW ReportW;
^~~~~~~
ingenwin.c: In function 'Ing_CpGProc':
ingenwin.c:895:6: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ans == ANS_NO)
^
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ingenwin.c:45:
../include/vibdefns.h:446:16: warning: 'ReportW' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Select Nlm_Select
^~~~~~~~~~
ingenwin.c:857:22: note: 'ReportW' was declared here
WindoW ReportW;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF macrodlg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from macrodlg.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
macrodlg.c: In function 'CloseMacroEditorWindowProc':
macrodlg.c:99:11: warning: unused variable 'do_remove' [-Wunused-variable]
Boolean do_remove = FALSE;
^~~~~~~~~
macrodlg.c: In function 'ExistingTextDialog':
macrodlg.c:1908:22: warning: variable 'ppt' set but not used [-Wunused-but-set-variable]
PrompT ppt;
^~~
macrodlg.c: In function 'SourceQualChoiceDialog':
macrodlg.c:3725:48: warning: variable 'b4' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3725:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3725:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3725:29: warning: variable 'b1' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c: In function 'SourceConstraintDialog':
macrodlg.c:3963:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:3963:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:3963:29: warning: variable 'b1' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c: In function 'CDSGeneProtQualConstraintDialog':
macrodlg.c:4277:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:4277:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:4277:29: warning: variable 'b1' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c: In function 'FeatureFieldTypeFromComplexConstraintType':
macrodlg.c:10273:3: warning: enumeration value 'eComplexConstraintType_seqid' not handled in switch [-Wswitch]
switch (constraint_type) {
^~~~~~
macrodlg.c:10273:3: warning: enumeration value 'eComplexConstraintType_string' not handled in switch [-Wswitch]
macrodlg.c:10273:3: warning: enumeration value 'eComplexConstraintType_loc' not handled in switch [-Wswitch]
macrodlg.c: In function 'TestApplyActionDialog':
macrodlg.c:12680:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'TestEditActionDialog':
macrodlg.c:12854:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'TestRemoveOutsideActionDialog':
macrodlg.c:13012:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'AddMacroActions':
macrodlg.c:19633:25: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE;
^~~~
macrodlg.c: In function 'PointerToSampleDialog':
macrodlg.c:19769:19: warning: variable 'max_char_per_line' set but not used [-Wunused-but-set-variable]
Int4 max_char_per_line;
^~~~~~~~~~~~~~~~~
macrodlg.c: In function 'SampleDialogCopy':
macrodlg.c:19889:53: warning: variable 'last_col' set but not used [-Wunused-but-set-variable]
Int2 start_col = 0, end_col = 0, first_col, last_col;
^~~~~~~~
macrodlg.c:19889:42: warning: variable 'first_col' set but not used [-Wunused-but-set-variable]
Int2 start_col = 0, end_col = 0, first_col, last_col;
^~~~~~~~~
macrodlg.c: In function 'SingleMacroAcceptButton':
macrodlg.c:21177:33: warning: variable 'num_features' set but not used [-Wunused-but-set-variable]
Int4 num_fields, num_features;
^~~~~~~~~~~~
macrodlg.c:21177:21: warning: variable 'num_fields' set but not used [-Wunused-but-set-variable]
Int4 num_fields, num_features;
^~~~~~~~~~
macrodlg.c: In function 'LaunchMacroTemplateEditor':
macrodlg.c:22877:23: warning: variable 'bfp' set but not used [-Wunused-but-set-variable]
BaseFormPtr bfp;
^~~
At top level:
macrodlg.c:9778:15: warning: 'LocOrStringConstraintDialog' defined but not used [-Wunused-function]
static DialoG LocOrStringConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
macrodlg.c: In function 'ApplyProductUpdateTableBtn':
macrodlg.c:26278:7: warning: 'lip' may be used uninitialized in this function [-Wmaybe-uninitialized]
FreeLog (lip);
^~~~~~~~~~~~~
macrodlg.c: In function 'RemoveSequencesActionDialog':
macrodlg.c:6490:15: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlg->dialog = (DialoG) p;
~~~~~~~~~~~~^~~~~~~~~~~~
macrodlg.c: In function 'ActionToSingleMacroActionForm':
macrodlg.c:21322:25: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 val, i;
^~~
In file included from ../include/vibrant.h:130:0,
from ../include/vibforms.h:46,
from macrodlg.c:48:
macrodlg.c: In function 'BuildEditMacroActionWindow':
../include/vibdefns.h:505:22: warning: 'indexer_only_group' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AlignObjects Nlm_AlignObjects
^~~~~~~~~~~~~~~~
macrodlg.c:14910:47: note: 'indexer_only_group' was declared here
GrouP p, g, parts_group, x, indexer_only_group;
^~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF biosrc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/biosrc.h:48,
from biosrc.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
biosrc.c: In function 'CreateBioSourceDialog':
biosrc.c:3506:18: warning: variable 'y' set but not used [-Wunused-but-set-variable]
PrompT y;
^
At top level:
biosrc.c:3182:26: warning: 'EnumListFromQualNameAssoc' defined but not used [-Wunused-function]
static EnumFieldAssocPtr EnumListFromQualNameAssoc (Nlm_QualNameAssocPtr qp)
^~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2991:16: warning: 'SubsourceDialogToSubSourcePtr' defined but not used [-Wunused-function]
static Pointer SubsourceDialogToSubSourcePtr (DialoG d)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2568:13: warning: 'SubSourcePtrToSubsourceDialog' defined but not used [-Wunused-function]
static void SubSourcePtrToSubsourceDialog (DialoG d, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2508:16: warning: 'OrgmodDialogToOrgModPtr' defined but not used [-Wunused-function]
static Pointer OrgmodDialogToOrgModPtr (DialoG d)
^~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2459:13: warning: 'OrgModPtrToOrgmodDialog' defined but not used [-Wunused-function]
static void OrgModPtrToOrgmodDialog (DialoG d, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cdrgn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/cdrgn.h:89,
from cdrgn.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cdrgn.c: In function 'ProductToSeqLocPtr':
cdrgn.c:1318:19: warning: variable 'rfp' set but not used [-Wunused-but-set-variable]
RnaFormPtr rfp = NULL;
^~~
cdrgn.c: In function 'CreateCodeBreakAlist':
cdrgn.c:1951:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
cdrgn.c: In function 'CodeBreakPtrToCodeBreakDialog':
cdrgn.c:2002:19: warning: variable 'aa' set but not used [-Wunused-but-set-variable]
Uint1 aa;
^~
cdrgn.c: In function 'PopulateAAPopup':
cdrgn.c:7044:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
At top level:
cdrgn.c:6854:13: warning: 'ConvertRnaRefNameToProductQual' defined but not used [-Wunused-function]
static void ConvertRnaRefNameToProductQual (SeqFeatPtr sfp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdrgn.c:6792:13: warning: 'RemoveQualByName' defined but not used [-Wunused-function]
static void RemoveQualByName (SeqFeatPtr sfp, CharPtr qual_name)
^~~~~~~~~~~~~~~~
cdrgn.c:6773:18: warning: 'FindOrAddQual' defined but not used [-Wunused-function]
static GBQualPtr FindOrAddQual (SeqFeatPtr sfp, CharPtr qual_name)
^~~~~~~~~~~~~
cdrgn.c:6330:15: warning: 'CreateMrnaUserObjectDialog' defined but not used [-Wunused-function]
static DialoG CreateMrnaUserObjectDialog (GrouP h, CharPtr label, SeqEntryPtr sep, BaseFormPtr bfp)
^~~~~~~~~~~~~~~~~~~~~~~~~~
cdrgn.c:6253:14: warning: 'check_rna_type' defined but not used [-Wunused-function]
static Uint1 check_rna_type (Uint1 type)
^~~~~~~~~~~~~~
cdrgn.c:2174:13: warning: 'AccessionToGi' defined but not used [-Wunused-function]
static Int4 AccessionToGi (CharPtr string)
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF import.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from import.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF pubdesc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/pubdesc.h:48,
from pubdesc.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pubdesc.c: In function 'SetPubdescImportExportItems':
pubdesc.c:2859:37: warning: comparison between pointer and integer
&&& pfp->currentPage == 1) {
^~
pubdesc.c: In function 'MakeReplaceAuthorsForm':
pubdesc.c:4289:24: warning: variable 'pepp' set but not used [-Wunused-but-set-variable]
PubdescEditProcsPtr pepp;
^~~~
pubdesc.c: In function 'DisplayDocSum':
pubdesc.c:4851:9: warning: variable 'lineheight' set but not used [-Wunused-but-set-variable]
Int2 lineheight;
^~~~~~~~~~
At top level:
pubdesc.c:5363:13: warning: 'Quit' defined but not used [-Wunused-function]
static void Quit (ButtoN b)
^~~~
pubdesc.c:5099:14: warning: 'AddAll' defined but not used [-Wunused-function]
static void AddAll(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st)
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqsub.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/seqsub.h:58,
from seqsub.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqsub.c: In function 'SeqSubmitFromTemplateEditor':
seqsub.c:3250:20: warning: variable 'omdp' set but not used [-Wunused-but-set-variable]
ObjMgrDataPtr omdp;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mapgene.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from mapgene.c:2:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mapgene.c: In function 'load_new_align':
mapgene.c:79:17: warning: variable 'match_slp' set but not used [-Wunused-but-set-variable]
SeqLocPtr slp, match_slp, t_slp;
^~~~~~~~~
mapgene.c: In function 'figure_loc_by_position':
mapgene.c:1039:20: warning: variable 'center' set but not used [-Wunused-but-set-variable]
Int4 start, stop, center;
^~~~~~
mapgene.c: In function 'cvt_loc_for_single_gene':
mapgene.c:1958:29: warning: variable 'p_align_offset' set but not used [-Wunused-but-set-variable]
Int4 offset, align_offset, p_align_offset;
^~~~~~~~~~~~~~
mapgene.c:1957:7: warning: unused variable 'shift' [-Wunused-variable]
Int4 shift = 0;
^~~~~
mapgene.c: In function 'print_header_for_center':
mapgene.c:2693:10: warning: variable 'link' set but not used [-Wunused-but-set-variable]
CharPtr link;
^~~~
mapgene.c: In function 'PrintGeneticMarkerForOneMap':
mapgene.c:3635:10: warning: variable 'link' set but not used [-Wunused-but-set-variable]
CharPtr link;
^~~~
At top level:
mapgene.c:3207:16: warning: 'convert_center_name_to_gifname' defined but not used [-Wunused-function]
static Boolean convert_center_name_to_gifname (CharPtr center_name, CharPtr gif_name)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mapgene.c:1788:13: warning: 'adjust_slp_list' defined but not used [-Wunused-function]
static void adjust_slp_list(ValNodePtr slp_list)
^~~~~~~~~~~~~~~
mapgene.c:1748:16: warning: 'merge_slp_list' defined but not used [-Wunused-function]
static Boolean merge_slp_list(ValNodePtr PNTR gene_slp_list, ValNodePtr slp_list)
^~~~~~~~~~~~~~
mapgene.c:1280:13: warning: 'change_anchor_to_front' defined but not used [-Wunused-function]
static void change_anchor_to_front(ValNodePtr msp_list, SeqIdPtr anchor_id)
^~~~~~~~~~~~~~~~~~~~~~
mapgene.c:200:13: warning: 'get_center_pointer' defined but not used [-Wunused-function]
static Int4 get_center_pointer(SeqLocPtr slp)
^~~~~~~~~~~~~~~~~~
mapgene.c:27:13: warning: 'print_this_id' defined but not used [-Wunused-function]
static void print_this_id (SeqIdPtr sip)
^~~~~~~~~~~~~
mapgene.c: In function 'PrintContigForOneMap':
mapgene.c:3181:4: warning: 'yac_num' may be used uninitialized in this function [-Wmaybe-uninitialized]
PrintHTMLContigAlign(band_name, contig_name, anp_list, fp, db, fish_list, yac_list, yac_num);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mapgene.c:3152:7: note: 'yac_num' was declared here
Int4 yac_num;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF prtgene.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/tofile.h:66,
from ../include/prtgene.h:3,
from prtgene.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
prtgene.c: In function 'print_sfp_ext':
prtgene.c:108:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(ufp->choice == 2) /*integer */
^~
prtgene.c:110:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
print_store_buf(temp, buf, buf_size, &len, fp);
^~~~~~~~~~~~~~~
prtgene.c: In function 'print_store_for_html':
prtgene.c:749:7: warning: variable 'white_sp' set but not used [-Wunused-but-set-variable]
Char white_sp;
^~~~~~~~
rm -f libncbidesk.a
ar cru libncbidesk.a drawseq.o dotmatrx.o fea2seg.o fstyle.o smdlg1.o smdlg2.o smdlg3.o smtools.o styleman.o stylemui.o glbpic.o layout.o saldist.o saled.o salfiles.o salpanel.o salparam.o salsa.o seqfltr.o seqgraph.o seqgrphx.o seqmtrx.o seqpcc.o seqanal.o aacomp.o seqscrl.o valdlg.o vsm.o vsmfile.o vsmutil.o udvgraph.o udvopen.o udvpanel.o dotvibrant.o dlgutil1.o dlgutil2.o e2trmlst.o e2docsum.o asn2graphic.o medview.o bspview.o gbfview.o gphview.o gphdraw.o gxydraw.o gtrdraw.o seqpanel.o ingengraph.o ingenext.o ingenwin.o macrodlg.o biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbidesk.a ../lib
ranlib ../lib/libncbidesk.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ddvclick.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvclick.c:248:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvclick.c: In function 'DDV_SendBSPSelectMsg_OLD':
ddvclick.c:979:13: warning: variable 'bDeselectAll' set but not used [-Wunused-but-set-variable]
Boolean bDeselectAll=TRUE;
^~~~~~~~~~~~
ddvclick.c: In function 'DDV_SendBSPSelectMsg':
ddvclick.c:1090:18: warning: variable 'bDeselectAll' set but not used [-Wunused-but-set-variable]
Boolean bDeselectAll=TRUE;
^~~~~~~~~~~~
ddvclick.c: In function 'DDV_DragProc':
ddvclick.c:2013:13: warning: unused variable 'cur_pgp' [-Wunused-variable]
ParaGPtr cur_pgp=NULL;
^~~~~~~
ddvclick.c: In function 'DDV_HoldProc':
ddvclick.c:2494:13: warning: unused variable 'Scroll' [-Wunused-variable]
Boolean Scroll=FALSE;
^~~~~~
ddvclick.c:2490:13: warning: unused variable 'cur_pgp' [-Wunused-variable]
ParaGPtr cur_pgp=NULL;
^~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvclick.c:252:
ddvclick.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvclick.c:252:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvclick.c:252:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvclick.c:252:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ddvclick.c:1823:13: warning: 'EraseOutline' defined but not used [-Wunused-function]
static void EraseOutline(PaneL p) {
^~~~~~~~~~~~
ddvclick.c:1811:16: warning: 'RectanglesAreSame' defined but not used [-Wunused-function]
static Boolean RectanglesAreSame(RecT rc1, RecT rc2) {
^~~~~~~~~~~~~~~~~
ddvclick.c:970:13: warning: 'DDV_SendBSPSelectMsg_OLD' defined but not used [-Wunused-function]
static void DDV_SendBSPSelectMsg_OLD(DdvMainPtr dmp,Int4 bsp_coord,Int4 SeqAlign_coord,
^~~~~~~~~~~~~~~~~~~~~~~~
ddvclick.c:611:13: warning: 'DDV_GetSeqAlignCoordGivenCol' defined but not used [-Wunused-function]
static Int4 DDV_GetSeqAlignCoordGivenCol(DdvMainPtr dmp, Int4 Disp_coord) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvclick.c: In function 'DDV_GetSeqNameGivenRow':
ddvclick.c:956:6: warning: 'sip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (!sip)
^
ddvclick.c: In function 'DDV_ReleaseProc':
ddvclick.c:1127:9: warning: 'pgp' may be used uninitialized in this function [-Wmaybe-uninitialized]
slp = SeqLocIntNew (bsp_coord_start, bsp_coord_stop, direction, pgp->sip);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvclick.c:1091:18: note: 'pgp' was declared here
ParaGPtr pgp;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ddvgraph.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvgraph.c:210:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvgraph.c: In function 'DDV_DrawSequence':
ddvgraph.c:701:31: warning: unused variable 'pos' [-Wunused-variable]
Int2 decal=1,i,x,y,pos=0;
^~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ddvgraph.c:215:
ddvgraph.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ddvgraph.c:215:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ddvgraph.c:215:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ddvgraph.c:215:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ddvopen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvopen.c:372:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvopen.c: In function 'DDV_GetAndCheckSeqAlign':
ddvopen.c:1739:8: warning: variable 'nRet' set but not used [-Wunused-but-set-variable]
Uint2 nRet=DVV_MSG_M_OK;
^~~~
ddvopen.c: In function 'DDV_FOpenAcceptProc':
ddvopen.c:1932:11: warning: variable 'nRet' set but not used [-Wunused-but-set-variable]
Uint2 nRet=DVV_MSG_M_OK,The_entityID;
^~~~
ddvopen.c: In function 'DDV_NetOpen_okProc':
ddvopen.c:2141:8: warning: variable 'AccessType' set but not used [-Wunused-but-set-variable]
Int2 AccessType,procval;
^~~~~~~~~~
ddvopen.c: In function 'DDV_StartMainWin_Slave':
ddvopen.c:2411:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
ddvopen.c:2417:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if (!w) return(NULL);
^~
ddvopen.c: In function 'DDV_ImportBioseqDlg':
ddvopen.c:2819:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
ddvopen.c: In function 'DDV_HideDlg':
ddvopen.c:3135:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
In file included from ../include/sqnutils.h:51:0,
from ../include/udviewer.h:219,
from ddvopen.c:376:
ddvopen.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/udviewer.h:228,
from ddvopen.c:376:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ddvopen.c:377:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ddvopen.c:377:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ddvopen.c:377:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ddvopen.c:377:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ddvopen.c:2111:16: warning: 'DDV_IsInt' defined but not used [-Wunused-function]
static Boolean DDV_IsInt(CharPtr szAccess)
^~~~~~~~~
ddvopen.c:1285:13: warning: 'DDV_NoConvert' defined but not used [-Wunused-function]
static void DDV_NoConvert(ButtoN g) {
^~~~~~~~~~~~~
ddvopen.c:1272:13: warning: 'DDV_Convert' defined but not used [-Wunused-function]
static void DDV_Convert(ButtoN g) {
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ddvpanel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvpanel.c:389:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvpanel.c: In function 'DDV_CreateViewerPanel':
ddvpanel.c:1177:8: warning: variable 'cxChar' set but not used [-Wunused-but-set-variable]
Int2 cxChar,cyChar;
^~~~~~
ddvpanel.c: In function 'DDV_DispStyles_OkProc':
ddvpanel.c:1543:21: warning: unused variable 'szBuf' [-Wunused-variable]
Char szBuf[15]={""};
^~~~~
ddvpanel.c: In function 'DDV_ExportTexte':
ddvpanel.c:2799:40: warning: variable 'browse' set but not used [-Wunused-but-set-variable]
ButtoN chk2,chk3,chk4,chk5,chk6,browse,ok;
^~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvpanel.c:392:
ddvpanel.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvpanel.c:392:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvpanel.c:392:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvpanel.c:392:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ddvpanel.c:3377:13: warning: 'write_annot' defined but not used [-Wunused-function]
static void write_annot(SeqAlignPtr align)
^~~~~~~~~~~
ddvpanel.c:3296:13: warning: 'DDV_MoveRightBoundaryRight' defined but not used [-Wunused-function]
static void DDV_MoveRightBoundaryRight(IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~~~
ddvpanel.c:3290:13: warning: 'DDV_MoveRightBoundaryLeft' defined but not used [-Wunused-function]
static void DDV_MoveRightBoundaryLeft(IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~~
ddvpanel.c:3284:13: warning: 'DDV_MoveLeftBoundaryRight' defined but not used [-Wunused-function]
static void DDV_MoveLeftBoundaryRight(IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~~
ddvpanel.c:3278:13: warning: 'DDV_MoveLeftBoundaryLeft' defined but not used [-Wunused-function]
static void DDV_MoveLeftBoundaryLeft(IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~
ddvpanel.c:3272:13: warning: 'DDV_MoveRowRight' defined but not used [-Wunused-function]
static void DDV_MoveRowRight(IteM i)
^~~~~~~~~~~~~~~~
ddvpanel.c:3266:13: warning: 'DDV_MoveRowLeft' defined but not used [-Wunused-function]
static void DDV_MoveRowLeft(IteM i)
^~~~~~~~~~~~~~~
ddvpanel.c:3024:13: warning: 'DDV_DeleteRow' defined but not used [-Wunused-function]
static void DDV_DeleteRow(IteM i)
^~~~~~~~~~~~~
ddvpanel.c: In function 'DDVExportTexteOkProc':
ddvpanel.c:2647:5: warning: 'bPrintGap' may be used uninitialized in this function [-Wmaybe-uninitialized]
DDV_DumpSAPInFastaFile(&(dmp->MSA_d.pgp_l),&dob, hFile,bPrintGap);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvpanel.c: In function 'DDV_SortPGPLineNum':
ddvpanel.c:2441:9: warning: 'pgp' may be used uninitialized in this function [-Wmaybe-uninitialized]
n+=pgp->nLines;
~~~^~~~~~~~
rm -f libddvlib.a
ar cru libddvlib.a ddvclick.o ddvgraph.o ddvopen.o ddvpanel.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libddvlib.a ../lib
ranlib ../lib/libddvlib.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF corematx.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from corematx.c:135:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF dvncode.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from dvncode.c:69:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objmmdb1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmmdb1.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmmdb1.c: In function 'BiostrucAsnRead':
objmmdb1.c:90:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiostrucIdFree':
objmmdb1.c:323:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'BiostrucIdAsnRead':
objmmdb1.c:358:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucSetAsnRead':
objmmdb1.c:547:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiostrucAnnotSetAsnRead':
objmmdb1.c:716:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiostrucResidueGraphSetAsnRead':
objmmdb1.c:885:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiostrucDescrFree':
objmmdb1.c:1015:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'BiostrucDescrAsnRead':
objmmdb1.c:1059:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucHistoryAsnRead':
objmmdb1.c:1270:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:1269:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucReplaceAsnRead':
objmmdb1.c:1450:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:1449:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'VersionOfDatabase_version_of_databaseFree':
objmmdb1.c:1618:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'BiostrucSourceAsnRead':
objmmdb1.c:1652:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'VersionOfDatabase_version_of_databaseAsnRead':
objmmdb1.c:1753:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucGraphAsnRead':
objmmdb1.c:2000:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiomolDescrFree':
objmmdb1.c:2138:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'BiomolDescrAsnRead':
objmmdb1.c:2188:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueGraphAsnRead':
objmmdb1.c:2445:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'MoleculeGraphAsnRead':
objmmdb1.c:2652:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'InterResidueBondAsnRead':
objmmdb1.c:2853:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:2852:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueAsnRead':
objmmdb1.c:3033:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3032:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueGraphPntrFree':
objmmdb1.c:3172:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'ResidueGraphPntrAsnRead':
objmmdb1.c:3207:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucGraphPntrAsnRead':
objmmdb1.c:3394:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3393:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucResidueGraphSetPntrAsnRead':
objmmdb1.c:3559:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3558:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomAsnRead':
objmmdb1.c:3725:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'IntraResidueBondAsnRead':
objmmdb1.c:3916:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3915:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ChiralCenterAsnRead':
objmmdb1.c:4088:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:4087:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomPntrAsnRead':
objmmdb1.c:4276:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:4275:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomPntrSetAsnRead':
objmmdb1.c:4430:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
In file included from ../include/strimprt.h:73:0,
from objmmdb1.c:5:
objmmdb1.c: At top level:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from objmmdb1.c:5:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
objmmdb1.c: In function 'BiostrucDescrAsnRead':
objmmdb1.c:1126:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb1.c: In function 'BiomolDescrAsnRead':
objmmdb1.c:2283:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objmmdb2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmmdb2.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmmdb2.c: In function 'BiostrucModelAsnRead':
objmmdb2.c:88:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'ModelDescrFree':
objmmdb2.c:241:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'ModelDescrAsnRead':
objmmdb2.c:288:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'ModelSpaceAsnRead':
objmmdb2.c:511:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:510:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'Coordinates_coordinatesFree':
objmmdb2.c:707:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'ModelCoordinateSetAsnRead':
objmmdb2.c:741:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'Coordinates_coordinatesAsnRead':
objmmdb2.c:829:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'ReferenceFrameAsnRead':
objmmdb2.c:1060:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:1059:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'CoordinatesFree':
objmmdb2.c:1190:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'CoordinatesAsnRead':
objmmdb2.c:1228:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'AtomicCoordinatesAsnRead':
objmmdb2.c:1417:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'Surface_surfaceFree':
objmmdb2.c:1636:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'SurfaceCoordinatesAsnRead':
objmmdb2.c:1682:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:1681:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'Surface_surfaceAsnRead':
objmmdb2.c:1762:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'DensityCoordinatesAsnRead':
objmmdb2.c:2026:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'ModelSpacePointsAsnRead':
objmmdb2.c:2258:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AtomicTemperatureFactorsFree':
objmmdb2.c:2398:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'AtomicTemperatureFactorsAsnRead':
objmmdb2.c:2433:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'AtomicOccupanciesAsnRead':
objmmdb2.c:2609:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AlternateConformationIdsAsnRead':
objmmdb2.c:2753:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'ConformationEnsembleAsnRead':
objmmdb2.c:2883:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'IsotropicTemperatureFactorsAsnRead':
objmmdb2.c:3046:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AnisotropicTemperatureFactorsAsnRead':
objmmdb2.c:3212:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'TMeshAsnRead':
objmmdb2.c:3416:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'TrianglesAsnRead':
objmmdb2.c:3615:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
In file included from ../include/strimprt.h:72:0,
from objmmdb2.c:5:
objmmdb2.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from objmmdb2.c:5:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from objmmdb2.c:5:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
objmmdb2.c: In function 'ModelDescrAsnRead':
objmmdb2.c:365:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'CoordinatesAsnRead':
objmmdb2.c:1278:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'AtomicTemperatureFactorsAsnRead':
objmmdb2.c:2479:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'ModelCoordinateSetAsnRead':
objmmdb2.c:875:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c:828:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb2.c: In function 'SurfaceCoordinatesAsnRead':
objmmdb2.c:1824:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c:1761:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objmmdb3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmmdb3.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmmdb3.c: In function 'BiostrucFeatureSetAsnRead':
objmmdb3.c:87:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ChemGraphPntrsFree':
objmmdb3.c:219:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'AtomPntrsAsnRead':
objmmdb3.c:442:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ChemGraphAlignmentAsnRead':
objmmdb3.c:624:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ChemGraphInteractionAsnRead':
objmmdb3.c:821:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'SphereAsnRead':
objmmdb3.c:1020:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ConeAsnRead':
objmmdb3.c:1188:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'CylinderAsnRead':
objmmdb3.c:1368:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BrickAsnRead':
objmmdb3.c:1553:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'TransformAsnRead':
objmmdb3.c:1792:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucFeatureSetDescrFree':
objmmdb3.c:1916:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'Location_locationFree':
objmmdb3.c:2156:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'BiostrucFeatureAsnRead':
objmmdb3.c:2201:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'Property_propertyFree':
objmmdb3.c:2716:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'ColorPropAsnRead':
objmmdb3.c:2792:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'CameraAsnRead':
objmmdb3.c:2979:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucScriptAsnRead':
objmmdb3.c:3163:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionPntrsAsnRead':
objmmdb3.c:3322:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionSimilarityAsnRead':
objmmdb3.c:3639:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'OtherFeatureAsnRead':
objmmdb3.c:3815:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucMoleculePntrAsnRead':
objmmdb3.c:3988:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'MoleculePntrsAsnRead':
objmmdb3.c:4330:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ResidueExplicitPntrsAsnRead':
objmmdb3.c:4492:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ResidueIntervalPntrAsnRead':
objmmdb3.c:4659:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionCoordinatesAsnRead':
objmmdb3.c:4830:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionBoundaryFree':
objmmdb3.c:4965:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'AlignStatsAsnRead':
objmmdb3.c:5196:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RealValueAsnRead':
objmmdb3.c:5437:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ModelSpacePointAsnRead':
objmmdb3.c:5597:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'MoveFree':
objmmdb3.c:5740:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'RotMatrixAsnRead':
objmmdb3.c:5948:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'TransMatrixAsnRead':
objmmdb3.c:6180:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'GLMatrixAsnRead':
objmmdb3.c:6358:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucScriptStepAsnRead':
objmmdb3.c:6658:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
In file included from ../include/strimprt.h:72:0,
from objmmdb3.c:5:
objmmdb3.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from objmmdb3.c:5:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from objmmdb3.c:5:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
objmmdb3.c: In function 'ChemGraphPntrsAsnRead':
objmmdb3.c:306:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'BiostrucFeatureSetDescrAsnRead':
objmmdb3.c:2019:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'RegionBoundaryAsnRead':
objmmdb3.c:5059:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'MoveAsnRead':
objmmdb3.c:5820:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'RegionPntrsAsnRead':
objmmdb3.c:3456:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c:3401:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb3.c: In function 'BiostrucFeatureAsnRead':
objmmdb3.c:2365:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c:2303:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objcn3d.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objcn3d.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objcn3d.c: In function 'Cn3dStyleDictionaryAsnRead':
objcn3d.c:87:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dUserAnnotationsAsnRead':
objcn3d.c:251:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dColorAsnRead':
objcn3d.c:415:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:414:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dBackboneStyleAsnRead':
objcn3d.c:604:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:603:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dGeneralStyleAsnRead':
objcn3d.c:787:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:786:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dBackboneLabelStyleAsnRead':
objcn3d.c:969:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:968:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dStyleSettingsAsnRead':
objcn3d.c:1171:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1170:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dStyleSettingsSetAsnRead':
objcn3d.c:1573:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dStyleTableItemAsnRead':
objcn3d.c:1702:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1701:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dResidueRangeAsnRead':
objcn3d.c:1866:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1865:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dMoleculeLocationAsnRead':
objcn3d.c:2028:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dObjectLocationAsnRead':
objcn3d.c:2190:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dUserAnnotationAsnRead':
objcn3d.c:2355:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dGLMatrixAsnRead':
objcn3d.c:2546:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:2545:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dVectorAsnRead':
objcn3d.c:2833:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:2832:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dViewSettingsAsnRead':
objcn3d.c:3005:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:3004:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
In file included from ../include/mapcn3d.h:8:0,
from objcn3d.c:5:
objcn3d.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/mapcn3d.h:8:0,
from objcn3d.c:5:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/mmdbapi1.h:232,
from ../include/mmdbapi.h:92,
from mmdbapi.c:116:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mmdbapi.c: In function 'MakeAModelstruc':
mmdbapi.c:192:11: warning: unused variable 'iCount' [-Wunused-variable]
Int4 iCount = 0;
^~~~~~
mmdbapi.c:189:11: warning: unused variable 'pdnmsCount' [-Wunused-variable]
PDNMS pdnmsCount = NULL;
^~~~~~~~~~
mmdbapi.c: In function 'AddPFBSelect':
mmdbapi.c:532:11: warning: unused variable 'pmsdStruc' [-Wunused-variable]
PMSD pmsdStruc = NULL;
^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbapi1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mmdbapi1.c:294:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mmdbapi1.c: In function 'FreeAtomicModelAsnLists':
mmdbapi1.c:1037:21: warning: unused variable 'pcoThis' [-Wunused-variable]
CoordinatesPtr pcoThis = NULL;
^~~~~~~
mmdbapi1.c: In function 'FetchBS':
mmdbapi1.c:1242:13: warning: unused variable 'bIsNetwork' [-Wunused-variable]
Boolean bIsNetwork = FALSE;
^~~~~~~~~~
mmdbapi1.c: In function 'FreeSurfaceModelAsnList':
mmdbapi1.c:1627:16: warning: variable 'pvnX' set but not used [-Wunused-but-set-variable]
ValNodePtr pvnX = NULL;
^~~~
mmdbapi1.c: In function 'MakeChemGraphNodeList':
mmdbapi1.c:2343:16: warning: variable 'pvnThis' set but not used [-Wunused-but-set-variable]
ValNodePtr pvnThis = NULL;
^~~~~~~
mmdbapi1.c: In function 'DoApplyTransform':
mmdbapi1.c:2573:8: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
mmdbapi1.c: In function 'DoReverseTransform':
mmdbapi1.c:2713:8: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
mmdbapi1.c: In function 'InstBSAnnotSet':
mmdbapi1.c:2860:8: warning: unused variable 'psfsThis' [-Wunused-variable]
PSFS psfsThis = NULL;
^~~~~~~~
mmdbapi1.c:2859:22: warning: unused variable 'pbsfThis' [-Wunused-variable]
BiostrucFeaturePtr pbsfThis = NULL;
^~~~~~~~
mmdbapi1.c:2855:9: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
mmdbapi1.c: In function 'BiosToSeq':
mmdbapi1.c:2978:19: warning: unused variable 'loc1' [-Wunused-variable]
ValNodePtr loc1 = NULL;
^~~~
mmdbapi1.c:2967:22: warning: unused variable 'pbsf' [-Wunused-variable]
BiostrucFeaturePtr pbsf=NULL;
^~~~
mmdbapi1.c: In function 'fnPBSFtoPSA':
mmdbapi1.c:3174:19: warning: unused variable 'loc1' [-Wunused-variable]
ValNodePtr loc1 = NULL;
^~~~
mmdbapi1.c: In function 'BiostrToSeqAnnotSet':
mmdbapi1.c:3408:19: warning: unused variable 'loc1' [-Wunused-variable]
ValNodePtr loc1 = NULL;
^~~~
mmdbapi1.c:3397:22: warning: unused variable 'pbsf' [-Wunused-variable]
BiostrucFeaturePtr pbsf=NULL;
^~~~
mmdbapi1.c: In function 'InstallAlignedSlave':
mmdbapi1.c:3877:9: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest;
^~~~~
mmdbapi1.c:3874:9: warning: unused variable 'psfsThis' [-Wunused-variable]
PSFS psfsThis = NULL;
^~~~~~~~
mmdbapi1.c: In function 'BiostrucAddFeature':
mmdbapi1.c:4184:11: warning: variable 'ncbiVast' set but not used [-Wunused-but-set-variable]
Boolean ncbiVast = FALSE;
^~~~~~~~
mmdbapi1.c:4182:11: warning: variable 'pdbFootnote' set but not used [-Wunused-but-set-variable]
Boolean pdbFootnote = FALSE;
^~~~~~~~~~~
mmdbapi1.c:4181:11: warning: variable 'pdbSite' set but not used [-Wunused-but-set-variable]
Boolean pdbSite = FALSE;
^~~~~~~
mmdbapi1.c:4172:15: warning: unused variable 'pdvnThis' [-Wunused-variable]
DValNodePtr pdvnThis = NULL;
^~~~~~~~
mmdbapi1.c: In function 'BiostrucAsnGet':
mmdbapi1.c:5289:18: warning: variable 'aop' set but not used [-Wunused-but-set-variable]
AsnOptionPtr aop;
^~~
mmdbapi1.c: In function 'BiosToSeq':
mmdbapi1.c:3127:20: warning: 'slavesip' may be used uninitialized in this function [-Wmaybe-uninitialized]
dsp->ids->next = slavesip;
~~~~~~~~~~~~~~~^~~~~~~~~~
mmdbapi1.c: In function 'BiostrToSeqAnnotSet':
mmdbapi1.c:3559:20: warning: 'slavesip' may be used uninitialized in this function [-Wmaybe-uninitialized]
dsp->ids->next = slavesip;
~~~~~~~~~~~~~~~^~~~~~~~~~
mmdbapi1.c: In function 'InstBSAnnotSet':
mmdbapi1.c:2885:13: warning: 'iMMDBId' may be used uninitialized in this function [-Wmaybe-uninitialized]
pdnmsThis = FindLoadedBiostruc(NULL, iMMDBId);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbapi2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mmdbapi2.c:159:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mmdbapi2.c: In function 'GetAtomLocs':
mmdbapi2.c:1471:9: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (pmadThis)
^
mmdbapi2.c: In function 'AssignAtomLocId':
mmdbapi2.c:1537:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest = 0;
^~~~~
mmdbapi2.c: In function 'AssignBackBone':
mmdbapi2.c:1686:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest = 0;
^~~~~
mmdbapi2.c: In function 'AssignVirtual':
mmdbapi2.c:1790:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest = 0;
^~~~~
mmdbapi2.c: In function 'AssignIons':
mmdbapi2.c:1846:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest = 0;
^~~~~
mmdbapi2.c: In function 'MolFromPDBChain':
mmdbapi2.c:1931:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest;
^~~~~
mmdbapi2.c: In function 'SeqStringFromMol':
mmdbapi2.c:1948:9: warning: unused variable 'iTest' [-Wunused-variable]
Int4 iTest =0;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbapi3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mmdbapi3.c:207:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mmdbapi3.c: In function 'WritePDBHeader':
mmdbapi3.c:840:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(org)
^~
mmdbapi3.c:845:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
src = orgstring;
^~~
mmdbapi3.c:840:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if(org)
^
mmdbapi3.c: In function 'WritePDBRemarks':
mmdbapi3.c:1389:8: warning: unused variable 'len' [-Wunused-variable]
int len;
^~~
mmdbapi3.c:1388:9: warning: unused variable 'pcThis' [-Wunused-variable]
Char pcThis[81];
^~~~~~
mmdbapi3.c:1387:21: warning: unused variable 'pbsdrLast' [-Wunused-variable]
BiostrucDescrPtr pbsdrLast = NULL;
^~~~~~~~~
mmdbapi3.c:1386:21: warning: unused variable 'pbsdrThis' [-Wunused-variable]
BiostrucDescrPtr pbsdrThis = NULL;
^~~~~~~~~
mmdbapi3.c: In function 'WritePDBConnect':
mmdbapi3.c:1610:9: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest;
^~~~~
mmdbapi3.c: In function 'WritePDBModelList':
mmdbapi3.c:1625:10: warning: variable 'iCount' set but not used [-Wunused-but-set-variable]
Int4 iCount;
^~~~~~
mmdbapi3.c: In function 'WriteKinAtom':
mmdbapi3.c:2287:11: warning: unused variable 'pcElName' [-Wunused-variable]
CharPtr pcElName = NULL;
^~~~~~~~
mmdbapi3.c: In function 'WriteFASTAMolecule':
mmdbapi3.c:3537:9: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int4 iTest =0;
^~~~~
mmdbapi3.c: In function 'WriteKinAtom':
mmdbapi3.c:2314:12: warning: 'iTemp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (iTemp < TempsKine[(iIndex-1)]) return; /* too low */
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbapi4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/mmdbapi1.h:232,
from ../include/mmdbapi.h:92,
from mmdbapi4.c:106:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mmdbapi4.c: In function 'RefreshSurface':
mmdbapi4.c:147:10: warning: unused variable 'iVal' [-Wunused-variable]
Int4 iVal = 0;
^~~~
mmdbapi4.c: In function 'FreeCoordinatesAsnLists':
mmdbapi4.c:335:28: warning: variable 'pdcThis' set but not used [-Wunused-but-set-variable]
DensityCoordinatesPtr pdcThis = NULL;
^~~~~~~
mmdbapi4.c: In function 'FreeRedundantAsn':
mmdbapi4.c:371:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
mmdbapi4.c:370:11: warning: unused variable 'pdnmmThis' [-Wunused-variable]
PDNMM pdnmmThis = NULL;
^~~~~~~~~
mmdbapi4.c:367:22: warning: unused variable 'pbsmThis' [-Wunused-variable]
BiostrucModelPtr pbsmThis = NULL;
^~~~~~~~
mmdbapi4.c: In function 'RefreshModelAsnMem':
mmdbapi4.c:474:13: warning: unused variable 'iCoordSets' [-Wunused-variable]
Int4 iCoordSets = 0;
^~~~~~~~~~
mmdbapi4.c:465:20: warning: unused variable 'pappThis' [-Wunused-variable]
AtomPntrsPtr pappThis = NULL;
^~~~~~~~
mmdbapi4.c:464:27: warning: unused variable 'pmspThis' [-Wunused-variable]
ModelSpacePointsPtr pmspThis = NULL;
^~~~~~~~
mmdbapi4.c:463:28: warning: unused variable 'pocThis' [-Wunused-variable]
AtomicOccupanciesPtr pocThis = NULL;
^~~~~~~
mmdbapi4.c:458:34: warning: unused variable 'paciThis' [-Wunused-variable]
AlternateConformationIdsPtr paciThis = NULL;
^~~~~~~~
mmdbapi4.c: In function 'RebuildChemGraphAsn':
mmdbapi4.c:931:15: warning: unused variable 'bOK' [-Wunused-variable]
Boolean bOK = TRUE;
^~~
mmdbapi4.c: In function 'WriteASNChemGraphOnly':
mmdbapi4.c:1192:10: warning: unused variable 'iHash' [-Wunused-variable]
Int4 iHash = 0;
^~~~~
mmdbapi4.c: In function 'FreeSingleModel':
mmdbapi4.c:1336:11: warning: unused variable 'pdnml' [-Wunused-variable]
PDNML pdnml = NULL;
^~~~~
mmdbapi4.c:1332:22: warning: unused variable 'pbsmTemp' [-Wunused-variable]
BiostrucModelPtr pbsmTemp = NULL;
^~~~~~~~
mmdbapi4.c: In function 'WriteAsnModelList':
mmdbapi4.c:1505:14: warning: unused variable 'paioAIP' [-Wunused-variable]
AsnIoPtr paioAIP = NULL;
^~~~~~~
mmdbapi4.c:1502:11: warning: unused variable 'pmldThis' [-Wunused-variable]
PMLD pmldThis = NULL;
^~~~~~~~
mmdbapi4.c:1498:11: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
mmdbapi4.c:1496:22: warning: unused variable 'pbsmThis' [-Wunused-variable]
BiostrucModelPtr pbsmThis = NULL;
^~~~~~~~
mmdbapi4.c:1495:17: warning: unused variable 'pBSThis' [-Wunused-variable]
BiostrucPtr pBSThis = NULL;
^~~~~~~
mmdbapi4.c:1494:13: warning: unused variable 'bFirst' [-Wunused-variable]
Boolean bFirst = TRUE;
^~~~~~
mmdbapi4.c:1493:10: warning: unused variable 'iTest' [-Wunused-variable]
Int2 iTest = 0;
^~~~~
mmdbapi4.c: In function 'BiostrucAnnotSetToSeqAnnot':
mmdbapi4.c:1741:19: warning: unused variable 'loc1' [-Wunused-variable]
ValNodePtr loc1 = NULL;
^~~~
mmdbapi4.c: In function 'WriteAsnModelList':
mmdbapi4.c:1632:13: warning: 'bRet' may be used uninitialized in this function [-Wmaybe-uninitialized]
return bRet;
^~~~
mmdbapi4.c: In function 'BiostrucAnnotSetToSeqAnnot':
mmdbapi4.c:1872:20: warning: 'slavesip' may be used uninitialized in this function [-Wmaybe-uninitialized]
dsp->ids->next = slavesip;
~~~~~~~~~~~~~~~^~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mmdbentr.c:65:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vastsubs.c
vastsubs.c: In function 'LoadSubsetTable':
vastsubs.c:212:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%d", &ndoms);
^~~~~~~~~~~~~~~~~~~~~~~~
vastsubs.c:239:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%d", &nsubs);
^~~~~~~~~~~~~~~~~~~~~~~~
vastsubs.c:258:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%d", &j);
^~~~~~~~~~~~~~~~~~~~
vastsubs.c:287:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%8c", domid);
^~~~~~~~~~~~~~~~~~~~~~~~
vastsubs.c:296:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%d", &n);
^~~~~~~~~~~~~~~~~~~~
vastsubs.c:302:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%d %d %d", &subset[j], &grps[j], &ranks[j]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vastsubs.c:304:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "\n");
^~~~~~~~~~~~~~~~
vastsubs.c:202:16: warning: 'len' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 i, j, n, len, strindex, ndoms, nsubs;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF prunebsc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/prunebsc.h:10,
from prunebsc.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
prunebsc.c: In function 'PruneFeatureSet':
prunebsc.c:220:22: warning: variable 'bsfpDie' set but not used [-Wunused-but-set-variable]
BiostrucFeaturePtr bsfpDie, bsfp, bsfpnew = NULL;
^~~~~~~
prunebsc.c: In function 'PruneModel':
prunebsc.c:272:30: warning: variable 'mcsDie' set but not used [-Wunused-but-set-variable]
ModelCoordinateSetPtr mcs, mcsDie, mcsnew = NULL;
^~~~~~
prunebsc.c: In function 'PruneBiostruc':
prunebsc.c:559:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (vnp = ValNodeFindNext(currentbp->descr, NULL, BiomolDescr_name))
^~
prunebsc.c:574:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (vnp = ValNodeFindNext(het->descr, NULL, BiomolDescr_name))
^~
prunebsc.c:663:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (vnp = ValNodeFindNext(bsfsp->descr, NULL, BiostrucFeatureSetDescr_name))
^~
In file included from ../include/ncbi.h:62:0,
from ../include/prunebsc.h:10,
from prunebsc.c:34:
../include/ncbistr.h:339:20: warning: 'feature_name' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringICmp Nlm_StringICmp
^~~~~~~~~~~~~~
prunebsc.c:522:25: note: 'feature_name' was declared here
CharPtr chnid, hetid, feature_name;
^~~~~~~~~~~~
prunebsc.c:649:23: warning: 'pirbnew' may be used uninitialized in this function [-Wmaybe-uninitialized]
pirbnew->next = pirb;
~~~~~~~~~~~~~~^~~~~~
prunebsc.c:591:26: warning: 'currenthet' may be used uninitialized in this function [-Wmaybe-uninitialized]
currenthet->next = het;
~~~~~~~~~~~~~~~~~^~~~~
prunebsc.c:701:24: warning: 'mol_id' may be used uninitialized in this function [-Wmaybe-uninitialized]
bsmpTail->next = PruneModel(bsmp, pvnIds, mol_id);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prunebsc.c:562:9: warning: 'chnid' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*chnid == *chain)
^~~~~~
prunebsc.c:182:7: warning: 'mtype' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(mtype)
^~~~~~
prunebsc.c:173:8: note: 'mtype' was declared here
Int4 mtype, molecule_id;
^~~~~
prunebsc.c:110:7: warning: 'mtype' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(mtype)
^~~~~~
prunebsc.c:102:8: note: 'mtype' was declared here
Int4 mtype;
^~~~~
prunebsc.c:127:25: warning: 'currentbp' may be used uninitialized in this function [-Wmaybe-uninitialized]
currentbp->next = newbp;
~~~~~~~~~~~~~~~~^~~~~~~
prunebsc.c:100:38: note: 'currentbp' was declared here
MoleculeGraphPtr newbp, bp = NULL, currentbp;
^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objcdd.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objcdd.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objcdd.c: In function 'CddIdFree':
objcdd.c:53:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'CddIdAsnRead':
objcdd.c:85:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddIdSetAsnRead':
objcdd.c:248:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:245:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddIdSetAsnWrite':
objcdd.c:301:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddAsnRead':
objcdd.c:401:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddSetAsnRead':
objcdd.c:796:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:793:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddSetAsnWrite':
objcdd.c:849:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddTreeAsnRead':
objcdd.c:932:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:931:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddTreeSetAsnRead':
objcdd.c:1143:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1140:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddTreeSetAsnWrite':
objcdd.c:1196:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddPrefNodesAsnRead':
objcdd.c:1276:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1275:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddPrefNodesAsnWrite':
objcdd.c:1365:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddProjectAsnRead':
objcdd.c:1472:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddOrgRefAsnRead':
objcdd.c:1661:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1660:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddOrgRefSetAsnRead':
objcdd.c:1830:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1827:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddOrgRefSetAsnWrite':
objcdd.c:1883:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddPrefNodeDescrFree':
objcdd.c:1923:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'CddPrefNodeDescrAsnRead':
objcdd.c:1958:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddPrefNodeDescrSetAsnRead':
objcdd.c:2121:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2118:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddPrefNodeDescrSetAsnWrite':
objcdd.c:2174:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'GlobalIdAsnRead':
objcdd.c:2253:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2252:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddRepeatAsnRead':
objcdd.c:2439:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2438:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddBookRefAsnRead':
objcdd.c:2615:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2614:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddDescrSetAsnRead':
objcdd.c:3170:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:3167:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddDescrSetAsnWrite':
objcdd.c:3223:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'MatrixAsnRead':
objcdd.c:3301:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'TriangleAsnRead':
objcdd.c:3489:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'UpdateCommentFree':
objcdd.c:3625:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'UpdateCommentAsnRead':
objcdd.c:3669:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'UpdateAlignAsnRead':
objcdd.c:3873:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'RejectIdAsnRead':
objcdd.c:4047:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'RejectIdAsnWrite':
objcdd.c:4122:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'FeatureEvidenceFree':
objcdd.c:4170:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'FeatureEvidenceAsnRead':
objcdd.c:4214:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'AlignAnnotAsnRead':
objcdd.c:4419:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'AlignAnnotSetAsnRead':
objcdd.c:4587:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4584:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'AlignAnnotSetAsnWrite':
objcdd.c:4640:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'DomainParentAsnRead':
objcdd.c:4718:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4717:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'SequenceTreeAsnRead':
objcdd.c:4898:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4897:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'AlgorithmTypeAsnRead':
objcdd.c:5085:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5084:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'SeqTreeNodeAsnRead':
objcdd.c:5387:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5386:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'Children_footprintAsnRead':
objcdd.c:5572:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5571:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'NodeAnnotationAsnRead':
objcdd.c:5862:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5861:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddViewerRectAsnRead':
objcdd.c:6027:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:6026:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddViewerAsnRead':
objcdd.c:6208:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddScriptAsnRead':
objcdd.c:6382:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:6381:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
In file included from objcdd.c:6:0:
objcdd.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from objcdd.c:6:0:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from objcdd.c:7:0:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
objcdd.c: In function 'CddDescrAsnRead':
objcdd.c:2994:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cddutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cddutil.c:336:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cddutil.c: In function 'CddGetPmIds':
cddutil.c:649:17: warning: unused variable 'bRefOpen' [-Wunused-variable]
Boolean bRefOpen = FALSE;
^~~~~~~~
cddutil.c: In function 'CddGetAnnotNames':
cddutil.c:807:19: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp, vnpHead = NULL;
^~~
cddutil.c: In function 'CddCheckForRepeats':
cddutil.c:1034:7: warning: the address of 'CddHasConsensus' will always evaluate as 'true' [-Waddress]
if (!CddHasConsensus) return FALSE;
^
cddutil.c:1013:23: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddMSLDenDiagToMSLDenSeg':
cddutil.c:1663:30: warning: variable 'lasts' set but not used [-Wunused-but-set-variable]
Int4 lastm, lasts;
^~~~~
cddutil.c:1663:23: warning: variable 'lastm' set but not used [-Wunused-but-set-variable]
Int4 lastm, lasts;
^~~~~
cddutil.c: In function 'SeqAlignInform':
cddutil.c:1938:22: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddAlignInform':
cddutil.c:2125:22: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddPssmInform':
cddutil.c:2248:22: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddPosFreqInform':
cddutil.c:2306:22: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddDenDiagCposComputation':
cddutil.c:2368:33: warning: variable 'RowHead' set but not used [-Wunused-but-set-variable]
ValNodePtr newRow, RowHead;
^~~~~~~
cddutil.c:2365:25: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddCposComputation':
cddutil.c:2571:33: warning: variable 'RowHead' set but not used [-Wunused-but-set-variable]
ValNodePtr newRow, RowHead;
^~~~~~~
cddutil.c:2568:25: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddRetrieveBioseqById':
cddutil.c:3379:15: warning: unused variable 'retcode' [-Wunused-variable]
Int2 retcode = 1;
^~~~~~~
cddutil.c:3377:15: warning: unused variable 'uid' [-Wunused-variable]
Int4 uid = 0;
^~~
cddutil.c: In function 'CddCalculateTriangle':
cddutil.c:3534:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL;
^~
cddutil.c:3534:31: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL;
^~
cddutil.c: In function 'CddCalculateQuerySim':
cddutil.c:3653:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL;
^~
cddutil.c:3653:31: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL;
^~
cddutil.c: In function 'CddConsensus':
cddutil.c:3853:49: warning: variable 'm_end' set but not used [-Wunused-but-set-variable]
Int4 m_last, m_frst, s_insert, m_end;
^~~~~
cddutil.c: In function 'CddCposCompPart1':
cddutil.c:4247:25: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddGetNewIndexForThreading':
cddutil.c:4392:14: warning: unused variable 'Index' [-Wunused-variable]
Int4 i, Index=0;
^~~~~
cddutil.c: In function 'CddCposComp':
cddutil.c:4474:33: warning: variable 'RowHead' set but not used [-Wunused-but-set-variable]
ValNodePtr newRow, RowHead;
^~~~~~~
cddutil.c: In function 'CddDenDiagCposComp2KBP':
cddutil.c:4745:59: warning: variable 'RowHead' set but not used [-Wunused-but-set-variable]
ValNodePtr ColumnHead, LetterHead, newRow, RowHead, newLetter;
^~~~~~~
cddutil.c: In function 'CddDumpTaxLinks':
cddutil.c:5727:16: warning: unused variable 'txid' [-Wunused-variable]
Int4 txid = 0, gi = 0;
^~~~
cddutil.c: At top level:
cddutil.c:6267:1: warning: "/*" within comment [-Wcomment]
/*---------------------------------------------------------------------------*/
In file included from ../include/cddutil.h:205:0,
from cddutil.c:353:
../include/objcdd.h:642:37: warning: 'Children_childrenFree' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:643:37: warning: 'Children_childrenAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:644:24: warning: 'Children_childrenAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:666:38: warning: 'Children_footprintFree' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr ));
^~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:667:38: warning: 'Children_footprintNew' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:668:38: warning: 'Children_footprintAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:669:24: warning: 'Children_footprintAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from cddutil.c:353:0:
../include/cddutil.h:589:25: warning: 'CddFindSeqIdInSeqLoc' declared 'static' but never defined [-Wunused-function]
static SeqIdPtr CddFindSeqIdInSeqLoc(SeqLocPtr location);
^~~~~~~~~~~~~~~~~~~~
cddutil.c:4661:16: warning: 'CddtakeMatrixCheckpoint' defined but not used [-Wunused-function]
static Boolean CddtakeMatrixCheckpoint(compactSearchItems *compactSearch,
^~~~~~~~~~~~~~~~~~~~~~~
In file included from cddutil.c:349:0:
../include/cdd.h:343:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/cdd.h:342:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/cdd.h:341:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/cdd.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "cdd.h24";
^~~~~~~~~~~
cddutil.c: In function 'CddCopyMSLDenDiag':
cddutil.c:3015:25: warning: 'ddpTail' may be used uninitialized in this function [-Wmaybe-uninitialized]
ddpTail->next = ddpNew;
~~~~~~~~~~~~~~^~~~~~~~
cddutil.c: In function 'CddCalculateTriangle':
cddutil.c:3469:22: warning: 'pscTail' may be used uninitialized in this function [-Wmaybe-uninitialized]
pscTail->next = psc; pscTail = psc; psc = NULL;
~~~~~~~~~~~~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cddposutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cddposutil.c:119:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cddposutil.c: In function 'CddfindThreshSequences':
cddposutil.c:359:15: warning: variable 'thisId' set but not used [-Wunused-but-set-variable]
SeqIdPtr thisId; /* Ids of target sequences in current SeqAlign */
^~~~~~
cddposutil.c: In function 'CddfindDenseDiagThreshSequences':
cddposutil.c:386:16: warning: variable 'thisId' set but not used [-Wunused-but-set-variable]
SeqIdPtr thisId; /* Ids of target sequences in current SeqAlign */
^~~~~~
cddposutil.c: In function 'CddposFreqsToMatrix':
cddposutil.c:1038:45: warning: operation on '*(*(posSearch->posPrivateMatrix + (sizetype)((unsigned int)length * 4u)) + (sizetype)((unsigned int)a * 4u))' may be undefined [-Wsequence-point]
posSearch->posPrivateMatrix[length][a] = posSearch->posPrivateMatrix[length][a] = BLAST_SCORE_MIN;
cddposutil.c: In function 'CddposDenseDiagDemographics':
cddposutil.c:1094:17: warning: unused variable 'is_new_id' [-Wunused-variable]
Boolean is_new_id = FALSE;
^~~~~~~~~
cddposutil.c:1093:17: warning: unused variable 'segIndex' [-Wunused-variable]
Int4 segIndex; /*Index for which piece we are at*/
^~~~~~~~
cddposutil.c:1092:25: warning: variable 'startS' set but not used [-Wunused-but-set-variable]
Int4 startQ, startS; /*Indices into array of starting positions*/
^~~~~~
cddposutil.c:1092:17: warning: variable 'startQ' set but not used [-Wunused-but-set-variable]
Int4 startQ, startS; /*Indices into array of starting positions*/
^~~~~~
cddposutil.c:1091:17: warning: unused variable 'curId' [-Wunused-variable]
SeqIdPtr curId; /*Used to compare seq. coming from different SeqAligns*/
^~~~~
cddposutil.c: In function 'CddSetUpSearchInternalByLoc':
cddposutil.c:1246:39: warning: unused variable 'last_length_adjustment' [-Wunused-variable]
index, length, length_adjustment=0, last_length_adjustment, min_query_length;
^~~~~~~~~~~~~~~~~~~~~~
cddposutil.c: In function 'CddSetUpSearchWithReadDb':
cddposutil.c:2040:43: warning: variable 'final_db_seq' set but not used [-Wunused-but-set-variable]
Int4 final_virtual_db_seq=0, final_db_seq=0;
^~~~~~~~~~~~
cddposutil.c:2006:28: warning: unused variable 'virtual_oid_bit' [-Wunused-variable]
Uint4 oid_bit, virtual_oid_bit;
^~~~~~~~~~~~~~~
cddposutil.c:2006:19: warning: unused variable 'oid_bit' [-Wunused-variable]
Uint4 oid_bit, virtual_oid_bit;
^~~~~~~
cddposutil.c:2005:30: warning: unused variable 'virtual_mask_index' [-Wunused-variable]
Int4 mask_index, virtual_mask_index;
^~~~~~~~~~~~~~~~~~
cddposutil.c:2005:18: warning: unused variable 'mask_index' [-Wunused-variable]
Int4 mask_index, virtual_mask_index;
^~~~~~~~~~
cddposutil.c:2004:19: warning: unused variable 'alias_oidlist' [-Wunused-variable]
OIDListPtr alias_oidlist;
^~~~~~~~~~~~~
cddposutil.c:2003:19: warning: unused variable 'use_private_gilist' [-Wunused-variable]
Boolean use_private_gilist = FALSE;
^~~~~~~~~~~~~~~~~~
cddposutil.c:2000:20: warning: unused variable 'vnp' [-Wunused-variable]
ValNodePtr vnp;
^~~
cddposutil.c: In function 'CddposReadAlignment':
cddposutil.c:2226:16: warning: variable 'alignPos' set but not used [-Wunused-but-set-variable]
Int4 alignPos, queryOffset, subjectOffset, matchLength;
^~~~~~~~
In file included from ../include/cddutil.h:205:0,
from cddposutil.c:131:
cddposutil.c: At top level:
../include/objcdd.h:642:37: warning: 'Children_childrenFree' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:643:37: warning: 'Children_childrenAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:644:24: warning: 'Children_childrenAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:666:38: warning: 'Children_footprintFree' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr ));
^~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:667:38: warning: 'Children_footprintNew' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:668:38: warning: 'Children_footprintAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:669:24: warning: 'Children_footprintAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from cddposutil.c:131:0:
../include/cddutil.h:507:27: warning: 'CddReadBlastOptions' declared 'static' but never defined [-Wunused-function]
static PGPBlastOptionsPtr CddReadBlastOptions(BioseqPtr bsp, Int4 iPseudo, CharPtr matrix_name);
^~~~~~~~~~~~~~~~~~~
../include/cddutil.h:512:13: warning: 'BlastKarlinBlkCopy' declared 'static' but never defined [-Wunused-function]
static void BlastKarlinBlkCopy(BLAST_KarlinBlkPtr kbp_in,BLAST_KarlinBlkPtr kbp_out);
^~~~~~~~~~~~~~~~~~
../include/cddutil.h:516:13: warning: 'CddputMatrixKbp' declared 'static' but never defined [-Wunused-function]
static void CddputMatrixKbp(FILE *checkFile, BLAST_KarlinBlkPtr kbp,
^~~~~~~~~~~~~~~
../include/cddutil.h:518:13: warning: 'CddputMatrixMatrix' declared 'static' but never defined [-Wunused-function]
static void CddputMatrixMatrix(FILE *checkFile,
^~~~~~~~~~~~~~~~~~
../include/cddutil.h:522:16: warning: 'CddtakeMatrixCheckpoint' declared 'static' but never defined [-Wunused-function]
static Boolean CddtakeMatrixCheckpoint(compactSearchItems *compactSearch,
^~~~~~~~~~~~~~~~~~~~~~~
../include/cddutil.h:589:25: warning: 'CddFindSeqIdInSeqLoc' declared 'static' but never defined [-Wunused-function]
static SeqIdPtr CddFindSeqIdInSeqLoc(SeqLocPtr location);
^~~~~~~~~~~~~~~~~~~~
../include/cddutil.h:591:25: warning: 'CddRelocateSeqLoc' declared 'static' but never defined [-Wunused-function]
static void CddRelocateSeqLoc(SeqLocPtr location, SeqIdPtr sip, Int4 *ali);
^~~~~~~~~~~~~~~~~
../include/cddutil.h:592:25: warning: 'CddSeqLocInExpAlign' declared 'static' but never defined [-Wunused-function]
static Int4 CddSeqLocInExpAlign(SeqLocPtr location, CddExpAlignPtr eap);
^~~~~~~~~~~~~~~~~~~
../include/cddutil.h:593:25: warning: 'CddFindSeqIdInAlignAnnot' declared 'static' but never defined [-Wunused-function]
static SeqIdPtr CddFindSeqIdInAlignAnnot(AlignAnnotPtr oldannot);
^~~~~~~~~~~~~~~~~~~~~~~~
../include/cddutil.h:623:24: warning: 'HitYet' declared 'static' but never defined [-Wunused-function]
static Boolean HitYet(Int4Ptr retlist, Int4 index, Int4 i);
^~~~~~
../include/cddutil.h:649:16: warning: 'CddFixForXML' declared 'static' but never defined [-Wunused-function]
static CharPtr CddFixForXML(CharPtr pc);
^~~~~~~~~~~~
cddposutil.c:971:13: warning: 'CddfreePosFreqs' defined but not used [-Wunused-function]
static void CddfreePosFreqs(Nlm_FloatHi ** posFreqs, Int4 length)
^~~~~~~~~~~~~~~
cddposutil.c: In function 'CddposComputeSequenceWeights':
cddposutil.c:840:35: warning: 'intervalSigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
posSearch->posSigma[qplace] = intervalSigma;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
cddposutil.c:832:68: warning: 'Sigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
posSearch->posA[thisSeq] = posSearch->posRowSigma[thisSeq]/Sigma;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
cddposutil.c: In function 'CddposDemographics':
cddposutil.c:1199:24: warning: 'retrievalOffset' may be used uninitialized in this function [-Wmaybe-uninitialized]
subjectOffset = curSegs->starts[startS] - retrievalOffset;
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cddposutil.c: In function 'CddSetUpSearchWithReadDb':
cddposutil.c:1740:48: warning: 'min_query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
if( 0 != BlastComputeLengthAdjustment(1/min_query_length,
~^~~~~~~~~~~~~~~~~
cddposutil.c:1246:63: note: 'min_query_length' was declared here
index, length, length_adjustment=0, last_length_adjustment, min_query_length;
^~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF objmime.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmime.c:73:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmime.c: In function 'NcbiMimeAsn1Free':
objmime.c:123:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'NcbiMimeAsn1AsnRead':
objmime.c:170:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'Data_dataFree':
objmime.c:377:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'EntrezGeneralAsnRead':
objmime.c:423:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c:422:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'Data_dataAsnRead':
objmime.c:517:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'BiostrucAlignAsnRead':
objmime.c:791:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucAlignSeqAsnRead':
objmime.c:1016:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucSeqAsnRead':
objmime.c:1208:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucSeqsAsnRead':
objmime.c:1402:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'SeqAlignData_seq_align_dataFree':
objmime.c:1599:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'BiostrucSeqsAlignsCddAsnRead':
objmime.c:1633:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'SeqAlignData_seq_align_dataAsnRead':
objmime.c:1720:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'BundleSeqsAlignsAsnRead':
objmime.c:1954:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
In file included from ../include/mapmime.h:4:0,
from objmime.c:78:
objmime.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/mapmime.h:4:0,
from objmime.c:78:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/mapmime.h:6:0,
from objmime.c:78:
../include/objcdd.h:642:37: warning: 'Children_childrenFree' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:643:37: warning: 'Children_childrenAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:644:24: warning: 'Children_childrenAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:666:38: warning: 'Children_footprintFree' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr ));
^~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:667:38: warning: 'Children_footprintNew' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:668:38: warning: 'Children_footprintAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:669:24: warning: 'Children_footprintAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~
objmime.c: In function 'NcbiMimeAsn1AsnRead':
objmime.c:232:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c: In function 'EntrezGeneralAsnRead':
objmime.c:579:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c:516:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmime.c: In function 'BiostrucSeqsAlignsCddAsnRead':
objmime.c:1766:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c:1719:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF strucapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from strucapi.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdalgs.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdatd.c
thrdatd.c: In function 'atd':
thrdatd.c:859:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) printf("%d ",sai->al[i]); printf("sai->al\n");
^~~
thrdatd.c:859:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) printf("%d ",sai->al[i]); printf("sai->al\n");
^~~~~~
thrdatd.c:860:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<sai->nmt;i++) printf("%d ",sai->sq[i]); printf("sai->sq\n");
^~~
thrdatd.c:860:51: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<sai->nmt;i++) printf("%d ",sai->sq[i]); printf("sai->sq\n");
^~~~~~
thrdatd.c:862:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) printf("%d ",sli->no[i]); printf("sli->no\n");
^~~
thrdatd.c:862:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) printf("%d ",sli->no[i]); printf("sli->no\n");
^~~~~~
thrdatd.c:863:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) printf("%d ",sli->co[i]); printf("sli->co\n");
^~~
thrdatd.c:863:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) printf("%d ",sli->co[i]); printf("sli->co\n");
^~~~~~
thrdatd.c:864:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<sli->nlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n");
^~~
thrdatd.c:864:51: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<sli->nlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n");
^~~~~~
thrdatd.c:865:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<sli->nmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n");
^~~
thrdatd.c:865:51: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<sli->nmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n");
^~~~~~
thrdatd.c:1014:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(k=0;k<nsc;k++) printf("%d ",sai->al[k]); printf("sai->al\n");
^~~
thrdatd.c:1014:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(k=0;k<nsc;k++) printf("%d ",sai->al[k]); printf("sai->al\n");
^~~~~~
thrdatd.c:1015:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(k=0;k<nmt;k++) printf("%d ",sai->sq[k]); printf("sai->sq\n");
^~~
thrdatd.c:1015:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(k=0;k<nmt;k++) printf("%d ",sai->sq[k]); printf("sai->sq\n");
^~~~~~
thrdatd.c:1017:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) printf("%d ",sli->no[i]); printf("sli->no\n");
^~~
thrdatd.c:1017:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) printf("%d ",sli->no[i]); printf("sli->no\n");
^~~~~~
thrdatd.c:1018:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) printf("%d ",sli->co[i]); printf("sli->co\n");
^~~
thrdatd.c:1018:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) printf("%d ",sli->co[i]); printf("sli->co\n");
^~~~~~
thrdatd.c:1019:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n");
^~~
thrdatd.c:1019:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n");
^~~~~~
thrdatd.c:1020:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n");
^~~
thrdatd.c:1020:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n");
^~~~~~
thrdatd.c:1244:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) free(spe->gss[i]); free(spe->gss);
^~~
thrdatd.c:1244:39: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) free(spe->gss[i]); free(spe->gss);
^~~~
thrdatd.c:1251:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<ndi; i++) free(spn->nrr[i]); free(spn->nrr);
^~~
thrdatd.c:1251:41: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<ndi; i++) free(spn->nrr[i]); free(spn->nrr);
^~~~
thrdatd.c:1255:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<ndi; i++) free(spn->nrp[i]); free(spn->nrp);
^~~
thrdatd.c:1255:41: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<ndi; i++) free(spn->nrp[i]); free(spn->nrp);
^~~~
thrdatd.c:1259:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<ndi; i++) free(spn->nrf[i]); free(spn->nrf);
^~~
thrdatd.c:1259:41: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<ndi; i++) free(spn->nrf[i]); free(spn->nrf);
^~~~
thrdatd.c:1260:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<ndi; i++) free(spn->frf[i]); free(spn->frf);
^~~
thrdatd.c:1260:41: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<ndi; i++) free(spn->frf[i]); free(spn->frf);
^~~~
thrdatd.c:201:8: warning: variable 'hh' set but not used [-Wunused-but-set-variable]
float hh;
^~
thrdatd.c:198:6: warning: variable 'rf' set but not used [-Wunused-but-set-variable]
int rf; /* Reference position for a core element */
^~
thrdatd.c:188:14: warning: unused variable 'm' [-Wunused-variable]
int i,j,k,l,m,n; /* Counters */
^
thrdatd.c:188:12: warning: unused variable 'l' [-Wunused-variable]
int i,j,k,l,m,n; /* Counters */
^
thrdatd.c:171:6: warning: variable 'nrp' set but not used [-Wunused-but-set-variable]
int nrp; /* Number of residue-peptide contacts in motif */
^~~
thrdatd.c:170:6: warning: variable 'nrr' set but not used [-Wunused-but-set-variable]
int nrr; /* Number of residue-residue contacts in motif */
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdbwfi.c
thrdbwfi.c: In function 'bwfi':
thrdbwfi.c:114:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
thrdbwfi.c:102:13: warning: 'nt' may be used uninitialized in this function [-Wmaybe-uninitialized]
ct=ttb->mx; for(i=0; i<=nt; i++) {
^~~
thrdbwfi.c:89:20: warning: 'nz' may be used uninitialized in this function [-Wmaybe-uninitialized]
cw=0.; ct=ttb->mx; for(i=0; i<=nz; i++) {
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdcpal.c
thrdcpal.c: In function 'cpal':
thrdcpal.c:210:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdcpll.c
thrdcpll.c: In function 'cpll':
thrdcpll.c:74:5: warning: variable 'nrt' set but not used [-Wunused-but-set-variable]
int nrt; /* Number of residue types */
^~~
thrdcpll.c:229:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
thrdcpll.c:220:15: warning: 'r2' may be used uninitialized in this function [-Wmaybe-uninitialized]
cl->rf.t2[k]=r2;
~~~~~~~~~~~~^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdcprl.c
thrdcprl.c: In function 'cprl':
thrdcprl.c:261:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdcxei.c
thrdcxei.c: In function 'cxei':
thrdcxei.c:94:15: warning: variable 'ms' set but not used [-Wunused-but-set-variable]
int ntot, ms;
^~
thrdcxei.c:205:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrddgri.c
thrddgri.c: In function 'g':
thrddgri.c:72:5: warning: variable 's0' set but not used [-Wunused-but-set-variable]
int s0;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdrsmp.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdsal0.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdsalr.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdsalu.c
thrdsalu.c: In function 'salu':
thrdsalu.c:83:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdsgoi.c
thrdsgoi.c: In function 'sgoi':
thrdsgoi.c:98:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<nsc; i++) si[i]=i; break; }
^~~
thrdsgoi.c:98:35: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<nsc; i++) si[i]=i; break; }
^~~~~
thrdsgoi.c:115:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<nsc; i++) to[i]=0; break; }
^~~
thrdsgoi.c:115:33: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<nsc; i++) to[i]=0; break; }
^~~~~
thrdsgoi.c:119:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<nsc; i++) to[i]=1; break; }
^~~
thrdsgoi.c:119:33: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<nsc; i++) to[i]=1; break; }
^~~~~
thrdsgoi.c:123:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdslo0.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdslor.c
thrdslor.c: In function 'slor':
thrdslor.c:90:6: warning: 'mp' may be used uninitialized in this function [-Wmaybe-uninitialized]
int *mp; /* Motif-derived loop length limits */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdslou.c
thrdslou.c: In function 'slou':
thrdslou.c:114:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdspci.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdspea.c
thrdspea.c: In function 'spea':
thrdspea.c:91:9: warning: variable 'nrt' set but not used [-Wunused-but-set-variable]
int nrt; /* Number of residue types in potential */
^~~
thrdspea.c:189:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdspel.c
thrdspel.c: In function 'spel':
thrdspel.c:88:9: warning: variable 'nrt' set but not used [-Wunused-but-set-variable]
int nrt; /* Number of residue types in potential */
^~~
thrdspel.c:188:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdspni.c
thrdspni.c: In function 'spni':
thrdspni.c:238:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdttb0.c
thrdttb0.c: In function 'ttb0':
thrdttb0.c:75:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdttbi.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF thrdzsc.c
thrdzsc.c: In function 'zsc':
thrdzsc.c:107:7: warning: unused variable 'gs' [-Wunused-variable]
int g,gs;
^~
thrdzsc.c:102:18: warning: unused variable 'zsc' [-Wunused-variable]
float tg,tgp,tgm,zsc; /* Energy of shuffled sequence */
^~~
thrdzsc.c:95:5: warning: unused variable 'ps' [-Wunused-variable]
int ps,ms,cs,
^~
thrdzsc.c:80:5: warning: unused variable 'temp' [-Wunused-variable]
int temp; /* Random index of the query sequence */
^~~~
thrdzsc.c:79:2: warning: unused variable 'kk' [-Wunused-variable]
kk,itr,ii,jj; /* Counters */
^~
thrdzsc.c:369:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
thrdzsc.c:357:39: warning: 'tg_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
ttb->zsc[i_max]=ScalingFactor*(tg_max-avg)/disp;
~~~~~~~^~~~~
rm -f libncbimmdb.a
ar cru libncbimmdb.a corematx.o dvncode.o objmmdb1.o objmmdb2.o objmmdb3.o objcn3d.o mmdbapi.o mmdbapi1.o mmdbapi2.o mmdbapi3.o mmdbapi4.o mmdbentr.o vastsubs.o prunebsc.o objcdd.o cddutil.o cddposutil.o objmime.o strucapi.o thrdalgs.o thrdatd.o thrdbwfi.o thrdcpal.o thrdcpll.o thrdcprl.o thrdcxei.o thrddgri.o thrdrsmp.o thrdsal0.o thrdsalr.o thrdsalu.o thrdsgoi.o thrdslo0.o thrdslor.o thrdslou.o thrdspci.o thrdspea.o thrdspel.o thrdspni.o thrdttb0.o thrdttbi.o thrdzsc.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbimmdb.a ../lib
ranlib ../lib/libncbimmdb.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF csim.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from csim.c:74:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
csim.c: In function 'set_pam_200':
csim.c:163:29: warning: missing braces around initializer [-Wmissing-braces]
static Int2 wgts[23][23] = { /* the PAM200 matrix */
^
csim.c:163:29: note: (near initialization for 'wgts')
csim.c:196:9: warning: array subscript has type 'char' [-Wchar-subscripts]
V[achars[i]][achars[j]]=10*(wgts[i][j]);
^
csim.c:196:20: warning: array subscript has type 'char' [-Wchar-subscripts]
V[achars[i]][achars[j]]=10*(wgts[i][j]);
^
csim.c: In function 'set_pam_file':
csim.c:228:13: warning: array subscript has type 'char' [-Wchar-subscripts]
V[alph[i]][alph[j]]=(Int2)(10*weight);
^
csim.c:228:22: warning: array subscript has type 'char' [-Wchar-subscripts]
V[alph[i]][alph[j]]=(Int2)(10*weight);
^
csim.c: In function 'big_pass':
csim.c:668:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[i]];
^
csim.c:692:23: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i, j, c, p+va[B[j]]) /* diagonal */
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c: In function 'diff1':
csim.c:799:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[1]];
^
csim.c:805:21: warning: array subscript has type 'char' [-Wchar-subscripts]
{ c = va[B[j]] - ( GAP(j-1) + GAP(N-j) );
^
csim.c:849:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[i]];
^
csim.c:853:43: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i+(s_ptr->I), (s_ptr->J)+j, c, s+v[A[i]][B[j]])
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:853:49: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i+(s_ptr->I), (s_ptr->J)+j, c, s+v[A[i]][B[j]])
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:874:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[i+1]];
^
csim.c:878:43: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i+1+s_ptr->I, j+1+s_ptr->J, c, s+v[A[i+1]][B[j+1]])
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:878:51: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i+1+s_ptr->I, j+1+s_ptr->J, c, s+v[A[i+1]][B[j+1]])
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:893:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (c > midc || CC[j] != DD[j] && RR[j] == SS[j])
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
csim.c: In function 'locate':
csim.c:974:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[i]];
^
csim.c:991:23: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i, j, c, p+va[B[j]]) /* diagonal */
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:1030:14: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[(plist->m1)]];
^
csim.c:1043:33: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG((plist->m1), j, c, p+va[B[j]]) /* diagonal */
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:1061:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~~~~~~^~~~~~~~~~
csim.c:1062:44: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| fi > rl && fj > cl ) )
~~~~~~~~^~~~~~~~~~
csim.c:1071:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~~~~~~^~~~~~~~~~
csim.c:1072:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| fi > rl && fj > cl ) )
~~~~~~~~^~~~~~~~~~
csim.c:1084:14: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[B[(plist->n1)]];
^
csim.c:1110:40: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i, (plist->n1), c, p+va[A[i]])
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:1128:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~~~~~~^~~~~~~~~~
csim.c:1129:29: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| fi > rl && fj > cl ) )
~~~~~~~~^~~~~~~~~~
csim.c:1138:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~~~~~~^~~~~~~~~~
csim.c:1139:47: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| fi > rl && fj > cl ) )
~~~~~~~~^~~~~~~~~~
csim.c:1144:29: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ( (plist->m1) == 1 && (plist->n1) == 1 || no_cross(flag, plist, &rl, &cl) )
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
csim.c: In function 'small_pass':
csim.c:1186:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[i]];
^
csim.c:1212:23: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i, j, c, p+va[B[j]]) /* diagonal */
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c: In function 'display':
csim.c:1360:5: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (i < M || j < N)
^
csim.c: In function 'set_pam_file':
csim.c:227:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%f", &weight); /**get the matrix**/
^~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
csim.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: csim.c,v 6.2 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
csim.c: In function 'SIM':
csim.c:1071:62: warning: 'dj' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~^~~~
csim.c:928:23: note: 'dj' was declared here
register Int4 di, dj; /* end-point associated with d */
^~
csim.c:1071:51: warning: 'di' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~^~~~
csim.c:928:19: note: 'di' was declared here
register Int4 di, dj; /* end-point associated with d */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF db_slist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/list.h:56,
from db_slist.c:97:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
db_slist.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: db_slist.c,v 6.2 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF dust.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from dust.c:102:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dust.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: dust.c,v 6.5 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_dust.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from blast_dust.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_dust.c:39:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF falign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from falign.c:92:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
falign.c: In function 'fbld_table':
falign.c:490:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*++q];
^
falign.c:494:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'bbld_table':
falign.c:517:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*--q];
^
falign.c:521:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'rcbld_table':
falign.c:544:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*--q];
^
falign.c:548:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'ex_table':
falign.c:567:42: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'free_all':
falign.c:668:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = cdiag_prev[l]) {
^~
falign.c: In function 'scan':
falign.c:688:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*++q];
^
falign.c:694:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c:710:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = diag_prev[len1+len2-1-pos]) {
^~
falign.c:719:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df=diag_prev[l]) {
^~
falign.c: In function 'fscan':
falign.c:763:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*++q];
^
falign.c:769:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'bscan':
falign.c:794:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*--q];
^
falign.c:800:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'rfscan':
falign.c:870:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*++q];
^
falign.c:876:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c:881:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = diag_prev[len1+se2-pos]) {
^~
falign.c:889:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = diag_prev[len1+se2-pos]) {
^~
falign.c: In function 'trcscan':
falign.c:1476:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*--q];
^
falign.c:1482:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'rclocal':
falign.c:1547:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = diag_prev[ocur_diag]) {
^~
falign.c: In function 'enterS':
falign.c:1897:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (s = findS(f->bgf)) {
^~
falign.c: In function 'local':
falign.c:1958:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = diag_prev[cur_diag]) {
^~
falign.c: In function 'align':
falign.c:1999:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = cdiag_prev[cur_diag]) {
^~
falign.c: In function 'calign':
falign.c:2054:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = cdiag_prev[cur_diag]) {
^~
falign.c: In function 'malign':
falign.c:2109:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = cdiag_prev[cur_diag]) {
^~
At top level:
falign.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: falign.c,v 6.3 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF g_any.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from g_any.c:89:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
g_any.c: In function 'k_align':
g_any.c:212:10: warning: array subscript has type 'char' [-Wchar-subscripts]
va = vv[A[i+1]];
^
g_any.c:229:26: warning: array subscript has type 'char' [-Wchar-subscripts]
if (j < J2) c = s + va[B[j+1]];
^
g_any.c:319:10: warning: array subscript has type 'char' [-Wchar-subscripts]
b2 = PP[t1][b1];
^
g_any.c:322:10: warning: array subscript has type 'char' [-Wchar-subscripts]
t2 = PT[t1][b1];
^
g_any.c: In function 'z_ALIGN':
g_any.c:367:7: warning: variable 'check_score' set but not used [-Wunused-but-set-variable]
Int4 check_score;
^~~~~~~~~~~
g_any.c: In function 'CHECK_SCORE':
g_any.c:492:13: warning: array subscript has type 'char' [-Wchar-subscripts]
score = vv[A[++i]][B[++j]] + score;
^
g_any.c:492:21: warning: array subscript has type 'char' [-Wchar-subscripts]
score = vv[A[++i]][B[++j]] + score;
^
At top level:
g_any.c:428:35: warning: 'CLINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:428:24: warning: 'BLINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:428:13: warning: 'ALINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: g_any.c,v 6.5 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF sim2.c
sim2.c: In function 'SIM2':
sim2.c:19:16: warning: unused variable 'compB' [-Wunused-variable]
CharPtr A, B, compB = NULL;
^~~~~
sim2.c:17:26: warning: unused variable 'sapC' [-Wunused-variable]
SeqAlignPtr sap = NULL, sapC=NULL, out_sap, out_sapC;
^~~~
At top level:
sim2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: sim2.c,v 6.1 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF sim3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from sim3.c:28:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sim3.c: In function 'locate':
sim3.c:103:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*p++];
^
sim3.c:105:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*p++];
^
sim3.c:113:48: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*p++];
^
sim3.c:115:57: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*p++];
^
sim3.c:129:48: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*p++];
^
sim3.c:133:57: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*p++];
^
sim3.c:152:45: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode1 = ((ecode1 & mask) << 2) + encoding[*q++];
^
sim3.c:155:57: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*p++];
^
At top level:
sim3.c:1067:16: warning: 'is_end_seg' defined but not used [-Wunused-function]
static Boolean is_end_seg(EditScriptPtr curr, EditScriptPtr head)
^~~~~~~~~~
sim3.c:1056:13: warning: 'get_current_pos' defined but not used [-Wunused-function]
static Int4 get_current_pos(Int4Ptr pos, Int4 length)
^~~~~~~~~~~~~~~
sim3.c:1048:13: warning: 'get_start_pos' defined but not used [-Wunused-function]
static Int4 get_start_pos(SeqLocPtr slp)
^~~~~~~~~~~~~
sim3.c:806:13: warning: 'Print_Script' defined but not used [-Wunused-function]
static void Print_Script(EditScriptPtr head, Int4 M, Int4 N, CharPtr A, CharPtr B)
^~~~~~~~~~~~
sim3.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: sim3.c,v 6.2 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
sim3.c: In function 'locate':
sim3.c:230:17: warning: 'paired_bj' may be used uninitialized in this function [-Wmaybe-uninitialized]
*j2 = paired_bj+1;
~~~~~~~~~^~
sim3.c:229:6: warning: 'paired_fj' may be used uninitialized in this function [-Wmaybe-uninitialized]
*j1 = paired_fj;
~~~~^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF sim4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from sim4.c:18:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sim4.c: In function 'sim4x':
sim4.c:630:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while(i1 = sgp->Blist[i].next) {
^~~~~
sim4.c: In function 'greedy':
sim4.c:1770:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (row == 0 && col == 0)
^
sim4.c:1794:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (row == 0)
^
sim4.c:1838:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (col == 0)
^
sim4.c:1962:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (row == m && col == n)
^
sim4.c:1991:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (row == m)
^
sim4.c:2037:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (col == n)
^
sim4.c: In function 'DISPLAY':
sim4.c:2625:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (a >= ALINE+50 || i >= M && j >= N)
~~~~~~~^~~~~~~~~
At top level:
sim4.c:2592:13: warning: 'DISPLAY' defined but not used [-Wunused-function]
static void DISPLAY(Int1 A[], Int1 B[], Int4 M, Int4 N, Int4 S[], Int4 AP, Int4 BP)
^~~~~~~
sim4.c:2563:13: warning: 'S2A' defined but not used [-Wunused-function]
static void S2A(EditScriptPtr head, Int4Ptr S)
^~~
sim4.c:2499:13: warning: 'Print_Script' defined but not used [-Wunused-function]
static void Print_Script(EditScriptPtr head, Int4 M, Int4 N, data_t *data)
^~~~~~~~~~~~
sim4.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: sim4.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
sim4.c: In function 'locate':
sim4.c:2919:19: warning: 'paired_bj' may be used uninitialized in this function [-Wmaybe-uninitialized]
*j2 = paired_bj + 1;
~~~~~~~~~~^~~
sim4.c:2918:7: warning: 'paired_fj' may be used uninitialized in this function [-Wmaybe-uninitialized]
*j1 = paired_fj;
~~~~^~~~~~~~~~~
sim4.c: In function 'greedy.isra.12':
sim4.c:2112:37: warning: 'forth' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (m-min_row[back]>=max_row[forth]) {
^
sim4.c:2112:22: warning: 'back' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (m-min_row[back]>=max_row[forth]) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF simutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from simutil.c:103:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
simutil.c: In function 'make_align':
simutil.c:495:9: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
At top level:
simutil.c:848:16: warning: 'is_alu_seq' defined but not used [-Wunused-function]
static Boolean is_alu_seq(CharPtr name)
^~~~~~~~~~
simutil.c:814:16: warning: 're_cal_score' defined but not used [-Wunused-function]
static FloatHi re_cal_score(RecordEndsPtr o_rep, RecordEndsPtr n_rep)
^~~~~~~~~~~~
simutil.c:344:17: warning: 'convert' defined but not used [-Wunused-function]
static ScorePtr convert(Int4Ptr x, Int4Ptr y, Int4Ptr start, Int4Ptr length, Int4 n, SeqLocPtr locx, SeqLocPtr locy, Int2Ptr numseg, FloatHiPtr SegScores)
^~~~~~~
simutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: simutil.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF slist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/list.h:56,
from slist.c:101:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
slist.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: slist.c,v 6.2 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF sec.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from sec.c:67:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sec.c: In function 'Region':
sec.c:268:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:268:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:292:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:292:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:321:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:321:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:345:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:345:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:428:35: warning: array subscript has type 'char' [-Wchar-subscripts]
diag_score = diag_score + V[seq1[i]][seq2[j]];
^
sec.c:428:44: warning: array subscript has type 'char' [-Wchar-subscripts]
diag_score = diag_score + V[seq1[i]][seq2[j]];
^
At top level:
sec.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: sec.c,v 6.1 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
sec.c: In function 'Region':
sec.c:504:11: warning: 'old_l' may be used uninitialized in this function [-Wmaybe-uninitialized]
LB[i] = old_l;
~~~~~~^~~~~~~
sec.c:72:37: warning: 'ppj' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Min(x,y) ((x) <= (y) ? (x) : (y))
^
sec.c:172:20: note: 'ppj' was declared here
Int4 pi, pj, ppi, ppj;
^~~
sec.c:172:15: warning: 'ppi' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 pi, pj, ppi, ppj;
^~~
sec.c:172:7: warning: 'pi' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 pi, pj, ppi, ppj;
^~
sec.c:502:10: warning: 'ej' may be used uninitialized in this function [-Wmaybe-uninitialized]
tr = Min(cj + Width, ej);
^
sec.c:163:15: warning: 'ei' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 bi, bj, ei, ej, t;
^~
sec.c:71:37: warning: 'bj' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Max(x,y) ((x) >= (y) ? (x) : (y))
^
sec.c:163:11: note: 'bj' was declared here
Int4 bi, bj, ei, ej, t;
^~
sec.c:462:16: warning: 'bi' may be used uninitialized in this function [-Wmaybe-uninitialized]
MemFree(LB+bi);
^
sec.c:463:16: warning: 'RB' may be used uninitialized in this function [-Wmaybe-uninitialized]
MemFree(RB+bi);
~~^~~
sec.c:462:16: warning: 'LB' may be used uninitialized in this function [-Wmaybe-uninitialized]
MemFree(LB+bi);
~~^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF tfuns.c
tfuns.c: In function 'find_orf':
tfuns.c:846:26: warning: unused variable 'into' [-Wunused-variable]
IntFuzzPtr infrom=NULL, into=NULL;
^~~~
tfuns.c:846:13: warning: unused variable 'infrom' [-Wunused-variable]
IntFuzzPtr infrom=NULL, into=NULL;
^~~~~~
At top level:
tfuns.c:956:13: warning: 'find_orf_from_circle' defined but not used [-Wunused-function]
static void find_orf_from_circle (SeqPortPtr spp, Boolean flagIsCircle,
^~~~~~~~~~~~~~~~~~~~
tfuns.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: tfuns.c,v 6.14 2007/10/10 16:10:17 bollin Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF toasn3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/gather.h:166,
from toasn3.c:10:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
toasn3.c: In function 'FindOrg':
toasn3.c:1311:17: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
toasn3.c: In function 'CheckQualsWithComm':
toasn3.c:1592:18: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toasn3.c: In function 'CheckQuals':
toasn3.c:1629:18: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toasn3.c: In function 'CountSourceFeat':
toasn3.c:2415:13: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
toasn3.c:2406:19: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
toasn3.c: In function 'TASNTrimInternalSemicolons':
toasn3.c:3986:12: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
CharPtr tmp;
^~~
toasn3.c: In function 'ImpFeatToProtRef':
toasn3.c:4672:13: warning: variable 'lfree' set but not used [-Wunused-but-set-variable]
Boolean lfree = FALSE, partial5, partial3;
^~~~~
toasn3.c: In function 'RemovePeptideImpFeats':
toasn3.c:4967:24: warning: variable 'ifp' set but not used [-Wunused-but-set-variable]
ImpFeatPtr ifp;
^~~
At top level:
toasn3.c:1572:16: warning: 'GetQualValue' defined but not used [-Wunused-function]
static CharPtr GetQualValue(GBQualPtr gbqual, CharPtr qual)
^~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from toasn3.c:19:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
toasn3.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: toasn3.c,v 6.133 2012/06/04 20:04:10 kans Exp $";
^~~~~
toasn3.c: In function 'GetOriginalBeforeAdjustment':
toasn3.c:4185:29: warning: 'last' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (last != NULL && last->choice != SEQLOC_INT) /* this is too weird */
~~~~^~~~~~~~
toasn3.c: In function 'FixNucProtSet':
toasn3.c:2057:21: warning: 'bseg' may be used uninitialized in this function [-Wmaybe-uninitialized]
bseg->descr = descr;
~~~~~~~~~~~~^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF toporg.c
toporg.c: In function 'ChkSegset':
toporg.c:62:51: warning: variable 'is_title' set but not used [-Wunused-but-set-variable]
Boolean is_org = FALSE, is_modif = FALSE, is_title = FALSE;
^~~~~~~~
toporg.c:61:17: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toporg.c:58:17: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
toporg.c:53:17: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp = NULL, set_vnp = NULL, upd_date_vnp = NULL;
^~~
toporg.c: In function 'ChkNucProt':
toporg.c:594:51: warning: variable 'is_title' set but not used [-Wunused-but-set-variable]
Boolean is_org = FALSE, is_modif = FALSE, is_title = FALSE;
^~~~~~~~
toporg.c: In function 'StripBSfromParts':
toporg.c:1280:17: warning: variable 'empty' set but not used [-Wunused-but-set-variable]
Boolean empty;
^~~~~
toporg.c:1279:17: warning: variable 'bsmp' set but not used [-Wunused-but-set-variable]
BSMapPtr bsmp;
^~~~
toporg.c:1278:29: warning: variable 'set_vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr descr, vnp, set_vnp;
^~~~~~~
toporg.c: In function 'MapsToGenref':
toporg.c:1944:17: warning: variable 'loc' set but not used [-Wunused-but-set-variable]
SeqLocPtr loc;
^~~
toporg.c:1939:17: warning: variable 'descr' set but not used [-Wunused-but-set-variable]
ValNodePtr descr = NULL, head, last, vnp;
^~~~~
toporg.c: In function 'FindOldLineage':
toporg.c:2521:17: warning: variable 'lineage' set but not used [-Wunused-but-set-variable]
CharPtr lineage;
^~~~~~~
toporg.c: In function 'ArePubsMergeableForFig':
toporg.c:4461:36: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
|| !cgp_fig->serial_number != cgp_nofig->serial_number) {
^~
toporg.c: In function 'StripBadTitleFromProteinProducts':
toporg.c:4968:22: warning: variable 'tech' set but not used [-Wunused-but-set-variable]
Uint1 tech;
^~~~
At top level:
toporg.c:3010:13: warning: 'BarCodeTechToKeyword' defined but not used [-Wunused-function]
static void BarCodeTechToKeyword (BioseqPtr bsp, Pointer userdata)
^~~~~~~~~~~~~~~~~~~~
toporg.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: toporg.c,v 6.197 2012/05/10 21:20:48 kans Exp $";
^~~~~
toporg.c: In function 'MergeEquivCitSubs':
toporg.c:3782:7: warning: 'csp1' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (DateMatch (csp1->date, csp2->date, FALSE) != 0) return FALSE;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
toporg.c:3802:18: note: 'csp1' was declared here
CitSubPtr csp1, csp2;
^~~~
toporg.c: In function 'CheckMaps':
toporg.c:1715:11: warning: 'to' may be used uninitialized in this function [-Wmaybe-uninitialized]
sip->to = to;
~~~~~~~~^~~~
toporg.c:1696:24: note: 'to' was declared here
Int4 from, to;
^~
toporg.c:1714:13: warning: 'from' may be used uninitialized in this function [-Wmaybe-uninitialized]
sip->from = from;
~~~~~~~~~~^~~~~~
toporg.c:1696:18: note: 'from' was declared here
Int4 from, to;
^~~~
toporg.c: In function 'ConvertSegSetToDeltaSeq':
toporg.c:6566:3: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqMgrClearFeatureIndexes (entityID, NULL);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF pobutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from ../include/pobutil.h:7,
from pobutil.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pobutil.c: In function 'build_repeat_feat':
pobutil.c:187:7: warning: unused variable 'c' [-Wunused-variable]
Char c='%';
^
pobutil.c: In function 'merge_StdSeg':
pobutil.c:1033:7: warning: variable 'start_1' set but not used [-Wunused-but-set-variable]
Int4 start_1, stop_1, start_2, stop_2;
^~~~~~~
pobutil.c:1031:7: warning: unused variable 'overlap' [-Wunused-variable]
Int4 overlap = -1;
^~~~~~~
In file included from ../include/ncbi.h:59:0,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from ../include/pobutil.h:7,
from pobutil.c:3:
pobutil.c: In function 'FindHumanRepeats':
../include/ncbimem.h:191:21: warning: 'memset' used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args]
#define Nlm_MemSet memset
^
../include/ncbimem.h:210:17: note: in expansion of macro 'Nlm_MemSet'
#define MemSet Nlm_MemSet
^~~~~~~~~~
pobutil.c:2380:2: note: in expansion of macro 'MemSet'
MemSet((Pointer) (&tmp), sizeof(ValNode), 0);
^~~~~~
../include/ncbimem.h:191:21: warning: 'memset' used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args]
#define Nlm_MemSet memset
^
../include/ncbimem.h:210:17: note: in expansion of macro 'Nlm_MemSet'
#define MemSet Nlm_MemSet
^~~~~~~~~~
pobutil.c:2381:2: note: in expansion of macro 'MemSet'
MemSet((Pointer) (&si), sizeof(SeqInt), 0);
^~~~~~
pobutil.c: In function 'AluFeat':
pobutil.c:2431:10: warning: variable 'my_userdata' set but not used [-Wunused-but-set-variable]
Pointer my_userdata;
^~~~~~~~~~~
At top level:
pobutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: pobutil.c,v 6.10 2007/05/07 13:30:54 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF stsutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from stsutil.c:88:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
stsutil.c: In function 'InitSTSSearch_r':
stsutil.c:270:10: warning: unused variable 'StsCount' [-Wunused-variable]
Int4 StsCount=0;
^~~~~~~~
stsutil.c: In function 'GetSTSEntry':
stsutil.c:635:13: warning: variable 'p' set but not used [-Wunused-but-set-variable]
CharPtr p;
^
stsutil.c: In function 'STSCalculateHash':
stsutil.c:753:26: warning: array subscript has type 'char' [-Wchar-subscripts]
if ((j = HashCode[*p++]) < 0)
^
stsutil.c: In function 'STSReverse':
stsutil.c:771:28: warning: array subscript has type 'char' [-Wchar-subscripts]
if ((*t = ComplCode[*s]) == 0)
^
stsutil.c: In function 'InitHashTable':
stsutil.c:910:21: warning: variable 'sts_uid' set but not used [-Wunused-but-set-variable]
CharPtr gb_uid, sts_uid;
^~~~~~~
stsutil.c:910:13: warning: variable 'gb_uid' set but not used [-Wunused-but-set-variable]
CharPtr gb_uid, sts_uid;
^~~~~~
stsutil.c:908:23: warning: variable 'gi' set but not used [-Wunused-but-set-variable]
Int4 id_sts, len, gi, StsCount = 0, StsInvalid =0;
^~
stsutil.c:908:10: warning: variable 'id_sts' set but not used [-Wunused-but-set-variable]
Int4 id_sts, len, gi, StsCount = 0, StsInvalid =0;
^~~~~~
stsutil.c:907:23: warning: unused variable 'error' [-Wunused-variable]
Int4 LineLength, error= FALSE;
^~~~~
At top level:
stsutil.c:892:13: warning: 'STSHashInitFree' defined but not used [-Wunused-function]
static void STSHashInitFree(STSHashInitPtr sts)
^~~~~~~~~~~~~~~
stsutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: stsutil.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF suggadj.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from suggadj.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
suggadj.c: In function 'score_possible_splice_sites':
suggadj.c:874:13: warning: array subscript has type 'char' [-Wchar-subscripts]
score = ( vx[seq_or_rev[putative_donor]]==3) ?10:0;
^
suggadj.c:875:13: warning: array subscript has type 'char' [-Wchar-subscripts]
score += (vx[seq_or_rev[putative_acceptor]]==3 )?10:0;
^
suggadj.c:878:14: warning: array subscript has type 'char' [-Wchar-subscripts]
score += ( vx[seq_or_rev[putative_donor+1]]==0 )?3:0;
^
suggadj.c:879:14: warning: array subscript has type 'char' [-Wchar-subscripts]
score += ( vx[seq_or_rev[putative_acceptor-1]]==2 )?3:0;
^
suggadj.c: In function 'check_split_codon':
suggadj.c:985:29: warning: array subscript has type 'char' [-Wchar-subscripts]
val_assuming_1_from_left= vx[seq_or_rev[left_ends+1]] * 16 +
^
suggadj.c:986:4: warning: array subscript has type 'char' [-Wchar-subscripts]
vx[seq_or_rev[right_starts-2]]*4+
^
suggadj.c:987:4: warning: array subscript has type 'char' [-Wchar-subscripts]
vx[seq_or_rev[right_starts-1]];
^
suggadj.c:998:29: warning: array subscript has type 'char' [-Wchar-subscripts]
val_assuming_2_from_left= vx[seq_or_rev[left_ends+1]] * 16 +
^
suggadj.c:999:4: warning: array subscript has type 'char' [-Wchar-subscripts]
vx[seq_or_rev[left_ends+2]] * 4 +
^
suggadj.c:1000:4: warning: array subscript has type 'char' [-Wchar-subscripts]
vx[seq_or_rev[right_starts-1]];
^
suggadj.c: In function 'overlapping_fixer':
suggadj.c:1370:18: warning: array subscript has type 'char' [-Wchar-subscripts]
test_val = vx[seq_or_rev[left_exon_ends]]*16 +
^
suggadj.c:1371:8: warning: array subscript has type 'char' [-Wchar-subscripts]
vx[seq_or_rev[right_exon_starts-1]];
^
suggadj.c:1373:20: warning: array subscript has type 'char' [-Wchar-subscripts]
test_val += vx[seq_or_rev[right_exon_starts-2]]*4;
^
suggadj.c:1375:20: warning: array subscript has type 'char' [-Wchar-subscripts]
test_val += vx[seq_or_rev[left_exon_ends+1]]*4;
^
At top level:
suggadj.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: suggadj.c,v 6.3 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF suggest.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from suggest.c:199:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
suggest.c: In function 'get_frames':
suggest.c:458:12: warning: array subscript has type 'char' [-Wchar-subscripts]
val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]];
^
suggest.c:458:26: warning: array subscript has type 'char' [-Wchar-subscripts]
val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]];
^
At top level:
suggest.c:1331:13: warning: 'ReportSuggestIntervalsError' defined but not used [-Wunused-function]
static void ReportSuggestIntervalsError (SeqRecPtr srp, CharPtr gen_txt)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
suggest.c:1222:1: warning: 'fprintf_m_stk_entry' defined but not used [-Wunused-function]
fprintf_m_stk_entry(FILE *fp, Int4 index, char *msg)
^~~~~~~~~~~~~~~~~~~
suggest.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: suggest.c,v 6.14 2009/04/10 17:22:14 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF suggslp.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from suggslp.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
suggslp.c: In function 'MakeReverseSequence':
suggslp.c:190:11: warning: array subscript has type 'char' [-Wchar-subscripts]
*t++ = r[*--s];
^
At top level:
suggslp.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: suggslp.c,v 6.6 2009/04/16 18:35:41 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blast.c:2572:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast.c: In function 'BlastReevaluateWithAmbiguities':
blast.c:2954:24: warning: variable 'query_end' set but not used [-Wunused-but-set-variable]
Uint1Ptr query_start, query_end, subject_real_start=NULL;
^~~~~~~~~
blast.c:2949:16: warning: variable 'hspcnt' set but not used [-Wunused-but-set-variable]
Int4 context, hspcnt, hspcnt_max, index, index1, status;
^~~~~~
blast.c: In function 'BlastGetVirtualOIDList':
blast.c:3179:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (virtual_oidlist = rdfp_chain->oidlist) {
^~
blast.c: In function 'BlastGetDbChunk':
blast.c:3210:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) {
^~
blast.c: In function 'BlastCreateQueryDNAP':
blast.c:4100:11: warning: variable 'strand_option' set but not used [-Wunused-but-set-variable]
Uint1 strand_option;
^~~~~~~~~~~~~
blast.c: In function 'BlastReapPartialHitlistByEvalue':
blast.c:6486:10: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
blast.c:6490:6: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if( !search->mult_queries )
^~
blast.c: In function 'BlastWordFinder_contig':
blast.c:7094:16: warning: variable 'bits_to_shift' set but not used [-Wunused-but-set-variable]
register Int4 bits_to_shift, min_diag_length, min_diag_mask;
^~~~~~~~~~~~~
blast.c: In function 'BlastWordExtend':
blast.c:7835:46: warning: variable 'leftscore' set but not used [-Wunused-but-set-variable]
BLAST_Score leftsum, rightsum, rightscore, leftscore;
^~~~~~~~~
blast.c: In function 'BlastNewWordExtend':
blast.c:7982:46: warning: variable 'leftscore' set but not used [-Wunused-but-set-variable]
BLAST_Score leftsum, rightsum, rightscore, leftscore;
^~~~~~~~~
blast.c: In function 'BlastNtWordFinder_mh':
blast.c:8843:23: warning: variable 'bits_to_shift' set but not used [-Wunused-but-set-variable]
register Int4 bits_to_shift, min_diag_length, min_diag_mask;
^~~~~~~~~~~~~
blast.c:8842:103: warning: variable 'compression_factor' set but not used [-Wunused-but-set-variable]
Int4 s_pos, q_off, s_off, offset, virtual_wordsize, wordsize, compressed_wordsize, compression_factor;
^~~~~~~~~~~~~~~~~~
blast.c: In function 'BlastNtWordFinder':
blast.c:9076:14: warning: variable 'bits_to_shift' set but not used [-Wunused-but-set-variable]
Int4 bits_to_shift, min_diag_length, min_diag_mask;
^~~~~~~~~~~~~
blast.c: In function 'BlastSaveCurrentHitlist':
blast.c:10115:11: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if( hitlist_max > 1 )
^
blast.c:9785:7: warning: variable 'query_length' set but not used [-Wunused-but-set-variable]
Int4 query_length;
^~~~~~~~~~~~
blast.c: In function 'SumHSPEvalue':
blast.c:10588:9: warning: variable 'gap_size' set but not used [-Wunused-but-set-variable]
Int4 gap_size, num, subject_length;
^~~~~~~~
blast.c: In function 'link_hsps':
blast.c:11267:10: warning: variable 'frame_change' set but not used [-Wunused-but-set-variable]
Boolean frame_change, linked_set, ignore_small_gaps;
^~~~~~~~~~~~
At top level:
blast.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast.c,v 6.451 2008/01/25 21:15:22 bealer Exp $";
^~~~~
blast.c: In function 'BLASTMergeHitLists.isra.4':
blast.c:6256:24: warning: 'op_type' may be used uninitialized in this function [-Wmaybe-uninitialized]
esp2->op_type = op_type;
~~~~~~~~~~~~~~^~~~~~~~~
blast.c:6058:10: note: 'op_type' was declared here
Uint1 op_type;
^~~~~~~
In file included from ../include/ncbi.h:59:0,
from blast.c:2572:
blast.c: In function 'blastMergeFilterLocs':
../include/ncbimem.h:232:23: warning: 'dup_slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
blast.c:3933:20: note: 'dup_slp' was declared here
SeqLocPtr slp, dup_slp, dup_head;
^~~~~~~
blast.c: In function 'BlastLinkHsps':
blast.c:10455:41: warning: 'orig_hitlist' may be used uninitialized in this function [-Wmaybe-uninitialized]
search->current_hitlist = orig_hitlist;
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blastutl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastutl.c:1836:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastutl.c: In function 'BlastSeqLocFilterEx':
blastutl.c:7554:11: warning: statement with no effect [-Wunused-value]
stop_timer("after repeat filtering");
^
blastutl.c: In function 'BlastPreliminaryGappedScore':
blastutl.c:9853:30: warning: variable 'query_length' set but not used [-Wunused-but-set-variable]
Int4 index, max_offset = 0, query_length, min_score;
^~~~~~~~~~~~
blastutl.c: In function 'BlastGetGappedScore':
blastutl.c:10282:11: warning: statement with no effect [-Wunused-value]
stop_timer("after BlastGappedScoreInternal");
^
At top level:
blastutl.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastutl.c,v 6.472 2010/12/10 18:47:12 madden Exp $";
^~~~~
blastutl.c: In function 'BlastNtFindWords':
blastutl.c:11445:10: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
end = MIN(end, len-initial_wordsize);
blastutl.c: In function 'BlastFindWords':
blastutl.c:11623:8: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
stop = MIN(stop, len);
blastutl.c:11711:18: warning: 'start_score2' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score2 += matrix[(Int4) *(str+index2)][*(words+index2)];
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:11717:15: warning: 'start_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
score += matrix[(Int4) *(str+wordsize-1)][index2];
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:11704:17: warning: 'first_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score = second_score+first_score;
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:11695:11: warning: 'diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
diff2 += diff;
~~~~~~^~~~~~~
blastutl.c: In function 'BlastNewFindWords_Old':
blastutl.c:11931:18: warning: 'start_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score2 += MtrxScorePosSearch(search->sbp,
blastutl.c:11924:17: warning: 'first_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score = second_score+first_score;
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:11915:11: warning: 'diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
diff2 += diff;
~~~~~~^~~~~~~
blastutl.c: In function 'BlastNewFindWordsEx':
blastutl.c:12124:30: warning: 'start_score2' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score2 += posMatrix[offset+index2][*(words+index2)];
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:12129:23: warning: 'start_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
score += posMatrix[offset+wordsize-1][index2];
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:12118:29: warning: 'first_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score = second_score + first_score;
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:12110:23: warning: 'diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
diff2 += diff;
~~~~~~^~~~~~~
blastutl.c: In function 'RealBlastGetGappedAlignmentTraceback':
blastutl.c:9008:42: warning: 'seqalign_array' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAlignPtr seqalign, seqalign_var, *seqalign_array;
^~~~~~~~~~~~~~
blastutl.c: In function 'SumBlastGetGappedAlignmentEx':
blastutl.c:9670:33: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
HeapSort(hsp_array+start,(stop-start),sizeof(BLAST_HSPPtr), score_compare_hsps);
~~~~~^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blastool.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastool.c:946:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastool.c: In function 'BlastScaleMatrix':
blastool.c:3032:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
blastool.c:3035:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if (new_lambda > lambda)
^~
blastool.c: In function 'OOFBlastHSPGetNumIdentical':
blastool.c:6081:9: warning: variable 'context' set but not used [-Wunused-but-set-variable]
Int2 context;
^~~~~~~
At top level:
blastool.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastool.c,v 6.292 2007/03/15 20:39:17 madden Exp $";
^~~~~
blastool.c: In function 'BlastCreateVirtualOIDList':
blastool.c:2556:24: warning: 'gilist' may be used uninitialized in this function [-Wmaybe-uninitialized]
BlastDoubleInt4Ptr gilist, real_gilist = NULL, *real_gilist_ptrs = NULL;
^~~~~~
blastool.c: In function 'BlastInsertList2Heap':
blastool.c:3595:31: warning: 'query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
context = hsp->query_offset / query_length;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
blastool.c: In function 'BlastFreeHeap':
blastool.c:3687:31: warning: 'query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
context = hsp->query_offset / query_length;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
blastool.c: In function 'BLASTFilterOverlapRegions':
blastool.c:4531:24: warning: 'next_tail' may be used uninitialized in this function [-Wmaybe-uninitialized]
tail->next = seqalign;
~~~~~~~~~~~^~~~~~~~~~
blastool.c: In function 'BlastPrintAlignInfo':
blastool.c:4800:23: warning: 'sap' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap->next = SeqAlignNew();
~~~~~~~~~~^~~~~~~~~~~~~~~
blastool.c: In function 'MegaBlastPrintAlignInfo':
blastool.c:963:17: warning: 'subject_seq_buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define fprintf blastool_fprintf
^~~~~~~~~~~~~~~~
blastool.c:5046:30: note: 'subject_seq_buffer' was declared here
CharPtr query_seq_buffer, subject_seq_buffer;
^~~~~~~~~~~~~~~~~~
blastool.c:963:17: warning: 'query_seq_buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define fprintf blastool_fprintf
^~~~~~~~~~~~~~~~
blastool.c:5046:12: note: 'query_seq_buffer' was declared here
CharPtr query_seq_buffer, subject_seq_buffer;
^~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blastconcat.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastconcat.c:89:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastconcat.c: In function 'BlastMakeFakeBspConcat':
blastconcat.c:648:12: warning: variable 'slp' set but not used [-Wunused-but-set-variable]
SeqLocPtr slp = NULL;
^~~
At top level:
blastconcat.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastconcat.c,v 1.14 2007/05/07 13:30:54 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF splutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from splutil.c:52:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
splutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: splutil.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gapxdrop.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/gapxdrop.h:150,
from gapxdrop.c:368:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gapxdrop.c: In function 'ALIGN_EX':
gapxdrop.c:864:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (s == 1)
^
gapxdrop.c:867:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (s == 2)
^
At top level:
gapxdrop.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: gapxdrop.c,v 6.76 2003/11/07 21:52:52 dondosha Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg0.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg0.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg0.c: In function 'g_band0_align':
bandalg0.c:273:9: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if(leftd >= 1)
^
At top level:
bandalg0.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg0.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg1.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg1.c: In function 'gband_quadratic':
bandalg1.c:54:14: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int4 c, i, j;
^
bandalg1.c: In function 'g_band1_align':
bandalg1.c:205:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if(leftd >= 1)
^
At top level:
bandalg1.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg1.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg2.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg2.c: In function 'gb_linear_align':
bandalg2.c:208:24: warning: variable 'misma' set but not used [-Wunused-but-set-variable]
register Int4 match, misma;
^~~~~
bandalg2.c:208:17: warning: variable 'match' set but not used [-Wunused-but-set-variable]
register Int4 match, misma;
^~~~~
bandalg2.c:207:18: warning: variable 'AA' set but not used [-Wunused-but-set-variable]
register Uint1 AA;
^~
At top level:
bandalg2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg2.c,v 6.5 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
bandalg2.c: In function 'gb_linear_align':
bandalg2.c:577:12: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
_INS(N - Y);
^
bandalg2.c:575:10: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
_DEL(M - X)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg3.c:37:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg3.c: In function 'gband_linear_qgap':
bandalg3.c:54:14: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int4 c, i, j;
^
At top level:
bandalg3.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg3.c,v 6.4 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
bandalg3.c: In function 'gband_linear_qgap':
bandalg3.c:314:16: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
else if(Y != rightd) _INS(rightd-Y)
^
bandalg3.c:185:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
bandalg3.c:313:21: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(X != M) _DEL(M - X)
^
bandalg3.c:185:25: note: 'X' was declared here
Int4 ib, best=MININT, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg4.c:37:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg4.c: In function 'g_band4_align_small':
bandalg4.c:826:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (e == 1)
^
bandalg4.c:829:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (e == 2)
^
bandalg4.c:630:8: warning: variable 'band' set but not used [-Wunused-but-set-variable]
Int4 band, j;
^~~~
At top level:
bandalg4.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg4.c,v 6.4 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
bandalg4.c: In function 'g_band4_align':
bandalg4.c:534:22: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(X != M || Y != N) regA = regB = 1;
~~^~~~
bandalg4.c:534:12: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(X != M || Y != N) regA = regB = 1;
~~^~~~
bandalg4.c:569:7: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
g_band4_align(A, B, r, r + rmid - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MAX(-r, low), rmid - 1, tb, 2, legA, legB, 1, 1, data);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bandalg4.c:857:37: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
else if (Y != rightd) _INS(rightd - Y);
^
bandalg4.c:640:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
In file included from bandalg4.c:37:0:
../include/bandalgn.h:140:76: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
data->last = (data->last < 0) ? (data->sapp[-1] -= (k)) : (*data->sapp++ = -(k));
^
bandalg4.c:640:25: note: 'X' was declared here
Int4 ib, best=MININT, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg5.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg5.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg5.c: In function 'gband_q3gap':
bandalg5.c:56:14: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int4 c, i, j;
^
bandalg5.c: In function 'g_band5_align':
bandalg5.c:292:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (e == 1)
^
bandalg5.c:295:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (e == 2)
^
At top level:
bandalg5.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg5.c,v 6.3 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
bandalg5.c: In function 'gband_q3gap':
bandalg5.c:320:6: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (Y != rightd) _INS(rightd - Y);
^
bandalg5.c:146:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
bandalg5.c:319:22: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (X != M) _DEL(M - X);
^
bandalg5.c:146:25: note: 'X' was declared here
Int4 ib, best=MININT, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF bandalgn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from bandalgn.c:118:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalgn.c: In function 'ExtendSeqAlign':
bandalgn.c:1113:22: warning: variable 'ddp' set but not used [-Wunused-but-set-variable]
DenseDiagPtr ddp;
^~~
bandalgn.c: In function 'CC_ExtendSeqAlign':
bandalgn.c:1188:22: warning: variable 'ddp' set but not used [-Wunused-but-set-variable]
DenseDiagPtr ddp;
^~~
At top level:
bandalgn.c:699:14: warning: 'HSblastna_to_ncbi4na' defined but not used [-Wunused-variable]
static Uint1 HSblastna_to_ncbi4na[] = { 1, /* A, 0 */
^~~~~~~~~~~~~~~~~~~~
bandalgn.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalgn.c,v 6.17 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
bandalgn.c: In function 'LocalBandToEditBlock':
bandalgn.c:463:20: warning: 'edit_block' may be used uninitialized in this function [-Wmaybe-uninitialized]
lbsp->edit_block = edit_block;
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
bandalgn.c: In function 'SetLowUpFromBlast':
bandalgn.c:1053:7: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (maxsc < val) {
^
bandalgn.c:1060:7: warning: 'alnlen' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (maxlen < alnlen) {
^
bandalgn.c:1070:9: warning: 'maxdi_up' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxy = MAX(maxy,maxdi_up);
bandalgn.c:1069:9: warning: 'mindi_low' may be used uninitialized in this function [-Wmaybe-uninitialized]
miny = MIN(miny,mindi_low);
bandalgn.c:1062:10: warning: 'maxdi' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxy = maxdi + width;
~~~~~^~~~~~~~~~~~~~~
bandalgn.c:1063:10: warning: 'mindi' may be used uninitialized in this function [-Wmaybe-uninitialized]
miny = mindi - width;
~~~~~^~~~~~~~~~~~~~~
bandalgn.c: In function 'GetAlignExtremes':
bandalgn.c:1309:7: warning: 'y2' may be used uninitialized in this function [-Wmaybe-uninitialized]
*yy2 = y2;
~~~~~^~~~
bandalgn.c:1308:7: warning: 'y1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*yy1 = y1;
~~~~~^~~~
bandalgn.c:1307:7: warning: 'x2' may be used uninitialized in this function [-Wmaybe-uninitialized]
*xx2 = x2;
~~~~~^~~~
bandalgn.c:1306:7: warning: 'x1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*xx1 = x1;
~~~~~^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blastkar.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastkar.c:648:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastkar.c:2373:25: warning: 'Altschul_prob' defined but not used [-Wunused-variable]
static BLAST_LetterProb Altschul_prob[] = {
^~~~~~~~~~~~~
blastkar.c:2347:25: warning: 'Dayhoff_prob' defined but not used [-Wunused-variable]
static BLAST_LetterProb Dayhoff_prob[] = {
^~~~~~~~~~~~
blastkar.c:1121:13: warning: 'blosum62_20_prefs' defined but not used [-Wunused-variable]
static Int4 blosum62_20_prefs[BLOSUM62_20_VALUES_MAX] = {
^~~~~~~~~~~~~~~~~
blastkar.c:1053:21: warning: 'blosum62_20_values' defined but not used [-Wunused-variable]
static Nlm_FloatHi blosum62_20_values[BLOSUM62_20_VALUES_MAX][8] = {
^~~~~~~~~~~~~~~~~~
blastkar.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastkar.c,v 6.115 2006/12/14 17:08:19 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF actutils.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/actutils.h:103,
from actutils.c:232:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
actutils.c: In function 'SlideToHit':
actutils.c:346:23: warning: variable 'done' set but not used [-Wunused-but-set-variable]
Boolean inIsland, done;
^~~~
actutils.c:346:13: warning: variable 'inIsland' set but not used [-Wunused-but-set-variable]
Boolean inIsland, done;
^~~~~~~~
actutils.c: In function 'ResolveSpinConflict':
actutils.c:1484:35: warning: unused variable 'row2_conflict' [-Wunused-variable]
Boolean row1_conflict = FALSE, row2_conflict = FALSE;
^~~~~~~~~~~~~
actutils.c:1484:12: warning: unused variable 'row1_conflict' [-Wunused-variable]
Boolean row1_conflict = FALSE, row2_conflict = FALSE;
^~~~~~~~~~~~~
actutils.c: In function 'ACT_FindBestAlnByDotPlot':
actutils.c:2002:20: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
actutils.c:2001:20: warning: variable 'start2' set but not used [-Wunused-but-set-variable]
Int4 start2;
^~~~~~
actutils.c:2000:20: warning: variable 'start1' set but not used [-Wunused-but-set-variable]
Int4 start1;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from actutils.c:232:
actutils.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
actutils.c:3132:13: warning: 'DumpAlignments' defined but not used [-Wunused-function]
static void DumpAlignments (SeqAlignPtr salp)
^~~~~~~~~~~~~~
actutils.c:2927:13: warning: 'MapBioseqToBioseqSpecial' defined but not used [-Wunused-function]
static Int4 MapBioseqToBioseqSpecial(SeqAlignPtr sap, Int4 begin, Int4 fin, Int4 pos, Int4 which_end)
^~~~~~~~~~~~~~~~~~~~~~~~
actutils.c:1654:16: warning: 'SpinsConflict' defined but not used [-Wunused-function]
static Boolean SpinsConflict (SQN_nPtr spin1, SQN_nPtr spin2, Int4 fuzz, Int4 strand)
^~~~~~~~~~~~~
actutils.c:1392:13: warning: 'am_fix_strand' defined but not used [-Wunused-function]
static void am_fix_strand(SeqAlignPtr sap, Uint1 strand1, Uint1 strand2)
^~~~~~~~~~~~~
actutils.c:1375:16: warning: 'am_isa_gap' defined but not used [-Wunused-function]
static Boolean am_isa_gap(Int4 start, Int4 prevstop, Uint1 strand)
^~~~~~~~~~
actutils.c:749:13: warning: 'StateTableSearch' defined but not used [-Wunused-function]
static void StateTableSearch (TextFsaPtr tbl, CharPtr txt, Int4Ptr state, Int4 pos, ACT_sitelistPtr PNTR asp_prev, ACT_sitelistPtr PNTR asp_head)
^~~~~~~~~~~~~~~~
actutils.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: actutils.c,v 6.56 2008/10/22 17:19:22 bollin Exp $";
^~~~~
In file included from ../include/ncbi.h:59:0,
from ../include/actutils.h:103,
from actutils.c:232:
actutils.c: In function 'GetOldBlastAlignmentPiece':
../include/ncbimem.h:232:23: warning: 'program' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
actutils.c:3089:25: note: 'program' was declared here
CharPtr program;
^~~~~~~
actutils.c: In function 'ACT_FindPeakScores':
actutils.c:1342:31: warning: 'ats_newprev' may be used uninitialized in this function [-Wmaybe-uninitialized]
ats_newprev->next = ats_new;
~~~~~~~~~~~~~~~~~~^~~~~~~~~
actutils.c:1321:28: warning: 'ats_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
ats_prev->next = ats;
~~~~~~~~~~~~~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF posit.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from posit.c:402:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
posit.c: In function 'posDemographics':
posit.c:1110:17: warning: variable 'numSeqAligns' set but not used [-Wunused-but-set-variable]
Int4 numseq, numSeqAligns; /*number of matching sequences and SeqAligns*/
^~~~~~~~~~~~
posit.c: In function 'posFreqsToMatrix':
posit.c:1679:45: warning: operation on '*(*(posSearch->posPrivateMatrix + (sizetype)((unsigned int)length * 4u)) + (sizetype)((unsigned int)a * 4u))' may be undefined [-Wsequence-point]
posSearch->posPrivateMatrix[length][a] = posSearch->posPrivateMatrix[length][a] = BLAST_SCORE_MIN;
posit.c: In function 'posComputePseudoFreqs':
posit.c:1840:16: warning: variable 'lambda' set but not used [-Wunused-but-set-variable]
Nlm_FloatHi lambda; /*Karlin-Altschul parameter*/
^~~~~~
posit.c: In function 'WposComputation':
posit.c:1988:13: warning: variable 'numSeqAligns' set but not used [-Wunused-but-set-variable]
Int4 i, numSeqAligns, numseq, qlength;
^~~~~~~~~~~~
posit.c: In function 'posPrintInformation':
posit.c:2319:8: warning: variable 'querySize' set but not used [-Wunused-but-set-variable]
Int4 querySize;
^~~~~~~~~
posit.c: In function 'posFindAlignmentDimensions':
posit.c:3064:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c:3070:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c:3079:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c:3086:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c: In function 'posPreprocessAlignment':
posit.c:3137:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c:3152:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c: In function 'posReadAlignment':
posit.c:3253:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextline, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
posit.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: posit.c,v 6.88 2011/10/25 14:33:16 boratyng Exp $";
^~~~~
posit.c: In function 'posFindAlignmentDimensions':
posit.c:3090:20: warning: 'testCountSeqs' may be used uninitialized in this function [-Wmaybe-uninitialized]
testCountSeqs++;
~~~~~~~~~~~~~^~
posit.c: In function 'posComputeSequenceWeights':
posit.c:1447:36: warning: 'intervalSigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
posSearch->posSigma[qplace] = intervalSigma;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
posit.c:1424:11: warning: 'Sigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (Sigma > 0) {
^
posit.c: In function 'posReadCheckpoint':
posit.c:2873:28: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (i < pssm->numColumns || j < pssm->numRows) {
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
posit.c:2702:11: note: 'j' was declared here
Int4 i, j, c;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF lookup.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from lookup.c:308:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
lookup.c: In function 'lookup_get_memory':
lookup.c:555:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
Uint8 extra = ((Uint8)mem_struct->current) & ((Uint8) 63);
^
In file included from ../include/blastdef.h:922:0,
from ../include/blast.h:470,
from lookup.c:309:
lookup.c: In function 'MegaBlastBuildLookupTable':
../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
#define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT
^
lookup.c:1047:35: note: in expansion of macro 'GET_EXTRA_CODE_18_OPT'
GET_EXTRA_CODE_18_OPT(seq)) & no_bit0;
^~~~~~~~~~~~~~~~~~~~~
../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
#define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT
^
lookup.c:1051:35: note: in expansion of macro 'GET_EXTRA_CODE_18_OPT'
GET_EXTRA_CODE_18_OPT(seq)) & no_bit0;
^~~~~~~~~~~~~~~~~~~~~
../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
#define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT
^
lookup.c:1078:31: note: in expansion of macro 'GET_EXTRA_CODE_18_OPT'
GET_EXTRA_CODE_18_OPT(seq) | bit0;
^~~~~~~~~~~~~~~~~~~~~
../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
#define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT
^
lookup.c:1082:31: note: in expansion of macro 'GET_EXTRA_CODE_18_OPT'
GET_EXTRA_CODE_18_OPT(seq) | bit0;
^~~~~~~~~~~~~~~~~~~~~
lookup.c:914:25: warning: variable 'extra_code' set but not used [-Wunused-but-set-variable]
register Int4 ecode, extra_code;
^~~~~~~~~~
At top level:
lookup.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: lookup.c,v 6.59 2005/07/28 14:57:10 coulouri Exp $";
^~~~~
lookup.c: In function 'MegaBlastBuildLookupTable':
lookup.c:975:10: warning: 'word_weight' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (word_weight >= 12) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF readdb.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2052:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
readdb.c: In function 'readdb_parse_db_names':
readdb.c:2498:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (**filenames == '"')
^
readdb.c: In function 's_GetBlastDirInfo':
readdb.c:2729:32: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess]
memset(blast_dir, 0, sizeof(blast_dir));
^
readdb.c: In function 'IndexFileExists':
readdb.c:3315:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (rdfp->cih)
^~
readdb.c:3321:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (rdbap->first_oid > 0) {
^~
readdb.c:3395:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (rdfp->cih && rdfp->aliasfilebit == 0)
^~
readdb.c:3401:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (rdbap->first_oid > 0) {
^~
readdb.c: In function 'FindBlastDBFileEx':
readdb.c:3475:33: warning: unused variable 'envp' [-Wunused-variable]
CharPtr buffer, buffer1, envp = NULL;
^~~~
readdb.c: In function 'readdb_new_internalEx':
readdb.c:3553:25: warning: unused variable 'envp' [-Wunused-variable]
CharPtr charptr, envp = NULL;
^~~~
readdb.c: In function 'readdb_get_link':
readdb.c:4747:12: warning: variable 'loaded_new' set but not used [-Wunused-but-set-variable]
Boolean loaded_new = FALSE;
^~~~~~~~~~
readdb.c:4746:24: warning: variable 'last_used' set but not used [-Wunused-but-set-variable]
ReadDBFILEPtr last, last_used, rdfp_var;
^~~~~~~~~
readdb.c: In function 'readdb_check_oid':
readdb.c:4891:38: warning: comparisons like 'X<=Y<=Z' do not have their mathematical meaning [-Wparentheses]
if (rdfp_var->start <= oid <= rdfp_var->stop)
~~~~~~~~~~~~~~~~^~~~~~
readdb.c: In function 'readdb_seqid2fasta':
readdb.c:5231:22: warning: unused variable 'dummy_gi' [-Wunused-variable]
Int4 dummy_gi = 0; /* Not used, should have been handled above. */
^~~~~~~~
readdb.c:5175:13: warning: unused variable 'chptr' [-Wunused-variable]
CharPtr chptr = NULL;
^~~~~
readdb.c: In function 'FDBuildOldStyleDefline':
readdb.c:6361:33: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess]
MemSet(defline, '\0', sizeof(defline));
^
readdb.c: In function 'FDBLoadMembershipsTable':
readdb.c:8260:21: warning: variable 'fn_name' set but not used [-Wunused-but-set-variable]
const char* fn_name = NULL;
^~~~~~~
readdb.c: In function 'SeqIdE2Index':
readdb.c:8608:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((tsip->version > 0) && (tsip->release == NULL))
^~
readdb.c:8610:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
break;
^~~~~
readdb.c:8613:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (tsip->version > 0)
^~
readdb.c:8615:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
break;
^~~~~
readdb.c:8572:13: warning: unused variable 'tmp' [-Wunused-variable]
CharPtr tmp, ptr=NULL;
^~~
readdb.c:8571:11: warning: unused variable 'tmptype' [-Wunused-variable]
Uint1 tmptype;
^~~~~~~
readdb.c: In function 'SeqIdSetE2Index':
readdb.c:8876:14: warning: variable 'oldanp' set but not used [-Wunused-but-set-variable]
SeqIdPtr oldanp;
^~~~~~
readdb.c: In function 'FindDBbyGI':
readdb.c:11392:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (gi > cih->maxgi)
^~
readdb.c:11395:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cigi = cih->ci + gi;
^~~~
readdb.c: In function 'Fastacmd_Search_ex':
readdb.c:12075:22: warning: variable 'guess_gi' set but not used [-Wunused-but-set-variable]
Int4 guess_gi = -1;
^~~~~~~~
readdb.c: In function 'DumpOneSequence':
readdb.c:12412:14: warning: unused variable 'numeric_id' [-Wunused-variable]
Boolean numeric_id = GetAccessionVersionFromSeqId(accn, &gi, &id, TRUE);
^~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from readdb.c:2062:
readdb.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
readdb.c:12824:1: warning: 'readdb_preload_index' defined but not used [-Wunused-function]
readdb_preload_index (ReadDBFILEPtr rdfp, Int4 first_db_seq,
^~~~~~~~~~~~~~~~~~~~
In file included from readdb.c:2055:0:
../include/ncbisami.h:191:14: warning: 'OneBit' defined but not used [-Wunused-variable]
static Uint1 OneBit[] = {0x80 , 0x40, 0x20, 0x10, 0x8, 0x4, 0x2, 0x1};
^~~~~~
../include/ncbisami.h:183:14: warning: 'PowersOfTwo' defined but not used [-Wunused-variable]
static Uint4 PowersOfTwo[] = {01,02,04,010,020,040,0100,0200,0400,01000,
^~~~~~~~~~~
readdb.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: readdb.c,v 6.548 2012/03/14 20:09:35 camacho Exp $";
^~~~~
readdb.c: In function 'readdb_get_taxonomy_names':
readdb.c:5674:28: warning: 'ufp_last' may be used uninitialized in this function [-Wmaybe-uninitialized]
ufp_last->next = ufp;
~~~~~~~~~~~~~~~^~~~~
readdb.c: In function 'readdb_get_descriptor':
readdb.c:6663:44: warning: 'new_defline_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
new_defline_length += StringLen(defline) + StringLen(id_buf);
^~
readdb.c: In function 'GetAccList':
readdb.c:11816:29: warning: 'AccListLast' may be used uninitialized in this function [-Wmaybe-uninitialized]
AccListLast->next = AccListTmp;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbisam.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbisam.c:198:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbisam.c: In function 'ISAMMakeStringIndex':
ncbisam.c:842:22: warning: unused variable 'file_pos' [-Wunused-variable]
Int4 file_pos = ftell(data->db_fd);
^~~~~~~~
ncbisam.c: In function 'ISAMInitSearch':
ncbisam.c:1399:10: warning: variable 'reserved2' set but not used [-Wunused-but-set-variable]
Int4 reserved2;
^~~~~~~~~
At top level:
ncbisam.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: ncbisam.c,v 6.34 2007/11/06 19:20:06 coulouri Exp $";
^~~~~
In file included from ../include/ncbi.h:59:0,
from ncbisam.c:198:
ncbisam.c: In function 'ISAMMakeIndex':
../include/ncbimem.h:232:23: warning: 'KeySamples' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
ncbisam.c:983:23: note: 'KeySamples' was declared here
Uint4Ptr KeyInfo, KeySamples;
^~~~~~~~~~
In file included from ../include/ncbi.h:59:0,
from ncbisam.c:198:
../include/ncbimem.h:232:23: warning: 'KeyDataSamples' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
ncbisam.c:984:34: note: 'KeyDataSamples' was declared here
NISAMKeyDataPtr KeyDataInfo, KeyDataSamples;
^~~~~~~~~~~~~~
ncbisam.c:984:21: warning: 'KeyDataInfo' may be used uninitialized in this function [-Wmaybe-uninitialized]
NISAMKeyDataPtr KeyDataInfo, KeyDataSamples;
^~~~~~~~~~~
ncbisam.c:983:14: warning: 'KeyInfo' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint4Ptr KeyInfo, KeySamples;
^~~~~~~
In file included from ../include/ncbi.h:59:0,
from ncbisam.c:198:
ncbisam.c: In function 'ISAMCreateDatabase':
../include/ncbimem.h:232:23: warning: 'prevterm' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
ncbisam.c:1181:13: note: 'prevterm' was declared here
CharPtr prevterm;
^~~~~~~~
In file included from ../include/ncbimsg.h:78:0,
from ../include/ncbi.h:60,
from ncbisam.c:198:
../include/ncbierr.h:246:23: warning: 'field_in' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define ErrLogPrintf Nlm_ErrLogPrintf
^~~~~~~~~~~~~~~~
ncbisam.c:1177:37: note: 'field_in' was declared here
unsigned long uid_in, uid_last, field_in;
^~~~~~~~
ncbisam.c: In function 'NISAMSearch':
ncbisam.c:1814:32: warning: 'KeyDataPageStart' may be used uninitialized in this function [-Wmaybe-uninitialized]
KeyDataPageStart = MemFree(KeyDataPageStart);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbisam.c:1812:28: warning: 'KeyPageStart' may be used uninitialized in this function [-Wmaybe-uninitialized]
KeyPageStart = MemFree(KeyPageStart);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
ncbisam.c:1750:36: warning: 'KeyPage' may be used uninitialized in this function [-Wmaybe-uninitialized]
Key = SwapUint4(KeyPage[current]);
^
ncbisam.c:1593:24: warning: 'SampleNum' may be used uninitialized in this function [-Wmaybe-uninitialized]
*Start = SampleNum * data->PageSize;
~~~~~~~~~~^~~~~~~~~~~~~~~~
ncbisam.c:1618:27: note: 'SampleNum' was declared here
Int4 Start = 0, Stop, SampleNum;
^~~~~~~~~
ncbisam.c: In function 'SISAMSearch':
ncbisam.c:2373:8: warning: 'SampleNum' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ( (SampleNum < 0) || (SampleNum >= data->NumSamples)) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbisort.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbisort.h:62,
from ../include/ncbisrti.h:60,
from ncbisort.c:83:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbisort.c: In function 'SORTFracCompare':
ncbisort.c:692:12: warning: type defaults to 'int' in declaration of 'tmpa' [-Wimplicit-int]
register tmpa = UCHAR(*a), tmpb = UCHAR(*b);
^~~~
ncbisort.c:692:30: warning: type defaults to 'int' in declaration of 'tmpb' [-Wimplicit-int]
register tmpa = UCHAR(*a), tmpb = UCHAR(*b);
^~~~
In file included from ncbisort.c:83:0:
ncbisort.c: At top level:
../include/ncbisrti.h:213:13: warning: 'inthandler' declared 'static' but never defined [-Wunused-function]
static void inthandler(int i);
^~~~~~~~~~
ncbisort.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: ncbisort.c,v 6.8 2006/05/10 20:47:17 camacho Exp $";
^~~~~
ncbisort.c: In function 'SORTMergeFPS':
ncbisort.c:1110:10: warning: 'savealloc' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (savealloc < lines[ord[0]].lines[cur[ord[0]]].length + 1) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salign.h:10,
from salign.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salign.c: In function 'BandAlignTwoSeqLocsFunc':
salign.c:173:13: warning: variable 'is_prot' set but not used [-Wunused-but-set-variable]
Boolean is_prot;
^~~~~~~
salign.c: In function 'SortBlastHits':
salign.c:391:15: warning: variable 'totalvalmax' set but not used [-Wunused-but-set-variable]
totalvalmax = INT4_MAX,
^~~~~~~~~~~
salign.c: In function 'link_solution':
salign.c:1188:15: warning: unused variable 'first' [-Wunused-variable]
Boolean first = TRUE;
^~~~~
At top level:
salign.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: salign.c,v 6.11 2009/01/21 17:09:18 bollin Exp $";
^~~~~
salign.c: In function 'SortBlastHits':
salign.c:454:6: warning: 'salpdup' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (salpdup!=NULL)
^
salign.c: In function 'TranslateSeqLoc.constprop':
salign.c:660:10: warning: 'slpp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return slpp;
^~~~
salign.c: In function 'BlastTwoSeqLocs':
salign.c:591:18: warning: 'strand2' may be used uninitialized in this function [-Wmaybe-uninitialized]
sit->strand = strand2;
~~~~~~~~~~~~^~~~~~~~~
salign.c:589:18: warning: 'strand1' may be used uninitialized in this function [-Wmaybe-uninitialized]
sit->strand = strand1;
~~~~~~~~~~~~^~~~~~~~~
salign.c: In function 'BlastBandAlignTwoSeqLocs.isra.4':
salign.c:1433:17: warning: 'tail' may be used uninitialized in this function [-Wmaybe-uninitialized]
tail->next = salptmp;
~~~~~~~~~~~^~~~~~~~~
salign.c:1408:15: note: 'tail' was declared here
tail,
^~~~
salign.c:1348:38: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
intronlg = (float)(abs(stop - start1) - alignlens)/(float)(j-1);
~~~~~^~~~~~~~
salign.c:1301:30: note: 'stop' was declared here
Int4 start, start1, stop;
^~~~
salign.c:1348:38: warning: 'start1' may be used uninitialized in this function [-Wmaybe-uninitialized]
intronlg = (float)(abs(stop - start1) - alignlens)/(float)(j-1);
~~~~~^~~~~~~~
salign.c:1301:22: note: 'start1' was declared here
Int4 start, start1, stop;
^~~~~~
salign.c:1270:38: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
intronlg = (float)(abs(stop - start1) - alignlen)/(float)(j-1);
~~~~~^~~~~~~~
salign.c:1229:30: note: 'stop' was declared here
Int4 start, start1, stop;
^~~~
salign.c:1270:38: warning: 'start1' may be used uninitialized in this function [-Wmaybe-uninitialized]
intronlg = (float)(abs(stop - start1) - alignlen)/(float)(j-1);
~~~~~^~~~~~~~
salign.c:1229:22: note: 'start1' was declared here
Int4 start, start1, stop;
^~~~~~
salign.c: In function 'SeqLocListToSeqAlign':
salign.c:1670:22: warning: 'master_slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
salpblast = BlastTwoSeqLocs (master_slp, slp, is_prot, msp);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF salptool.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from salptool.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salptool.c: In function 'MergeTwoDspBySIM4':
salptool.c:285:10: warning: variable 'has_overlap' set but not used [-Wunused-but-set-variable]
Boolean has_overlap;
^~~~~~~~~~~
salptool.c:281:7: warning: variable 'gap' set but not used [-Wunused-but-set-variable]
Int4 gap=0,gap_1, gap_2;
^~~
salptool.c: In function 'extend_dsp_ends':
salptool.c:1329:21: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
salptool.c:1331:4: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if(extend_len > 0)
^~
salptool.c:1346:21: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
salptool.c:1348:4: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if(extend_len > 0)
^~
salptool.c:1363:21: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
salptool.c:1365:4: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if(extend_len > 0)
^~
salptool.c:1380:21: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
salptool.c:1382:4: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if(extend_len > 0)
^~
In file included from ../include/sqnutils.h:51:0,
from salptool.c:12:
salptool.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from salptool.c:14:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
salptool.c:1518:24: warning: 'OrderBestHits' defined but not used [-Wunused-function]
static int LIBCALLBACK OrderBestHits(Pointer ptr1, Pointer ptr2)
^~~~~~~~~~~~~
salptool.c:1468:13: warning: 'showtextalign_fromalign' defined but not used [-Wunused-function]
static void showtextalign_fromalign (SeqAlignPtr salp, CharPtr path, FILE *fp)
^~~~~~~~~~~~~~~~~~~~~~~
salptool.c:1453:13: warning: 'getlengthforid' defined but not used [-Wunused-function]
static Int4 getlengthforid (SeqIdPtr sip)
^~~~~~~~~~~~~~
salptool.c:1267:16: warning: 'need_recompute' defined but not used [-Wunused-function]
static Boolean need_recompute(SeqAlignPtr align, Int4 m_len, Int4 s_len)
^~~~~~~~~~~~~~
salptool.c:838:13: warning: 'SeqLocTrimPolyATail' defined but not used [-Wunused-function]
static void SeqLocTrimPolyATail(SeqLocPtr loc_2, BioseqPtr bsp_2) {
^~~~~~~~~~~~~~~~~~~
salptool.c:46:13: warning: 'SeqAnnotWrite' defined but not used [-Wunused-function]
static void SeqAnnotWrite(SeqAlignPtr align)
^~~~~~~~~~~~~
salptool.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: salptool.c,v 6.57 2008/07/07 18:52:31 bollin Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urkutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from urkutil.c:59:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkutil.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urkpcc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkpcc.h:54,
from urkpcc.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkpcc.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkpcc.c,v 6.13 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urkptpf.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from urkptpf.c:65:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkptpf.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkptpf.c,v 6.33 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urkepi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkepi.h:54,
from urkepi.c:59:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkepi.c: In function 'PredictEpiI0':
urkepi.c:214:21: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[*seq] += 1;
^
urkepi.c:239:58: warning: array subscript has type 'char' [-Wchar-subscripts]
episcore = DownArrayScore (episcore, epip->epiarray[*seq]);
^
urkepi.c:240:21: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[*seq] += 1;
^
urkepi.c:241:56: warning: array subscript has type 'char' [-Wchar-subscripts]
episcore = UpArrayScore (episcore, epip->epiarray[*seq]);
^
urkepi.c:263:58: warning: array subscript has type 'char' [-Wchar-subscripts]
episcore = DownArrayScore (episcore, epip->epiarray[*(seq-window)]);
^
urkepi.c:264:21: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[*(seq-window)] -= 1;
^
urkepi.c:265:56: warning: array subscript has type 'char' [-Wchar-subscripts]
episcore = UpArrayScore (episcore, epip->epiarray[*(seq-window)]);
^
urkepi.c: In function 'OptimizeEpiComp':
urkepi.c:605:14: warning: array subscript has type 'char' [-Wchar-subscripts]
bin[seq[i]] += 1;
^
urkepi.c:621:14: warning: array subscript has type 'char' [-Wchar-subscripts]
bin[seq[i]] += 1;
^
urkepi.c:651:15: warning: array subscript has type 'char' [-Wchar-subscripts]
if (fbin[seq[i]] > expect)
^
urkepi.c:657:15: warning: array subscript has type 'char' [-Wchar-subscripts]
if (fbin[seq[i]] > expect)
^
urkepi.c: In function 'OptimizeEpiHP':
urkepi.c:782:27: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[seq[j]] += 1;
^
urkepi.c:797:27: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[seq[j]] += 1;
^
urkepi.c:837:25: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[seq[n]] -= 1;
^
urkepi.c: In function 'OptimizeEpiProbFunc':
urkepi.c:982:27: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[seq[n]] += 1;
^
urkepi.c:994:27: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[seq[n]] += 1;
^
At top level:
urkepi.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkepi.c,v 6.19 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
urkepi.c: In function 'FilterEpi':
urkepi.c:1053:21: warning: 'right' may be used uninitialized in this function [-Wmaybe-uninitialized]
cfap->right = right;
~~~~~~~~~~~~^~~~~~~
urkepi.c:936:56: note: 'right' was declared here
Int4 i, n, j, k, start, stop, loop, fact, left, right;
^~~~~
urkepi.c:1052:20: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized]
cfap->left = left;
~~~~~~~~~~~^~~~~~
urkepi.c:936:50: note: 'left' was declared here
Int4 i, n, j, k, start, stop, loop, fact, left, right;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urkfltr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkfltr.h:51,
from urkfltr.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkfltr.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkfltr.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urkdust.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkdust.h:51,
from urkdust.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkdust.c: In function 'DustMe_h':
urkdust.c:196:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(dcvp->curlevel <= newlevel) && dcvp->curend == loop+1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
urkdust.c: In function 'DustForGraph':
urkdust.c:776:17: warning: variable 'drphead' set but not used [-Wunused-but-set-variable]
DustRegionPtr drphead;
^~~~~~~
At top level:
urkdust.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkdust.c,v 6.10 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urksigu.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urksigu.h:57,
from urksigu.c:59:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urksigu.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urksigu.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seg.c
seg.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seg.c,v 6.19 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
seg.c: In function 'getprob':
seg.c:935:15: warning: 'ans2' may be used uninitialized in this function [-Wmaybe-uninitialized]
ans = ans1 + ans2 - totseq;
~~~~~^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urkbias.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from urkbias.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkbias.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkbias.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urkcnsrt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkcnsrt.h:60,
from urkcnsrt.c:80:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkcnsrt.c:1203:13: warning: 'ScanFrame' defined but not used [-Wunused-function]
static void ScanFrame (BioseqPtr bsp, SeqLocPtr slp, Int4 frame,
^~~~~~~~~
urkcnsrt.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkcnsrt.c,v 6.21 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
urkcnsrt.c: In function 'Scan3Frames':
urkcnsrt.c:1312:34: warning: 'length' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 i, n, start, stop, length, chunk;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF urktree.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urktree.h:51,
from urktree.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urktree.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urktree.c,v 6.6 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF pseed3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from pseed3.c:176:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pseed3.c: In function 'SeedPruneHitsFromSeedReturn':
pseed3.c:230:17: warning: variable 'curSegs' set but not used [-Wunused-but-set-variable]
DenseSegPtr curSegs, testSegs; /*Used to extract ids from curSeqAlign, testSeqAlign*/
^~~~~~~
pseed3.c: In function 'seedEngineCore':
pseed3.c:507:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, &numPatOccur, &effectiveOccurrences, program_flag, unfilter_query, query, search->sbp->query_length, is_dna, patternSearch, seedSearch, showDiagnostics, &(search->error_return), info_vnp, hitArraySz)) {
^~~~~
pseed3.c: In function 'output_hits':
pseed3.c:1202:10: warning: variable 'posBaseIndex' set but not used [-Wunused-but-set-variable]
Int4 posBaseIndex; /*loop index for copying pos results arrays*/
^~~~~~~~~~~~
pseed3.c: In function 'init_order':
pseed3.c:1483:38: warning: array subscript has type 'char' [-Wchar-subscripts]
seedSearch->order[seedSearch->pchars[i]] = i;
^
pseed3.c:1483:19: warning: array subscript has type 'char' [-Wchar-subscripts]
seedSearch->order[seedSearch->pchars[i]] = i;
^
pseed3.c:1487:33: warning: array subscript has type 'char' [-Wchar-subscripts]
seedSearch->charMultiple[i] = 0;
^
pseed3.c:1489:30: warning: array subscript has type 'char' [-Wchar-subscripts]
if (seedSearch->standardProb[i] > seedepsilon) {
^
pseed3.c:1490:22: warning: array subscript has type 'char' [-Wchar-subscripts]
matrixRow = matrix[i];
^
pseed3.c:1493:34: warning: array subscript has type 'char' [-Wchar-subscripts]
if (seedSearch->standardProb[j] > seedepsilon)
^
pseed3.c:1494:42: warning: array subscript has type 'char' [-Wchar-subscripts]
rowSum += seedSearch->standardProb[j]*exp(-(seedSearch->paramLambda)*matrixRow[j]);
^
pseed3.c:1494:86: warning: array subscript has type 'char' [-Wchar-subscripts]
rowSum += seedSearch->standardProb[j]*exp(-(seedSearch->paramLambda)*matrixRow[j]);
^
pseed3.c:1496:28: warning: array subscript has type 'char' [-Wchar-subscripts]
seedSearch->charMultiple[i] = rowSum;
^
At top level:
pseed3.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: pseed3.c,v 6.54 2008/10/31 18:51:07 madden Exp $";
^~~~~
pseed3.c: In function 'seedParallelFill':
pseed3.c:712:68: warning: iteration 100 invokes undefined behavior [-Waggressive-loop-optimizations]
returnData->seedSearch->name_space[i] = seedSearch->name_space[i];
~~~~~~~~~~~~~~~~~~~~~~^~~
pseed3.c:711:4: note: within this loop
for( i = 0; i <= BUF_SIZE; i++)
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF pattern1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from pattern1.c:80:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pattern1.c: In function 'init_pattern':
pattern1.c:286:52: warning: array subscript has type 'char' [-Wchar-subscripts]
positionProbability = seedSearch->standardProb[seedSearch->order[c]];
^
pattern1.c:303:53: warning: array subscript has type 'char' [-Wchar-subscripts]
positionProbability += seedSearch->standardProb[seedSearch->order[c]];
^
pattern1.c:317:53: warning: array subscript has type 'char' [-Wchar-subscripts]
positionProbability -= seedSearch->standardProb[seedSearch->order[c]];
^
pattern1.c: In function 'find_hitsS_DNA':
pattern1.c:534:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) {
^~
pattern1.c:547:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) {
^~
pattern1.c: At top level:
pattern1.c:744:8: warning: return type defaults to 'int' [-Wimplicit-int]
static and(Int4 *result, Int4 *a, Int4 *b, patternSearchItems *patternSearch)
^~~
pattern1.c: In function 'and':
pattern1.c:750:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (result[i] = (a[i] & b[i]))
^~
pattern1.c: In function 'align':
pattern1.c:1102:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (leftd >= 1)
^
pattern1.c: In function 'pat_output':
pattern1.c:1637:2: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
pattern1.c:1639:11: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
ValNodeCopyStr(info_vnp, 0, buffer);
^~~~~~~~~~~~~~
At top level:
pattern1.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: pattern1.c,v 6.22 2006/08/04 21:11:17 papadopo Exp $";
^~~~~
pattern1.c: In function 'get_patL':
pattern1.c:1348:42: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
*end = wordIndex*BITS_PACKED_PER_WORD+j;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
pattern1.c: In function 'align':
pattern1.c:1158:8: warning: 'CDrow' may be used uninitialized in this function [-Wmaybe-uninitialized]
score = (CDrow-1)->CC;
~~~~~~^~~~~~~~~~~~~~~
pattern1.c: In function 'get_patLL':
pattern1.c:1393:5: warning: 'pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j = 0; j < pos; j+= wordIndex) {
^~~
pattern1.c: In function 'init_pattern':
pattern1.c:192:11: warning: 'tj' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 tj; /*temporary copy of j*/
^~
pattern1.c: In function 'align_of_pattern':
pattern1.c:1562:19: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized]
local_score += ALIGN_B(querySeq-1, dbSeq-1, queryMatchOffset, dbMatchOffset,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BAND_LOW, BAND_HIGH, matrix, gap_open, gap_extend, alignScript, data);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF impatool.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from impatool.c:73:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
impatool.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: impatool.c,v 6.16 2006/06/30 18:44:40 camacho Exp $";
^~~~~
impatool.c: In function 'IMPALAPrintHelp':
impatool.c:301:20: warning: 'ret_buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
ret_buffer = MemFree(ret_buffer);
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF posit2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from posit2.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
posit2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: posit2.c,v 6.12 2006/09/18 20:54:27 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mbalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/mbalign.h:4,
from mbalign.c:176:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mbalign.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: mbalign.c,v 6.43 2006/02/02 17:57:34 papadopo Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF vecscrn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vecscrn.h:74,
from vecscrn.c:103:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vecscrn.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: vecscrn.c,v 6.137 2005/12/27 14:46:44 madden Exp $";
^~~~~
vecscrn.c: In function 'VSPrintOverviewFromSeqLocs':
vecscrn.c:1085:8: warning: 'tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp = tmp->next;
~~~~^~~~~~~~~~~
vecscrn.c: In function 'VSPrintListFromSeqLocs':
vecscrn.c:1191:8: warning: 'tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp = tmp->next;
~~~~^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF mblast.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mblast.c:710:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mblast.c: In function 'BioseqMegaBlastEngineCore':
mblast.c:961:12: warning: statement with no effect [-Wunused-value]
stop_timer("BioseqBlastEngineCore: before do_the_blast_run()");
^
mblast.c:987:12: warning: statement with no effect [-Wunused-value]
stop_timer("MegaBlastEngineCore: after do_the_blast_run()");
^
mblast.c:942:14: warning: variable 'seqalign' set but not used [-Wunused-but-set-variable]
SeqAlignPtr seqalign, PNTR seqalignp;
^~~~~~~~
mblast.c: In function 'MegaBlastSetUpSearchInternalByLoc':
mblast.c:1167:16: warning: variable 'avglen' set but not used [-Wunused-but-set-variable]
Nlm_FloatHi avglen;
^~~~~~
mblast.c: In function 'MegaBlastPackAlignmentsByQuery':
mblast.c:1829:14: warning: variable 'slp' set but not used [-Wunused-but-set-variable]
SeqLocPtr slp;
^~~
mblast.c: In function 'MegaBlastWordFinder_disc_1b':
mblast.c:2372:32: warning: variable 'mask' set but not used [-Wunused-but-set-variable]
register Int4 s_off, ecode, mask, q_off, extra_code;
^~~~
At top level:
mblast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: mblast.c,v 6.215 2006/09/21 13:42:37 madden Exp $";
^~~~~
mblast.c: In function 'MegaBlastPackAlignmentsByQuery':
mblast.c:1864:19: warning: 'sap' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap->next = seqalign_var;
~~~~~~~~~~^~~~~~~~~~~~~~
mblast.c: In function 'MegaBlastWordFinder_disc':
mblast.c:2250:53: warning: 'ecode2' may be used uninitialized in this function [-Wmaybe-uninitialized]
(((PV_ARRAY_TYPE) 1)<<(ecode2&PV_ARRAY_MASK))) == 0))) {
~~~~~~~^~~~~~~~~~~~~~~
mblast.c:2151:47: warning: 'ecode1' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (q_off = lookup->mb_lt->hashtable[ecode1]; q_off>0;
^
mblast.c: In function 'MegaBlastWordFinder':
mblast.c:2711:51: warning: 'ecode2' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (q_off = lookup->mb_lt->hashtable2[ecode2]; q_off>0;
^
mblast.c:2373:17: note: 'ecode2' was declared here
Int4 ecode1, ecode2;
^~~~~~
mblast.c:2475:52: warning: 'ecode1' may be used uninitialized in this function [-Wmaybe-uninitialized]
(((PV_ARRAY_TYPE) 1)<<(ecode1&PV_ARRAY_MASK))) == 0)
~~~~~~~^~~~~~~~~~~~~~~
mblast.c:2373:9: note: 'ecode1' was declared here
Int4 ecode1, ecode2;
^~~~~~
mblast.c: In function 'MegaBlastGapInfoToSeqAlign':
mblast.c:3504:16: warning: 'seqalign' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAlignPtr seqalign, seqalign_var, sap;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF rpsutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/rpsutil.h:128,
from rpsutil.c:281:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rpsutil.c: In function 'RPSBlastSearchLight':
rpsutil.c:1838:10: warning: variable 'status' set but not used [-Wunused-but-set-variable]
Int2 status;
^~~~~~
rpsutil.c: In function 'RPSBgetCddHits':
rpsutil.c:2210:21: warning: variable 'found_score' set but not used [-Wunused-but-set-variable]
Boolean found_score = FALSE;
^~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from rpsutil.c:282:
rpsutil.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
rpsutil.c: In function 'getAuxInformation':
rpsutil.c:398:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%s",underlyingMatrixName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:404:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%d\n", gap_open);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:405:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%d\n", gap_extend);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:406:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Kungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:407:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Hungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:408:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &maxLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:409:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &dbLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:410:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%lf", &privateScalingFactor);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:415:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &maxLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:416:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &(rpsinfo->karlinK[index]));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
rpsutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: rpsutil.c,v 6.76 2007/05/07 13:30:54 kans Exp $";
^~~~~
rpsutil.c: In function 'RPSAlignTraceBack':
rpsutil.c:1444:32: warning: 'posMatrix' may be used uninitialized in this function [-Wmaybe-uninitialized]
search->sbp->posMatrix = posMatrix;
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
rpsutil.c:1433:22: warning: 'rev_subject_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
seqalign = BlastGetGapAlgnTbck (search, 0, TRUE, FALSE,
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
subject, subject_length,
~~~~~~~~~~~~~~~~~~~~~~~~
rev_subject, rev_subject_length);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c: In function 'RPSCalcEValue':
rpsutil.c:1269:30: warning: 'posMatrix' may be used uninitialized in this function [-Wmaybe-uninitialized]
search->sbp->posMatrix = posMatrix;
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF kappa.c
kappa.c: In function 'Kappa_SequenceGetProteinRange':
kappa.c:1399:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
kappa.c: At top level:
kappa.c:2203:5: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
Kappa_SequenceGetRange,
^~~~~~~~~~~~~~~~~~~~~~
kappa.c:2203:5: note: (near initialization for 'redo_align_callbacks.get_range')
kappa.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: kappa.c,v 6.93 2012/04/30 12:45:01 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF xmlblast.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/xmlblast.h:89,
from xmlblast.c:171:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
xmlblast.c: In function 'PSIXmlInit':
xmlblast.c:1239:13: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = FALSE;
^~~~~~
At top level:
xmlblast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: xmlblast.c,v 6.41 2007/05/07 13:30:54 kans Exp $";
^~~~~
xmlblast.c: In function 'BXMLGetSeqLineForStdSeg':
xmlblast.c:373:28: warning: 'genetic_code2' may be used uninitialized in this function [-Wmaybe-uninitialized]
CharPtr genetic_code1, genetic_code2;
^~~~~~~~~~~~~
xmlblast.c: In function 'BXMLSeqAlignToHits':
xmlblast.c:867:36: warning: 'hspp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if((hspp->next = BXMLGetHspFromSeqAlign(sap2, is_aa, chain,
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
is_ooframe, mask_loc)) == NULL)
~~~~~~~~~~~~~~~~~~~~~~
xmlblast.c: In function 'SeqAlignToHits':
xmlblast.c:1646:24: warning: 'hspp' may be used uninitialized in this function [-Wmaybe-uninitialized]
hspp->next = GetHspFromSeqAlign(sap2, ungapped, &hsp_count);
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF bxmlobj.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from bxmlobj.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bxmlobj.c: In function 'BlastOutputAsnRead':
bxmlobj.c:96:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c: In function 'ParametersAsnRead':
bxmlobj.c:361:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c:360:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
bxmlobj.c: In function 'IterationAsnRead':
bxmlobj.c:613:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c: In function 'StatisticsAsnRead':
bxmlobj.c:829:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c:828:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
bxmlobj.c: In function 'HitAsnRead':
bxmlobj.c:1039:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c: In function 'HspAsnRead':
bxmlobj.c:1244:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c:1243:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
At top level:
bxmlobj.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bxmlobj.c,v 6.11 2006/09/18 15:20:39 bealer Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF dotseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from ../include/tofasta.h:47,
from ../include/dotseq.h:63,
from dotseq.c:86:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dotseq.c:96:36: warning: missing braces around initializer [-Wmissing-braces]
static Int4 DOTblosum62[24][24] = {
^
dotseq.c:96:36: note: (near initialization for 'DOTblosum62')
dotseq.c: In function 'DOT_BuildPLookup':
dotseq.c:887:31: warning: variable 'found_ambig' set but not used [-Wunused-but-set-variable]
Boolean EXACTMATCH, found_ambig, saved_index = FALSE;
^~~~~~~~~~~
dotseq.c:885:19: warning: unused variable 'threshold' [-Wunused-variable]
Int4 threshold=13; /* one-hit heuristics T must be at least 13*/
^~~~~~~~~
dotseq.c:883:19: warning: unused variable 'index' [-Wunused-variable]
Int4 index = 0;
^~~~~
dotseq.c: In function 'DOT_ComputeHits':
dotseq.c:1043:47: warning: variable 'q_end' set but not used [-Wunused-but-set-variable]
Uint1Ptr s, subject0, s_end, q_end;
^~~~~
dotseq.c:1041:19: warning: unused variable 'saved_index' [-Wunused-variable]
Boolean saved_index = FALSE;
^~~~~~~~~~~
dotseq.c:1039:19: warning: unused variable 'threshold' [-Wunused-variable]
Int4 threshold=13;
^~~~~~~~~
dotseq.c: In function 'DOT_SPI_FindBestAlnByDotPlot':
dotseq.c:2016:20: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
dotseq.c:2015:20: warning: variable 'start2' set but not used [-Wunused-but-set-variable]
Int4 start2;
^~~~~~
dotseq.c:2014:20: warning: variable 'start1' set but not used [-Wunused-but-set-variable]
Int4 start1;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from dotseq.c:87:
dotseq.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
dotseq.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: dotseq.c,v 6.14 2006/07/13 17:16:20 bollin Exp $";
^~~~~
dotseq.c: In function 'DOT_BuildHitList':
dotseq.c:1310:19: warning: 'index' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 index;
^~~~~
dotseq.c:1309:19: warning: 'hitlist' may be used uninitialized in this function [-Wmaybe-uninitialized]
DOTDiagPtr PNTR hitlist;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF spidey.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/spidey.h:102,
from spidey.c:259:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
spidey.c: In function 'SPI_PrintResult':
spidey.c:1736:21: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
Int4 offset;
^~~~~~
spidey.c: In function 'SPI_AlnSinglemRNAToPieces':
spidey.c:2850:19: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if (spot->from == spot->to == 0)
~~~~~~~~~~~^~~~~~~~~~~
spidey.c: In function 'SPI_FillInLastmRNAHoles':
spidey.c:6295:21: warning: variable 'internal' set but not used [-Wunused-but-set-variable]
Boolean internal;
^~~~~~~~
spidey.c: In function 'SPI_FindBestAlnByDotPlot':
spidey.c:6441:20: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
spidey.c:6440:20: warning: variable 'start2' set but not used [-Wunused-but-set-variable]
Int4 start2;
^~~~~~
spidey.c:6439:20: warning: variable 'start1' set but not used [-Wunused-but-set-variable]
Int4 start1;
^~~~~~
spidey.c: In function 'SPI_ConnectAlnPieces':
spidey.c:7810:30: warning: variable 'tmparray' set but not used [-Wunused-but-set-variable]
SPI_FragPtr PNTR tmparray;
^~~~~~~~
spidey.c:7796:25: warning: variable 'sfpprev' set but not used [-Wunused-but-set-variable]
SPI_FragPtr sfpprev;
^~~~~~~
spidey.c: In function 'SPI_AdjustSplicesInPieces':
spidey.c:8444:23: warning: variable 'minus' set but not used [-Wunused-but-set-variable]
Boolean minus;
^~~~~
spidey.c: In function 'SPI_CheckMrnaOrder':
spidey.c:10292:35: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if ((ival->strand == Seq_strand_plus == ival2->strand
spidey.c:10296:38: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
|| (ival->strand == Seq_strand_minus == ival2->strand
spidey.c:10309:35: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if ((ival->strand == Seq_strand_plus == ival2->strand
spidey.c:10311:38: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
|| (ival->strand == Seq_strand_plus == ival2->strand
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/spidey.h:103,
from spidey.c:259:
spidey.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
spidey.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: spidey.c,v 6.73 2006/06/01 14:55:31 kskatz Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF motif.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/motif.h:45,
from motif.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
motif.c: In function 'MOT_FindPolyA':
motif.c:86:18: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
Uint1 buf[MOT_WINSIZE];
^~~
motif.c: In function 'MOT_FindKozak':
motif.c:216:18: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
Uint1 buf[MOT_WINSIZE];
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from ../include/motif.h:48,
from motif.c:47:
motif.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
motif.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: motif.c,v 6.7 2007/05/07 13:30:54 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blfmtutl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blfmtutl.c:172:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blfmtutl.c: In function 'CBStatisticsGetReference':
blfmtutl.c:590:4: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
} else
^~~~
blfmtutl.c:592:4: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
add_string_to_bufferEx("Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,", &ret_buffer, &ret_buffer_length, TRUE);
^~~~~~~~~~~~~~~~~~~~~~
At top level:
blfmtutl.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blfmtutl.c,v 1.43 2011/10/28 14:24:13 coulouri Exp $";
^~~~~
blfmtutl.c: In function 'BlastPrintTabularResults':
blfmtutl.c:1113:13: warning: 'alignments_count' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (--alignments_count < 0)
^
blfmtutl.c:1331:19: warning: 's_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
s_end += s_shift;
~~~~~~^~~~~~~~~~
blfmtutl.c:1330:21: warning: 's_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
s_start += s_shift;
~~~~~~~~^~~~~~~~~~
blfmtutl.c:1329:19: warning: 'q_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
q_end += q_shift;
~~~~~~^~~~~~~~~~
blfmtutl.c:1328:21: warning: 'q_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
q_start += q_shift;
~~~~~~~~^~~~~~~~~~
blfmtutl.c:1077:24: warning: 'query_id' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (slp && SeqIdComp(query_id, SeqLocId(slp)) != SIC_YES)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blfmtutl.c: In function 'BlastSetUserErrorString':
blfmtutl.c:1392:26: warning: 'title' may be used uninitialized in this function [-Wmaybe-uninitialized]
CharPtr buf_start, ptr, title;
^~~~~
rm -f libncbitool.a
ar cru libncbitool.a csim.o db_slist.o dust.o blast_dust.o falign.o g_any.o sim2.o sim3.o sim4.o simutil.o slist.o sec.o tfuns.o toasn3.o toporg.o pobutil.o stsutil.o suggadj.o suggest.o suggslp.o blast.o blastutl.o blastool.o blastconcat.o splutil.o gapxdrop.o bandalg0.o bandalg1.o bandalg2.o bandalg3.o bandalg4.o bandalg5.o bandalgn.o blastkar.o actutils.o posit.o lookup.o readdb.o ncbisam.o ncbisort.o salign.o salptool.o urkutil.o urkpcc.o urkptpf.o urkepi.o urkfltr.o urkdust.o urksigu.o seg.o urkbias.o urkcnsrt.o urktree.o pseed3.o pattern1.o impatool.o posit2.o mbalign.o vecscrn.o mblast.o rpsutil.o kappa.o xmlblast.o bxmlobj.o dotseq.o spidey.o motif.o blfmtutl.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbitool.a ../lib
ranlib ../lib/libncbitool.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF matrix_frequency_data.c
matrix_frequency_data.c:31:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF compo_mode_condition.c
compo_mode_condition.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF composition_adjustment.c
composition_adjustment.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF nlm_linear_algebra.c
nlm_linear_algebra.c:31:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF optimize_target_freq.c
optimize_target_freq.c:86:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF compo_heap.c
compo_heap.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF smith_waterman.c
smith_waterman.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF redo_alignment.c
redo_alignment.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF unified_pvalues.c
unified_pvalues.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
rm -f libblastcompadj.a
ar cru libblastcompadj.a matrix_frequency_data.o compo_mode_condition.o composition_adjustment.o nlm_linear_algebra.o optimize_target_freq.o compo_heap.o smith_waterman.o redo_alignment.o unified_pvalues.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libblastcompadj.a ../lib
ranlib ../lib/libblastcompadj.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gdfontg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/gifgen.h:115,
from gdfontg.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gdfontmb.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/gifgen.h:115,
from gdfontmb.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gdfontt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/gifgen.h:115,
from gdfontt.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF pictogif.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from pictogif.c:50:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gdfontl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/gifgen.h:115,
from gdfontl.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gdfonts.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/gifgen.h:115,
from gdfonts.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -DWIN_GIF -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbidrwg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ncbidrwg.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbidrwg.c: In function 'Nlm_ClearRgn':
ncbidrwg.c:6081:16: warning: variable 'ntool' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool;
^~~~~
ncbidrwg.c: In function 'Nlm_DiffRgn':
ncbidrwg.c:6273:16: warning: variable 'ntool3' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool3;
^~~~~~
ncbidrwg.c:6272:16: warning: variable 'ntool2' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool2;
^~~~~~
ncbidrwg.c:6271:16: warning: variable 'ntool1' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool1;
^~~~~~
ncbidrwg.c: In function 'Nlm_XorRgn':
ncbidrwg.c:6324:16: warning: variable 'ntool3' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool3;
^~~~~~
ncbidrwg.c:6323:16: warning: variable 'ntool2' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool2;
^~~~~~
ncbidrwg.c:6322:16: warning: variable 'ntool1' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool1;
^~~~~~
ncbidrwg.c: In function 'Nlm_EqualRgn':
ncbidrwg.c:6353:16: warning: variable 'ntool2' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool2;
^~~~~~
ncbidrwg.c:6352:16: warning: variable 'ntool1' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool1;
^~~~~~
ncbidrwg.c: In function 'Nlm_EmptyRgn':
ncbidrwg.c:6381:17: warning: variable 'ntool' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool;
^~~~~
ncbidrwg.c: In function 'Nlm_CopyPixmap':
ncbidrwg.c:7040:25: warning: variable 'height' set but not used [-Wunused-but-set-variable]
Nlm_Int2 height;
^~~~~~
ncbidrwg.c:7039:25: warning: variable 'width' set but not used [-Wunused-but-set-variable]
Nlm_Int2 width;
^~~~~
ncbidrwg.c: In function 'Nlm_GetColorRGB':
ncbidrwg.c:1373:10: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (Nlm_Uint4)i;
^~~~~~~~~~~~
rm -f libvibgif.a
ar cru libvibgif.a gdfontg.o gdfontmb.o gdfontt.o pictogif.o gdfontl.o gdfonts.o ncbidrwg.o drawing.o mapping.o picture.o ncbimain.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libvibgif.a ../lib
ranlib ../lib/libvibgif.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF algorend.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/viewer3d.h:125,
from algorend.c:584:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
algorend.c: In function 'ColorFromSS':
algorend.c:893:10: warning: unused variable 'rsult' [-Wunused-variable]
Int2 rsult = 0;
^~~~~
algorend.c: In function 'Cn3D_RenWire':
algorend.c:1400:10: warning: unused variable 'pmldThis' [-Wunused-variable]
PMLD pmldThis = NULL;
^~~~~~~~
algorend.c:1399:11: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
algorend.c:1398:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
algorend.c: In function 'Cn3D_ColSeqCons':
algorend.c:1795:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
pars->ConsColAlg = (Nlm_Int2) GetObjectExtra(i);
^
algorend.c: In function 'RenderObject':
algorend.c:3135:25: warning: variable 'fZTo' set but not used [-Wunused-but-set-variable]
FloatLo fXTo, fYTo, fZTo;
^~~~
algorend.c:3135:19: warning: variable 'fYTo' set but not used [-Wunused-but-set-variable]
FloatLo fXTo, fYTo, fZTo;
^~~~
algorend.c:3135:13: warning: variable 'fXTo' set but not used [-Wunused-but-set-variable]
FloatLo fXTo, fYTo, fZTo;
^~~~
algorend.c:3134:29: warning: variable 'fZFrom' set but not used [-Wunused-but-set-variable]
FloatLo fXFrom, fYFrom, fZFrom;
^~~~~~
algorend.c:3134:21: warning: variable 'fYFrom' set but not used [-Wunused-but-set-variable]
FloatLo fXFrom, fYFrom, fZFrom;
^~~~~~
algorend.c:3134:13: warning: variable 'fXFrom' set but not used [-Wunused-but-set-variable]
FloatLo fXFrom, fYFrom, fZFrom;
^~~~~~
algorend.c: In function 'RenderLabel':
algorend.c:3393:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
algorend.c: In function 'RenderBond':
algorend.c:3554:10: warning: variable 'pmsdParent' set but not used [-Wunused-but-set-variable]
PMSD pmsdParent = NULL;
^~~~~~~~~~
algorend.c: In function 'RenderHalfWormBond':
algorend.c:3673:10: warning: variable 'pmsdParent' set but not used [-Wunused-but-set-variable]
PMSD pmsdParent;
^~~~~~~~~~
algorend.c:3671:24: warning: variable 'pmad2' set but not used [-Wunused-but-set-variable]
PMAD pmad0, pmad1, pmad2, pmad3;
^~~~~
algorend.c: In function 'RenderAnAtom':
algorend.c:3758:10: warning: unused variable 'pmadFrom' [-Wunused-variable]
PMAD pmadFrom = NULL;
^~~~~~~~
algorend.c:3757:10: warning: variable 'pmsdParent' set but not used [-Wunused-but-set-variable]
PMSD pmsdParent = NULL;
^~~~~~~~~~
algorend.c: In function 'RenderAllAtom':
algorend.c:3829:9: warning: variable 'iMenu' set but not used [-Wunused-but-set-variable]
int iMenu;
^~~~~
algorend.c:3815:11: warning: unused variable 'pvnmbThis' [-Wunused-variable]
PVNMB pvnmbThis = NULL;
^~~~~~~~~
algorend.c:3811:11: warning: unused variable 'pvnmaThis' [-Wunused-variable]
PVNMA pvnmaThis = NULL;
^~~~~~~~~
algorend.c: In function 'RenderGraph':
algorend.c:4498:10: warning: unused variable 'bReservedThis' [-Wunused-variable]
Byte bReservedThis = 0;
^~~~~~~~~~~~~
algorend.c: In function 'LabelChainTermini':
algorend.c:4772:14: warning: unused variable 'pmbdThis' [-Wunused-variable]
PMBD pmbdThis = NULL;
^~~~~~~~
algorend.c:4771:15: warning: unused variable 'pvnmbThis' [-Wunused-variable]
PVNMB pvnmbThis = NULL;
^~~~~~~~~
algorend.c: In function 'RenderMolecule':
algorend.c:4871:11: warning: variable 'pdnmmThis' set but not used [-Wunused-but-set-variable]
PDNMM pdnmmThis = NULL;
^~~~~~~~~
algorend.c: In function 'fnARLoop':
algorend.c:5556:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest;
^~~~~
algorend.c: In function 'AlgorithmicRendering':
algorend.c:5684:10: warning: unused variable 'i' [-Wunused-variable]
Int2 i = 0;
^
algorend.c:5683:10: warning: unused variable 'Cn3d_LayerNow_sofar' [-Wunused-variable]
Int2 Cn3d_LayerNow_sofar = 0;
^~~~~~~~~~~~~~~~~~~
algorend.c: In function 'Do3DOrigin':
algorend.c:5756:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
algorend.c:5751:13: warning: variable 'fTo' set but not used [-Wunused-but-set-variable]
FloatLo fTo[3];
^~~
algorend.c:5750:13: warning: variable 'fFrom' set but not used [-Wunused-but-set-variable]
FloatLo fFrom[3];
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from algorend.c:598:
algorend.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
algorend.c:2265:13: warning: 'LabelGroupOnOffProc' defined but not used [-Wunused-function]
static void LabelGroupOnOffProc(GrouP g)
^~~~~~~~~~~~~~~~~~~
algorend.c:717:16: warning: 'Cn3d_CopyToNode' defined but not used [-Wunused-variable]
static Boolean Cn3d_CopyToNode = FALSE;
^~~~~~~~~~~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
algorend.c: In function 'RenderLabel':
../include/pictur3d.h:235:27: warning: 'iX' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddText3D Nlm_AddText3D
^~~~~~~~~~~~~
algorend.c:3389:10: note: 'iX' was declared here
Int4 iX, iY, iZ;
^~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:235:27: warning: 'iY' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddText3D Nlm_AddText3D
^~~~~~~~~~~~~
algorend.c:3389:14: note: 'iY' was declared here
Int4 iX, iY, iZ;
^~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:235:27: warning: 'iZ' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddText3D Nlm_AddText3D
^~~~~~~~~~~~~
algorend.c:3389:18: note: 'iZ' was declared here
Int4 iX, iY, iZ;
^~
algorend.c:3444:41: warning: 'fZCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fZt = (fZCen - fZFrom) + (fZCen - fZTo);
~~~~~~~^~~~~~~
algorend.c:3443:41: warning: 'fYCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~
algorend.c:3442:41: warning: 'fXCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~
algorend.c:3444:41: warning: 'fZTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fZt = (fZCen - fZFrom) + (fZCen - fZTo);
~~~~~~~^~~~~~~
algorend.c:3443:41: warning: 'fYTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~
algorend.c:3442:41: warning: 'fXTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~
algorend.c:3444:22: warning: 'fZFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fZt = (fZCen - fZFrom) + (fZCen - fZTo);
~~~~~~~^~~~~~~~~
algorend.c:3443:22: warning: 'fYFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~~~
algorend.c:3442:22: warning: 'fXFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~~~
algorend.c: In function 'MasterChangeRenderProc.isra.1':
algorend.c:1316:33: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
pars->SolventRender = k;
~~~~~~~~~~~~~~~~~~~~^~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
algorend.c: In function 'RenderObject':
../include/pictur3d.h:234:27: warning: 'iXFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3136:10: note: 'iXFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:234:27: warning: 'iYFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3136:18: note: 'iYFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:234:27: warning: 'iZFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3136:26: note: 'iZFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:234:27: warning: 'iXTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3137:10: note: 'iXTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:234:27: warning: 'iYTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3137:16: note: 'iYTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:234:27: warning: 'iZTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3137:22: note: 'iZTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
algorend.c: In function 'Do3DOrigin':
../include/pictur3d.h:232:27: warning: 'iXFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5752:10: note: 'iXFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:232:27: warning: 'iYFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5752:18: note: 'iYFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:232:27: warning: 'iZFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5752:26: note: 'iZFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:232:27: warning: 'iXTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5753:10: note: 'iXTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:232:27: warning: 'iYTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5753:16: note: 'iYTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:232:27: warning: 'iZTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5753:22: note: 'iZTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dmsel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmsel.c:60:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dopen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dopen.c:394:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dopen.c: In function 'Cn3D_OpenStart':
cn3dopen.c:722:10: warning: unused variable 'iBioseq' [-Wunused-variable]
Int4 iBioseq = 0;
^~~~~~~
cn3dopen.c: In function 'MMDB_ReadMime':
cn3dopen.c:1000:19: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
cn3dopen.c:989:25: warning: unused variable 'pbsasThis' [-Wunused-variable]
BiostrucAlignSeqPtr pbsasThis = NULL;
^~~~~~~~~
cn3dopen.c: In function 'Cn3D_NetOpenBiostruc':
cn3dopen.c:1310:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dopen.c:412:
cn3dopen.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from cn3dopen.c:413:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
cn3dopen.c:431:15: warning: 'Cn3D_bOpenBrowse' defined but not used [-Wunused-variable]
static ButtoN Cn3D_bOpenBrowse;
^~~~~~~~~~~~~~~~
cn3dopen.c:430:15: warning: 'Cn3D_wOpen' defined but not used [-Wunused-variable]
static WindoW Cn3D_wOpen;
^~~~~~~~~~
cn3dopen.c: In function 'MMDB_ReadMime':
cn3dopen.c:529:9: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAM_ReplaceGI(salp);
^~~~~~~~~~~~~~~~~~~
cn3dopen.c:513:15: note: 'salp' was declared here
SeqAlign *salp;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dsave.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dsave.c:157:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dsave.c: In function 'Cn3D_ExportAsnNow':
cn3dsave.c:375:11: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
cn3dsave.c:372:24: warning: variable 'pbsfThis' set but not used [-Wunused-but-set-variable]
BiostrucFeaturePtr pbsfThis;
^~~~~~~~
cn3dsave.c:366:10: warning: unused variable 'pmsdSlave' [-Wunused-variable]
PMSD pmsdSlave = NULL, pmsdMaster = NULL;
^~~~~~~~~
cn3dsave.c:362:27: warning: variable 'FirstSlave' set but not used [-Wunused-but-set-variable]
Boolean iCn3d = TRUE, FirstSlave = FALSE;
^~~~~~~~~~
cn3dsave.c:357:13: warning: unused variable 'pcSave' [-Wunused-variable]
CharPtr pcSave = NULL;
^~~~~~
cn3dsave.c: In function 'Cn3D_SaveBiostruc':
cn3dsave.c:524:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dsave.c:523:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dsave.c:518:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dsave.c: In function 'Cn3D_ExportDictNow':
cn3dsave.c:598:13: warning: unused variable 'pcSave' [-Wunused-variable]
CharPtr pcSave = NULL;
^~~~~~
cn3dsave.c:596:10: warning: unused variable 'iCount' [-Wunused-variable]
Int4 iCount = 0;
^~~~~~
cn3dsave.c: In function 'Cn3D_SaveDictionary':
cn3dsave.c:629:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dsave.c:624:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dsave.c: In function 'Cn3D_SaveSub':
cn3dsave.c:688:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
IteM i;
^
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dsave.c:171:
cn3dsave.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
cn3dsave.c:184:15: warning: 'Cn3D_bFeatOn' defined but not used [-Wunused-variable]
static ButtoN Cn3D_bFeatOn;
^~~~~~~~~~~~
In file included from cn3dsave.c:165:0:
../include/asnmime.h:119:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnmime.h:118:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnmime.h:117:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/asnmime.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnmime.h12";
^~~~~~~~~~~
cn3dsave.c: In function 'Cn3D_GetSubSet.isra.1':
cn3dsave.c:289:24: warning: 'isep' may be used uninitialized in this function [-Wmaybe-uninitialized]
isep->next = SeqEntryNew();
~~~~~~~~~~~^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dxprt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dxprt.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportPDB':
cn3dxprt.c:209:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dxprt.c:208:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dxprt.c:203:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportKin':
cn3dxprt.c:381:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dxprt.c:380:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dxprt.c:375:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportSub':
cn3dxprt.c:513:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
IteM i;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dwin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dwin.c:647:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dwin.c:733:1: warning: missing braces around initializer [-Wmissing-braces]
{
^
cn3dwin.c:733:1: note: (near initialization for 'Cn3d_PaletteRGB')
cn3dwin.c: In function 'Viewer3DGroups':
cn3dwin.c:1728:10: warning: unused variable 'groups' [-Wunused-variable]
Int2 groups = 0;
^~~~~~
cn3dwin.c: In function 'Viewer3DViewer':
cn3dwin.c:1784:10: warning: unused variable 'groups' [-Wunused-variable]
Int2 groups = 0;
^~~~~~
cn3dwin.c: In function 'Cn3D_AlignEdit':
cn3dwin.c:1936:10: warning: unused variable 'iCount' [-Wunused-variable]
Int2 iCount = 0;
^~~~~~
cn3dwin.c:1935:10: warning: variable 'pmmdThis' set but not used [-Wunused-but-set-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dwin.c:1933:17: warning: unused variable 'salp' [-Wunused-variable]
SeqAlignPtr salp = NULL;
^~~~
cn3dwin.c:1931:29: warning: variable 'pmsdSlave' set but not used [-Wunused-but-set-variable]
PMSD pmsdMaster = NULL, pmsdSlave = NULL;
^~~~~~~~~
cn3dwin.c:1930:11: warning: unused variable 'pdnmsSlave' [-Wunused-variable]
PDNMS pdnmsSlave = NULL;
^~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/udviewer.h:219,
from cn3dwin.c:665:
cn3dwin.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/udviewer.h:228,
from cn3dwin.c:665:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
cn3dwin.c:1626:13: warning: 'HLmolecule_MA' defined but not used [-Wunused-function]
static void HLmolecule_MA(MAPtr ma,
^~~~~~~~~~~~~
cn3dwin.c:1428:13: warning: 'HLatom_MA' defined but not used [-Wunused-function]
static void HLatom_MA(MAPtr ma,
^~~~~~~~~
cn3dwin.c:929:13: warning: 'Cn3D_MoveCB' defined but not used [-Wunused-function]
static void Cn3D_MoveCB(IteM i)
^~~~~~~~~~~
cn3dwin.c:922:13: warning: 'Cn3D_ZoomCB' defined but not used [-Wunused-function]
static void Cn3D_ZoomCB(IteM i)
^~~~~~~~~~~
cn3dwin.c:688:13: warning: 'Cn3D_iModelCtrl' defined but not used [-Wunused-variable]
static IteM Cn3D_iModelCtrl = NULL;
^~~~~~~~~~~~~~~
cn3dwin.c:682:13: warning: 'Cn3D_iLabelCtrl' defined but not used [-Wunused-variable]
static IteM Cn3D_iLabelCtrl = NULL;
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/cn3dmain.h:182,
from cn3dentr.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dmsg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmsg.c:254:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmsg.c: In function 'SeqStrucMediaMsgFunc':
cn3dmsg.c:593:19: warning: variable 'omudp' set but not used [-Wunused-but-set-variable]
OMUserDataPtr omudp = NULL;
^~~~~
In file included from ../include/sqnutils.h:51:0,
from cn3dmsg.c:267:
cn3dmsg.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dmsg.c:271:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dmatn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmatn.c:173:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmatn.c: In function 'FindMM':
cn3dmatn.c:217:29: warning: unused variable 'pdnmsThisSlave' [-Wunused-variable]
PDNMS pdnmsThis = NULL, pdnmsThisSlave = NULL;
^~~~~~~~~~~~~~
cn3dmatn.c: In function 'DoMediaHL':
cn3dmatn.c:249:10: warning: variable 'MainAtom' set but not used [-Wunused-but-set-variable]
Byte MainAtom = 0;
^~~~~~~~
cn3dmatn.c:247:10: warning: unused variable 'paldThis' [-Wunused-variable]
PALD paldThis = NULL;
^~~~~~~~
cn3dmatn.c:246:11: warning: unused variable 'pvnalThis' [-Wunused-variable]
PVNAL pvnalThis = NULL;
^~~~~~~~~
cn3dmatn.c:245:10: warning: unused variable 'pmadThis' [-Wunused-variable]
PMAD pmadThis = NULL;
^~~~~~~~
cn3dmatn.c:244:11: warning: unused variable 'pvnmaThis' [-Wunused-variable]
PVNMA pvnmaThis = NULL;
^~~~~~~~~
cn3dmatn.c: In function 'Cn3DCheckAndDoHighlight':
cn3dmatn.c:372:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dmatn.c:371:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dmodl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmodl.c: In function 'Cn3DCheckNoSingleHighlight':
cn3dmodl.c:353:11: warning: unused variable 'pdnmgThis' [-Wunused-variable]
PDNMG pdnmgThis = NULL;
^~~~~~~~~
cn3dmodl.c: In function 'Cn3DCheckHighlighted':
cn3dmodl.c:364:29: warning: unused variable 'pmsdSlave' [-Wunused-variable]
PMSD pmsdMaster = NULL, pmsdSlave = NULL;
^~~~~~~~~
cn3dmodl.c: In function 'Cn3D_ReSetVisibleStatus':
cn3dmodl.c:508:10: warning: unused variable 'pmgd' [-Wunused-variable]
PMGD pmgd = NULL;
^~~~
cn3dmodl.c:507:11: warning: unused variable 'pdnmg' [-Wunused-variable]
PDNMG pdnmg = NULL;
^~~~~
cn3dmodl.c:506:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'fnAlignList':
cn3dmodl.c:996:25: warning: unused variable 'itemtype' [-Wunused-variable]
Uint2 entityID = 0, itemtype = 0;
^~~~~~~~
cn3dmodl.c:996:11: warning: unused variable 'entityID' [-Wunused-variable]
Uint2 entityID = 0, itemtype = 0;
^~~~~~~~
cn3dmodl.c:995:14: warning: unused variable 'sipThis' [-Wunused-variable]
SeqIdPtr sipThis = NULL;
^~~~~~~
cn3dmodl.c:993:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'SynchronizeModVisibleStatus':
cn3dmodl.c:1065:11: warning: unused variable 'pdnmg' [-Wunused-variable]
PDNMG pdnmg = NULL;
^~~~~
cn3dmodl.c:1064:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'SetResidueVisibilities':
cn3dmodl.c:1201:11: warning: unused variable 'pvnmoThis' [-Wunused-variable]
PVNMO pvnmoThis = NULL;
^~~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dmodl.c:319:
cn3dmodl.c: At top level:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dmodl.c:323:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dshim.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/cn3dmain.h:182,
from cn3dshim.c:131:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dmesh.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmesh.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmesh.c: In function 'Cn3D_MeshAcceptProc':
cn3dmesh.c:103:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dmesh.c: In function 'Cn3D_OpenMesh':
cn3dmesh.c:151:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dmesh.c: In function 'Cn3D_MeshAcceptProc':
cn3dmesh.c:111:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d", &(Mesh.NumVert), &(Mesh.NumEdge),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.NumTri));
~~~~~~~~~~~~~~~
cn3dmesh.c:119:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%lf %lf %lf %lf %lf %lf %f %f %f %d %d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[0]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[1]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[2]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[0]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[1]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[2]), &fDummy, &fDummy, &fDummy,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&lDummy, &lDummy, &lDummy);
~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmesh.c:129:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d %d %d", &Mesh.Edges[i].Vertex[0],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Edges[i].Vertex[1], &lDummy, &lDummy, &lDummy);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmesh.c:133:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d %d %d %d %d %d %d", &Mesh.Tri[i].Edge[0],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Edge[1], &Mesh.Tri[i].Edge[2],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Vertex[0], &Mesh.Tri[i].Vertex[1],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Vertex[2], &lDummy, &Mesh.Tri[i].Atom,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&lDummy);
~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dstyl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dstyl.c:72:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dstyl.c: In function 'GetThisSpecialAlgorRenderSet':
cn3dstyl.c:459:27: warning: unused variable 'sfipThis' [-Wunused-variable]
SpecialFeatureInfoPtr sfipThis = NULL;
^~~~~~~~
cn3dstyl.c: In function 'GetSpecialAlgorRenderSet':
cn3dstyl.c:641:10: warning: unused variable 'parsThis' [-Wunused-variable]
PARS parsThis = NULL;
^~~~~~~~
cn3dstyl.c:640:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'ChangeSpecialLabelsProc':
cn3dstyl.c:866:44: warning: unused variable 'PDBOn' [-Wunused-variable]
Boolean NumOn = FALSE, NameOn = FALSE, PDBOn = FALSE, WhiteOn =
^~~~~
cn3dstyl.c: In function 'lFeatureEditedAction':
cn3dstyl.c:1136:10: warning: unused variable 'val' [-Wunused-variable]
Int4 val = 0;
^~~
cn3dstyl.c: In function 'bFeatureMoveAction':
cn3dstyl.c:1153:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'bFeatureEditAction':
cn3dstyl.c:1176:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'ModelControls':
cn3dstyl.c:1364:19: warning: variable 'ppt13' set but not used [-Wunused-but-set-variable]
PrompT ppt12, ppt13, ppt14;
^~~~~
cn3dstyl.c:1362:36: warning: variable 'ppt5' set but not used [-Wunused-but-set-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10,
^~~~
cn3dstyl.c:1362:12: warning: variable 'ppt1' set but not used [-Wunused-but-set-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10,
^~~~
cn3dstyl.c: In function 'GetBiostrucFeatureLocationForHihglightedResidues':
cn3dstyl.c:1728:30: warning: variable 'SingleInterval' set but not used [-Wunused-but-set-variable]
Boolean Started = FALSE, SingleInterval, UserDefinedFeatureFound =
^~~~~~~~~~~~~~
cn3dstyl.c:1725:20: warning: variable 'iMolCurrent' set but not used [-Wunused-but-set-variable]
Int2 iMol = 0, iMolCurrent = 0;
^~~~~~~~~~~
cn3dstyl.c: In function 'MakeBiostrucFeatureSetForUserDefinedFeature':
cn3dstyl.c:2122:60: warning: unused variable 'bsfsp_tail' [-Wunused-variable]
BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail =
^~~~~~~~~~
cn3dstyl.c:2122:41: warning: unused variable 'bsfsp_head' [-Wunused-variable]
BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail =
^~~~~~~~~~
cn3dstyl.c: In function 'GetUserDefinedFeature':
cn3dstyl.c:2196:27: warning: unused variable 'sfipThis' [-Wunused-variable]
SpecialFeatureInfoPtr sfipThis = NULL;
^~~~~~~~
cn3dstyl.c: In function 'Cn3DIndexUserDefinedFeature':
cn3dstyl.c:2551:23: warning: variable 'sfpThis' set but not used [-Wunused-but-set-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c:2549:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dstyl.c:2548:11: warning: unused variable 'pdnmmHead' [-Wunused-variable]
PDNMM pdnmmHead = NULL;
^~~~~~~~~
cn3dstyl.c:2547:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dstyl.c:89:
cn3dstyl.c: At top level:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c:456:30: warning: 'GetThisSpecialAlgorRenderSet' defined but not used [-Wunused-function]
static SpecialFeatureInfoPtr GetThisSpecialAlgorRenderSet(Int2 id)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c:149:15: warning: 'bResetFeatureTitle' defined but not used [-Wunused-variable]
static ButtoN bResetFeatureTitle;
^~~~~~~~~~~~~~~~~~
cn3dstyl.c:144:14: warning: 'Cn3D_pupModelStyleItem' defined but not used [-Wunused-variable]
static PopuP Cn3D_pupModelStyleItem;
^~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c: In function 'CopyLocation':
cn3dstyl.c:496:27: warning: 'rsipNewHead' may be used uninitialized in this function [-Wmaybe-uninitialized]
rspNew->data.ptrvalue = (VoidPtr) rsipNewHead;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqcons.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from seqcons.c:112:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from seqcons.c:115:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/alignmgr2.h:111,
from ../include/actutils.h:105,
from seqcons.c:116:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
seqcons.c:263:19: warning: 'CSC_Blosum62Fields' defined but not used [-Wunused-const-variable=]
static const char CSC_Blosum62Fields[CSC_BLOSUMSIZE] =
^~~~~~~~~~~~~~~~~~
seqcons.c: In function 'CSC_Algorithm_ByBlosum62':
seqcons.c:402:43: warning: 'minScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
scale = 1.0 - 1.0 * (score[i] - minScore) / (maxScore - minScore);
~~~~~~~~~~^~~~~~~~~~~
seqcons.c:402:67: warning: 'maxScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
scale = 1.0 - 1.0 * (score[i] - minScore) / (maxScore - minScore);
~~~~~~~~~~^~~~~~~~~~~
rm -f libncbicn3d.a
ar cru libncbicn3d.a algorend.o cn3dmsel.o cn3dopen.o cn3dsave.o cn3dxprt.o cn3dwin.o cn3dentr.o cn3dmsg.o cn3dmatn.o cn3dmodl.o cn3dshim.o cn3dmesh.o cn3dstyl.o seqcons.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbicn3d.a ../lib
ranlib ../lib/libncbicn3d.a
mv algorend.o algorend.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL algorend.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/shim3d.h:153,
from algorend.c:582:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
algorend.c: In function 'Cn3D_SetOGLFont':
algorend.c:791:24: warning: unused variable 'currentUnderlined' [-Wunused-variable]
currentUnderlined = FALSE;
^~~~~~~~~~~~~~~~~
algorend.c:790:45: warning: unused variable 'currentItalic' [-Wunused-variable]
static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE,
^~~~~~~~~~~~~
algorend.c:790:24: warning: unused variable 'currentBold' [-Wunused-variable]
static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE,
^~~~~~~~~~~
algorend.c:789:40: warning: unused variable 'currentSize' [-Wunused-variable]
static Nlm_Int2 currentIndex = -1, currentSize = -1;
^~~~~~~~~~~
algorend.c:789:21: warning: unused variable 'currentIndex' [-Wunused-variable]
static Nlm_Int2 currentIndex = -1, currentSize = -1;
^~~~~~~~~~~~
algorend.c: In function 'ColorFromSS':
algorend.c:893:10: warning: unused variable 'rsult' [-Wunused-variable]
Int2 rsult = 0;
^~~~~
algorend.c: In function 'Cn3D_RenWire':
algorend.c:1400:10: warning: unused variable 'pmldThis' [-Wunused-variable]
PMLD pmldThis = NULL;
^~~~~~~~
algorend.c:1399:11: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
algorend.c:1398:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
algorend.c: In function 'Cn3D_ColSeqCons':
algorend.c:1795:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
pars->ConsColAlg = (Nlm_Int2) GetObjectExtra(i);
^
algorend.c: In function 'MasterChangeLabelsProc':
algorend.c:2075:44: warning: unused variable 'TopOn' [-Wunused-variable]
Boolean NumOn, NameOn, PDBOn, WhiteOn, TopOn;
^~~~~
algorend.c:2073:13: warning: unused variable 'k' [-Wunused-variable]
Int2 i, k, nameval;
^
algorend.c: In function 'ResetLabelCtrls':
algorend.c:2272:25: warning: variable 'size' set but not used [-Wunused-but-set-variable]
Int2 i, val, style, size, termStyle;
^~~~
algorend.c: In function 'LabelControls':
algorend.c:2434:19: warning: variable 'ppt11' set but not used [-Wunused-but-set-variable]
PrompT ppt10, ppt11;
^~~~~
algorend.c:2431:36: warning: unused variable 'ppt7' [-Wunused-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt7, ppt8, ppt9;
^~~~
algorend.c: In function 'Cn3D_SetQualityFromAppParams':
algorend.c:2649:9: warning: unused variable 'i' [-Wunused-variable]
int i;
^
algorend.c: In function 'OGL_Quality':
algorend.c:2769:23: warning: unused variable 'q' [-Wunused-variable]
Nlm_PrompT bp, p, q;
^
algorend.c:2769:20: warning: variable 'p' set but not used [-Wunused-but-set-variable]
Nlm_PrompT bp, p, q;
^
algorend.c:2769:16: warning: variable 'bp' set but not used [-Wunused-but-set-variable]
Nlm_PrompT bp, p, q;
^~
algorend.c: In function 'RenderControls':
algorend.c:2893:12: warning: variable 'ppt5' set but not used [-Wunused-but-set-variable]
PrompT ppt5;
^~~~
algorend.c: In function 'RenderObject':
algorend.c:3138:10: warning: unused variable 'iCylRadius' [-Wunused-variable]
Int4 iCylRadius;
^~~~~~~~~~
algorend.c:3137:22: warning: unused variable 'iZTo' [-Wunused-variable]
Int4 iXTo, iYTo, iZTo;
^~~~
algorend.c:3137:16: warning: unused variable 'iYTo' [-Wunused-variable]
Int4 iXTo, iYTo, iZTo;
^~~~
algorend.c:3137:10: warning: unused variable 'iXTo' [-Wunused-variable]
Int4 iXTo, iYTo, iZTo;
^~~~
algorend.c:3136:26: warning: unused variable 'iZFrom' [-Wunused-variable]
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
algorend.c:3136:18: warning: unused variable 'iYFrom' [-Wunused-variable]
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
algorend.c:3136:10: warning: unused variable 'iXFrom' [-Wunused-variable]
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
algorend.c:3133:10: warning: unused variable 'i' [-Wunused-variable]
Int4 i = 0;
^
algorend.c: In function 'RenderLabel':
algorend.c:3394:10: warning: variable 'paldPrim' set but not used [-Wunused-but-set-variable]
PALD paldPrim = NULL;
^~~~~~~~
algorend.c:3393:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
algorend.c:3389:18: warning: unused variable 'iZ' [-Wunused-variable]
Int4 iX, iY, iZ;
^~
algorend.c:3389:14: warning: unused variable 'iY' [-Wunused-variable]
Int4 iX, iY, iZ;
^~
algorend.c:3389:10: warning: unused variable 'iX' [-Wunused-variable]
Int4 iX, iY, iZ;
^~
algorend.c: In function 'RenderBond':
algorend.c:3554:10: warning: variable 'pmsdParent' set but not used [-Wunused-but-set-variable]
PMSD pmsdParent = NULL;
^~~~~~~~~~
algorend.c: In function 'RenderHalfWormBond':
algorend.c:3673:10: warning: variable 'pmsdParent' set but not used [-Wunused-but-set-variable]
PMSD pmsdParent;
^~~~~~~~~~
algorend.c:3671:24: warning: variable 'pmad2' set but not used [-Wunused-but-set-variable]
PMAD pmad0, pmad1, pmad2, pmad3;
^~~~~
algorend.c: In function 'RenderAnAtom':
algorend.c:3758:10: warning: unused variable 'pmadFrom' [-Wunused-variable]
PMAD pmadFrom = NULL;
^~~~~~~~
algorend.c: In function 'RenderAllAtom':
algorend.c:3829:9: warning: variable 'iMenu' set but not used [-Wunused-but-set-variable]
int iMenu;
^~~~~
algorend.c:3815:11: warning: unused variable 'pvnmbThis' [-Wunused-variable]
PVNMB pvnmbThis = NULL;
^~~~~~~~~
algorend.c:3811:11: warning: unused variable 'pvnmaThis' [-Wunused-variable]
PVNMA pvnmaThis = NULL;
^~~~~~~~~
algorend.c: In function 'RenderGraph':
algorend.c:4498:10: warning: unused variable 'bReservedThis' [-Wunused-variable]
Byte bReservedThis = 0;
^~~~~~~~~~~~~
algorend.c: In function 'LabelChainTermini':
algorend.c:4772:14: warning: unused variable 'pmbdThis' [-Wunused-variable]
PMBD pmbdThis = NULL;
^~~~~~~~
algorend.c:4771:15: warning: unused variable 'pvnmbThis' [-Wunused-variable]
PVNMB pvnmbThis = NULL;
^~~~~~~~~
algorend.c: In function 'RenderMolecule':
algorend.c:4871:11: warning: variable 'pdnmmThis' set but not used [-Wunused-but-set-variable]
PDNMM pdnmmThis = NULL;
^~~~~~~~~
algorend.c: In function 'fnARLoop':
algorend.c:5556:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest;
^~~~~
algorend.c: In function 'AlgorithmicRendering':
algorend.c:5684:10: warning: unused variable 'i' [-Wunused-variable]
Int2 i = 0;
^
algorend.c:5683:10: warning: unused variable 'Cn3d_LayerNow_sofar' [-Wunused-variable]
Int2 Cn3d_LayerNow_sofar = 0;
^~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from algorend.c:598:
algorend.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
algorend.c:789:21: warning: 'currentIndex' defined but not used [-Wunused-variable]
static Nlm_Int2 currentIndex = -1, currentSize = -1;
^~~~~~~~~~~~
algorend.c:789:40: warning: 'currentSize' defined but not used [-Wunused-variable]
static Nlm_Int2 currentIndex = -1, currentSize = -1;
^~~~~~~~~~~
algorend.c:790:24: warning: 'currentBold' defined but not used [-Wunused-variable]
static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE,
^~~~~~~~~~~
algorend.c:790:45: warning: 'currentItalic' defined but not used [-Wunused-variable]
static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE,
^~~~~~~~~~~~~
algorend.c:791:24: warning: 'currentUnderlined' defined but not used [-Wunused-variable]
currentUnderlined = FALSE;
^~~~~~~~~~~~~~~~~
algorend.c:2265:13: warning: 'LabelGroupOnOffProc' defined but not used [-Wunused-function]
static void LabelGroupOnOffProc(GrouP g)
^~~~~~~~~~~~~~~~~~~
algorend.c:717:16: warning: 'Cn3d_CopyToNode' defined but not used [-Wunused-variable]
static Boolean Cn3d_CopyToNode = FALSE;
^~~~~~~~~~~~~~~
algorend.c: In function 'MasterChangeRenderProc':
algorend.c:1316:33: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
pars->SolventRender = k;
~~~~~~~~~~~~~~~~~~~~^~~
algorend.c: In function 'RenderLabel':
algorend.c:3448:15: warning: 'fZCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fZCen += fZt / l;
~~~~~~^~~~~~~~~~
algorend.c:3443:41: warning: 'fYCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~
algorend.c:3442:41: warning: 'fXCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~
algorend.c:3449:41: warning: 'fZTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fYCen - fYFrom) * (fZCen - fZTo) - (fZCen - fZFrom) * (fYCen - fYTo);
~~~~~~~^~~~~~~
algorend.c:3443:41: warning: 'fYTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~
algorend.c:3442:41: warning: 'fXTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~
algorend.c:3449:58: warning: 'fZFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fYCen - fYFrom) * (fZCen - fZTo) - (fZCen - fZFrom) * (fYCen - fYTo);
~~~~~~~^~~~~~~~~
algorend.c:3443:22: warning: 'fYFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~~~
algorend.c:3442:22: warning: 'fXFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~~~
mv algorend.o algorend.glo
mv algorend.tmp algorend.o
mv cn3dmsel.o cn3dmsel.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmsel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmsel.c:60:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv cn3dmsel.o cn3dmsel.glo
mv cn3dmsel.tmp cn3dmsel.o
mv cn3dopen.o cn3dopen.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dopen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dopen.c:394:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dopen.c: In function 'Cn3D_OpenStart':
cn3dopen.c:722:10: warning: unused variable 'iBioseq' [-Wunused-variable]
Int4 iBioseq = 0;
^~~~~~~
cn3dopen.c: In function 'MMDB_ReadMime':
cn3dopen.c:1000:19: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
cn3dopen.c:989:25: warning: unused variable 'pbsasThis' [-Wunused-variable]
BiostrucAlignSeqPtr pbsasThis = NULL;
^~~~~~~~~
cn3dopen.c: In function 'Cn3D_NetOpenBiostruc':
cn3dopen.c:1310:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dopen.c:412:
cn3dopen.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from cn3dopen.c:413:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
cn3dopen.c:431:15: warning: 'Cn3D_bOpenBrowse' defined but not used [-Wunused-variable]
static ButtoN Cn3D_bOpenBrowse;
^~~~~~~~~~~~~~~~
cn3dopen.c:430:15: warning: 'Cn3D_wOpen' defined but not used [-Wunused-variable]
static WindoW Cn3D_wOpen;
^~~~~~~~~~
cn3dopen.c: In function 'MMDB_ReadMime':
cn3dopen.c:529:9: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAM_ReplaceGI(salp);
^~~~~~~~~~~~~~~~~~~
cn3dopen.c:513:15: note: 'salp' was declared here
SeqAlign *salp;
^~~~
mv cn3dopen.o cn3dopen.glo
mv cn3dopen.tmp cn3dopen.o
mv cn3dsave.o cn3dsave.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dsave.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dsave.c:157:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dsave.c: In function 'Cn3D_AddMatrix':
cn3dsave.c:206:41: warning: unused variable 'bsfsp_new' [-Wunused-variable]
BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_new = NULL;
^~~~~~~~~
cn3dsave.c: In function 'Cn3D_ExportAsnNow':
cn3dsave.c:375:11: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
cn3dsave.c:372:24: warning: variable 'pbsfThis' set but not used [-Wunused-but-set-variable]
BiostrucFeaturePtr pbsfThis;
^~~~~~~~
cn3dsave.c:366:10: warning: unused variable 'pmsdSlave' [-Wunused-variable]
PMSD pmsdSlave = NULL, pmsdMaster = NULL;
^~~~~~~~~
cn3dsave.c:362:27: warning: variable 'FirstSlave' set but not used [-Wunused-but-set-variable]
Boolean iCn3d = TRUE, FirstSlave = FALSE;
^~~~~~~~~~
cn3dsave.c:357:13: warning: unused variable 'pcSave' [-Wunused-variable]
CharPtr pcSave = NULL;
^~~~~~
cn3dsave.c: In function 'Cn3D_SaveBiostruc':
cn3dsave.c:524:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dsave.c:523:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dsave.c:518:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dsave.c: In function 'Cn3D_ExportDictNow':
cn3dsave.c:598:13: warning: unused variable 'pcSave' [-Wunused-variable]
CharPtr pcSave = NULL;
^~~~~~
cn3dsave.c:596:10: warning: unused variable 'iCount' [-Wunused-variable]
Int4 iCount = 0;
^~~~~~
cn3dsave.c: In function 'Cn3D_SaveDictionary':
cn3dsave.c:629:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dsave.c:624:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dsave.c: In function 'Cn3D_SaveSub':
cn3dsave.c:688:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
IteM i;
^
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dsave.c:171:
cn3dsave.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
cn3dsave.c:184:15: warning: 'Cn3D_bFeatOn' defined but not used [-Wunused-variable]
static ButtoN Cn3D_bFeatOn;
^~~~~~~~~~~~
In file included from cn3dsave.c:165:0:
../include/asnmime.h:119:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnmime.h:118:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnmime.h:117:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/asnmime.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnmime.h12";
^~~~~~~~~~~
cn3dsave.c: In function 'Cn3D_GetSubSet.isra.1':
cn3dsave.c:289:24: warning: 'isep' may be used uninitialized in this function [-Wmaybe-uninitialized]
isep->next = SeqEntryNew();
~~~~~~~~~~~^~~~~~~~~~~~~~~
mv cn3dsave.o cn3dsave.glo
mv cn3dsave.tmp cn3dsave.o
mv cn3dxprt.o cn3dxprt.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dxprt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dxprt.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportPDB':
cn3dxprt.c:209:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dxprt.c:208:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dxprt.c:203:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportKin':
cn3dxprt.c:381:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dxprt.c:380:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dxprt.c:375:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportSub':
cn3dxprt.c:513:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
IteM i;
^
mv cn3dxprt.o cn3dxprt.glo
mv cn3dxprt.tmp cn3dxprt.o
mv cn3dwin.o cn3dwin.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dwin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dwin.c:647:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dwin.c:733:1: warning: missing braces around initializer [-Wmissing-braces]
{
^
cn3dwin.c:733:1: note: (near initialization for 'Cn3d_PaletteRGB')
cn3dwin.c: In function 'Cn3D_Default_HLColor':
cn3dwin.c:982:27: warning: variable 'colorB' set but not used [-Wunused-but-set-variable]
Uint1 colorR, colorG, colorB;
^~~~~~
cn3dwin.c:982:19: warning: variable 'colorG' set but not used [-Wunused-but-set-variable]
Uint1 colorR, colorG, colorB;
^~~~~~
cn3dwin.c:982:11: warning: variable 'colorR' set but not used [-Wunused-but-set-variable]
Uint1 colorR, colorG, colorB;
^~~~~~
cn3dwin.c: In function 'Cn3D_RedrawEx':
cn3dwin.c:1251:19: warning: unused variable 'iColor' [-Wunused-variable]
DDV_ColorCell iColor;
^~~~~~
cn3dwin.c: In function 'fnPreCHLresidue':
cn3dwin.c:1543:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dwin.c: In function 'Viewer3DGroups':
cn3dwin.c:1728:10: warning: unused variable 'groups' [-Wunused-variable]
Int2 groups = 0;
^~~~~~
cn3dwin.c: In function 'Cn3D_AlignEdit':
cn3dwin.c:1936:10: warning: unused variable 'iCount' [-Wunused-variable]
Int2 iCount = 0;
^~~~~~
cn3dwin.c:1935:10: warning: variable 'pmmdThis' set but not used [-Wunused-but-set-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dwin.c:1933:17: warning: unused variable 'salp' [-Wunused-variable]
SeqAlignPtr salp = NULL;
^~~~
cn3dwin.c:1931:29: warning: variable 'pmsdSlave' set but not used [-Wunused-but-set-variable]
PMSD pmsdMaster = NULL, pmsdSlave = NULL;
^~~~~~~~~
cn3dwin.c:1930:11: warning: unused variable 'pdnmsSlave' [-Wunused-variable]
PDNMS pdnmsSlave = NULL;
^~~~~~~~~~
cn3dwin.c: In function 'Cn3DWin':
cn3dwin.c:2364:5: warning: implicit declaration of function 'Nlm_SetOGLContext' [-Wimplicit-function-declaration]
Nlm_SetOGLContext(NULL, NULL, NULL, NULL);
^~~~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/udviewer.h:219,
from cn3dwin.c:665:
cn3dwin.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/udviewer.h:228,
from cn3dwin.c:665:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
cn3dwin.c:1626:13: warning: 'HLmolecule_MA' defined but not used [-Wunused-function]
static void HLmolecule_MA(MAPtr ma,
^~~~~~~~~~~~~
cn3dwin.c:1428:13: warning: 'HLatom_MA' defined but not used [-Wunused-function]
static void HLatom_MA(MAPtr ma,
^~~~~~~~~
cn3dwin.c:1349:25: warning: 'DoHighlightSeg' defined but not used [-Wunused-function]
static void LIBCALLBACK DoHighlightSeg(PFB pfbThis,
^~~~~~~~~~~~~~
cn3dwin.c:979:13: warning: 'Cn3D_Default_HLColor' defined but not used [-Wunused-function]
static void Cn3D_Default_HLColor(IteM i)
^~~~~~~~~~~~~~~~~~~~
cn3dwin.c:953:13: warning: 'Cn3D_BgColor' defined but not used [-Wunused-function]
static void Cn3D_BgColor(IteM i)
^~~~~~~~~~~~
cn3dwin.c:936:13: warning: 'Cn3D_Default_BgColor' defined but not used [-Wunused-function]
static void Cn3D_Default_BgColor(IteM i)
^~~~~~~~~~~~~~~~~~~~
cn3dwin.c:929:13: warning: 'Cn3D_MoveCB' defined but not used [-Wunused-function]
static void Cn3D_MoveCB(IteM i)
^~~~~~~~~~~
cn3dwin.c:922:13: warning: 'Cn3D_ZoomCB' defined but not used [-Wunused-function]
static void Cn3D_ZoomCB(IteM i)
^~~~~~~~~~~
cn3dwin.c:719:14: warning: 'Cn3D_gViewCtrl' defined but not used [-Wunused-variable]
static GrouP Cn3D_gViewCtrl;
^~~~~~~~~~~~~~
cn3dwin.c:713:14: warning: 'Cn3D_gViewer' defined but not used [-Wunused-variable]
static GrouP Cn3D_gViewer;
^~~~~~~~~~~~
cn3dwin.c:688:13: warning: 'Cn3D_iModelCtrl' defined but not used [-Wunused-variable]
static IteM Cn3D_iModelCtrl = NULL;
^~~~~~~~~~~~~~~
cn3dwin.c:682:13: warning: 'Cn3D_iLabelCtrl' defined but not used [-Wunused-variable]
static IteM Cn3D_iLabelCtrl = NULL;
^~~~~~~~~~~~~~~
cn3dwin.c:676:14: warning: 'Cn3D_Vy' defined but not used [-Wunused-variable]
static Uint2 Cn3D_Vy, Cn3D_Rx;
^~~~~~~
mv cn3dwin.o cn3dwin.glo
mv cn3dwin.tmp cn3dwin.o
mv cn3dentr.o cn3dentr.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/cn3dmain.h:182,
from cn3dentr.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv cn3dentr.o cn3dentr.glo
mv cn3dentr.tmp cn3dentr.o
mv cn3dmsg.o cn3dmsg.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmsg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmsg.c:254:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmsg.c: In function 'SeqStrucMediaMsgFunc':
cn3dmsg.c:593:19: warning: variable 'omudp' set but not used [-Wunused-but-set-variable]
OMUserDataPtr omudp = NULL;
^~~~~
In file included from ../include/sqnutils.h:51:0,
from cn3dmsg.c:267:
cn3dmsg.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dmsg.c:271:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv cn3dmsg.o cn3dmsg.glo
mv cn3dmsg.tmp cn3dmsg.o
mv cn3dmatn.o cn3dmatn.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmatn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmatn.c:173:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmatn.c: In function 'FindMM':
cn3dmatn.c:217:29: warning: unused variable 'pdnmsThisSlave' [-Wunused-variable]
PDNMS pdnmsThis = NULL, pdnmsThisSlave = NULL;
^~~~~~~~~~~~~~
cn3dmatn.c: In function 'DoMediaHL':
cn3dmatn.c:249:10: warning: variable 'MainAtom' set but not used [-Wunused-but-set-variable]
Byte MainAtom = 0;
^~~~~~~~
cn3dmatn.c:247:10: warning: unused variable 'paldThis' [-Wunused-variable]
PALD paldThis = NULL;
^~~~~~~~
cn3dmatn.c:246:11: warning: unused variable 'pvnalThis' [-Wunused-variable]
PVNAL pvnalThis = NULL;
^~~~~~~~~
cn3dmatn.c:245:10: warning: unused variable 'pmadThis' [-Wunused-variable]
PMAD pmadThis = NULL;
^~~~~~~~
cn3dmatn.c:244:11: warning: unused variable 'pvnmaThis' [-Wunused-variable]
PVNMA pvnmaThis = NULL;
^~~~~~~~~
cn3dmatn.c: In function 'Cn3DCheckAndDoHighlight':
cn3dmatn.c:372:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dmatn.c:371:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
mv cn3dmatn.o cn3dmatn.glo
mv cn3dmatn.tmp cn3dmatn.o
mv cn3dmodl.o cn3dmodl.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmodl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmodl.c: In function 'Cn3DCheckNoSingleHighlight':
cn3dmodl.c:353:11: warning: unused variable 'pdnmgThis' [-Wunused-variable]
PDNMG pdnmgThis = NULL;
^~~~~~~~~
cn3dmodl.c: In function 'Cn3DCheckHighlighted':
cn3dmodl.c:364:29: warning: unused variable 'pmsdSlave' [-Wunused-variable]
PMSD pmsdMaster = NULL, pmsdSlave = NULL;
^~~~~~~~~
cn3dmodl.c: In function 'Cn3D_ReSetVisibleStatus':
cn3dmodl.c:508:10: warning: unused variable 'pmgd' [-Wunused-variable]
PMGD pmgd = NULL;
^~~~
cn3dmodl.c:507:11: warning: unused variable 'pdnmg' [-Wunused-variable]
PDNMG pdnmg = NULL;
^~~~~
cn3dmodl.c:506:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'fnAlignList':
cn3dmodl.c:996:25: warning: unused variable 'itemtype' [-Wunused-variable]
Uint2 entityID = 0, itemtype = 0;
^~~~~~~~
cn3dmodl.c:996:11: warning: unused variable 'entityID' [-Wunused-variable]
Uint2 entityID = 0, itemtype = 0;
^~~~~~~~
cn3dmodl.c:995:14: warning: unused variable 'sipThis' [-Wunused-variable]
SeqIdPtr sipThis = NULL;
^~~~~~~
cn3dmodl.c:993:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'SynchronizeModVisibleStatus':
cn3dmodl.c:1065:11: warning: unused variable 'pdnmg' [-Wunused-variable]
PDNMG pdnmg = NULL;
^~~~~
cn3dmodl.c:1064:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'SetResidueVisibilities':
cn3dmodl.c:1201:11: warning: unused variable 'pvnmoThis' [-Wunused-variable]
PVNMO pvnmoThis = NULL;
^~~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dmodl.c:319:
cn3dmodl.c: At top level:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dmodl.c:323:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
mv cn3dmodl.o cn3dmodl.glo
mv cn3dmodl.tmp cn3dmodl.o
mv cn3dshim.o cn3dshim.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dshim.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/cn3dmain.h:182,
from cn3dshim.c:131:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dshim.c: In function 'Cn3D_Size':
cn3dshim.c:413:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis;
^~~~~~~~
cn3dshim.c:412:11: warning: unused variable 'pdnmsSlave' [-Wunused-variable]
PDNMS pdnmsSlave;
^~~~~~~~~~
cn3dshim.c: In function 'Cn3D_SizeCB':
cn3dshim.c:391:36: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations]
BoundBox->x[i] = pflvDataThis[i / (int) 2];
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dshim.c:390:17: note: within this loop
for (i = 0; i < 6; i++) {
^~~
cn3dshim.c:399:36: warning: iteration 1 invokes undefined behavior [-Waggressive-loop-optimizations]
BoundBox->x[i + 1]) BoundBox->x[i + 1] =
~~~~~~~~~~~^~~~~~~
cn3dshim.c:395:17: note: within this loop
for (i = 0; i < 6; i += 2) { /* check to see if the atom lies outside the bound box */
^~~
mv cn3dshim.o cn3dshim.glo
mv cn3dshim.tmp cn3dshim.o
mv cn3dmesh.o cn3dmesh.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmesh.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmesh.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmesh.c: In function 'Cn3D_MeshAcceptProc':
cn3dmesh.c:103:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dmesh.c: In function 'Cn3D_OpenMesh':
cn3dmesh.c:151:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dmesh.c: In function 'Cn3D_MeshAcceptProc':
cn3dmesh.c:111:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d", &(Mesh.NumVert), &(Mesh.NumEdge),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.NumTri));
~~~~~~~~~~~~~~~
cn3dmesh.c:119:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%lf %lf %lf %lf %lf %lf %f %f %f %d %d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[0]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[1]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[2]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[0]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[1]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[2]), &fDummy, &fDummy, &fDummy,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&lDummy, &lDummy, &lDummy);
~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmesh.c:129:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d %d %d", &Mesh.Edges[i].Vertex[0],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Edges[i].Vertex[1], &lDummy, &lDummy, &lDummy);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmesh.c:133:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d %d %d %d %d %d %d", &Mesh.Tri[i].Edge[0],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Edge[1], &Mesh.Tri[i].Edge[2],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Vertex[0], &Mesh.Tri[i].Vertex[1],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Vertex[2], &lDummy, &Mesh.Tri[i].Atom,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&lDummy);
~~~~~~~~
mv cn3dmesh.o cn3dmesh.glo
mv cn3dmesh.tmp cn3dmesh.o
mv cn3dstyl.o cn3dstyl.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dstyl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dstyl.c:72:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dstyl.c: In function 'GetThisSpecialAlgorRenderSet':
cn3dstyl.c:459:27: warning: unused variable 'sfipThis' [-Wunused-variable]
SpecialFeatureInfoPtr sfipThis = NULL;
^~~~~~~~
cn3dstyl.c: In function 'GetSpecialAlgorRenderSet':
cn3dstyl.c:641:10: warning: unused variable 'parsThis' [-Wunused-variable]
PARS parsThis = NULL;
^~~~~~~~
cn3dstyl.c:640:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'ChangeSpecialLabelsProc':
cn3dstyl.c:867:16: warning: unused variable 'TopOn' [-Wunused-variable]
FALSE, TopOn = FALSE;
^~~~~
cn3dstyl.c:866:44: warning: unused variable 'PDBOn' [-Wunused-variable]
Boolean NumOn = FALSE, NameOn = FALSE, PDBOn = FALSE, WhiteOn =
^~~~~
cn3dstyl.c:864:17: warning: unused variable 'k' [-Wunused-variable]
Int2 i = 0, k = 0, nameval = 0;
^
cn3dstyl.c: In function 'ModelSetLabelCtrls':
cn3dstyl.c:1059:37: warning: variable 'size' set but not used [-Wunused-but-set-variable]
Int2 i = 0, val = 0, style = 0, size = 0;
^~~~
cn3dstyl.c: In function 'lFeatureEditedAction':
cn3dstyl.c:1136:10: warning: unused variable 'val' [-Wunused-variable]
Int4 val = 0;
^~~
cn3dstyl.c: In function 'bFeatureMoveAction':
cn3dstyl.c:1153:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'bFeatureEditAction':
cn3dstyl.c:1176:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'ModelControls':
cn3dstyl.c:1364:19: warning: variable 'ppt13' set but not used [-Wunused-but-set-variable]
PrompT ppt12, ppt13, ppt14;
^~~~~
cn3dstyl.c:1363:9: warning: unused variable 'ppt11' [-Wunused-variable]
ppt11;
^~~~~
cn3dstyl.c:1362:60: warning: unused variable 'ppt9' [-Wunused-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10,
^~~~
cn3dstyl.c:1362:36: warning: variable 'ppt5' set but not used [-Wunused-but-set-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10,
^~~~
cn3dstyl.c:1362:12: warning: variable 'ppt1' set but not used [-Wunused-but-set-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10,
^~~~
cn3dstyl.c: In function 'GetBiostrucFeatureLocationForHihglightedResidues':
cn3dstyl.c:1728:30: warning: variable 'SingleInterval' set but not used [-Wunused-but-set-variable]
Boolean Started = FALSE, SingleInterval, UserDefinedFeatureFound =
^~~~~~~~~~~~~~
cn3dstyl.c:1725:20: warning: variable 'iMolCurrent' set but not used [-Wunused-but-set-variable]
Int2 iMol = 0, iMolCurrent = 0;
^~~~~~~~~~~
cn3dstyl.c: In function 'MakeBiostrucFeatureSetForUserDefinedFeature':
cn3dstyl.c:2122:60: warning: unused variable 'bsfsp_tail' [-Wunused-variable]
BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail =
^~~~~~~~~~
cn3dstyl.c:2122:41: warning: unused variable 'bsfsp_head' [-Wunused-variable]
BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail =
^~~~~~~~~~
cn3dstyl.c: In function 'GetUserDefinedFeature':
cn3dstyl.c:2196:27: warning: unused variable 'sfipThis' [-Wunused-variable]
SpecialFeatureInfoPtr sfipThis = NULL;
^~~~~~~~
cn3dstyl.c: In function 'Cn3DIndexUserDefinedFeature':
cn3dstyl.c:2551:23: warning: variable 'sfpThis' set but not used [-Wunused-but-set-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c:2549:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dstyl.c:2548:11: warning: unused variable 'pdnmmHead' [-Wunused-variable]
PDNMM pdnmmHead = NULL;
^~~~~~~~~
cn3dstyl.c:2547:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dstyl.c:89:
cn3dstyl.c: At top level:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c:456:30: warning: 'GetThisSpecialAlgorRenderSet' defined but not used [-Wunused-function]
static SpecialFeatureInfoPtr GetThisSpecialAlgorRenderSet(Int2 id)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c:149:15: warning: 'bResetFeatureTitle' defined but not used [-Wunused-variable]
static ButtoN bResetFeatureTitle;
^~~~~~~~~~~~~~~~~~
cn3dstyl.c:144:14: warning: 'Cn3D_pupModelStyleItem' defined but not used [-Wunused-variable]
static PopuP Cn3D_pupModelStyleItem;
^~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c: In function 'CopyLocation':
cn3dstyl.c:496:27: warning: 'rsipNewHead' may be used uninitialized in this function [-Wmaybe-uninitialized]
rspNew->data.ptrvalue = (VoidPtr) rsipNewHead;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
mv cn3dstyl.o cn3dstyl.glo
mv cn3dstyl.tmp cn3dstyl.o
mv seqcons.o seqcons.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL seqcons.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from seqcons.c:112:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from seqcons.c:115:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/alignmgr2.h:111,
from ../include/actutils.h:105,
from seqcons.c:116:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
seqcons.c:263:19: warning: 'CSC_Blosum62Fields' defined but not used [-Wunused-const-variable=]
static const char CSC_Blosum62Fields[CSC_BLOSUMSIZE] =
^~~~~~~~~~~~~~~~~~
seqcons.c: In function 'CSC_Algorithm_ByBlosum62':
seqcons.c:402:43: warning: 'minScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
scale = 1.0 - 1.0 * (score[i] - minScore) / (maxScore - minScore);
~~~~~~~~~~^~~~~~~~~~~
seqcons.c:402:67: warning: 'maxScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
scale = 1.0 - 1.0 * (score[i] - minScore) / (maxScore - minScore);
~~~~~~~~~~^~~~~~~~~~~
mv seqcons.o seqcons.glo
mv seqcons.tmp seqcons.o
rm -f libncbicn3dOGL.a
ar cru libncbicn3dOGL.a algorend.glo cn3dmsel.glo cn3dopen.glo cn3dsave.glo cn3dxprt.glo cn3dwin.glo cn3dentr.glo cn3dmsg.glo cn3dmatn.glo cn3dmodl.glo cn3dshim.glo cn3dmesh.glo cn3dstyl.glo seqcons.glo
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbicn3dOGL.a ../lib
ranlib ../lib/libncbicn3dOGL.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF aa_ungapped.c
aa_ungapped.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_diagnostics.c
blast_diagnostics.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_engine.c
blast_engine.c:57:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_extend.c
blast_extend.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_filter.c
blast_filter.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_gapalign.c
blast_gapalign.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_hits.c
blast_hits.c: In function 'Blast_HSPResultsFromHSPStreamWithLimitEx':
blast_hits.c:3499:13: warning: variable 'rm_hsps' set but not used [-Wunused-but-set-variable]
Boolean rm_hsps = FALSE;
^~~~~~~
At top level:
blast_hits.c:3212:12: warning: 's_SortHspWrapEvalue' defined but not used [-Wunused-function]
static int s_SortHspWrapEvalue(const void *x, const void *y)
^~~~~~~~~~~~~~~~~~~
blast_hits.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_itree.c
blast_itree.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_lookup.c
blast_lookup.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_message.c
blast_message.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_options.c
blast_options.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seg.c
blast_seg.c:38:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seqsrc.c
blast_seqsrc.c:38:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_sw.c
blast_sw.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_setup.c
blast_setup.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_stat.c
blast_stat.c: In function 's_BlastGumbelBlkNew':
blast_stat.c:818:21: warning: unused variable 'retv' [-Wunused-variable]
Blast_GumbelBlk* retv;
^~~~
At top level:
blast_stat.c:5081:15: warning: 's_CalculateNormalProbability' defined but not used [-Wunused-function]
static double s_CalculateNormalProbability(double x_, double eps_)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_stat.c:52:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_traceback.c
blast_traceback.c:52:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
blast_traceback.c: In function 'Blast_TracebackFromHSPList':
blast_traceback.c:393:25: warning: 'qe' may be used uninitialized in this function [-Wmaybe-uninitialized]
Blast_HSPInit(qs, qe, ss, se, qs, ss,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hsp->context, hsp->query.frame,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hsp->subject.frame, 0, &new_esp, &new_hsp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_traceback.c:365:22: note: 'qe' was declared here
Int4 qs, qe, ss, se, es, ee, os;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_util.c
blast_util.c: In function 'BlastProgram2Number':
blast_util.c:309:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (strcasecmp("phiblastp", program) == 0)
^~
blast_util.c:312:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return 0;
^~~~~~
At top level:
blast_util.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gapinfo.c
gapinfo.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF greedy_align.c
greedy_align.c:38:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF link_hsps.c
link_hsps.c: In function 's_FwdCompareHSPs':
link_hsps.c:138:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (h1->context > h2->context)
^~
link_hsps.c:141:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (h1->query.offset < h2->query.offset)
^~
At top level:
link_hsps.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF lookup_wrap.c
lookup_wrap.c:39:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF na_ungapped.c
na_ungapped.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_math.c
ncbi_math.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_std.c
ncbi_std.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF pattern.c
pattern.c:58:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF phi_extend.c
phi_extend.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF phi_lookup.c
phi_lookup.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF lookup_util.c
lookup_util.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_encoding.c
blast_encoding.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_psi.c
blast_psi.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_psi_priv.c
blast_psi_priv.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_kappa.c
blast_kappa.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF matrix_freq_ratios.c
matrix_freq_ratios.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_hspstream.c
blast_hspstream.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_parameters.c
blast_parameters.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_posit.c
blast_posit.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF phi_gapalign.c
phi_gapalign.c:57:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_program.c
blast_program.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_query_info.c
blast_query_info.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_tune.c
blast_tune.c:37:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_aalookup.c
blast_aalookup.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_nalookup.c
blast_nalookup.c:38:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_aascan.c
blast_aascan.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_nascan.c
blast_nascan.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_dynarray.c
blast_dynarray.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF split_query.c
split_query.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF gencode_singleton.c
gencode_singleton.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF index_ungapped.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF hspfilter_collector.c
hspfilter_collector.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
rm -f libblast.a
ar cru libblast.a aa_ungapped.o blast_diagnostics.o blast_engine.o blast_extend.o blast_filter.o blast_gapalign.o blast_hits.o blast_itree.o blast_lookup.o blast_message.o blast_options.o blast_seg.o blast_seqsrc.o blast_sw.o blast_setup.o blast_stat.o blast_traceback.o blast_util.o gapinfo.o greedy_align.o link_hsps.o lookup_wrap.o na_ungapped.o ncbi_math.o ncbi_std.o pattern.o phi_extend.o phi_lookup.o lookup_util.o blast_encoding.o blast_psi.o blast_psi_priv.o blast_kappa.o matrix_freq_ratios.o blast_hspstream.o blast_parameters.o blast_posit.o phi_gapalign.o blast_program.o blast_query_info.o blast_tune.o blast_aalookup.o blast_nalookup.o blast_aascan.o blast_nascan.o blast_dynarray.o split_query.o gencode_singleton.o index_ungapped.o hspfilter_collector.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libblast.a ../lib
ranlib ../lib/libblast.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_api.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/algo/blast/api/blast_tabular.h:42,
from ../include/algo/blast/api/blast_api.h:47,
from blast_api.c:38:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_api.c: In function 's_BlastRPSInfoInit':
blast_api.c:149:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%s", buffer);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:151:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%d", &info->aux_info.gap_open_penalty);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:152:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%d", &info->aux_info.gap_extend_penalty);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:153:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%le", &info->aux_info.ungapped_k);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:154:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%le", &info->aux_info.ungapped_h);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:155:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%d", &info->aux_info.max_db_seq_length);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:156:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%d", &info->aux_info.db_length);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:157:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%lf", &info->aux_info.scale_factor);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:161:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%d", &seq_size); /* not used */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:162:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%le", &info->aux_info.karlin_k[i]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_input.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:85,
from blast_input.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_input.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_input.c,v 1.32 2008/06/09 17:28:41 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_format.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/algo/blast/api/blast_format.h:45,
from blast_format.c:38:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_format.c: In function 's_MBXmlInit':
blast_format.c:255:13: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = FALSE;
^~~~~~
blast_format.c: In function 's_LoadMatrix':
blast_format.c:673:20: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]][pchars[j]] = pack_matrix->scores[(i*dim)+j];
^
blast_format.c:673:31: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]][pchars[j]] = pack_matrix->scores[(i*dim)+j];
^
At top level:
blast_format.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_format.c,v 1.119 2011/05/26 20:59:45 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_mtlock.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/ncbithr.h:87,
from blast_mtlock.c:39:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_mtlock.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_options_api.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_prelim.c
blast_prelim.c: In function 'Blast_PrelimSearchThreadRun':
blast_prelim.c:100:9: warning: variable 'status' set but not used [-Wunused-but-set-variable]
Int2 status = 0;
^~~~~~
At top level:
blast_prelim.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_prelim.c,v 1.8 2006/05/24 21:17:50 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_returns.c
blast_returns.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_returns.c,v 1.39 2010/06/10 13:44:46 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from blast_seq.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_seq.c: In function 's_SeqLocFillSequenceBuffer':
blast_seq.c:529:10: warning: variable 'seq_code' set but not used [-Wunused-but-set-variable]
Uint1 seq_code, strand;
^~~~~~~~
At top level:
blast_seq.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_seq.c,v 1.89 2008/06/09 17:29:14 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seqalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from ../include/algo/blast/api/blast_seqalign.h:42,
from blast_seqalign.c:35:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_seqalign.c: In function 's_HSPListToSeqAlignUngapped':
blast_seqalign.c:343:26: warning: variable 'hspset_cnt_old' set but not used [-Wunused-but-set-variable]
Int4 hsp_cnt, index2, hspset_cnt_old;
^~~~~~~~~~~~~~
At top level:
blast_seqalign.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_seqalign.c,v 1.64 2010/02/12 20:54:54 maning Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_tabular.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/algo/blast/api/blast_tabular.h:42,
from blast_tabular.c:35:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_tabular.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_tabular.c,v 1.41 2009/06/01 14:33:38 maning Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF repeats_filter.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:85,
from ../include/algo/blast/api/repeats_filter.h:41,
from repeats_filter.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
repeats_filter.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: repeats_filter.c,v 1.19 2007/12/19 21:56:48 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqsrc_multiseq.c
seqsrc_multiseq.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seqsrc_multiseq.c,v 1.28 2011/05/26 20:59:45 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF seqsrc_readdb.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from ../include/algo/blast/api/seqsrc_readdb.h:38,
from seqsrc_readdb.c:35:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqsrc_readdb.c: In function 's_ReaddbGetNextChunk':
seqsrc_readdb.c:375:11: warning: variable 'real_readdb_entries' set but not used [-Wunused-but-set-variable]
Uint4 real_readdb_entries;
^~~~~~~~~~~~~~~~~~~
At top level:
seqsrc_readdb.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seqsrc_readdb.c,v 1.60 2011/05/26 20:59:45 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF twoseq_api.c
twoseq_api.c: In function 's_TwoSeqBasicFillOptions':
twoseq_api.c:100:10: warning: unused variable 'status' [-Wunused-variable]
Int2 status = 0;
^~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/algo/blast/api/twoseq_api.h:41,
from twoseq_api.c:45:
twoseq_api.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF dust_filter.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:85,
from ../include/algo/blast/api/dust_filter.h:41,
from dust_filter.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dust_filter.c: In function 's_GetFilteringLocations':
dust_filter.c:171:32: warning: unused variable 'filter_slp_rev' [-Wunused-variable]
BlastSeqLoc* filter_slp_rev = NULL;
^~~~~~~~~~~~~~
At top level:
dust_filter.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: dust_filter.c,v 1.12 2007/12/19 22:05:56 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF blast_message_api.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from blast_message_api.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -D_PNG -I../include -DWIN_MOTIF hspfilter_queue.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/ncbithr.h:87,
from hspfilter_queue.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
hspfilter_queue.c: In function 's_BlastHSPQueueInit':
hspfilter_queue.c:65:24: warning: unused variable 'q_data' [-Wunused-variable]
BlastHSPQueueData * q_data = data;
^~~~~~
At top level:
hspfilter_queue.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
rm -f libblastapi.a
ar cru libblastapi.a blast_api.o blast_input.o blast_format.o blast_mtlock.o blast_options_api.o blast_prelim.o blast_returns.o blast_seq.o blast_seqalign.o blast_tabular.o repeats_filter.o seqsrc_multiseq.o seqsrc_readdb.o twoseq_api.o dust_filter.o blast_message_api.o hspfilter_queue.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libblastapi.a ../lib
ranlib ../lib/libblastapi.a
gcc -o asntool -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -DWIN_MOTIF -L../shlib asntool.c asncode.c ../lib/libncbi.a -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asntool.c:64:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asncode.c:52:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asncode.c: In function 'AsnCode_SETOF_base_or_user':
asncode.c:1518:20: warning: variable 'real_type' set but not used [-Wunused-but-set-variable]
Int2 real_type;
^~~~~~~~~
asncode.c:1517:20: warning: variable 'valslot' set but not used [-Wunused-but-set-variable]
CharPtr valslot;
^~~~~~~
asncode.c: In function 'userobj_and_basetype_SETOF':
asncode.c:2472:20: warning: variable 'valslot' set but not used [-Wunused-but-set-variable]
CharPtr valslot;
^~~~~~~
asncode.c: In function 'AsnCodeIsReallyChoice':
asncode.c:3201:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (now_atp)
^
asncode.c: In function 'AsnCodeFunctionWriteFuncChoiceStart':
asncode.c:3623:20: warning: variable 'obj_use' set but not used [-Wunused-but-set-variable]
CharPtr obj_use = which_node->obj_name;
^~~~~~~
asncode.c: In function 'AsnCodeIter':
asncode.c:4237:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (iter->atp != NULL)
^
asncode.c: In function 'AsnCode':
asncode.c:4316:48: warning: variable 'objnamety' set but not used [-Wunused-but-set-variable]
CharPtr objnameuc = NULL, objnamemc = NULL, objnamety = NULL;
^~~~~~~~~
At top level:
asncode.c:291:17: warning: 'defbyte' defined but not used [-Wunused-variable]
static CharPtr defbyte = "ASNCODE_BYTEVAL_SLOT";
^~~~~~~
asncode.c:290:17: warning: 'defbool' defined but not used [-Wunused-variable]
static CharPtr defbool = "ASNCODE_BOOLVAL_SLOT";
^~~~~~~
asncode.c:289:17: warning: 'defreal' defined but not used [-Wunused-variable]
static CharPtr defreal = "ASNCODE_REALVAL_SLOT";
^~~~~~~
asncode.c:288:17: warning: 'defbigint' defined but not used [-Wunused-variable]
static CharPtr defbigint = "ASNCODE_BIGINTVAL_SLOT";
^~~~~~~~~
asncode.c:286:17: warning: 'defptr' defined but not used [-Wunused-variable]
static CharPtr defptr = "ASNCODE_PTRVAL_SLOT";
^~~~~~
../lib/libncbi.a(ncbifile.o): In function `Nlm_TmpNam':
./build/ncbifile.c:1209: warning: the use of `tempnam' is dangerous, better use `mkstemp'
cp -p asntool ../bin
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -C build -f makenet.unx LCL=lnx CC="gcc " LDFLAGS1="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"' -fPIE -pie -Wl,-z,relro -Wl,-z,now" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" NCBI_LINKINGLIBDIR="../shlib" \
CFLAGS1="-c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"' -fPIC" \
LDFLAGS="-Wl,-z,relro -Wl,-z,now" \
NETENTREZVERSION="2.02c2ASN1SPEC6" \
BLIB31=libvibnet.a OGLLIBS="-lGLU -lGL -lpng " all libncbimla.a libnetblast.a libncbitxc2.a libncbiid1.a shlib
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
./ln-if-absent ../connect/test/*.c .
./ln-if-absent ../network/entrez/client/*.h ../include
./ln-if-absent ../network/entrez/client/*.c .
./ln-if-absent ../network/medarch/client/*.h ../include
./ln-if-absent ../network/medarch/client/*.c .
./ln-if-absent ../network/taxonomy/client/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/taxonomy/client/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/taxon1/common/*.h ../include
./ln-if-absent ../network/taxon1/common/*.c .
./ln-if-absent ../network/taxon1/taxon2/*.h ../include
./ln-if-absent ../network/taxon1/taxon2/*.c .
./ln-if-absent ../network/id0arch/client/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/id0arch/client/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/id1arch/*.h ../include
./ln-if-absent ../network/id1arch/*.c .
./ln-if-absent ../network/id2arch/*.h ../include
./ln-if-absent ../network/id2arch/*.c .
./ln-if-absent ../network/spell/client/*.h ../include
./ln-if-absent ../network/spell/client/*.c .
./ln-if-absent ../network/suggest/client/*.h ../include
./ln-if-absent ../network/suggest/client/*.c .
./ln-if-absent ../network/blast3/client/*.h ../include
./ln-if-absent ../network/blast3/client/*.c .
./ln-if-absent ../tools/taxblast.h ../include
./ln-if-absent ../tools/taxblast.c .
./ln-if-absent /*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/misc/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/misc/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ssparse/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ssparse/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libparsn/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libparsn/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/smart/smartnet/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/smart/smartnet/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/www/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/www/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/query/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/query/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/ctlib/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/ctlib/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/oslib/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/oslib/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/idloadlib/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/idloadlib/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/nsclilib/*.h ../include
./ln-if-absent ../network/nsclilib/*.c .
./ln-if-absent ../network/vibnet/*.c .
./ln-if-absent ../network/vibnet/*.h ../include
./ln-if-absent ../cdromlib/*.h ../include
./ln-if-absent ../network/wwwblast/Src/*.c .
./ln-if-absent ../cdromlib/accentr.c .
./ln-if-absent ../cdromlib/accutils.c .
./ln-if-absent ../sequin/*.* .
./ln-if-absent ../demo/entrez.c .
./ln-if-absent ../demo/seqget.c .
./ln-if-absent ../demo/entrcmd.c .
./ln-if-absent ../demo/batch.c .
./ln-if-absent ../demo/qbatch.c .
./ln-if-absent ../demo/elecpcr.c .
./ln-if-absent ../demo/asn2fast.c .
./ln-if-absent ../demo/asn2asn.c .
./ln-if-absent ../demo/cleanasn.c .
./ln-if-absent ../demo/cspeedtest.c .
./ln-if-absent ../demo/sqn2agp.c .
./ln-if-absent ../demo/sugint.c .
./ln-if-absent ../demo/fetchent.c .
./ln-if-absent ../demo/udvmain.c .
./ln-if-absent ../demo/rtestval.c .
./ln-if-absent ../demo/aceread_tst.c .
./ln-if-absent ../demo/asn2ff.c .
./ln-if-absent ../demo/asn2gb.c .
./ln-if-absent ../demo/asn2fsa.c .
./ln-if-absent ../demo/asn2all.c .
./ln-if-absent ../demo/gene2xml.c .
./ln-if-absent ../demo/asnval.c .
./ln-if-absent ../demo/asndisc.c .
./ln-if-absent ../demo/asnbarval.c .
./ln-if-absent ../demo/aceread_tst.c .
./ln-if-absent ../demo/asnmacro.c .
./ln-if-absent ../demo/asnstrip.c .
./ln-if-absent ../demo/tbl2asn.c .
./ln-if-absent ../demo/raw2delt.c .
./ln-if-absent ../demo/flint.c .
./ln-if-absent ../demo/xlint.c .
./ln-if-absent ../demo/diffshift.c .
./ln-if-absent ../demo/gbseqget.c .
./ln-if-absent ../demo/insdseqget.c .
./ln-if-absent ../demo/nps2gps.c .
./ln-if-absent ../demo/testent2.c .
./ln-if-absent ../demo/trna2sap.c .
./ln-if-absent ../demo/trna2tbl.c .
./ln-if-absent ../demo/entrez2.c .
./ln-if-absent ../demo/condense.c .
./ln-if-absent ../demo/spideymain.c .
./ln-if-absent ../demo/dotmain.c .
./ln-if-absent ../demo/ingenmain.c .
./ln-if-absent ../demo/bl2seq.c .
./ln-if-absent ../demo/blastall.c .
./ln-if-absent ../demo/blast_driver.c .
./ln-if-absent ../demo/src_chk.c .
./ln-if-absent ../demo/tbl_chk.c .
./ln-if-absent ../demo/srchnt.c ../demo/srchaa.c ../demo/mts.c ../demo/sigme.c ../demo/dst.c ../demo/ccp.c ../demo/epi.c ../demo/twop.c ../demo/cnsrt.c ../demo/cnsgn.c ../demo/ccpv.c ../demo/dustv.c ../demo/epiv.c ../demo/sigmev.c ../demo/twopv.c ../demo/cnsrtv.c ../demo/cnsgnv.c ../demo/searchv.c .
./ln-if-absent ../network/entrez/server/*.* .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/suggest/server/*.* .
chmod -R ug+rw,o+r .
echo Waiting...go
Waiting...go
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_lib_.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ni_types.h:84,
from ../include/ncbinet.h:84,
from ni_lib_.c:76:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_debug.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ni_debug.c:55:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_service.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ni_service.c:122:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ni_service.c: In function 's_GenericGetService':
ni_service.c:199:19: warning: unused variable 'c' [-Wunused-variable]
CONNECTOR c;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_error.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ni_types.h:84,
from ../include/ncbinet.h:84,
from ../include/ni_error.h:76,
from ni_error.c:72:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rm -f libnetcli.a
ar cru libnetcli.a ni_lib_.o ni_debug.o ni_service.o ni_error.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libnetcli.a ../lib
ranlib ../lib/libnetcli.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from netentr.c:161:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netentr.c: In function 's_NetEntTLEvalCount':
netentr.c:798:5: warning: "/*" within comment [-Wcomment]
/*MsgSetReadTimeout(Entrez_ni, 60);*/
netentr.c: In function 's_NetDocSumListGet':
netentr.c:856:18: warning: variable 'amp' set but not used [-Wunused-but-set-variable]
AsnModulePtr amp;
^~~
netentr.c: In function 's_NetTermListByTerm':
netentr.c:1212:9: warning: variable 'terms_to_read' set but not used [-Wunused-but-set-variable]
int terms_to_read;
^~~~~~~~~~~~~
netentr.c:1200:14: warning: unused variable 'asnout' [-Wunused-variable]
AsnIoPtr asnout = Entrez_asnout;
^~~~~~
netentr.c: In function 's_NetTermListByPage':
netentr.c:1343:14: warning: unused variable 'asnout' [-Wunused-variable]
AsnIoPtr asnout = Entrez_asnout;
^~~~~~
netentr.c: In function 'NetEntTLEval':
netentr.c:675:12: warning: 'lsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return lsp;
^~~
netentr.c: In function 'NetEntTLEvalCount':
netentr.c:800:8: warning: 'atp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (atp == ENTREZ_BACK_eval_count)
^
netentr.c:782:16: note: 'atp' was declared here
AsnTypePtr atp;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netlib.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from netlib.c:82:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netlib.c: In function 'BoolExprAsnWrite':
netlib.c:307:16: warning: unused variable 'n' [-Wunused-variable]
static int n = 0;
^
At top level:
netlib.c:307:16: warning: 'n' defined but not used [-Wunused-variable]
netlib.c:96:16: warning: 'loaded' defined but not used [-Wunused-variable]
static Boolean loaded = FALSE;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objneten.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asnneten.h:9,
from objneten.c:86:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objneten.c: In function 'NetEntAsnLoad':
objneten.c:106:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (loaded)
^~
objneten.c:108:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
loaded = TRUE;
^~~~~~
objneten.c: In function 'EntrezNeighborTextAsnRead':
objneten.c:2938:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c: In function 'ChildLinkAsnRead':
objneten.c:3148:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c: In function 'EntrezHierarchyAsnRead':
objneten.c:3442:15: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c: In function 'EntrezBlastreqAsnRead':
objneten.c:3705:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:3704:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objneten.c: In function 'EntrezExtraInfoAsnRead':
objneten.c:3911:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:3910:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objneten.c: In function 'ClusterArticlesAsnRead':
objneten.c:4262:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:4261:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objneten.c: In function 'ClusterRespAsnRead':
objneten.c:4455:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c: In function 'DateConstraintsAsnRead':
objneten.c:4622:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c: In function 'DateVectorAsnRead':
objneten.c:4785:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:4784:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objneten.c: In function 'GetByFidAsnRead':
objneten.c:4963:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:4962:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objneten.c: In function 'GetFeatIdsAsnRead':
objneten.c:5133:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:5132:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
rm -f libnetentr.a
ar cru libnetentr.a netentr.o netlib.o objneten.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libnetentr.a ../lib
ranlib ../lib/libnetentr.a
./ln-if-absent accentr.c Naccentr.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -D_NETENT_ Naccentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from Naccentr.c:297:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
Naccentr.c:357:93: warning: missing braces around initializer [-Wmissing-braces]
Uint1 AdaptiveDocSumMatrix[MAX_CHUNK_IN_ADAPTIVE_MATRIX+1][MAX_SECS_IN_ADAPTIVE_MATRIX+1] = {
^
Naccentr.c:357:93: note: (near initialization for 'AdaptiveDocSumMatrix')
Naccentr.c: In function 'EntrezDocSumListGet':
Naccentr.c:1409:14: warning: variable 'actual' set but not used [-Wunused-but-set-variable]
Int2 actual;
^~~~~~
Naccentr.c: In function 'EntrezGIForSeqIdFunc':
Naccentr.c:3283:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! gi) return OM_MSG_RET_OK;
^~
Naccentr.c:3285:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sip2 = ValNodeNew(NULL);
^~~~
rm -f libncbiNacc.a
ar cru libncbiNacc.a Naccentr.o accutils.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbiNacc.a ../lib
ranlib ../lib/libncbiNacc.a
./ln-if-absent accentr.c Caccentr.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -D_NET_AND_CD_ Caccentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from Caccentr.c:297:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
Caccentr.c:357:93: warning: missing braces around initializer [-Wmissing-braces]
Uint1 AdaptiveDocSumMatrix[MAX_CHUNK_IN_ADAPTIVE_MATRIX+1][MAX_SECS_IN_ADAPTIVE_MATRIX+1] = {
^
Caccentr.c:357:93: note: (near initialization for 'AdaptiveDocSumMatrix')
Caccentr.c: In function 'EntrezDocSumListGet':
Caccentr.c:1409:14: warning: variable 'actual' set but not used [-Wunused-but-set-variable]
Int2 actual;
^~~~~~
Caccentr.c: In function 'EntrezGIForSeqIdFunc':
Caccentr.c:3283:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! gi) return OM_MSG_RET_OK;
^~
Caccentr.c:3285:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sip2 = ValNodeNew(NULL);
^~~~
rm -f libncbiCacc.a
ar cru libncbiCacc.a Caccentr.o accutils.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbiCacc.a ../lib
ranlib ../lib/libncbiCacc.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netcnfg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from netcnfg.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" trmlst.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from trmlst.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
trmlst.c: In function 'FetchFromTermList':
trmlst.c:1048:16: warning: variable 'numRead' set but not used [-Wunused-but-set-variable]
Int2 numRead;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" docsum.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from docsum.c:252:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
docsum.c: In function 'ImportDocSumForm':
docsum.c:2298:21: warning: unused variable 'sephead' [-Wunused-variable]
SeqEntryPtr sephead = NULL;
^~~~~~~
docsum.c:2296:21: warning: unused variable 'is_na' [-Wunused-variable]
Boolean is_na = TRUE;
^~~~~
docsum.c:2290:21: warning: unused variable 'choice' [-Wunused-variable]
Uint1 choice = 0;
^~~~~~
docsum.c: In function 'SaveDocsumProject':
docsum.c:3042:16: warning: variable 'sfp' set but not used [-Wunused-but-set-variable]
SummFormPtr sfp;
^~~
docsum.c: In function 'LaunchStructureViewer':
docsum.c:4192:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
docsum.c:439:15: warning: 'checkmark' defined but not used [-Wunused-variable]
static Uint1 checkmark [] = {
^~~~~~~~~
docsum.c: In function 'FetchLocalBioseq':
docsum.c:1223:6: warning: 'str' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (str == NULL) return failed;
^
rm -f libvibnet.a
ar cru libvibnet.a netcnfg.o trmlst.o docsum.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libvibnet.a ../lib
ranlib ../lib/libvibnet.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -DNLM_OBJ_INCL=\"mapmla.h\" objmla.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmla.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmla.c: In function 'MlaRequestFree':
objmla.c:49:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmla.c: In function 'MlaRequestAsnRead':
objmla.c:96:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmla.c: In function 'TitleMsgAsnRead':
objmla.c:447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmla.c:446:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmla.c: In function 'TitleMsgListAsnRead':
objmla.c:612:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmla.c: In function 'MlaRequestAsnRead':
objmla.c:249:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmla.c: In function 'MlaBackAsnRead':
objmla.c:902:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" medarch.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ni_types.h:84,
from ../include/ncbinet.h:84,
from medarch.c:122:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
medarch.c:758:8: warning: 's_MedArchPubSetEntryGetUid' defined but not used [-Wunused-function]
/*FCN*/s_MedArchPubSetEntryGetUid (
^~~~~~~~~~~~~~~~~~~~~~~~~~
medarch.c:710:8: warning: 's_MedArchPubSetEntryGetPmId' defined but not used [-Wunused-function]
/*FCN*/s_MedArchPubSetEntryGetPmId (
^~~~~~~~~~~~~~~~~~~~~~~~~~~
medarch.c: In function 'MedArchPubSetCreate':
medarch.c:1693:9: warning: 'pubSetEAtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
MedlineEntryAsnWrite (lastmep, aip, pubSetEAtp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/ni_types.h:85:0,
from ../include/ncbinet.h:84,
from medarch.c:122:
../include/asn.h:465:27: warning: 'pubSetAtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AsnEndStruct(x,y) AsnCloseStruct(x, y, NULL)
^~~~~~~~~~~~~~
medarch.c:1625:16: note: 'pubSetAtp' was declared here
AsnTypePtr pubSetAtp;
^~~~~~~~~
medarch.c:1655:5: warning: 'startAtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
AsnWrite (aip, startAtp, NULL);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" medutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/medutil.h:79,
from medutil.c:58:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rm -f libncbimla.a
ar cru libncbimla.a objmla.o medarch.o medutil.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbimla.a ../lib
ranlib ../lib/libncbimla.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objblst3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objblst3.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objblst3.c: In function 'BlastSearchAsnRead':
objblst3.c:91:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:90:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastRequestFree':
objblst3.c:287:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objblst3.c: In function 'BlastRequestAsnRead':
objblst3.c:337:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'Cutoff2_cutoff2Free':
objblst3.c:999:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objblst3.c: In function 'BlastParametersAsnRead':
objblst3.c:1027:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'Cutoff2_cutoff2AsnRead':
objblst3.c:1422:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'Cutoff_cutoffAsnRead':
objblst3.c:1788:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'Cutoff_cutoffFree':
objblst3.c:1871:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objblst3.c: In function 'BlastMatrixAsnRead':
objblst3.c:1936:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'BlastDbinfoAsnRead':
objblst3.c:2153:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:2152:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastMaskAsnRead':
objblst3.c:2357:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'BlastKABlkAsnRead':
objblst3.c:2517:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:2516:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastErrorAsnRead':
objblst3.c:2697:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:2696:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastPhialignAsnRead':
objblst3.c:2861:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'BlastDbinfoGetAsnRead':
objblst3.c:3022:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3021:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastSeqIdAsnRead':
objblst3.c:3187:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3186:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastSequenceAsnRead':
objblst3.c:3364:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3363:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastPartsAsnRead':
objblst3.c:3532:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'BlastQueuedAsnRead':
objblst3.c:3694:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3693:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastProgressAsnRead':
objblst3.c:3846:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3845:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastDeflineAsnRead':
objblst3.c:4000:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3999:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastVersionAsnRead':
objblst3.c:4168:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:4167:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'MegaBlastHitAsnRead':
objblst3.c:4335:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:4334:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'MegaBlastResultsAsnRead':
objblst3.c:4546:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'BlastRequestAsnRead':
objblst3.c:430:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objblst3.c: In function 'BlastResponseAsnRead':
objblst3.c:791:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objblst3.c: In function 'BlastParametersAsnRead':
objblst3.c:1474:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objblst3.c:1421:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objblst3.c:1840:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objblst3.c:1787:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netblap3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ni_types.h:84,
from ../include/ncbinet.h:84,
from netblap3.c:359:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netblap3.c: In function 'BlastNetBioseqFetchFunc':
netblap3.c:1835:16: warning: variable 'omdp' set but not used [-Wunused-but-set-variable]
OMUserDataPtr omdp;
^~~~
netblap3.c: In function 'MegaBlastSeqLocNetCore':
netblap3.c:2049:8: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID = 0;
^~~~~~~~
In file included from ../include/netblap3.h:135:0,
from netblap3.c:364:
netblap3.c: At top level:
../include/objblst3.h:180:35: warning: 'Cutoff2_cutoff2Free' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr ));
^~~~~~~~~~~~~~~~~~~
../include/objblst3.h:181:35: warning: 'Cutoff2_cutoff2AsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:182:24: warning: 'Cutoff2_cutoff2AsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:199:33: warning: 'Cutoff_cutoffFree' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr ));
^~~~~~~~~~~~~~~~~
../include/objblst3.h:200:33: warning: 'Cutoff_cutoffAsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:201:24: warning: 'Cutoff_cutoffAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
netblap3.c:452:1: warning: 'BlastResetOldHook' defined but not used [-Wunused-function]
BlastResetOldHook(void)
^~~~~~~~~~~~~~~~~
netblap3.c:445:1: warning: 'BlastGetErrorStatus' defined but not used [-Wunused-function]
BlastGetErrorStatus(void)
^~~~~~~~~~~~~~~~~~~
netblap3.c:438:1: warning: 'BlastSetErrorStatus' defined but not used [-Wunused-function]
BlastSetErrorStatus(Boolean status)
^~~~~~~~~~~~~~~~~~~
netblap3.c:430:1: warning: 'BlastSetErrorHook' defined but not used [-Wunused-function]
BlastSetErrorHook(void)
^~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:134:0,
from netblap3.c:364:
../include/blstspc.h:229:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/blstspc.h:228:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/blstspc.h:227:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/blstspc.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "blstspc.h23";
^~~~~~~~~~~
netblap3.c: In function 'BlastNetMatrixToBlastMatrix':
netblap3.c:1212:35: warning: 'index2' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (index1 != blast_matrix->rows || index2 != blast_matrix->columns)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
netblap3.c: In function 'TraditionalBlastReportEngine':
netblap3.c:2570:11: warning: 'next_seqalign' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (seqalign) {
^
rm -f libnetblast.a
ar cru libnetblast.a objblst3.o netblap3.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libnetblast.a ../lib
ranlib ../lib/libnetblast.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objtax1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objtax1.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objtax1.c: In function 'Taxon1ReqFree':
objtax1.c:49:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtax1.c: In function 'Taxon1ReqAsnRead':
objtax1.c:96:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1InfoAsnRead':
objtax1.c:467:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:466:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1ErrorAsnRead':
objtax1.c:1067:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1066:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1NameAsnRead':
objtax1.c:1232:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1231:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1DataAsnRead':
objtax1.c:1418:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1417:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon2DataAsnRead':
objtax1.c:1606:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c: In function 'Taxon1ReqAsnRead':
objtax1.c:265:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax1.c: In function 'Taxon1RespAsnRead':
objtax1.c:868:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/utilpub.h:4,
from taxutil.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
taxutil.c: In function 'taxname_match':
taxutil.c:66:24: warning: unused variable 'taxstr' [-Wunused-variable]
CharPtr taxstr = NULL;
^~~~~~
taxutil.c: In function 'get_lineage':
taxutil.c:140:28: warning: 'onp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return Nlm_StringSave(onp->lineage);
~~~^~~~~~~~~
taxutil.c: In function 'get_gcode':
taxutil.c:160:23: warning: 'onp' may be used uninitialized in this function [-Wmaybe-uninitialized]
gclp->genomic = onp->gcode;
~~~^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -c -o tc2dproc.o -DTAXSERVICE tc2proc.c
tc2proc.c: In function 'getIdByOrgRef':
tc2proc.c:407:17: warning: unused variable 'om_flag' [-Wunused-variable]
Boolean om_flag= FALSE;
^~~~~~~
tc2proc.c: In function 'bldLineage':
tc2proc.c:1095:10: warning: unused variable 'rank' [-Wunused-variable]
Int2 rank= 0;
^~~~
tc2proc.c: In function 'storedTaxId':
tc2proc.c:2114:17: warning: unused variable 'object_id' [-Wunused-variable]
ObjectIdPtr object_id;
^~~~~~~~~
tc2proc.c: In function 'tax1e_needUpdate':
tc2proc.c:2181:13: warning: unused variable 'hit_name' [-Wunused-variable]
CharPtr hit_name;
^~~~~~~~
tc2proc.c:2180:13: warning: unused variable 'need_search_name' [-Wunused-variable]
Boolean need_search_name= TRUE;
^~~~~~~~~~~~~~~~
tc2proc.c:2179:9: warning: unused variable 'is_species' [-Wunused-variable]
int is_species;
^~~~~~~~~~
tc2proc.c:2176:19: warning: unused variable 'res' [-Wunused-variable]
Taxon1DataPtr res;
^~~
At top level:
tc2proc.c:403:13: warning: 'getIdByOrgRef' defined but not used [-Wunused-function]
static Int4 getIdByOrgRef(CharPtr sname, OrgNamePtr orNm)
^~~~~~~~~~~~~
tc2proc.c: In function 'mergeOrgMod':
tc2proc.c:1619:22: warning: 'lst' may be used uninitialized in this function [-Wmaybe-uninitialized]
lst->next= src;
~~~~~~~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -c -o txcdproc.o -DTAXSERVICE txcdproc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ni_types.h:84,
from ../include/ncbinet.h:84,
from txcdproc.c:116:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" parttree.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/txclient.h:70,
from parttree.c:79:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
parttree.c: In function 'tax_ptree_addSubtree':
parttree.c:392:13: warning: unused variable 'need_remove' [-Wunused-variable]
Boolean need_remove= FALSE;
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxcs.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxblast.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from taxblast.c:158:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
taxblast.c: In function 'TXBHtmlReportInternal':
taxblast.c:1294:37: warning: variable 'linlines' set but not used [-Wunused-but-set-variable]
Int2 numtaxa, numorgs, numhits, linlines, longname;
^~~~~~~~
taxblast.c: In function 'RDTaxLookupReset':
taxblast.c:1985:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
At top level:
taxblast.c:1902:13: warning: 'getTotalTaxIdCount' defined but not used [-Wunused-function]
static Int4 getTotalTaxIdCount(TreeCursorPtr cursor)
^~~~~~~~~~~~~~~~~~
taxblast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: taxblast.c,v 6.30 2008/07/18 19:26:35 madden Exp $";
^~~~~
taxblast.c: In function 'TXBGetTargetGi.isra.2':
taxblast.c:501:12: warning: 'gi' may be used uninitialized in this function [-Wmaybe-uninitialized]
return gi;
^~
rm -f libncbitxc2.a
ar cru libncbitxc2.a objtax1.o taxutil.o tc2dproc.o txcdproc.o parttree.o taxcs.o taxblast.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbitxc2.a ../lib
ranlib ../lib/libncbitxc2.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" id1gen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from id1gen.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
id1gen.c: In function 'ID1serverRequestFree':
id1gen.c:49:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
id1gen.c: In function 'ID1serverRequestAsnRead':
id1gen.c:90:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
id1gen.c: In function 'ID1serverMaxcomplexAsnRead':
id1gen.c:348:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
id1gen.c:347:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
id1gen.c: In function 'ID1SeqHistAsnRead':
id1gen.c:530:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
id1gen.c:529:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
id1gen.c: In function 'ID1SeqEntryInfoAsnRead':
id1gen.c:979:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
id1gen.c:978:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
id1gen.c: In function 'ID1blobInfoAsnRead':
id1gen.c:1147:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
id1gen.c:1146:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
id1gen.c: In function 'ID1serverDebugAsnRead':
id1gen.c:1368:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
id1gen.c: In function 'ID1serverBackAsnRead':
id1gen.c:811:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
id1gen.c: In function 'ID1serverRequestAsnRead':
id1gen.c:186:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" id1arch.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from id1arch.c:31:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
id1arch.c: In function 'ID1ArchSeqEntryGet':
id1arch.c:173:7: warning: unused variable 'retval' [-Wunused-variable]
Int4 retval = 0;
^~~~~~
id1arch.c: In function 'ID1ArchGIGet':
id1arch.c:486:10: warning: unused variable 'retval' [-Wunused-variable]
Int4 retval = 0;
^~~~~~
id1arch.c: In function 'SeqHistPrintTable':
id1arch.c:553:59: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=]
sprintf(repl_date,"%0.2d/%0.2d/%0.4d",
^~~~~~~~~~~~~~~~~~~
id1arch.c:553:59: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=]
id1arch.c:553:59: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=]
id1arch.c:563:47: warning: spurious trailing '%' in format [-Wformat=]
fprintf(fp,"%-20d%-20s%",old_gi,repl_date);
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" accid1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from ../include/seqmgr.h:48,
from accid1.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
accid1.c: In function 's_ID1BioseqFetchFunc':
accid1.c:262:9: warning: unused variable 'retcode' [-Wunused-variable]
Int2 retcode=0;
^~~~~~~
rm -f libncbiid1.a
ar cru libncbiid1.a id1gen.o id1arch.o accid1.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbiid1.a ../lib
ranlib ../lib/libncbiid1.a
mkdir ../shlib
rm -f ../shlib/*.a
ln ../lib/*.a ../shlib
cd ../shlib; make -f ../make/makeshlb.unx `ls *.a | sed "s/\.a/.so.6/"` SH1="gcc -o" SH2="-shared *.o"
make[3]: Entering directory '/<<PKGBUILDDIR>>/shlib'
gcc -shared -Wl,-soname=libblastcompadj.so.6 -o libblastcompadj.so.6.1.20120620 \
-Wl,--whole-archive libblastcompadj.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
-lm
gcc -shared -Wl,-soname=libncbi.so.6 -o libncbi.so.6.1.20120620 \
-Wl,--whole-archive libncbi.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
-lm
libncbi.a(ncbifile.o): In function `Nlm_TmpNam':
./build/ncbifile.c:1209: warning: the use of `tempnam' is dangerous, better use `mkstemp'
gcc -shared -Wl,-soname=libblast.so.6 -o libblast.so.6.1.20120620 \
-Wl,--whole-archive libblast.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libblastcompadj.so.6.1.20120620 libncbi.so.6.1.20120620 -lm
ln -s libblast.so.6.1.20120620 libblast.so.6
ln -s libblast.so.6.1.20120620 libblast.so
gcc -shared -Wl,-soname=libncbiobj.so.6 -o libncbiobj.so.6.1.20120620 \
-Wl,--whole-archive libncbiobj.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbi.so.6.1.20120620 -lm
gcc -shared -Wl,-soname=libncbitool.so.6 -o libncbitool.so.6.1.20120620 \
-Wl,--whole-archive libncbitool.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libblastcompadj.so.6.1.20120620 libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620 -lm
gcc -shared -Wl,-soname=libblastapi.so.6 -o libblastapi.so.6.1.20120620 \
-Wl,--whole-archive libblastapi.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libblast.so.6.1.20120620 libncbitool.so.6.1.20120620 libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620 -lm
ln -s libblastapi.so.6.1.20120620 libblastapi.so.6
ln -s libblastapi.so.6.1.20120620 libblastapi.so
ln -s libblastcompadj.so.6.1.20120620 libblastcompadj.so.6
ln -s libblastcompadj.so.6.1.20120620 libblastcompadj.so
gcc -shared -Wl,-soname=libnetcli.so.6 -o libnetcli.so.6.1.20120620 \
-Wl,--whole-archive libnetcli.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbi.so.6.1.20120620
gcc -shared -Wl,-soname=libncbiid1.so.6 -o libncbiid1.so.6.1.20120620 \
-Wl,--whole-archive libncbiid1.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiobj.so.6.1.20120620 libnetcli.so.6.1.20120620 libncbi.so.6.1.20120620
gcc -shared -Wl,-soname=libncbimmdb.so.6 -o libncbimmdb.so.6.1.20120620 \
-Wl,--whole-archive libncbimmdb.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiid1.so.6.1.20120620 libncbitool.so.6.1.20120620 libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620 -lm
gcc -shared -Wl,-soname=libvibrantOGL.so.6 -o libvibrantOGL.so.6.1.20120620 \
-Wl,--whole-archive libvibrantOGL.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620 -lGLU -lGL -lpng -lXm -lXmu -lXt -lX11 -lm
gcc -shared -Wl,-soname=libncbidesk.so.6 -o libncbidesk.so.6.1.20120620 \
-Wl,--whole-archive libncbidesk.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libblastapi.so.6.1.20120620 libncbimmdb.so.6.1.20120620 libncbitool.so.6.1.20120620 libvibrantOGL.so.6.1.20120620 libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620 -lm
gcc -shared -Wl,-soname=libddvlib.so.6 -o libddvlib.so.6.1.20120620 \
-Wl,--whole-archive libddvlib.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbidesk.so.6.1.20120620 libvibrantOGL.so.6.1.20120620 libncbitool.so.6.1.20120620 libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620
ln -s libddvlib.so.6.1.20120620 libddvlib.so.6
ln -s libddvlib.so.6.1.20120620 libddvlib.so
ln -s libncbi.so.6.1.20120620 libncbi.so.6
ln -s libncbi.so.6.1.20120620 libncbi.so
ln -s libncbiNacc.so.6.1.20120620 libncbiCacc.so.6.1.20120620
ln -s libncbiCacc.so.6.1.20120620 libncbiCacc.so.6
ln -s libncbiCacc.so.6.1.20120620 libncbiCacc.so
gcc -shared -Wl,-soname=libncbicdr.so.6 -o libncbicdr.so.6.1.20120620 \
-Wl,--whole-archive libncbicdr.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620
gcc -shared -Wl,-soname=libncbiNacc.so.6 -o libncbiNacc.so.6.1.20120620 \
-Wl,--whole-archive libncbiNacc.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbicdr.so.6.1.20120620 libnetentr.a libnetcli.so.6.1.20120620 libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620 -lm
ln -s libncbiNacc.so.6.1.20120620 libncbiNacc.so.6
ln -s libncbiNacc.so.6.1.20120620 libncbiNacc.so
ln -s libncbiNacc.so.6.1.20120620 libncbiacc.so.6.1.20120620
ln -s libncbiacc.so.6.1.20120620 libncbiacc.so.6
ln -s libncbiacc.so.6.1.20120620 libncbiacc.so
ln -s libncbicdr.so.6.1.20120620 libncbicdr.so.6
ln -s libncbicdr.so.6.1.20120620 libncbicdr.so
ln -s libncbicn3dOGL.so.6.1.20120620 libncbicn3d.so.6.1.20120620
ln -s libncbicn3d.so.6.1.20120620 libncbicn3d.so.6
ln -s libncbicn3d.so.6.1.20120620 libncbicn3d.so
gcc -shared -Wl,-soname=libncbicn3dOGL.so.6 -o libncbicn3dOGL.so.6.1.20120620 \
-Wl,--whole-archive libncbicn3dOGL.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiNacc.so.6.1.20120620 libddvlib.so.6.1.20120620 libncbidesk.so.6.1.20120620 libncbimmdb.so.6.1.20120620 libncbitool.so.6.1.20120620 libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620 libvibrantOGL.so.6.1.20120620 -lm
ln -s libncbicn3dOGL.so.6.1.20120620 libncbicn3dOGL.so.6
ln -s libncbicn3dOGL.so.6.1.20120620 libncbicn3dOGL.so
ln -s libncbidesk.so.6.1.20120620 libncbidesk.so.6
ln -s libncbidesk.so.6.1.20120620 libncbidesk.so
ln -s libncbiid1.so.6.1.20120620 libncbiid1.so.6
ln -s libncbiid1.so.6.1.20120620 libncbiid1.so
gcc -shared -Wl,-soname=libncbimla.so.6 -o libncbimla.so.6.1.20120620 \
-Wl,--whole-archive libncbimla.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiobj.so.6.1.20120620 libnetcli.so.6.1.20120620 libncbi.so.6.1.20120620
ln -s libncbimla.so.6.1.20120620 libncbimla.so.6
ln -s libncbimla.so.6.1.20120620 libncbimla.so
ln -s libncbimmdb.so.6.1.20120620 libncbimmdb.so.6
ln -s libncbimmdb.so.6.1.20120620 libncbimmdb.so
ln -s libncbiobj.so.6.1.20120620 libncbiobj.so.6
ln -s libncbiobj.so.6.1.20120620 libncbiobj.so
ln -s libncbitool.so.6.1.20120620 libncbitool.so.6
ln -s libncbitool.so.6.1.20120620 libncbitool.so
gcc -shared -Wl,-soname=libncbitxc2.so.6 -o libncbitxc2.so.6.1.20120620 \
-Wl,--whole-archive libncbitxc2.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbitool.so.6.1.20120620 libnetcli.so.6.1.20120620 libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620 -lm
ln -s libncbitxc2.so.6.1.20120620 libncbitxc2.so.6
ln -s libncbitxc2.so.6.1.20120620 libncbitxc2.so
gcc -shared -Wl,-soname=libnetblast.so.6 -o libnetblast.so.6.1.20120620 \
-Wl,--whole-archive libnetblast.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbitool.so.6.1.20120620 libnetcli.so.6.1.20120620 libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620
ln -s libnetblast.so.6.1.20120620 libnetblast.so.6
ln -s libnetblast.so.6.1.20120620 libnetblast.so
ln -s libnetcli.so.6.1.20120620 libnetcli.so.6
ln -s libnetcli.so.6.1.20120620 libnetcli.so
ln -s libncbiNacc.so.6.1.20120620 libnetentr.so.6.1.20120620
ln -s libnetentr.so.6.1.20120620 libnetentr.so.6
ln -s libnetentr.so.6.1.20120620 libnetentr.so
gcc -shared -Wl,-soname=libvibgif.so.6 -o libvibgif.so.6.1.20120620 \
-Wl,--whole-archive libvibgif.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbi.so.6.1.20120620 -lm
ln -s libvibgif.so.6.1.20120620 libvibgif.so.6
ln -s libvibgif.so.6.1.20120620 libvibgif.so
gcc -shared -Wl,-soname=libvibnet.so.6 -o libvibnet.so.6.1.20120620 \
-Wl,--whole-archive libvibnet.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiNacc.so.6.1.20120620 libncbidesk.so.6.1.20120620 libncbimmdb.so.6.1.20120620 libvibrantOGL.so.6.1.20120620 libncbitool.so.6.1.20120620 libncbicdr.so.6.1.20120620 libncbiobj.so.6.1.20120620 libncbi.so.6.1.20120620
ln -s libvibnet.so.6.1.20120620 libvibnet.so.6
ln -s libvibnet.so.6.1.20120620 libvibnet.so
ln -s libvibrantOGL.so.6.1.20120620 libvibrant.so.6.1.20120620
ln -s libvibrant.so.6.1.20120620 libvibrant.so.6
ln -s libvibrant.so.6.1.20120620 libvibrant.so
ln -s libvibrantOGL.so.6.1.20120620 libvibrantOGL.so.6
ln -s libvibrantOGL.so.6.1.20120620 libvibrantOGL.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/shlib'
rm -f ../shlib/*.a
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -C build clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
rm -f *.[acho] *.glo
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -C build all LCL=lnx CC="gcc " LDFLAGS1="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"' -fPIE -pie -Wl,-z,relro -Wl,-z,now" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" NCBI_LINKINGLIBDIR="../shlib" \
CFLAGS1="-c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"' -D_PNG" \
LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \
LIB30=libncbicn3d.a LIB45=libddvlib.a LIB400=libvibrantOGL.a LIB3000=libncbicn3dOGL.a
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
chmod -R ug+rw,o+r . ../include
./ln-if-absent ../corelib/tsprintf.h ../include
./ln-if-absent ../corelib/gifgen.h ../include
./ln-if-absent ../corelib/ncbi*.h ../include
./ln-if-absent ../corelib/tree*.h ../include
./ln-if-absent ../corelib/regex.h ../include
./ln-if-absent ../corelib/matrix.h ../include
./ln-if-absent ../corelib/binary.h ../include
./ln-if-absent ../corelib/morefile/*.h ../include
./ln-if-absent ../corelib/morefile/*.c .
./ln-if-absent ../link/macmet/MoreCarbonAccessors.h ../include
./ln-if-absent ../corelib/ncbilcl.lnx ../include/ncbilcl.h
./ln-if-absent ../corelib/*.c .
./ln-if-absent ../corelib/core*.h .
./ln-if-absent ../asnlib/*.h .
rm -f ../include/asn.h
mv asn.h ../include
./ln-if-absent ../asnlib/*.c .
./ln-if-absent ../connect/*.c .
./ln-if-absent ../connect/ncbi_ansi_ext.h .
./ln-if-absent ../connect/ncbi_assert.h .
./ln-if-absent ../connect/ncbi_priv.h .
./ln-if-absent ../connect/ncbi_comm.h .
./ln-if-absent ../connect/ncbi_config.h .
./ln-if-absent ../connect/ncbi_connssl.h .
./ln-if-absent ../connect/ncbi_lbsm.h .
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../connect/ncbi_lbsm_ipc.h .
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../connect/ncbi_host_infop.h .
./ln-if-absent ../connect/ncbi_server_infop.h .
./ln-if-absent ../connect/ncbi_servicep.h .
./ln-if-absent ../connect/ncbi_socketp.h .
./ln-if-absent ../connect/ncbi_dispd.h .
./ln-if-absent ../connect/ncbi_lbsmd.h .
./ln-if-absent ../connect/ncbi_local.h .
./ln-if-absent ../connect/ncbi_lb.h .
./ln-if-absent ../connect/ncbi_version.h .
./ln-if-absent ../connect/ncbi_base64.h .
./ln-if-absent ../connect/urlquery.h ../include
mkdir ../include/connect
mkdir: cannot create directory '../include/connect': File exists
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
chmod ug+rw,o+r ../include/connect
cp -fp ../connect/ncbi_*.h ../connect/connect_export.h ../include/connect
./ln-if-absent ../util/tables/*.c .
mkdir -p ../include/util/tables
cp -fp ../util/tables/*.h ../include/util/tables
./ln-if-absent ../util/creaders/*.c .
mkdir -p ../include/util/creaders
cp -fp ../util/creaders/*.h ../include/util/creaders
./ln-if-absent ../ctools/*.c .
./ln-if-absent ../ctools/*.h .
mkdir ../include/ctools
mkdir: cannot create directory '../include/ctools': File exists
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
chmod ug+rw,o+r ../include/ctools
cp -fp ../ctools/*.h ../include/ctools
./ln-if-absent ../object/*.c .
./ln-if-absent ../object/*.h ../include
./ln-if-absent ../access/*.c .
./ln-if-absent ../access/*.h ../include
./ln-if-absent ../asnstat/*.h ../include
./ln-if-absent ../api/*.h ../include
./ln-if-absent ../api/*.c .
./ln-if-absent ../api/*.inc .
./ln-if-absent ../cdromlib/*.h ../include
./ln-if-absent ../cdromlib/*.c .
./ln-if-absent ../vibrant/*.h ../include
./ln-if-absent ../vibrant/*.c .
./ln-if-absent ../desktop/*.h ../include
./ln-if-absent ../desktop/*.c .
./ln-if-absent ../biostruc/*.h ../include
./ln-if-absent ../biostruc/*.c .
./ln-if-absent ../biostruc/cdd/*.h ../include
./ln-if-absent ../biostruc/cdd/*.c .
./ln-if-absent ../biostruc/cn3d/*.h ../include
./ln-if-absent ../biostruc/cn3d/*.c .
./ln-if-absent ../tools/*.h ../include
./ln-if-absent ../tools/*.c .
./ln-if-absent ../cn3d/*.h ../include
./ln-if-absent ../cn3d/*.c .
./ln-if-absent ../gif/*.c .
./ln-if-absent ../gif/*.h ../include
./ln-if-absent ../ddv/*.h ../include
./ln-if-absent ../ddv/*.c .
./ln-if-absent ../regexp/*.c .
./ln-if-absent ../regexp/*.h ../include
./ln-if-absent ../internal/compr/*.c .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/compr/*.h ../include
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libindx/*.c .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libindx/*.h ../include
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libpars/*.c .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libpars/*.h ../include
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/*.c .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/*.dat .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideochr*.h ../include
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideoorgs.h .
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.c .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.dat .
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.h ../include
set: No match.
makefile:679: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ncbidraw.c ncbidrwg.c
./ln-if-absent ncbithr.c ncbithrs.c
./ln-if-absent ../network/nsclilib/*.h ../include
./ln-if-absent ../network/blast3/client/*.h ../include
./ln-if-absent ../network/id1arch/*.h ../include
./ln-if-absent ../network/id2arch/*.h ../include
mkdir -p ../include/algo/blast/core
./ln-if-absent ../algo/blast/core/*.c .
./ln-if-absent ../algo/blast/core/*.h .
./ln-if-absent ../algo/blast/core/*.inl .
cp -fp ../algo/blast/core/*.h ../include/algo/blast/core
mkdir -p ../include/algo/blast/composition_adjustment
./ln-if-absent ../algo/blast/composition_adjustment/*.c .
cp -fp ../algo/blast/composition_adjustment/*.h \
../include/algo/blast/composition_adjustment
mkdir -p ../include/algo/blast/api
./ln-if-absent ../algo/blast/api/*.c .
cp -fp ../algo/blast/api/*.h ../include/algo/blast/api
chmod -R ug+rw,o+r .
echo Waiting...go
Waiting...go
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbithr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ncbithr.c:289:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbithr.c: In function 's_TlsDestroyAll':
ncbithr.c:2529:11: warning: variable 'err_code' set but not used [-Wunused-but-set-variable]
int err_code = 0;
^~~~~~~~
cp -p ncbithr.o ../lib
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbimain.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbimain.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbimain.c:82:1: warning: return type defaults to 'int' [-Wimplicit-int]
main(int argc, char *argv[])
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbibs.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbibs.c:55:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbibs.c: In function 'Nlm_BSSeek':
ncbibs.c:448:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sp == bsp->seekptr) /* already in right position */
^~
ncbibs.c:451:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
bsp->seekptr = sp;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF wwwutils.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbiwww.h:106,
from wwwutils.c:150:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbierr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from corepriv.h:85,
from ncbierr.c:235:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/string.h:635:0,
from ../include/ncbilcl.h:156,
from ../include/ncbi.h:57,
from corepriv.h:85,
from ncbierr.c:235:
In function 'strncat',
inlined from 'ErrMsgRoot_fopen.isra.1' at ncbierr.c:955:13:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbienv.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from corepriv.h:85,
from ncbienv.c:306:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbifile.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbifile.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbiprop.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from corepriv.h:85,
from ncbiprop.c:104:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbimath.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbimath.h:69,
from ncbimath.c:90:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbimem.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbimem.c:163:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbimisc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbimisc.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbimisc.c: In function 'Nlm_MD5Final':
ncbimisc.c:2250:26: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
^
ncbimisc.c: In function 'XmlPathSuffixIs':
ncbimisc.c:2947:58: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (StringHasNoText (parentFilter) || parent != NULL && StringICmp (parent->name, parentFilter) == 0) {
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbimsg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from corepriv.h:85,
from ncbimsg.c:167:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbistr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbistr.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbisgml.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbisgml.c:80:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/string.h:635:0,
from ../include/ncbilcl.h:156,
from ../include/ncbi.h:57,
from ncbisgml.c:80:
In function 'strncat',
inlined from 'Nlm_Sgml2Ascii' at ncbisgml.c:284:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'Nlm_Sgml2Ascii' at ncbisgml.c:265:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'Nlm_Sgml2AsciiLen' at ncbisgml.c:354:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'Nlm_Sgml2AsciiLen' at ncbisgml.c:340:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbitime.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbitime.c:77:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbilang.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbilang.c:57:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asnbufo.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asnbufo.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asndebin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asndebin.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asndebin.c: In function 'AsnBinReadVal':
asndebin.c:545:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
asndebin.c:548:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if (atp == NULL)
^~
asndebin.c:614:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* empty sequence written */
^~~~
asndebin.c:616:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
while (atp2 != NULL)
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asnenbin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnenbin.c:88:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asngen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asngen.c:80:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asngen.c: In function 'AsnFindNthPieceOfObject':
asngen.c:540:16: warning: variable 'aeop' set but not used [-Wunused-but-set-variable]
AsnExpOptPtr aeop;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asnio.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnio.c:150:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asnio.c: In function 'AsnIoWriteBlock':
asnio.c:765:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* use alternative write function */
^~~~
asnio.c:768:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if (retval != bytes_to_write)
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asnlex.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnlex.c:104:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asnlex.c: In function 'AsnTxtReadId':
asnlex.c:250:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((token == END_STRUCT) && ((isa == SEQ_TYPE) || (isa == SET_TYPE)))
^~
asnlex.c:253:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (token != IDENT)
^~
asnlex.c: In function 'AsnTxtReadVal':
asnlex.c:397:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* empty sequence written */
^~~~
asnlex.c:399:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
while (atp2 != NULL)
^~~~~
At top level:
asnlex.c:1322:13: warning: 'AsnLexWordUTF8' defined but not used [-Wunused-function]
static Int2 AsnLexWordUTF8 (AsnIoPtr aip)
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asnlext.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnlext.c:57:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asnout.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnout.c:79:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asnout.c: In function 'AsnOutput':
asnout.c:159:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
asnout.c:162:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
for (i = 0; i < 12; i++)
^~~
asnout.c:213:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! loader)
^~
asnout.c:216:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
attvp = p.root_tmpvalue.next;
^~~~~
asnout.c:270:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! loader)
^~
asnout.c:273:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
attp = p.root_tmptype.next;
^~~~
asnout.c:450:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! loader)
^~
asnout.c:453:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
i = 1;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asnprint.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asnprint.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asnprint.c: In function 'GetXMLModuleName':
asnprint.c:102:2: warning: statement with no effect [-Wunused-value]
for (currmod; currmod != NULL; currmod = currmod->next)
^~~
asnprint.c: In function 'AsnPrintCloseStruct':
asnprint.c:1771:7: warning: variable 'isa' set but not used [-Wunused-but-set-variable]
Int2 isa;
^~~
asnprint.c: In function 'AsnPrintModuleXMLInc':
asnprint.c:2092:10: warning: variable 'ptr' set but not used [-Wunused-but-set-variable]
CharPtr ptr;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asntypes.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asntypes.c:111:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asntypes.c: In function 'AsnEnumTypeStr':
asntypes.c:1383:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((atp->type->isa != ENUM_TYPE) && (atp->type->isa != INTEGER_TYPE))
^~
asntypes.c:1386:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
avnp = (AsnValxNodePtr) atp->branch;
^~~~
asntypes.c: In function 'AsnTreeLoad':
asntypes.c:1274:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%d %d %d", &numval, &numtype, &nummod);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asntypes.c:1288:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%d %s %ld %lf %d", &isa, name, &intvalue, &realvalue, &next);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asntypes.c:1301:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%d %s %d %d %d %d %d %d %d %d %d %d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&isa, name, &tagclass, &tagnumber, bools, bools+1, bools+2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bools+3, bools+4, &defaultvalue, &type, &branch, &next);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asntypes.c:1333:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%s %s %d %d", name, fname, &type, &next);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asngenob.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asngenob.c:72:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gifgen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from gifgen.c:137:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF togif.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from togif.c:111:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
togif.c: In function 'gdImageCreateFromGif':
togif.c:961:12: warning: variable 'AspectRatio' set but not used [-Wunused-but-set-variable]
int AspectRatio;
^~~~~~~~~~~
togif.c:960:12: warning: variable 'Background' set but not used [-Wunused-but-set-variable]
int Background;
^~~~~~~~~~
togif.c:959:12: warning: variable 'ColorResolution' set but not used [-Wunused-but-set-variable]
int ColorResolution;
^~~~~~~~~~~~~~~
gcc -DNCBI_NOTHREADS_AVAIL -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbithrs.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ncbithrs.c:289:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbithrs.c: In function 's_TlsDestroyAll':
ncbithrs.c:2529:11: warning: unused variable 'err_code' [-Wunused-variable]
int err_code = 0;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -DHAVE_STRING_H -DREGEX_MALLOC regex.c
regex.c: In function 're_match_2':
regex.c:2368:11: warning: unused variable 'destination' [-Wunused-variable]
char *destination; \
^
regex.c:3768:19: note: in expansion of macro 'PUSH_FAILURE_POINT'
PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
^~~~~~~~~~~~~~~~~~
regex.c:2368:11: warning: unused variable 'destination' [-Wunused-variable]
char *destination; \
^
regex.c:3915:11: note: in expansion of macro 'PUSH_FAILURE_POINT'
PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
^~~~~~~~~~~~~~~~~~
regex.c:2368:11: warning: unused variable 'destination' [-Wunused-variable]
char *destination; \
^
regex.c:3968:11: note: in expansion of macro 'PUSH_FAILURE_POINT'
PUSH_FAILURE_POINT (p + mcnt, d, -2);
^~~~~~~~~~~~~~~~~~
regex.c:4071:25: warning: variable 'sdummy' set but not used [-Wunused-but-set-variable]
const char *sdummy;
^~~~~~
regex.c:4070:28: warning: variable 'pdummy' set but not used [-Wunused-but-set-variable]
unsigned char *pdummy;
^~~~~~
regex.c:2368:11: warning: unused variable 'destination' [-Wunused-variable]
char *destination; \
^
regex.c:4107:11: note: in expansion of macro 'PUSH_FAILURE_POINT'
PUSH_FAILURE_POINT (0, 0, -2);
^~~~~~~~~~~~~~~~~~
regex.c:2368:11: warning: unused variable 'destination' [-Wunused-variable]
char *destination; \
^
regex.c:4120:11: note: in expansion of macro 'PUSH_FAILURE_POINT'
PUSH_FAILURE_POINT (0, 0, -2);
^~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF tsprintf.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbiargs.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbiargs.c:82:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF tree.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/treemgr.h:67,
from tree.c:79:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF matrix.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/matrix.h:44,
from matrix.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_socket.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_socket.c:37:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbi_socket.c: In function 's_GetLocalPort':
ncbi_socket.c:386:50: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
if (getsockname(fd, (struct sockaddr*) &sin, &sinlen) == 0
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:127:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getsockname (int __fd, __SOCKADDR_ARG __addr,
^~~~~~~~~~~
ncbi_socket.c: In function 's_IsConnected':
ncbi_socket.c:2435:73: warning: pointer targets in passing argument 5 of 'getsockopt' differ in signedness [-Wpointer-sign]
if (getsockopt(sock->sock, SOL_SOCKET, SO_ERROR, (void*) error, &len)
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:219:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getsockopt (int __fd, int __level, int __optname,
^~~~~~~~~~
ncbi_socket.c: In function 'TRIGGER_Create':
ncbi_socket.c:4002:18: warning: unused variable 'x_id' [-Wunused-variable]
unsigned int x_id = ++s_ID_Counter;
^~~~
ncbi_socket.c: In function 's_CreateListening':
ncbi_socket.c:4454:50: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
x_error = getsockname(x_lsock, &addr.sa, &addrlen) != 0
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:127:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getsockname (int __fd, __SOCKADDR_ARG __addr,
^~~~~~~~~~~
ncbi_socket.c: In function 's_Accept':
ncbi_socket.c:4722:49: warning: pointer targets in passing argument 3 of 'accept' differ in signedness [-Wpointer-sign]
if ((x_sock = accept(lsock->sock, &addr.sa, &addrlen)) == SOCK_INVALID) {
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:243:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int accept (int __fd, __SOCKADDR_ARG __addr,
^~~~~~
ncbi_socket.c: In function 's_CreateOnTop':
ncbi_socket.c:5174:35: warning: pointer targets in passing argument 3 of 'getpeername' differ in signedness [-Wpointer-sign]
if (getpeername(fd, &peer.sa, &peerlen) != 0) {
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:141:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getpeername (int __fd, __SOCKADDR_ARG __addr,
^~~~~~~~~~~
ncbi_socket.c:5210:43: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
if (getsockname(fd, &peer.sa, &peerlen) != 0)
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:127:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getsockname (int __fd, __SOCKADDR_ARG __addr,
^~~~~~~~~~~
ncbi_socket.c: In function 'DSOCK_Bind':
ncbi_socket.c:6609:53: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
x_error = getsockname(sock->sock, &addr.sa, &addrlen) != 0
^
In file included from ncbi_socketp.h:53:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/sys/socket.h:127:12: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
extern int getsockname (int __fd, __SOCKADDR_ARG __addr,
^~~~~~~~~~~
ncbi_socket.c: In function 'DSOCK_RecvMsg':
ncbi_socket.c:7002:52: warning: pointer targets in passing argument 6 of 'recvfrom' differ in signedness [-Wpointer-sign]
(struct sockaddr*) &sin, &sinlen);
^
In file included from /usr/include/arm-linux-gnueabihf/sys/socket.h:280:0,
from ncbi_socketp.h:53,
from ncbi_connssl.h:37,
from ncbi_socket.c:38:
/usr/include/arm-linux-gnueabihf/bits/socket2.h:64:1: note: expected 'socklen_t * restrict {aka unsigned int * restrict}' but argument is of type 'TSOCK_socklen_t * {aka int *}'
recvfrom (int __fd, void *__restrict __buf, size_t __n, int __flags,
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_buffer.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_types.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_core.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_core.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_core_c.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_core_c.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_util.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_util.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_priv.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_assert.h:35,
from ncbi_priv.h:55,
from ncbi_priv.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_ansi_ext.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_ansi_ext.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_connection.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_assert.h:35,
from ncbi_priv.h:55,
from ncbi_connection.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_assert.h:35,
from ncbi_priv.h:55,
from ncbi_connector.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_connutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_connutil.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_file_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_file_connector.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_heapmgr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_assert.h:35,
from ncbi_priv.h:55,
from ncbi_heapmgr.c:114:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_http_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_http_connector.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_memory_connector.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_lbsmd_stub.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_host_info.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_server_info.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_server_info.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_service.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_service.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_version.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_version.h:37,
from ncbi_version.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_service_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_service_connector.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_ftp_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_ftp_connector.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_dispd.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_dispd.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_lb.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_local.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_local.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_socket_connector.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_socket_connector.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urlquery.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from urlquery.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF binary.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/binary.h:60,
from binary.c:59:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_sendmail.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ncbi_config.h:38,
from ncbi_ansi_ext.h:37,
from ncbi_sendmail.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_base64.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn_connection.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF raw_scoremat.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF drwnflpt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from drwnflpt.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF drwnfspc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from drwnfspc.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF drwnmfls.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from drwnmfls.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rm -f libncbi.a
ar cru libncbi.a ncbimain.o ncbibs.o wwwutils.o ncbierr.o ncbienv.o ncbifile.o ncbiprop.o ncbimath.o ncbimem.o ncbimisc.o ncbimsg.o ncbistr.o ncbisgml.o ncbitime.o ncbilang.o asnbufo.o asndebin.o asnenbin.o asngen.o asnio.o asnlex.o asnlext.o asnout.o asnprint.o asntypes.o asngenob.o gifgen.o togif.o ncbithrs.o regex.o tsprintf.o ncbiargs.o tree.o matrix.o ncbi_socket.o ncbi_buffer.o ncbi_types.o ncbi_core.o ncbi_core_c.o ncbi_util.o ncbi_priv.o ncbi_ansi_ext.o ncbi_connection.o ncbi_connector.o ncbi_connutil.o ncbi_file_connector.o ncbi_heapmgr.o ncbi_http_connector.o ncbi_memory_connector.o ncbi_lbsmd_stub.o ncbi_host_info.o ncbi_server_info.o ncbi_service.o ncbi_version.o ncbi_service_connector.o ncbi_ftp_connector.o ncbi_dispd.o ncbi_lb.o ncbi_local.o ncbi_socket_connector.o urlquery.o binary.o ncbi_sendmail.o ncbi_base64.o asn_connection.o raw_scoremat.o drwnflpt.o drwnfspc.o drwnmfls.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbi.a ../lib
ranlib ../lib/libncbi.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objacces.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asnacces.h:9,
from objacces.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objacces.c: In function 'LinkSetAsnWrite':
objacces.c:137:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:140:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (lsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objacces.c: In function 'LinkSetAsnRead':
objacces.c:211:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:214:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
lsp = LinkSetNew();
^~~
objacces.c:215:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (lsp == NULL)
^~
objacces.c:218:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objacces.c:221:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:223:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* get the num */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objalign.h:103,
from objalign.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objalign.c: In function 'CommonSeqAlignLabelFunc':
objalign.c:135:27: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
CharPtr curr, typelabel, tmp;
^~~
objalign.c: In function 'SeqAlignAsnRead':
objalign.c:595:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:598:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sap = SeqAlignNew();
^~~
objalign.c:599:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sap == NULL)
^~
objalign.c:602:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'DenseDiagAsnWrite':
objalign.c:1018:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1021:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ddp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c: In function 'DenseDiagAsnRead':
objalign.c:1108:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1111:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ddp = DenseDiagNew();
^~~
objalign.c:1112:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ddp == NULL)
^~
objalign.c:1115:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'DenseSegAsnWrite':
objalign.c:1264:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1267:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (dsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c: In function 'DenseSegAsnRead':
objalign.c:1368:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1371:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
dsp = DenseSegNew();
^~~
objalign.c:1372:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dsp == NULL)
^~
objalign.c:1375:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'StdSegAsnWrite':
objalign.c:1553:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1556:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c:1573:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! SeqLocSetAsnWrite(ssp->loc, aip, STD_SEG_loc, STD_SEG_loc_E))
^~
objalign.c:1576:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ssp->scores != NULL)
^~
objalign.c: In function 'StdSegAsnRead':
objalign.c:1618:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1621:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ssp = StdSegNew();
^~~
objalign.c:1622:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ssp == NULL)
^~
objalign.c:1625:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'SeqAlignSetAsnWrite':
objalign.c:1696:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1700:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
oldsap = sap;
^~~~~~
objalign.c: In function 'PackSegAsnWrite':
objalign.c:1884:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1887:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (psp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnCloseStruct(aip, PACKED_SEG_starts, (Pointer)psp->starts))
^~
objalign.c:1919:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
av.ptrvalue = psp->present;
^~
objalign.c: In function 'PackSegAsnRead':
objalign.c:1989:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1992:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
psp = PackSegNew();
^~~
objalign.c:1993:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (psp == NULL)
^~
objalign.c:1996:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'SplicedSegAsnRead':
objalign.c:2169:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseSegAsnRead':
objalign.c:2409:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedExonAsnRead':
objalign.c:2600:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedSegModifierFree':
objalign.c:2858:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'ProductPosFree':
objalign.c:3031:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'SplicedExonChunkFree':
objalign.c:3204:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'SpliceSiteAsnRead':
objalign.c:3446:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'ProtPosAsnRead':
objalign.c:3600:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseAlignAsnRead':
objalign.c:3769:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseSegExtAsnRead':
objalign.c:3988:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedSegModifierAsnRead':
objalign.c:2938:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objalign.c: In function 'SplicedExonChunkAsnRead':
objalign.c:3305:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objall.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/objall.h:64,
from objall.c:63:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objbibli.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asnbibli.h:9,
from objbibli.c:110:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objbibli.c: In function 'AffilAsnRead':
objbibli.c:205:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:208:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
afp = AffilNew();
^~~
objbibli.c: In function 'AffilAsnWrite':
objbibli.c:293:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:296:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (afp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'AuthListFree':
objbibli.c:453:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (alp->affil != NULL)
^~
objbibli.c:455:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return (AuthListPtr)MemFree(alp);
^~~~~~
objbibli.c: In function 'AuthListAsnRead':
objbibli.c:484:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:487:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
alp = AuthListNew();
^~~
objbibli.c: In function 'AuthListAsnWrite':
objbibli.c:578:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:581:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (alp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:583:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)alp)) /* open AuthList SEQUENCE */
^~
objbibli.c:586:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
av.ptrvalue = alp->names;
^~
objbibli.c: In function 'AuthorFree':
objbibli.c:670:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ap->affil != NULL)
^~
objbibli.c:672:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return (AuthorPtr)MemFree(ap);
^~~~~~
objbibli.c: In function 'AuthorAsnRead':
objbibli.c:700:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:703:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ap = AuthorNew();
^~
objbibli.c: In function 'AuthorAsnWrite':
objbibli.c:772:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:775:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ap == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitArtAsnRead':
objbibli.c:916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:919:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cap = CitArtNew();
^~~
objbibli.c: In function 'CitArtAsnWrite':
objbibli.c:1018:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1021:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cap == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1023:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)cap)) /* open the SEQUENCE */
^~
objbibli.c:1026:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cap->title != NULL)
^~
objbibli.c: In function 'ImprintAsnRead':
objbibli.c:1141:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1144:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ip = ImprintNew();
^~
objbibli.c: In function 'ImprintAsnWrite':
objbibli.c:1240:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1243:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitRetractAsnRead':
objbibli.c:1378:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1381:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
crp = CitRetractNew();
^~~
objbibli.c: In function 'CitRetractAsnWrite':
objbibli.c:1432:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1435:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (crp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitJourAsnRead':
objbibli.c:1509:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1512:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cjp = CitJourNew();
^~~
objbibli.c: In function 'CitJourAsnWrite':
objbibli.c:1561:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1564:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cjp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1570:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! ImprintAsnWrite(cjp->imp, aip, CIT_JOUR_imp))
^~
objbibli.c:1572:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cjp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitBookAsnRead':
objbibli.c:1661:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1664:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cbp = CitBookNew();
^~~
objbibli.c: In function 'CitBookAsnWrite':
objbibli.c:1729:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1732:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1745:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! ImprintAsnWrite(cbp->imp, aip, CIT_BOOK_imp))
^~
objbibli.c:1747:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cbp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitProcAsnWrite':
objbibli.c:1864:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1867:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1884:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnCloseStruct(aip, CIT_PROC_meet, (Pointer)cpp->otherdata))
^~
objbibli.c:1886:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cpp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitLetAsnWrite':
objbibli.c:1978:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1981:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (clp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitPatAsnRead':
objbibli.c:2072:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2075:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cpp = CitPatNew();
^~~
objbibli.c: In function 'CitPatAsnWrite':
objbibli.c:2194:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2197:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'IdPatAsnRead':
objbibli.c:2325:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2328:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
idp = IdPatNew();
^~~
objbibli.c: In function 'IdPatAsnWrite':
objbibli.c:2391:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2394:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (idp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitGenAsnRead':
objbibli.c:2523:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2526:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cgp = CitGenNew();
^~~
objbibli.c: In function 'CitGenAsnWrite':
objbibli.c:2604:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2607:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cgp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'TitleAsnWrite':
objbibli.c:2800:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2803:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (tp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitSubFree':
objbibli.c:2882:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (csp == NULL)
^~
objbibli.c:2885:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
AuthListFree(csp->authors);
^~~~~~~~~~~~
objbibli.c: In function 'CitSubAsnRead':
objbibli.c:2916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2919:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
csp = CitSubNew();
^~~
objbibli.c:2931:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2934:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (atp == CIT_SUB_imp)
^~
objbibli.c: In function 'CitSubAsnWrite':
objbibli.c:3002:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3005:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (csp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:3009:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AuthListAsnWrite(csp->authors, aip, CIT_SUB_authors))
^~
objbibli.c:3012:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (csp->imp != NULL)
^~
objbibli.c: In function 'PatPrioritySetAsnRead':
objbibli.c:3665:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ppp == NULL)
^~
objbibli.c:3668:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (head == NULL)
^~
objbibli.c:3686:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3688:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ppp->date = DateAsnRead(aip, atp);
^~~
objbibli.c: In function 'PatPrioritySetAsnWrite':
objbibli.c:3724:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, set, (Pointer)ppp)) /* open the SEQUENCE OF */
^~
objbibli.c:3727:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
for (tmp = ppp; tmp != NULL; tmp = tmp->next)
^~~
objbibli.c: In function 'ArticleIdAsnRead':
objbibli.c:3818:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3821:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
aidp = ArticleIdNew();
^~~~
objbibli.c: In function 'ArticleIdAsnWrite':
objbibli.c:3894:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3897:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (aidp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'PubStatusDateAsnRead':
objbibli.c:4006:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:4009:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
psdp = PubStatusDateNew();
^~~~
objbibli.c: In function 'PubStatusDateAsnWrite':
objbibli.c:4058:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:4061:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (psdp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objfeat.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objfeat.h:48,
from objfeat.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objfeat.c: In function 'ModelEvidenceSupportAsnRead':
objfeat.c:1494:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ExperimentSupportAsnRead':
objfeat.c:1739:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ProgramIdAsnRead':
objfeat.c:1921:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'EvidenceBasisAsnRead':
objfeat.c:2088:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'InferenceSupportAsnRead':
objfeat.c:2252:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ModelEvidenceItemAsnRead':
objfeat.c:2465:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SeqFeatSupportAsnRead':
objfeat.c:2667:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAQualAsnRead':
objfeat.c:4192:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAQualSetAsnRead':
objfeat.c:4341:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAGenAsnRead':
objfeat.c:4469:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'GeneNomenclatureAsnRead':
objfeat.c:4649:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'OrgNameMatch':
objfeat.c:5890:28: warning: self-comparison always evaluates to false [-Wtautological-compare]
|| onp2->mgcode != onp2->mgcode
^~
objfeat.c: In function 'TaxElementAsnWrite':
objfeat.c:7320:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)tep))
^~
objfeat.c:7323:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
av.intvalue = (Int4)(tep->fixed_level);
^~
objfeat.c: In function 'PCRPrimerAsnRead':
objfeat.c:8191:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRPrimerSetAsnRead':
objfeat.c:8333:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRReactionAsnRead':
objfeat.c:8454:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRReactionSetAsnRead':
objfeat.c:8597:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneRefAsnRead':
objfeat.c:8724:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneSeqSetAsnRead':
objfeat.c:8914:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneSeqAsnRead':
objfeat.c:9044:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SomaticOriginAsnRead':
objfeat.c:9393:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SomaticOriginConditionAsnRead':
objfeat.c:9472:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'VariationRefAsnRead':
objfeat.c:9551:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ConsequenceAsnWrite':
objfeat.c:10112:12: warning: variable 'av' set but not used [-Wunused-but-set-variable]
DataVal av;
^~
objfeat.c: In function 'Consequence_loss_of_heterozygosityAsnRead':
objfeat.c:10572:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_frameshiftAsnRead':
objfeat.c:10650:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'VarRefDataFree':
objfeat.c:10750:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'VarRefDataSetAsnRead':
objfeat.c:10803:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_elementFree':
objfeat.c:10997:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'VariationInstAsnRead':
objfeat.c:11126:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: At top level:
objfeat.c:11275:1: warning: "/*" within comment [-Wcomment]
/**************************************************
objfeat.c: In function 'VariantPropertiesAsnRead':
objfeat.c:11304:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PhenotypeAsnRead':
objfeat.c:11625:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PopulationDataAsnRead':
objfeat.c:11821:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ExtLocAsnRead':
objfeat.c:12034:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Seq_seqFree':
objfeat.c:12199:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'DeltaItemAsnRead':
objfeat.c:12232:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_elementAsnRead':
objfeat.c:10539:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objfeat.c: In function 'CodeBreakAsnWrite':
objfeat.c:3647:11: warning: 'tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (! AsnWrite(aip, tmp, &av)) goto erret;
^~~~~~~~~~~~~~~~~~~~~~~
objfeat.c: In function 'VarRefDataAsnRead':
objfeat.c:10965:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objgen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asngen.h:9,
from objgen.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objgen.c: In function 'DateClean':
objgen.c:161:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dp == NULL)
^~
objgen.c:164:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
memset(dp, 0, sizeof(NCBI_Date));
^~~~~~
objgen.c: In function 'DateAsnWrite':
objgen.c:399:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:402:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (dp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'DateAsnRead':
objgen.c:492:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:495:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
dp = DateNew();
^~
objgen.c:496:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dp == NULL)
^~
objgen.c:499:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */
^~
objgen.c: In function 'DbtagFree':
objgen.c:750:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt == NULL)
^~
objgen.c:753:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
dbt->tag = ObjectIdFree(dbt->tag);
^~~
objgen.c: In function 'DbtagAsnRead':
objgen.c:782:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:785:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
dbt = DbtagNew();
^~~
objgen.c:786:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt == NULL)
^~
objgen.c:789:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */
^~
objgen.c:797:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt->tag == NULL)
^~
objgen.c:800:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
atp = AsnReadId(aip, amp, atp); if (atp == NULL) goto erret; /* END_STRUCT */
^~~
objgen.c: In function 'DbtagAsnWrite':
objgen.c:831:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:834:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (dbt == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'ObjectIdAsnRead':
objgen.c:976:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:979:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */
^~
objgen.c:985:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oid == NULL)
^~
objgen.c:987:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (atp == OBJECT_ID_id)
^~
objgen.c: In function 'ObjectIdAsnWrite':
objgen.c:1020:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1023:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (oid == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'NameStdFree':
objgen.c:1153:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (nsp == NULL)
^~
objgen.c:1156:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
for (i = 0; i < 7; i++)
^~~
objgen.c: In function 'NameStdAsnRead':
objgen.c:1187:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1190:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
nsp = NameStdNew();
^~~
objgen.c:1191:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (nsp == NULL)
^~
objgen.c:1194:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */
^~
objgen.c: In function 'NameStdAsnWrite':
objgen.c:1250:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1253:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (nsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'PersonIdFree':
objgen.c:1345:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pid == NULL)
^~
objgen.c:1348:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (pid->choice == 1) /* Dbtag */
^~
objgen.c: In function 'PersonIdAsnWrite':
objgen.c:1441:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1444:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (pid == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'IntFuzzAsnRead':
objgen.c:1657:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1660:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ifp = IntFuzzNew();
^~~
objgen.c:1661:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ifp == NULL)
^~
objgen.c:1664:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE (nothing) */
^~
objgen.c: In function 'UserFieldAsnRead':
objgen.c:1915:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1918:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ufp = UserFieldNew();
^~~
objgen.c: In function 'UserObjectAsnRead':
objgen.c:2395:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:2398:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
uop = UserObjectNew();
^~~
objgen.c:2399:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (uop == NULL)
^~
objgen.c:2402:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objloc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:85,
from objloc.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objloc.c: In function 'SeqIdAsnWrite':
objloc.c:313:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:316:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqIdAsnRead':
objloc.c:441:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:444:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
anp = ValNodeNew(NULL);
^~~
objloc.c: In function 'SeqIdDup':
objloc.c:585:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oldid == NULL)
^~
objloc.c:588:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
newid = ValNodeNew(NULL);
^~~~~
objloc.c: In function 'SeqIdSetAsnRead':
objloc.c:749:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, atp, &av) <= 0) /* end struct */
^~
objloc.c:751:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (first == NULL)
^~
objloc.c: In function 'SeqIdSetAsnWrite':
objloc.c:783:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp2 == NULL)
^~
objloc.c:786:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, settype); goto erret; }
^~
objloc.c: In function 'TextSeqIdAsnWrite':
objloc.c:861:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:864:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (tsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'TextSeqIdAsnRead':
objloc.c:929:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:932:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
tsip = TextSeqIdNew();
^~~~
objloc.c:933:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (tsip == NULL)
^~
objloc.c:936:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PatentSeqIdAsnWrite':
objloc.c:1013:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1016:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (psip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PatentSeqIdAsnRead':
objloc.c:1061:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1064:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
psip = PatentSeqIdNew();
^~~~
objloc.c:1065:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (psip == NULL)
^~
objloc.c:1068:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'GiimAsnWrite':
objloc.c:1144:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1147:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (gip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'GiimAsnRead':
objloc.c:1207:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (gip == NULL)
^~
objloc.c:1210:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PDBSeqIdAsnWrite':
objloc.c:1295:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1298:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (pdbsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PDBSeqIdAsnRead':
objloc.c:1356:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1359:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
pdbsip = PDBSeqIdNew();
^~~~~~
objloc.c:1360:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pdbsip == NULL)
^~
objloc.c:1363:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'SeqLocAsnWrite':
objloc.c:1508:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1511:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocAsnRead':
objloc.c:1602:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1605:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
anp = ValNodeNew(NULL);
^~~
objloc.c:1606:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (anp == NULL)
^~
objloc.c:1609:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the CHOICE value (nothing) */
^~
objloc.c: In function 'SeqLocMixAsnWrite':
objloc.c:1716:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1719:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocEquivAsnWrite':
objloc.c:1783:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1786:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocSetAsnWrite':
objloc.c:1851:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp2 == NULL)
^~
objloc.c:1854:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, set); goto erret; }
^~
objloc.c: In function 'SeqLocSetAsnRead':
objloc.c:1918:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, atp, &av) <= 0) /* read END_STRUCT */
^~
objloc.c:1920:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (first == NULL)
^~
objloc.c: In function 'SeqIntAsnWrite':
objloc.c:2000:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2003:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (sip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqIntAsnRead':
objloc.c:2071:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2074:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sip = SeqIntNew();
^~~
objloc.c:2075:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sip == NULL)
^~
objloc.c:2078:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PackSeqIntAsnWrite':
objloc.c:2155:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2157:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
oldsip = sip;
^~~~~~
objloc.c:2161:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)oldsip))
^~
objloc.c:2163:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
for ( ;sip != NULL; sip = sip->next)
^~~
objloc.c: In function 'SeqPntAsnWrite':
objloc.c:2285:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2288:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (spp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqPntAsnRead':
objloc.c:2348:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2351:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
spp = SeqPntNew();
^~~
objloc.c:2352:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (spp == NULL)
^~
objloc.c:2355:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PackSeqPntAsnWrite':
objloc.c:2453:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2456:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (pspp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PackSeqPntAsnRead':
objloc.c:2525:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2528:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
pspp = PackSeqPntNew();
^~~~
objloc.c:2529:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pspp == NULL)
^~
objloc.c:2532:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'SeqBondAsnWrite':
objloc.c:2696:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2699:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqBondAsnRead':
objloc.c:2748:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2751:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sbp = SeqBondNew();
^~~
objloc.c:2752:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sbp == NULL)
^~
objloc.c:2755:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objmedli.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmedli.h:80,
from objmedli.c:101:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmedli.c: In function 'MedlineMeshAsnRead':
objmedli.c:245:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objmedli.c:248:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
mmp = MedlineMeshNew();
^~~
objmedli.c: In function 'DocRefFree':
objmedli.c:1177:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (drp == NULL)
^~
objmedli.c:1180:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return (DocRefPtr)MemFree(drp);
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objpub.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objpub.h:70,
from objpub.c:122:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objpub.c: In function 'PubSetAsnRead':
objpub.c:824:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, settype, &av) <= 0) /* read START_STRUCT */
^~
objpub.c:827:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (settype == PUB_SET_pub)
^~
objpub.c:894:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, settype, &av) <= 0) /* read END_STRUCT for SET OF */
^~
objpub.c:896:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (anp == NULL)
^~
objpub.c: In function 'PubLabelUnique':
objpub.c:1353:17: warning: unused variable 'pmid' [-Wunused-variable]
Int4 muid = 0, pmid = 0;
^~~~
objpub.c:1353:7: warning: unused variable 'muid' [-Wunused-variable]
Int4 muid = 0, pmid = 0;
^~~~
objpub.c: In function 'PubSetAsnRead':
objpub.c:869:13: warning: 'func' may be used uninitialized in this function [-Wmaybe-uninitialized]
pnt = (* func)(aip, atp);
~~~~^~~~~~~~~~~~~~~~~~~~
objpub.c:880:25: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
cit->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objres.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from objres.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objscoremat.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objscoremat.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objscoremat.c: In function 'PssmAsnRead':
objscoremat.c:93:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmIntermediateDataAsnRead':
objscoremat.c:336:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmFinalDataAsnRead':
objscoremat.c:544:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmParametersAsnRead':
objscoremat.c:759:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmWithParametersAsnRead':
objscoremat.c:936:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'BlockPropertyAsnRead':
objscoremat.c:1102:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'CoreBlockAsnRead':
objscoremat.c:1275:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'LoopConstraintAsnRead':
objscoremat.c:1463:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'CoreDefAsnRead':
objscoremat.c:1626:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'FormatRpsDbParametersAsnRead':
objscoremat.c:1794:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from objseq.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objseq.c: In function 'LinkageEvidenceAsnRead':
objseq.c:1603:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objseq.c: In function 'SeqGapAsnRead':
objseq.c:1755:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objseq.c: In function 'SeqDescrAsnWriteExtra':
objseq.c:2023:48: warning: variable 'had_anp' set but not used [-Wunused-but-set-variable]
Boolean retval = FALSE, had_extra = FALSE, had_anp = FALSE;
^~~~~~~
objseq.c: In function 'AnnotIdAsnWrite':
objseq.c:4806:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:4808:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
break;
^~~~~
objseq.c:4814:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:4816:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
break;
^~~~~
objseq.c: In function 'AnnotDescAsnWrite':
objseq.c:5191:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:5193:12: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
break;
^~~~~
objseq.c: In function 'BioseqAsnRead':
objseq.c:977:21: warning: 'osp' may be used uninitialized in this function [-Wmaybe-uninitialized]
else if (osp->load_by_id) /* don't load it */
~~~^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objblock.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objblock.h:70,
from objblock.c:71:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objblock.c: In function 'EMBLBlockFree':
objblock.c:891:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ebp == NULL)
^~
objblock.c:894:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
DateFree(ebp->creation_date);
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objcode.c
objcode.c:45:51: warning: "/*" within comment [-Wcomment]
* environment variables to allow reading from data/*.val, replaced tabs in source code with spaces
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objcode.h:64,
from objcode.c:102:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objsset.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from objsset.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objsset.c: In function 'BioseqSetFree':
objsset.c:363:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (bsp == NULL)
^~
objsset.c:366:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (bsp->idx.parentptr == NULL || bsp->idx.parenttype == OBJ_SEQSUB) {
^~
objsset.c: In function 'SeqEntryFree':
objsset.c:876:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (sep->choice == 2)
^~
objsset.c:879:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return (SeqEntryPtr)MemFree(sep);
^~~~~~
objsset.c: In function 'SeqEntryFreeComponents':
objsset.c:896:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (sep->choice == 2)
^~
objsset.c:899:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return sep;
^~~~~~
objsset.c: In function 'SeqEntryAsnGet':
objsset.c:1071:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (retcode == 1) /* just after a Bioseq */
^~
objsset.c:1073:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
av.ptrvalue = (Pointer) osp;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objsub.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asnsubmt.h:9,
from objsub.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objsub.c: In function 'SubmitAsnLoad':
objsub.c:338:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (loaded)
^~
objsub.c:341:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! SeqSetAsnLoad ())
^~
objsub.c:344:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnLoad())
^~
objsub.c:347:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ObjMgrTypeLoad(OBJ_SEQSUB, "Seq-submit", seqsubtypename, "Sequence Data Submission",
^~~~~~~~~~~~~~
objsub.c: In function 'SeqSubmitAsnWrite':
objsub.c:452:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:455:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:457:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)ssp))
^~
objsub.c:460:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! SubmitBlockAsnWrite(ssp->sub, aip, SEQ_SUBMIT_sub)) goto erret;
^~
objsub.c: In function 'SeqSubmitAsnRead':
objsub.c:534:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:537:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ssp = SeqSubmitNew();
^~~
objsub.c:538:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ssp == NULL)
^~
objsub.c:541:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objsub.c: In function 'SubmitBlockAsnWrite':
objsub.c:677:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:680:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:682:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)sbp))
^~
objsub.c:685:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (! ContactInfoAsnWrite(sbp->contact, aip, SUBMIT_BLOCK_contact))
^~
objsub.c: In function 'SubmitBlockAsnRead':
objsub.c:763:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:766:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
oldatp = atp;
^~~~~~
objsub.c:768:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sbp == NULL)
^~
objsub.c:771:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objsub.c: In function 'ContactInfoAsnWrite':
objsub.c:935:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:938:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:940:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)cip))
^~
objsub.c:943:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (cip->name != NULL)
^~
objsub.c: In function 'ContactInfoAsnRead':
objsub.c:1059:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:1061:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
oldatp = atp;
^~~~~~
objsub.c:1064:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (cip == NULL)
^~
objsub.c:1067:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objprt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objprt.h:67,
from objprt.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objprt.c: In function 'PrintFormEnumAsnRead':
objprt.c:934:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ptr == NULL) return NULL;
^
objprt.c:951:19: note: 'ptr' was declared here
PrintFormEnumPtr ptr;
^~~
objprt.c: In function 'PrintFormTextAsnRead':
objprt.c:1051:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ptr == NULL) return NULL;
^
objprt.c:1067:19: note: 'ptr' was declared here
PrintFormTextPtr ptr;
^~~
objprt.c: In function 'PrintFormBooleanAsnRead':
objprt.c:877:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormBooleanFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormAsnRead':
objprt.c:591:6: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp = PrintFormFree(vnp);
~~~~^~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormatAsnRead':
objprt.c:429:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormatFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintTemplateAsnRead':
objprt.c:247:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintTemplateFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormBlockAsnRead':
objprt.c:755:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormBlockFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'UserFormatAsnRead':
objprt.c:1209:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=UserFormatFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objfdef.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objfeat.h:48,
from ../include/objfdef.h:48,
from objfdef.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objalignloc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objalignloc.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objalignloc.c: In function 'AlignLocSetAsnRead':
objalignloc.c:69:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c: In function 'Loc_locFree':
objalignloc.c:196:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalignloc.c: In function 'AlignLocAsnRead':
objalignloc.c:233:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:232:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'Loc_locAsnRead':
objalignloc.c:313:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignIdFree':
objalignloc.c:525:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalignloc.c: In function 'AlignIdAsnRead':
objalignloc.c:557:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignBoxAsnRead':
objalignloc.c:746:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:745:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignRowsAsnRead':
objalignloc.c:925:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:924:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignColumnsAsnRead':
objalignloc.c:1086:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:1085:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignIdAsnRead':
objalignloc.c:613:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objtable.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objtable.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objtable.c: In function 'SeqTableColumnInfoAsnRead':
objtable.c:87:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c:86:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtable.c: In function 'SeqTableColumnAsnRead':
objtable.c:268:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c:267:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtable.c: In function 'SeqTableColumnAsnWrite':
objtable.c:364:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objtable.c: In function 'SeqTableAsnRead':
objtable.c:472:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'CommonStringTableAsnRead':
objtable.c:654:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'CommonStringTableAsnWrite':
objtable.c:729:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objtable.c: In function 'CommonBytesTableAsnRead':
objtable.c:815:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'CommonBytesTableAsnWrite':
objtable.c:890:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objtable.c: In function 'SeqTableSingleDataFree':
objtable.c:1220:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtable.c: In function 'SeqTableSingleDataAsnRead':
objtable.c:1264:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtable.c: In function 'SeqTableMultiDataAsnRead':
objtable.c:1106:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtable.c: In function 'SeqTableSingleDataAsnRead':
objtable.c:1349:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtable.c: In function 'SeqTableSparseIndexAsnRead':
objtable.c:1554:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objpubme.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objpubme.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objpubme.c: In function 'PubmedEntryAsnRead':
objpubme.c:89:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objpubme.c: In function 'PubmedUrlAsnRead':
objpubme.c:285:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objpubme.c:284:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objmdrs.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmdrs.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmdrs.c: In function 'MedlarsEntryAsnRead':
objmdrs.c:85:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmdrs.c: In function 'MedlarsRecordAsnRead':
objmdrs.c:256:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmdrs.c:255:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objproj.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objproj.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objproj.c: In function 'ProjectAsnRead':
objproj.c:116:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objproj.c:115:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objproj.c: In function 'ProjectDescrAsnRead':
objproj.c:718:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objproj.c: In function 'ProjdescFree':
objproj.c:852:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objproj.c: In function 'ProjdescAsnRead':
objproj.c:893:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/mmdbapi.h:92,
from ../include/mapproj.h:45,
from objproj.c:5:
objproj.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/mmdbapi.h:92,
from ../include/mapproj.h:45,
from objproj.c:5:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/mmdbapi.h:92,
from ../include/mapproj.h:45,
from objproj.c:5:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/mmdbapi.h:92,
from ../include/mapproj.h:45,
from objproj.c:5:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
objproj.c: In function 'ProjdescAsnRead':
objproj.c:953:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objproj.c: In function 'ProjectItemAsnRead':
objproj.c:536:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objgbseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objgbseq.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objgbseq.c: In function 'GBSetAsnRead':
objgbseq.c:68:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBSeqAsnRead':
objgbseq.c:229:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBReferenceAsnRead':
objgbseq.c:725:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBCommentAsnRead':
objgbseq.c:963:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBStrucCommentAsnRead':
objgbseq.c:1127:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBFeatureAsnRead':
objgbseq.c:1295:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBFeatureSetAsnRead':
objgbseq.c:1519:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBAltSeqDataAsnRead':
objgbseq.c:1683:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBXrefAsnRead':
objgbseq.c:1846:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBCommentParagraphAsnRead':
objgbseq.c:2012:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBCommentItemAsnRead':
objgbseq.c:2163:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBStrucCommentItemAsnRead':
objgbseq.c:2330:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBIntervalAsnRead':
objgbseq.c:2506:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBQualifierAsnRead':
objgbseq.c:2716:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBAltSeqItemAsnRead':
objgbseq.c:2887:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objtseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objtseq.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objtseq.c: In function 'TSeqAsnRead':
objtseq.c:89:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtseq.c: In function 'TSeqSetAsnRead':
objtseq.c:322:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtseq.c: In function 'BioseqToTSeq':
objtseq.c:448:8: warning: variable 'seqcode' set but not used [-Wunused-but-set-variable]
Uint1 seqcode;
^~~~~~~
objtseq.c: In function 'BioseqToMiniTSeq':
objtseq.c:560:8: warning: variable 'seqcode' set but not used [-Wunused-but-set-variable]
Uint1 seqcode;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objinsdseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objinsdseq.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objinsdseq.c: In function 'INSDSetAsnRead':
objinsdseq.c:68:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDSeqAsnRead':
objinsdseq.c:229:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDReferenceAsnRead':
objinsdseq.c:725:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDCommentAsnRead':
objinsdseq.c:963:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDStrucCommentAsnRead':
objinsdseq.c:1127:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDFeatureAsnRead':
objinsdseq.c:1295:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDFeatureSetAsnRead':
objinsdseq.c:1519:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDAltSeqDataAsnRead':
objinsdseq.c:1683:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDXrefAsnRead':
objinsdseq.c:1846:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDCommentParagraphAsnRead':
objinsdseq.c:2012:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDCommentItemAsnRead':
objinsdseq.c:2163:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDStrucCommentItemAsnRead':
objinsdseq.c:2330:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDIntervalAsnRead':
objinsdseq.c:2506:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDQualifierAsnRead':
objinsdseq.c:2716:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDAltSeqItemAsnRead':
objinsdseq.c:2887:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objmacro.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmacro.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmacro.c: In function 'AECRActionAsnRead':
objmacro.c:87:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:86:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseActionAsnRead':
objmacro.c:269:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:268:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MacroActionListAsnRead':
objmacro.c:472:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:469:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MacroActionListAsnWrite':
objmacro.c:525:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SuspectRuleSetAsnRead':
objmacro.c:586:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:583:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SuspectRuleSetAsnWrite':
objmacro.c:639:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'WordSubstitutionAsnRead':
objmacro.c:719:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c: In function 'WordSubstitutionSetAsnRead':
objmacro.c:884:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:881:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'WordSubstitutionSetAsnWrite':
objmacro.c:937:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'StringConstraintAsnRead':
objmacro.c:1025:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1024:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StringConstraintSetAsnRead':
objmacro.c:1266:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1263:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'StringConstraintSetAsnWrite':
objmacro.c:1319:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'LocationPosConstraintFree':
objmacro.c:1359:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationPosConstraintAsnRead':
objmacro.c:1388:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationConstraintAsnRead':
objmacro.c:1587:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1586:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalValAsnRead':
objmacro.c:1800:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1799:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalValChoiceFree':
objmacro.c:1927:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FeatQualLegalValChoiceAsnRead':
objmacro.c:1959:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalSetAsnRead':
objmacro.c:2111:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2108:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'FeatQualLegalSetAsnWrite':
objmacro.c:2164:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'FeatQualChoiceFree':
objmacro.c:2204:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FeatQualChoiceAsnRead':
objmacro.c:2236:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldAsnRead':
objmacro.c:2415:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2414:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldLegalAsnRead':
objmacro.c:2579:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2578:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldPairAsnRead':
objmacro.c:2742:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2741:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaFeatTypeFree':
objmacro.c:2882:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'RnaFeatTypeAsnRead':
objmacro.c:2914:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaQualAsnRead':
objmacro.c:3162:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3161:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaQualPairAsnRead':
objmacro.c:3327:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3326:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualPairAsnRead':
objmacro.c:3500:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3499:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualChoiceFree':
objmacro.c:3625:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SourceQualChoiceAsnRead':
objmacro.c:3654:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualTextValAsnRead':
objmacro.c:3869:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3868:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualValChoiceFree':
objmacro.c:3996:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SourceQualValChoiceAsnRead':
objmacro.c:4028:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualValSetAsnRead':
objmacro.c:4224:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4221:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SourceQualValSetAsnWrite':
objmacro.c:4277:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'CDSGeneProtFieldPairAsnRead':
objmacro.c:4353:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4352:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldFree':
objmacro.c:4478:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MolinfoFieldAsnRead':
objmacro.c:4507:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoMoleculePairAsnRead':
objmacro.c:4732:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4731:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoTechniquePairAsnRead':
objmacro.c:4893:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4892:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoCompletednessPairAsnRead':
objmacro.c:5054:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5053:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoMolClassPairAsnRead':
objmacro.c:5215:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5214:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoTopologyPairAsnRead':
objmacro.c:5376:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5375:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoStrandPairAsnRead':
objmacro.c:5537:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5536:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldPairFree':
objmacro.c:5662:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MolinfoFieldPairAsnRead':
objmacro.c:5709:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldListAsnRead':
objmacro.c:5901:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5898:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MolinfoFieldListAsnWrite':
objmacro.c:5954:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MolinfoFieldConstraintAsnRead':
objmacro.c:6032:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6031:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StructuredCommentFieldFree':
objmacro.c:6160:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'StructuredCommentFieldAsnRead':
objmacro.c:6192:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StructuredCommentFieldPairAsnRead':
objmacro.c:6386:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6385:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StructuredCommentFieldPairAsnWrite':
objmacro.c:6461:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'DBLinkFieldPairAsnRead':
objmacro.c:6553:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6552:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldConstraintAsnRead':
objmacro.c:6715:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6714:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeFree':
objmacro.c:6843:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeAsnRead':
objmacro.c:6872:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintAsnRead':
objmacro.c:7087:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7086:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PublicationConstraintAsnRead':
objmacro.c:7253:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7252:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceConstraintAsnRead':
objmacro.c:7432:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7431:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtPseudoConstraintAsnRead':
objmacro.c:7621:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7620:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtConstraintFieldFree':
objmacro.c:7746:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'CDSGeneProtConstraintFieldAsnRead':
objmacro.c:7775:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtQualConstraintAsnRead':
objmacro.c:7948:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7947:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtQualConstraintAsnWrite':
objmacro.c:8030:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'FieldConstraintAsnRead':
objmacro.c:8129:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:8128:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldConstraintAsnWrite':
objmacro.c:8204:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'FieldTypeFree':
objmacro.c:8260:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FieldTypeAsnRead':
objmacro.c:8304:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintFree':
objmacro.c:8511:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintAsnRead':
objmacro.c:8540:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'QuantityConstraintFree':
objmacro.c:8718:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'QuantityConstraintAsnRead':
objmacro.c:8747:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceConstraintAsnRead':
objmacro.c:8945:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:8944:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TranslationConstraintAsnRead':
objmacro.c:9170:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9169:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConstraintChoiceFree':
objmacro.c:9322:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConstraintChoiceAsnRead':
objmacro.c:9384:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConstraintChoiceSetAsnRead':
objmacro.c:9616:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9613:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'ConstraintChoiceSetAsnWrite':
objmacro.c:9669:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'TextMarkerFree':
objmacro.c:9709:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TextMarkerAsnRead':
objmacro.c:9741:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TextPortionAsnRead':
objmacro.c:9937:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9936:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldEditAsnRead':
objmacro.c:10153:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10152:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldPairTypeFree':
objmacro.c:10300:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FieldPairTypeAsnRead':
objmacro.c:10350:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyActionAsnRead':
objmacro.c:10567:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10566:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditActionAsnRead':
objmacro.c:10744:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10743:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditActionAsnWrite':
objmacro.c:10819:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'TextTransformFree':
objmacro.c:10875:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TextTransformAsnRead':
objmacro.c:10910:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TextTransformSetAsnRead':
objmacro.c:11081:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11078:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'TextTransformSetAsnWrite':
objmacro.c:11134:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'ConvertActionAsnRead':
objmacro.c:11214:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11213:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CopyActionAsnRead':
objmacro.c:11406:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11405:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SwapActionAsnRead':
objmacro.c:11572:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11571:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SwapActionAsnWrite':
objmacro.c:11647:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'AECRParseActionAsnRead':
objmacro.c:11745:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11744:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveActionAsnRead':
objmacro.c:11961:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11960:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveActionAsnWrite':
objmacro.c:12029:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'RemoveOutsideActionAsnRead':
objmacro.c:12119:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:12118:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ActionChoiceFree':
objmacro.c:12259:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ActionChoiceAsnRead':
objmacro.c:12312:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcOrgChoiceFree':
objmacro.c:12499:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcOrgChoiceAsnRead':
objmacro.c:12528:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcOrgAsnRead':
objmacro.c:12711:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:12710:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcGeneralIdFree':
objmacro.c:12839:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcGeneralIdAsnRead':
objmacro.c:12871:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcFree':
objmacro.c:13027:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcAsnRead':
objmacro.c:13065:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseDstOrgAsnRead':
objmacro.c:13319:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:13318:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseDestFree':
objmacro.c:13447:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseDestAsnRead':
objmacro.c:13485:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationIntervalAsnRead':
objmacro.c:13693:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:13692:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationChoiceFree':
objmacro.c:13818:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationChoiceAsnRead':
objmacro.c:13850:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceListAsnRead':
objmacro.c:14024:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14021:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SequenceListAsnWrite':
objmacro.c:14077:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SequenceListChoiceFree':
objmacro.c:14117:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SequenceListChoiceAsnRead':
objmacro.c:14149:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyFeatureActionAsnRead':
objmacro.c:14338:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14337:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveFeatureActionAsnRead':
objmacro.c:14602:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14601:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFromCDSOptionsAsnRead':
objmacro.c:14766:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14765:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureSrcOptionsFree':
objmacro.c:14900:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConvertFeatureSrcOptionsAsnRead':
objmacro.c:14932:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RegionTypeAsnRead':
objmacro.c:15099:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15098:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureDstOptionsFree':
objmacro.c:15215:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConvertFeatureDstOptionsAsnRead':
objmacro.c:15250:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureActionAsnRead':
objmacro.c:15464:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15463:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditLocationStrandAsnRead':
objmacro.c:15670:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15669:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'Partial5SetActionAsnRead':
objmacro.c:15831:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15830:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'Partial3SetActionAsnRead':
objmacro.c:15992:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15991:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PartialBothSetActionAsnRead':
objmacro.c:16153:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16152:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ExtendToFeatureAsnRead':
objmacro.c:16315:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16314:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationEditTypeFree':
objmacro.c:16452:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationEditTypeAsnRead':
objmacro.c:16499:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditFeatureLocationActionAsnRead':
objmacro.c:16774:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16773:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoBlockAsnRead':
objmacro.c:16971:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16970:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoBlockAsnWrite':
objmacro.c:17053:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'RemoveDescriptorActionAsnRead':
objmacro.c:17151:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17150:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AutodefActionAsnRead':
objmacro.c:17317:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c: In function 'FixPubCapsActionAsnRead':
objmacro.c:17488:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17487:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SortFieldsActionAsnRead':
objmacro.c:17690:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17689:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixAuthorCapsAsnRead':
objmacro.c:17866:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17865:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixCapsActionFree':
objmacro.c:17982:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixCapsActionAsnRead':
objmacro.c:18017:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixFormatActionFree':
objmacro.c:18189:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixFormatActionAsnRead':
objmacro.c:18218:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveDuplicateFeatureActionAsnRead':
objmacro.c:18422:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18421:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'GeneXrefTypeAsnRead':
objmacro.c:18613:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18612:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'XrefTypeFree':
objmacro.c:18747:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'XrefTypeAsnRead':
objmacro.c:18779:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveXrefsActionAsnRead':
objmacro.c:18948:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18947:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveXrefsActionAsnWrite':
objmacro.c:19023:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MakeGeneXrefActionAsnRead':
objmacro.c:19116:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19115:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AuthorFixActionAsnRead':
objmacro.c:19281:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19280:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'UpdateSequencesActionAsnRead':
objmacro.c:19447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19446:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CreateTSAIdsSrcFree':
objmacro.c:19574:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'CreateTSAIdsSrcAsnRead':
objmacro.c:19606:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CreateTSAIdsActionAsnRead':
objmacro.c:19787:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19786:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AutofixActionAsnRead':
objmacro.c:19966:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19965:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixSetsActionFree':
objmacro.c:20084:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixSetsActionAsnRead':
objmacro.c:20113:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TableMatchTypeFree':
objmacro.c:20269:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TableMatchTypeAsnRead':
objmacro.c:20301:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TableMatchAsnRead':
objmacro.c:20547:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:20546:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyTableExtraDataFree':
objmacro.c:20675:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ApplyTableExtraDataAsnRead':
objmacro.c:20704:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyTableActionAsnRead':
objmacro.c:20877:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:20876:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AddFileActionAsnRead':
objmacro.c:21057:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21056:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AddDescriptorListActionAsnRead':
objmacro.c:21225:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21224:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AddDescriptorListActionAsnWrite':
objmacro.c:21300:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'RemoveSequencesActionAsnRead':
objmacro.c:21393:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21392:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveSequencesActionAsnWrite':
objmacro.c:21461:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MacroActionChoiceFree':
objmacro.c:21512:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MacroActionChoiceAsnRead':
objmacro.c:21613:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SearchFuncFree':
objmacro.c:22093:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SearchFuncAsnRead':
objmacro.c:22131:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SimpleReplaceAsnRead':
objmacro.c:22400:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:22399:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ReplaceFuncFree':
objmacro.c:22536:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ReplaceFuncAsnRead':
objmacro.c:22571:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ReplaceRuleAsnRead':
objmacro.c:22751:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:22750:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SuspectRuleAsnRead':
objmacro.c:22921:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:22920:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualChoiceAsnRead':
objmacro.c:3727:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SourceQualValChoiceAsnRead':
objmacro.c:4098:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MolinfoFieldAsnRead':
objmacro.c:4587:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MolinfoFieldPairAsnRead':
objmacro.c:5771:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'StructuredCommentFieldAsnRead':
objmacro.c:6251:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FieldTypeAsnRead':
objmacro.c:8390:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ConstraintChoiceAsnRead':
objmacro.c:9466:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcGeneralIdAsnRead':
objmacro.c:12930:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixCapsActionAsnRead':
objmacro.c:18084:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixFormatActionAsnRead':
objmacro.c:18284:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixSetsActionAsnRead':
objmacro.c:20172:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MacroActionChoiceAsnRead':
objmacro.c:21852:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationPosConstraintAsnRead':
objmacro.c:1447:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'RnaFeatTypeAsnRead':
objmacro.c:3008:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeAsnRead':
objmacro.c:6945:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintAsnRead':
objmacro.c:8613:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'QuantityConstraintAsnRead':
objmacro.c:8806:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'TextMarkerAsnRead':
objmacro.c:9800:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FieldPairTypeAsnRead':
objmacro.c:10416:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ActionChoiceAsnRead':
objmacro.c:12382:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcOrgChoiceAsnRead':
objmacro.c:12580:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcAsnRead':
objmacro.c:13160:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseDestAsnRead':
objmacro.c:13552:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationChoiceAsnRead':
objmacro.c:13906:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ConvertFeatureDstOptionsAsnRead':
objmacro.c:15320:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationEditTypeAsnRead':
objmacro.c:16603:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'TableMatchTypeAsnRead':
objmacro.c:20392:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SearchFuncAsnRead':
objmacro.c:22236:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objent2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objent2.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objent2.c: In function 'Entrez2IdListAsnRead':
objent2.c:87:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:86:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2BooleanExpAsnRead':
objent2.c:276:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2BooleanElementFree':
objent2.c:414:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'Entrez2BooleanElementAsnRead':
objent2.c:455:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LimitsAsnRead':
objent2.c:664:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:663:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2BooleanTermAsnRead':
objent2.c:841:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:840:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2RequestAsnRead':
objent2.c:1037:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1036:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'E2RequestFree':
objent2.c:1198:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'E2RequestAsnRead':
objent2.c:1251:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2EvalBooleanAsnRead':
objent2.c:1488:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1487:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermQueryAsnRead':
objent2.c:1664:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1663:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermPosAsnRead':
objent2.c:1842:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1841:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2HierQueryAsnRead':
objent2.c:2028:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2027:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2GetLinksAsnRead':
objent2.c:2215:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2214:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2IdAsnRead':
objent2.c:2409:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2408:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DtFilterAsnRead':
objent2.c:2573:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2572:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2ReplyAsnRead':
objent2.c:2750:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2749:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'E2ReplyFree':
objent2.c:2922:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'E2ReplyAsnRead':
objent2.c:2978:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2InfoAsnRead':
objent2.c:3224:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2BooleanReplyAsnRead':
objent2.c:3395:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:3394:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumListAsnRead':
objent2.c:3572:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2TermListAsnRead':
objent2.c:3733:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2HierNodeAsnRead':
objent2.c:3905:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2LinkSetAsnRead':
objent2.c:4104:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4103:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkCountListAsnRead':
objent2.c:4280:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2DbInfoAsnRead':
objent2.c:4446:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2FieldInfoAsnRead':
objent2.c:4685:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4684:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkInfoAsnRead':
objent2.c:4928:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4927:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumFieldInfoAsnRead':
objent2.c:5126:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5125:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumAsnRead':
objent2.c:5301:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2DocsumDataAsnRead':
objent2.c:5463:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5462:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermAsnRead':
objent2.c:5629:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5628:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkCountAsnRead':
objent2.c:5811:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5810:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2BooleanElementAsnRead':
objent2.c:522:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objent2.c: In function 'E2ReplyAsnRead':
objent2.c:3062:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ent2api.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ent2api.h:45,
from ent2api.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF pmfapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from pmfapi.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pmfapi.c: In function 'PubMedSynchronousQuery':
pmfapi.c:1224:58: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("PubMedWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'PubSeqSynchronousQueryEx':
pmfapi.c:1458:58: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'PubSeqSynchronousQueryTI':
pmfapi.c:1636:58: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'PubSeqSynchronousQuerySRA':
pmfapi.c:1717:58: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'GiRevHistSynchronousQuery':
pmfapi.c:1790:61: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("GiRevHistWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'GiAccVerSynchronousQuery':
pmfapi.c:1842:60: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("GiAccVerWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'AccnRevHistSynchronousQuery':
pmfapi.c:1893:63: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("AccnRevHistWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'GiSeqIdSetSynchronousQuery':
pmfapi.c:1944:62: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("GiSeqIdSetWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
pmfapi.c: In function 'AccnListSynchronousQuery':
pmfapi.c:1994:60: warning: 'starttime' may be used uninitialized in this function [-Wmaybe-uninitialized]
printf ("AccnListWaitForReply %ld\n", (long) (stoptime - starttime));
~~~~~~~~~~^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objtax3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objtax3.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objtax3.c: In function 'Taxon3RequestAsnRead':
objtax3.c:86:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'T3RequestFree':
objtax3.c:200:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtax3.c: In function 'SequenceOfIntAsnRead':
objtax3.c:418:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'Taxon3ReplyAsnRead':
objtax3.c:547:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'T3ReplyFree':
objtax3.c:661:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtax3.c: In function 'T3ErrorAsnRead':
objtax3.c:872:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'T3DataAsnRead':
objtax3.c:1071:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'Value_valueFree':
objtax3.c:1252:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtax3.c: In function 'T3StatusFlagsAsnRead':
objtax3.c:1282:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'T3RefreshFlagsAsnRead':
objtax3.c:1606:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
In file included from ../include/strimprt.h:72:0,
from objtax3.c:5:
objtax3.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from objtax3.c:5:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from objtax3.c:5:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from objtax3.c:5:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
objtax3.c: In function 'T3RequestAsnRead':
objtax3.c:297:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax3.c: In function 'T3ReplyAsnRead':
objtax3.c:741:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax3.c: In function 'T3StatusFlagsAsnRead':
objtax3.c:1420:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax3.c:1361:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF tax3api.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from tax3api.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
tax3api.c: In function 'Tax3SynchronousQuery':
tax3api.c:188:27: warning: variable 't3' set but not used [-Wunused-but-set-variable]
time_t t1, t2, t3;
^~
tax3api.c: In function 'CheckSuggestedFixes':
tax3api.c:753:20: warning: variable 'tep' set but not used [-Wunused-but-set-variable]
T3ErrorPtr tep;
^~~
tax3api.c: In function 'TryNewSuggestedFixes':
tax3api.c:865:20: warning: variable 'tep' set but not used [-Wunused-but-set-variable]
T3ErrorPtr tep;
^~~
tax3api.c: In function 'GetSuggestedNamesFromRank':
tax3api.c:1114:20: warning: variable 'tep' set but not used [-Wunused-but-set-variable]
T3ErrorPtr tep;
^~~
tax3api.c: In function 'BioSourceFromBioSample':
tax3api.c:3220:16: warning: unused variable 'max' [-Wunused-variable]
time_t max = 0;
^~~
At top level:
tax3api.c:3003:13: warning: 'AddBioSourcesToChecklist' defined but not used [-Wunused-function]
static void AddBioSourcesToChecklist (ValNodePtr biop_list, ValNodePtr check_list)
^~~~~~~~~~~~~~~~~~~~~~~~
tax3api.c:2345:16: warning: 'StringIsExactMatchForOrgRef' defined but not used [-Wunused-function]
static Boolean StringIsExactMatchForOrgRef (CharPtr str, OrgRefPtr org)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
tax3api.c:1886:16: warning: 'EndsWithSp' defined but not used [-Wunused-function]
static Boolean EndsWithSp (CharPtr str)
^~~~~~~~~~
tax3api.c:616:28: warning: 'TaxFixItemOrigIsOk' defined but not used [-Wunused-function]
static Boolean LIBCALLBACK TaxFixItemOrigIsOk (ValNodePtr vnp)
^~~~~~~~~~~~~~~~~~
tax3api.c:361:16: warning: 'HasMisspellingFlag' defined but not used [-Wunused-function]
static Boolean HasMisspellingFlag (T3DataPtr t)
^~~~~~~~~~~~~~~~~~
tax3api.c:297:13: warning: 'SaveTaxon3Request' defined but not used [-Wunused-function]
static void SaveTaxon3Request (Taxon3RequestPtr t3rp, CharPtr path)
^~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objegkludge.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objegkludge.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objentgene.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objentgene.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objentgene.c: In function 'EntrezgeneAsnRead':
objentgene.c:103:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c: In function 'EntrezgeneSetAsnRead':
objentgene.c:411:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:408:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objentgene.c: In function 'EntrezgeneSetAsnWrite':
objentgene.c:464:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objentgene.c: In function 'GeneTrackAsnRead':
objentgene.c:545:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c: In function 'GeneCommentaryAsnRead':
objentgene.c:764:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c: In function 'Method_methodFree':
objentgene.c:1056:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objentgene.c: In function 'MapsAsnRead':
objentgene.c:1087:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1086:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'Method_methodAsnRead':
objentgene.c:1167:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'GeneSourceAsnRead':
objentgene.c:1408:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1407:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'XtraTermsAsnRead':
objentgene.c:1622:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1621:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'OtherSourceAsnRead':
objentgene.c:1792:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1791:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'MapsAsnRead':
objentgene.c:1219:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objentgene.c:1166:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objmla2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmla2.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmla2.c: In function 'Mla2RequestFree':
objmla2.c:49:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmla2.c: In function 'Mla22RequestAsnRead':
objmla2.c:96:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmla2.c: In function 'TitleMsg2AsnRead':
objmla2.c:447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmla2.c:446:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmla2.c: In function 'TitleMsgList2AsnRead':
objmla2.c:612:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmla2.c: In function 'Mla22RequestAsnRead':
objmla2.c:249:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmla2.c: In function 'Mla2BackAsnRead':
objmla2.c:902:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mla2api.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/mla2api.h:45,
from mla2api.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF qblastapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from qblastapi.c:120:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
qblastapi.c: In function 'SecondQBlastCallback':
qblastapi.c:259:15: warning: variable 'waiting' set but not used [-Wunused-but-set-variable]
Boolean waiting = FALSE;
^~~~~~~
qblastapi.c: In function 'BLASTGetSeqAnnotByRIDEx':
qblastapi.c:823:18: warning: variable 'status' set but not used [-Wunused-but-set-variable]
EIO_Status status;
^~~~~~
qblastapi.c: In function 'BLASTGetQueryBioseqByRIDEx':
qblastapi.c:868:18: warning: variable 'status' set but not used [-Wunused-but-set-variable]
EIO_Status status;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vecscnapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from vecscnapi.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objmim.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmim.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmim.c: In function 'MimSetAsnRead':
objmim.c:86:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimDateAsnRead':
objmim.c:248:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:247:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimEntryAsnRead':
objmim.c:447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimCitAsnRead':
objmim.c:907:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:906:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimTextAsnRead':
objmim.c:1093:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:1092:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimEditItemAsnRead':
objmim.c:1272:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:1271:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimAllelicVariantAsnRead':
objmim.c:1443:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimIndexTermAsnRead':
objmim.c:1634:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimReferenceAsnRead':
objmim.c:1812:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimLinkAsnRead':
objmim.c:2187:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2186:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimAuthorAsnRead':
objmim.c:2360:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2359:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimPageAsnRead':
objmim.c:2525:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2524:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objvalid.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objvalid.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objvalid.c: In function 'FieldRuleAsnRead':
objvalid.c:88:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:87:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objvalid.c: In function 'FieldSetAsnRead':
objvalid.c:256:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:253:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'FieldSetAsnWrite':
objvalid.c:309:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'DependentFieldRuleAsnRead':
objvalid.c:390:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:389:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objvalid.c: In function 'DependentFieldSetAsnRead':
objvalid.c:573:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:570:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'DependentFieldSetAsnWrite':
objvalid.c:626:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'CommentRuleAsnRead':
objvalid.c:708:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:707:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objvalid.c: In function 'CommentSetAsnRead':
objvalid.c:898:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:895:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'CommentSetAsnWrite':
objvalid.c:951:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mimapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mimapi.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cddapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cddapi.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqport.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from seqport.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqport.c: In function 'productLoc_to_locationLoc':
seqport.c:4153:13: warning: variable 'is_cdregion' set but not used [-Wunused-but-set-variable]
Boolean is_cdregion = FALSE;
^~~~~~~~~~~
seqport.c: In function 'NaLocFromNaInterval':
seqport.c:4483:8: warning: variable 'p_end_pos' set but not used [-Wunused-but-set-variable]
Int4 p_end_pos; /*the end of the product sequence in the current loc*/
^~~~~~~~~
seqport.c: In function 'dnaLoc_to_aaLoc':
seqport.c:4599:18: warning: variable 'cds_right' set but not used [-Wunused-but-set-variable]
Int4 cds_left, cds_right;
^~~~~~~~~
seqport.c:4599:8: warning: variable 'cds_left' set but not used [-Wunused-but-set-variable]
Int4 cds_left, cds_right;
^~~~~~~~
seqport.c: In function 'DeltaRevComp':
seqport.c:5281:21: warning: variable 'dspnext' set but not used [-Wunused-but-set-variable]
DeltaSeqPtr dsp, dspnext;
^~~~~~~
seqport.c: In function 'SeqSearchEnterNucWord':
seqport.c:6822:18: warning: variable 'patLen' set but not used [-Wunused-but-set-variable]
Int2 next, patLen, state;
^~~~~~
seqport.c: In function 'ProtSearchEnterProtWord':
seqport.c:7696:18: warning: variable 'patLen' set but not used [-Wunused-but-set-variable]
Int2 next, patLen, state;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from seqport.c:62:
seqport.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF sequtil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from sequtil.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequtil.c: In function 'GetPointsForLeftAndRightOffsets':
sequtil.c:7959:11: warning: variable 'first_strand' set but not used [-Wunused-but-set-variable]
Uint1 first_strand, last_strand;
^~~~~~~~~~~~
sequtil.c: In function 'SeqPointWriteEx':
sequtil.c:8492:15: warning: variable 'fuzzlen' set but not used [-Wunused-but-set-variable]
Int4 fuzzlen, id_len;
^~~~~~~
sequtil.c: In function 'TaxNameFromCommon':
sequtil.c:8647:42: warning: missing braces around initializer [-Wmissing-braces]
static Nlm_TaxCommon taxcommon[40] = {
^
sequtil.c:8647:42: note: (near initialization for 'taxcommon')
sequtil.c: In function 'GetBestScoreAndEvalueFromScorePtr':
sequtil.c:9470:48: warning: variable 'sum_set' set but not used [-Wunused-but-set-variable]
Boolean score_set=FALSE, evalue_set=FALSE, sum_set=FALSE, bit_set=FALSE;
^~~~~~~
sequtil.c: In function 'SeqIdFromAccessionEx':
sequtil.c:10070:38: warning: variable 'sip2' set but not used [-Wunused-but-set-variable]
SeqIdPtr sip2;
^~~~
sequtil.c: In function 'SeqLocCoverage':
sequtil.c:6875:12: warning: 'sip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqIdPtr sip;
^~~
sequtil.c: In function 'SeqLocCompareEx.part.18':
sequtil.c:5792:29: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
for (i = 0; i < num; i++)
^~~
sequtil.c:5792:29: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF prtutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objprt.h:67,
from ../include/prtutil.h:69,
from prtutil.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
prtutil.c: In function 'StdFormatPrint':
prtutil.c:1422:10: warning: unused variable 'ptr' [-Wunused-variable]
CharPtr ptr = NULL;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF simple.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/simple.h:63,
from simple.c:68:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from simple.c:69:0:
../include/all.h:7192:0: warning: "RNA_QUAL" redefined
#define RNA_QUAL &at[2231]
../include/all.h:5745:0: note: this is the location of the previous definition
#define RNA_QUAL &at[1023]
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF tofasta.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from ../include/tofasta.h:47,
from tofasta.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
tofasta.c: In function 'DoSpecialDefline':
tofasta.c:1407:22: warning: variable 'gene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr gene = NULL;
^~~~
tofasta.c: In function 'CreateDefLineExEx':
tofasta.c:4801:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (vnp != NULL)
^~
tofasta.c:4803:15: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (title != NULL) {
^~
tofasta.c: In function 'FastaToSeqEntryInternalExEx':
tofasta.c:2736:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(buffer+1, BuffSize, fd);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tofasta.c:2761:13: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(buffer+i+1, FTSE_BUFF_CHUNK, fd);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
tofasta.c:3479:19: warning: 'GatherGenesForCDS' defined but not used [-Wunused-function]
static ValNodePtr GatherGenesForCDS(SeqLocPtr slp)
^~~~~~~~~~~~~~~~~
tofasta.c:3445:19: warning: 'GatherSeqFeatProt' defined but not used [-Wunused-function]
static SeqFeatPtr GatherSeqFeatProt(BioseqPtr bsp)
^~~~~~~~~~~~~~~~~
tofasta.c:3359:19: warning: 'GetCDSProtUnindexed' defined but not used [-Wunused-function]
static SeqFeatPtr GetCDSProtUnindexed (
^~~~~~~~~~~~~~~~~~~
tofasta.c:3196:19: warning: 'IndexedGatherDescrOnBioseq' defined but not used [-Wunused-function]
static ValNodePtr IndexedGatherDescrOnBioseq (ItemInfoPtr iip, BioseqPtr bsp, Uint1 choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~
tofasta.c:3101:16: warning: 'get_descr' defined but not used [-Wunused-function]
static Boolean get_descr (GatherContextPtr gcp)
^~~~~~~~~
tofasta.c:3072:16: warning: 'get_descr_on_top' defined but not used [-Wunused-function]
static Boolean get_descr_on_top (GatherContextPtr gcp)
^~~~~~~~~~~~~~~~
tofasta.c: In function 'FastaReadSequenceInternalEx':
tofasta.c:2611:27: warning: 'mask_to' may be used uninitialized in this function [-Wmaybe-uninitialized]
mask_sint->to = mask_to;
~~~~~~~~~~~~~~^~~~~~~~~
tofasta.c: In function 'FastaToSeqEntryInternalExEx':
tofasta.c:2852:13: warning: 'fd' may be used uninitialized in this function [-Wmaybe-uninitialized]
ungetc(ch, fd);
^~~~~~~~~~~~~~
tofasta.c:2672:25: warning: 'firstchar' may be used uninitialized in this function [-Wmaybe-uninitialized]
const Char PNTR firstchar;
^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF tofile.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from tofile.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF tomedlin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmedli.h:80,
from tomedlin.c:150:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF valid.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from valid.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
valid.c: In function 'Valid1GatherProc':
valid.c:2238:22: warning: variable 'sc_valid' set but not used [-Wunused-but-set-variable]
EFieldValid sc_valid;
^~~~~~~~
valid.c: In function 'ValidateSeqIdCase':
valid.c:3342:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'ValidateGenProdSet':
valid.c:5551:19: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'CountAdjacentProc':
valid.c:6193:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'ValidateBioseqInst':
valid.c:6584:19: warning: variable 'tech' set but not used [-Wunused-but-set-variable]
Uint1 tech;
^~~~
valid.c:6526:19: warning: variable 'prot' set but not used [-Wunused-but-set-variable]
SeqFeatPtr prot;
^~~~
valid.c: In function 'ValidateBioSource':
valid.c:13688:19: warning: variable 'id' set but not used [-Wunused-but-set-variable]
Int4 id;
^~
valid.c: In function 'ValidateDblink':
valid.c:14737:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'ValidateSeqDescrCommon':
valid.c:14795:19: warning: variable 'pdp' set but not used [-Wunused-but-set-variable]
PubdescPtr pdp;
^~~
valid.c: In function 'ValidateBioseqContextIndexed':
valid.c:17742:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (bvsp->is_mrna || cdscount == 1 && genecount < 2) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
valid.c:17154:41: warning: variable 'utr3gene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr cdsgene, utr5gene, utr3gene;
^~~~~~~~
valid.c: In function 'ValidateBarcodeIndexNumber':
valid.c:18667:21: warning: variable 'bin_len' set but not used [-Wunused-but-set-variable]
Int4 bin_len;
^~~~~~~
valid.c: In function 'ValidateBioseqContext':
valid.c:18775:19: warning: variable 'taxname' set but not used [-Wunused-but-set-variable]
CharPtr taxname = NULL;
^~~~~~~
valid.c: In function 'ValidateRptUnit':
valid.c:20323:32: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean badchars, found, just_nuc_letters, multi_rpt_unit;
^~~~~
valid.c: In function 'CheckForCommonCDSProduct':
valid.c:22238:19: warning: variable 'is_nw' set but not used [-Wunused-but-set-variable]
Boolean is_nw = FALSE;
^~~~~
valid.c:22235:19: warning: variable 'is_nc' set but not used [-Wunused-but-set-variable]
Boolean is_nc = FALSE;
^~~~~
valid.c: In function 'CheckForIllegalDbxref':
valid.c:22617:16: warning: variable 'id' set but not used [-Wunused-but-set-variable]
Int4 id;
^~
valid.c: In function 'ValidateAnticodon':
valid.c:23348:53: warning: variable 'circular' set but not used [-Wunused-but-set-variable]
ordered = TRUE, adjacent = FALSE, circular = FALSE, exception = FALSE;
^~~~~~~~
valid.c:23347:19: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = TRUE, tmpval, mixed_strand = FALSE, unmarked_strand = FALSE,
^~~~~~
valid.c: In function 'IsGeneXrefRedundant':
valid.c:24599:17: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
valid.c: In function 'ValidateSeqFeat':
valid.c:24763:19: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
valid.c:24741:19: warning: variable 'pdp' set but not used [-Wunused-but-set-variable]
PubdescPtr pdp;
^~~
valid.c: In function 'CdTransCheck':
valid.c:26675:19: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'SpliceCheckEx':
valid.c:27477:19: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
valid.c: In function 'CdsProductIdCheck':
valid.c:27823:15: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'ValidateSeqLoc':
valid.c:27887:19: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = TRUE, tmpval, mixed_strand = FALSE, unmarked_strand = FALSE,
^~~~~~
valid.c:27886:24: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
SeqLocPtr tmp, prev;
^~~~
valid.c: In function 'SortSeqGraphProc':
valid.c:28260:26: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (gip2->right < gip2->right) {
^
At top level:
valid.c:24281:16: warning: 'CouldExtendPartial' defined but not used [-Wunused-function]
static Boolean CouldExtendPartial (SeqLocPtr slp, Boolean partial5)
^~~~~~~~~~~~~~~~~~
valid.c:18342:28: warning: 'MultiGeneOverlapFree' defined but not used [-Wunused-function]
static MultiGeneOverlapPtr MultiGeneOverlapFree (MultiGeneOverlapPtr m)
^~~~~~~~~~~~~~~~~~~~
valid.c:18292:19: warning: 'ListFeaturesContainedInLocation' defined but not used [-Wunused-function]
static ValNodePtr ListFeaturesContainedInLocation (BioseqPtr bsp, SeqLocPtr slp, Uint1 seqfeatChoice, Uint1 featdefChoice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
valid.c:13056:16: warning: 'CountryIsClosestToLatLon' defined but not used [-Wunused-function]
static Boolean CountryIsClosestToLatLon (
^~~~~~~~~~~~~~~~~~~~~~~~
valid.c:12959:16: warning: 'LatLonInRange' defined but not used [-Wunused-function]
static Boolean LatLonInRange (
^~~~~~~~~~~~~
valid.c:12157:16: warning: 'LatLonIsValid' defined but not used [-Wunused-function]
static Boolean LatLonIsValid (CharPtr name)
^~~~~~~~~~~~~
valid.c:9394:16: warning: 'ConsistentWithC' defined but not used [-Wunused-function]
static Boolean ConsistentWithC (Char ch)
^~~~~~~~~~~~~~~
valid.c:6450:13: warning: 'ReportLongSeqId' defined but not used [-Wunused-function]
static void ReportLongSeqId (SeqIdPtr sip, ValidStructPtr vsp, Int4 max_len)
^~~~~~~~~~~~~~~
valid.c:5438:13: warning: 'CheckMutSetSources' defined but not used [-Wunused-function]
static void CheckMutSetSources (BioSourcePtr biop, Pointer userdata)
^~~~~~~~~~~~~~~~~~
valid.c:4089:13: warning: 'FindLongIdsThatCollideWhenTruncated' defined but not used [-Wunused-function]
static void FindLongIdsThatCollideWhenTruncated (SeqEntryPtr sep, ValidStructPtr vsp, Int4 trunc_len)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
valid.c:1415:16: warning: 'IsNotUnclassifiedExcept' defined but not used [-Wunused-function]
static Boolean IsNotUnclassifiedExcept (ValidStructPtr vsp)
^~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF valapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from valapi.c:50:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
valapi.c: In function 'DoesStringMatchExpression':
valapi.c:253:15: warning: variable 'errstr' set but not used [-Wunused-but-set-variable]
const char *errstr;
^~~~~~
valapi.c: In function 'ReorderStructuredCommentFields':
valapi.c:777:82: warning: unused variable 'ufp_last' [-Wunused-variable]
UserFieldPtr ufp, ufp_prev = NULL, new_list = NULL, new_prev = NULL, ufp_next, ufp_last = NULL;
^~~~~~~~
valapi.c:777:72: warning: unused variable 'ufp_next' [-Wunused-variable]
UserFieldPtr ufp, ufp_prev = NULL, new_list = NULL, new_prev = NULL, ufp_next, ufp_last = NULL;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF alignmgr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/alignmgr.h:261,
from alignmgr.c:584:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
alignmgr.c: In function 'AlnMgrIndexParentSA':
alignmgr.c:1607:19: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
sap->saip = (Pointer)AMAlignIndexFree(amaip);
^
alignmgr.c: In function 'AlnMgrGetNthBlockRange':
alignmgr.c:4182:21: warning: variable 'amaip' set but not used [-Wunused-but-set-variable]
AMAlignIndexPtr amaip;
^~~~~
alignmgr.c: In function 'AlnMgrMakeFakeMultipleEx':
alignmgr.c:5157:21: warning: variable 'nogap' set but not used [-Wunused-but-set-variable]
Boolean nogap;
^~~~~
alignmgr.c: In function 'AlnMgrMapBioseqToBioseq':
alignmgr.c:10840:19: warning: variable 'gap' set but not used [-Wunused-but-set-variable]
Uint1 gap;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from alignmgr.c:584:
alignmgr.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
alignmgr.c:10572:16: warning: 'am_merge_after_edit' defined but not used [-Wunused-function]
static Boolean am_merge_after_edit (SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~~~
alignmgr.c:6650:16: warning: 'AlnMgrJaggedIndex' defined but not used [-Wunused-function]
static Boolean AlnMgrJaggedIndex(SeqAlignPtr sap, AMmsmsPtr ams_head, AMmsmsPtr *ams_mhead, Int4 numrows)
^~~~~~~~~~~~~~~~~
alignmgr.c:6123:18: warning: 'AlnMgrConstructOverlaps' defined but not used [-Wunused-function]
static AMmsmsPtr AlnMgrConstructOverlaps(AMmsmsPtr ams_head)
^~~~~~~~~~~~~~~~~~~~~~~
alignmgr.c:5405:13: warning: 'AlnMgrMergeNeighbors' defined but not used [-Wunused-function]
static void AlnMgrMergeNeighbors(SeqAlignPtr salp)
^~~~~~~~~~~~~~~~~~~~
alignmgr.c: In function 'AlnMgrUnpackSeqAlign':
alignmgr.c:1149:33: warning: 'sap_segs_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap_segs_prev->next = (SeqAlignPtr)(sap_segs->segs);
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr.c: In function 'AlnMgrGetNthSeqRangeInSA':
alignmgr.c:4115:19: warning: 'tmp_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
*stop = tmp_end;
~~~~~~^~~~~~~~~
alignmgr.c:4113:20: warning: 'tmp_beg' may be used uninitialized in this function [-Wmaybe-uninitialized]
*start = tmp_beg;
~~~~~~~^~~~~~~~~
alignmgr.c: In function 'am_print_seqalign_indexes':
alignmgr.c:2416:30: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j=0; j<(saip->ssdp[i]->numsect); j++)
~~~~^~~~~~
alignmgr.c:2481:34: warning: 'amaip' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j=0; j<(amaip->amadp[i]->numseg); j++)
~~~~~^~~~~~~
alignmgr.c: In function 'am_is_consistent':
alignmgr.c:10114:13: warning: 'n' may be used uninitialized in this function [-Wmaybe-uninitialized]
AlnMgrGetNthUnalignedForNthRow(sap, n, i, &u_start, &u_stop);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr.c: In function 'AlnMgrGetSubAlign':
alignmgr.c:9097:15: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
salp = am_cleanupsalp(salp);
~~~~~^~~~~~~~~~~~~~~~~~~~~~
alignmgr.c: In function 'AlnMgrMakeMultByIntersectOnMaster':
alignmgr.c:5592:4: warning: 'sip_tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqIdFree(sip_tmp);
^~~~~~~~~~~~~~~~~~
alignmgr.c:5885:21: warning: 'sip_tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
sip_tmp = sip_tmp->next;
~~~~~~~~^~~~~~~~~~~~~~~
alignmgr.c:5846:18: note: 'sip_tmp' was declared here
SeqIdPtr sip_tmp;
^~~~~~~
alignmgr.c:5883:17: warning: 'sip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (SAM_OrderSeqID(sip_tmp, sip) == 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr.c:5844:18: note: 'sip' was declared here
SeqIdPtr sip;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF aliparse.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/aliparse.h:12,
from aliparse.c:9:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
aliparse.c: In function 's_IsInterleaved':
aliparse.c:929:37: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(s_configInfo.useMaybes == FALSE) &&
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
(seqLinePtr->maybe == FALSE))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aliparse.c:823:20: warning: variable 'isMaybe' set but not used [-Wunused-but-set-variable]
Boolean isMaybe;
^~~~~~~
aliparse.c: In function 's_ProcessInterId':
aliparse.c:1000:15: warning: variable 'errPtr' set but not used [-Wunused-but-set-variable]
ErrInfoPtr errPtr;
^~~~~~
aliparse.c: In function 's_ProcessInterSeq':
aliparse.c:1090:15: warning: variable 'errPtr' set but not used [-Wunused-but-set-variable]
ErrInfoPtr errPtr = NULL;
^~~~~~
aliparse.c: In function 's_AnalyzeInterleaved':
aliparse.c:1193:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aliparse.c: In function 's_ProcessContigId':
aliparse.c:1385:18: warning: variable 'errPtr' set but not used [-Wunused-but-set-variable]
ErrInfoPtr errPtr;
^~~~~~
aliparse.c: In function 's_ProcessContigSeq':
aliparse.c:1476:18: warning: variable 'errPtr' set but not used [-Wunused-but-set-variable]
ErrInfoPtr errPtr;
^~~~~~
aliparse.c: In function 's_AnalyzeContiguous':
aliparse.c:1603:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aliparse.c: In function 's_CheckContext':
aliparse.c:2150:33: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(seqLinePtr->maybe == TRUE) &&
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
(s_configInfo.useMaybes == TRUE))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aliparse.c:2131:20: warning: variable 'errPtr' set but not used [-Wunused-but-set-variable]
ErrInfoPtr errPtr;
^~~~~~
aliparse.c: In function 'PrintOutMultAlign':
aliparse.c:3161:10: warning: statement with no effect [-Wunused-value]
for (d; d<spacer; d++)
^~~
aliparse.c: In function 'ALI_ConvertToNCBIData':
aliparse.c:3227:17: warning: variable 'sdp' set but not used [-Wunused-but-set-variable]
SeqDescrPtr sdp;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/aliparse.h:15,
from aliparse.c:9:
aliparse.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
aliparse.c:57:18: warning: 's_SegCompare' declared 'static' but never defined [-Wunused-function]
static int s_SegCompare(const void *i,
^~~~~~~~~~~~
aliparse.c:3186:13: warning: 'PrintOutSegs' defined but not used [-Wunused-function]
static void PrintOutSegs(SeqAlignPtr sap)
^~~~~~~~~~~~
aliparse.c:3130:13: warning: 'PrintOutMultAlign' defined but not used [-Wunused-function]
static void PrintOutMultAlign(SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~
aliparse.c:449:13: warning: 's_FreeRowList' defined but not used [-Wunused-function]
static void s_FreeRowList (ValNodePtr rowList)
^~~~~~~~~~~~~
aliparse.c: In function 's_GetRowIdString':
aliparse.c:543:20: warning: 'newIdStr' may be used uninitialized in this function [-Wmaybe-uninitialized]
CharPtr newIdStr;
^~~~~~~~
aliparse.c: In function 's_ProcessMaybes':
aliparse.c:696:21: warning: 'lastSeqPart' may be used uninitialized in this function [-Wmaybe-uninitialized]
lastSeqPart->next = newSeqPart;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from ../include/ncbi.h:62:0,
from ../include/aliparse.h:12,
from aliparse.c:9:
../include/ncbistr.h:337:19: warning: 'currentIdStr' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringCmp Nlm_StringCmp
^~~~~~~~~~~~~
aliparse.c:631:18: note: 'currentIdStr' was declared here
CharPtr currentIdStr;
^~~~~~~~~~~~
aliparse.c: In function 'Ali_Read':
aliparse.c:1355:14: warning: 'previousLength' may be used uninitialized in this function [-Wmaybe-uninitialized]
errPtr = Ali_AddError (&(fileInfoPtr->errors),ERR_SEQ_LENGTH_MISMATCH,
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
previousLength,
~~~~~~~~~~~~~~~
s_configInfo.declaredInfo.seqLength);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aliparse.c:1154:20: note: 'previousLength' was declared here
Int4 previousLength;
^~~~~~~~~~~~~~
aliparse.c:927:18: warning: 'seqLinePtr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (seqLinePtr->sequence != NULL)
~~~~~~~~~~^~~~~~~~~~
aliparse.c:820:20: note: 'seqLinePtr' was declared here
SeqLineInfoPtr seqLinePtr;
^~~~~~~~~~
aliparse.c:760:3: warning: 'cLineType' may be used uninitialized in this function [-Wmaybe-uninitialized]
fprintf(stderr,"%04d: MAYBE SEQUENCE[%c] : %s\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqLinePtr->rowNum,
~~~~~~~~~~~~~~~~~~~
cLineType,
~~~~~~~~~~
seqLinePtr->sequence);
~~~~~~~~~~~~~~~~~~~~~
aliparse.c:723:20: note: 'cLineType' was declared here
Char cLineType;
^~~~~~~~~
aliparse.c: In function 'ALI_ConvertToNCBIData':
aliparse.c:3276:4: warning: 'sep_new' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAlignAddInSeqEntry (sep_head, sanp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF aliread.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from aliread.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/aliparse.h:15,
from aliread.c:6:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF alignval.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from alignval.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
alignval.c: In function 'ValidateSeqlengthInDenseSeg':
alignval.c:1214:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if(stptrtemp[j+i*aligndim]+lenptrtemp[i]>bslen)
^
alignval.c: In function 'PercentStringMatch':
alignval.c:1495:32: warning: variable 'max_len' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, min_len, k, max_len;
^~~~~~~
alignval.c: In function 'CheckAlnSeqLens':
alignval.c:1893:12: warning: variable 'aln_len' set but not used [-Wunused-but-set-variable]
Int4 aln_len, start, stop;
^~~~~~~
alignval.c: In function 'ValidateSeqAlign':
alignval.c:1991:16: warning: variable 'ans' set but not used [-Wunused-but-set-variable]
MsgAnswer ans;
^~~
alignval.c: In function 'GetAlignmentColumnPercentIdentities':
alignval.c:2371:14: warning: variable 'num_match' set but not used [-Wunused-but-set-variable]
Int4 num_match;
^~~~~~~~~
alignval.c: In function 'WeightedAlignmentPercentIdentity':
alignval.c:2681:14: warning: variable 'num_match' set but not used [-Wunused-but-set-variable]
Int4 num_match;
^~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from alignval.c:57:
alignval.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
alignval.c:1891:13: warning: 'CheckAlnSeqLens' defined but not used [-Wunused-function]
static void CheckAlnSeqLens (SeqAlignPtr salp)
^~~~~~~~~~~~~~~
alignval.c:1476:16: warning: 'IsSipContainedInStdseg' defined but not used [-Wunused-function]
static Boolean IsSipContainedInStdseg(SeqIdPtr sip, StdSegPtr ssp)
^~~~~~~~~~~~~~~~~~~~~~
alignval.c:568:13: warning: 'delete_bioseqs' defined but not used [-Wunused-function]
static void delete_bioseqs (ValNodePtr ids, Uint2 entityID)
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF sqnutil1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/sqnutils.h:48,
from sqnutil1.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sqnutil1.c: In function 'GeneExtendFunc':
sqnutil1.c:2514:18: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
sqnutil1.c: In function 'ParseAnticodon':
sqnutil1.c:3961:14: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil1.c: In function 'ParseCodeBreak':
sqnutil1.c:4081:17: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil1.c: In function 'CleanOrgModListEx':
sqnutil1.c:6276:48: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
} else if (last->subtype == omp->subtype &&
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
StringICmp (last->subname, omp->subname) == 0 ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil1.c: In function 'CleanUpPubdescAuthors':
sqnutil1.c:9213:20: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
ValNodePtr PNTR prev;
^~~~
sqnutil1.c: In function 'RemoveUnnecessaryGeneXrefs':
sqnutil1.c:14155:24: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil1.c: In function 'LinkTwoFeatures':
sqnutil1.c:18204:25: warning: variable 'prev_xref' set but not used [-Wunused-but-set-variable]
SeqFeatXrefPtr xref, prev_xref, next_xref;
^~~~~~~~~
sqnutil1.c: In function 'RemoveBadCodonRecognizedCallback':
sqnutil1.c:18750:13: warning: variable 'rcodon' set but not used [-Wunused-but-set-variable]
Uint1 rcodon [4];
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from sqnutil1.c:63:
sqnutil1.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
sqnutil1.c:10364:16: warning: 'CleanUpSgml' defined but not used [-Wunused-function]
static CharPtr CleanUpSgml (
^~~~~~~~~~~
sqnutil1.c:10250:13: warning: 'SortGoTermsSfp' defined but not used [-Wunused-function]
static void SortGoTermsSfp (
^~~~~~~~~~~~~~
sqnutil1.c:7645:16: warning: 'IsStringSingleToken' defined but not used [-Wunused-function]
static Boolean IsStringSingleToken (CharPtr str)
^~~~~~~~~~~~~~~~~~~
sqnutil1.c:5290:13: warning: 'CleanupConsSplice' defined but not used [-Wunused-function]
static void CleanupConsSplice (GBQualPtr gbq)
^~~~~~~~~~~~~~~~~
sqnutil1.c:2509:16: warning: 'GeneExtendFunc' defined but not used [-Wunused-function]
static Boolean GeneExtendFunc (GatherContextPtr gcp)
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF sqnutil2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/sqnutils.h:48,
from sqnutil2.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sqnutil2.c: In function 'FindResidueByName':
sqnutil2.c:5197:11: warning: variable 'last' set but not used [-Wunused-but-set-variable]
Uint1 last;
^~~~
sqnutil2.c: In function 'ReadFeatureTableEx':
sqnutil2.c:7202:18: warning: variable 'isnote' set but not used [-Wunused-but-set-variable]
Boolean isnote;
^~~~~~
sqnutil2.c:7194:18: warning: variable 'endsinspace' set but not used [-Wunused-but-set-variable]
Boolean endsinspace;
^~~~~~~~~~~
sqnutil2.c: In function 'SeqEntryCopyReplace':
sqnutil2.c:9199:8: warning: variable 'type' set but not used [-Wunused-but-set-variable]
Uint1 type = 0;
^~~~
sqnutil2.c: In function 'StreamingReadBioseq':
sqnutil2.c:10024:10: warning: variable 'level' set but not used [-Wunused-but-set-variable]
Int2 level;
^~~~~
sqnutil2.c: In function 'StreamAsnForDescriptors':
sqnutil2.c:10257:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (rval = StreamingReadSeqEntry (aip, sp, &sr)) {
^~~~~
sqnutil2.c: In function 'StreamingReadWriteSeqSubmit':
sqnutil2.c:10637:1: warning: label 'ret' defined but not used [-Wunused-label]
ret:
^~~
sqnutil2.c: In function 'WriteAsnWithReplacedDescriptors':
sqnutil2.c:10676:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (rval = StreamingReadWriteSeqEntry(desc_stream_list, aip_in, aip_out, sp)) {
^~~~~
sqnutil2.c: In function 'ReadFeatureTableFile':
sqnutil2.c:11627:18: warning: variable 'begin' set but not used [-Wunused-but-set-variable]
Int4 begin;
^~~~~
sqnutil2.c: In function 'ReadFastaOnly':
sqnutil2.c:11821:18: warning: variable 'seqid' set but not used [-Wunused-but-set-variable]
Char seqid [2048];
^~~~~
sqnutil2.c: In function 'ReadDeltaFastaWithEmptyDefline':
sqnutil2.c:12352:29: warning: variable 'seqid' set but not used [-Wunused-but-set-variable]
Char line [4096], seqid [2048];
^~~~~
sqnutil2.c: In function 'SortSeqGraphProc':
sqnutil2.c:12908:26: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (gip2->right < gip2->right) {
^
sqnutil2.c: In function 'PrintQualityScoresToBuffer':
sqnutil2.c:12958:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil2.c: In function 'GetScoresbySeqId':
sqnutil2.c:13367:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil2.c: In function 'IsStringInSpanInList':
sqnutil2.c:17223:11: warning: variable 'str_val' set but not used [-Wunused-but-set-variable]
Int4 str_val;
^~~~~~~
sqnutil2.c:17221:27: warning: variable 'suffix_len' set but not used [-Wunused-but-set-variable]
Int4 prefix_len = 0, suffix_len;
^~~~~~~~~~
sqnutil2.c: In function 'CreateStructuredCommentsFromFile':
sqnutil2.c:19251:35: warning: variable 'vnp_h' set but not used [-Wunused-but-set-variable]
ValNodePtr table, header, line, vnp_h, vnp_l, tmp;
^~~~~
sqnutil2.c: In function 'AlignmentIntervalToString':
sqnutil2.c:19615:14: warning: variable 'target_strand' set but not used [-Wunused-but-set-variable]
Uint1 target_strand;
^~~~~~~~~~~~~
sqnutil2.c:19614:14: warning: variable 'seq_len' set but not used [-Wunused-but-set-variable]
Int4 seq_len;
^~~~~~~
sqnutil2.c: In function 'AdjustForConsensusSpliceCallback':
sqnutil2.c:20781:33: warning: variable 'partial5_last' set but not used [-Wunused-but-set-variable]
Boolean partial5, partial3, partial5_last, partial3_last, first = TRUE;
^~~~~~~~~~~~~
sqnutil2.c: In function 'RemoveGIProc':
sqnutil2.c:21356:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from sqnutil2.c:58:
sqnutil2.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
sqnutil2.c:16055:13: warning: 'RevCompFeatsOnBioseq' defined but not used [-Wunused-function]
static void RevCompFeatsOnBioseq (BioseqPtr bsp)
^~~~~~~~~~~~~~~~~~~~
sqnutil2.c:8266:16: warning: 'DoesSeqEntryAccessionMatchList' defined but not used [-Wunused-function]
static Boolean DoesSeqEntryAccessionMatchList (SeqEntryPtr sep, ValNodePtr accn_list)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil2.c:4661:16: warning: 'IsNonSeqChar' defined but not used [-Wunused-function]
static Boolean IsNonSeqChar (Char ch, Boolean is_prot)
^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF sqnutil3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/sqnutils.h:48,
from sqnutil3.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sqnutil3.c: In function 'BspLinkCDSmRNAbyOverlap':
sqnutil3.c:526:22: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil3.c: In function 'CautiousSeqEntryCleanup':
sqnutil3.c:2265:16: warning: variable 'taxserver' set but not used [-Wunused-but-set-variable]
Boolean taxserver;
^~~~~~~~~
sqnutil3.c: In function 'ConvertSegSetsToDeltaSequences':
sqnutil3.c:3376:17: warning: variable 'bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr bsp, new_bsp = NULL;
^~~
sqnutil3.c:3370:26: warning: variable 'prev_sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sub_sep, prev_sep, next_sep;
^~~~~~~~
sqnutil3.c: In function 'MakeSequinDataFromAlignmentEx':
sqnutil3.c:5124:32: warning: variable 'num_sets' set but not used [-Wunused-but-set-variable]
Int4 index, curr_seg, num_sets;
^~~~~~~~
sqnutil3.c:5118:26: warning: variable 'salp_last' set but not used [-Wunused-but-set-variable]
SeqAlignPtr salp_list, salp_last;
^~~~~~~~~
sqnutil3.c:5118:15: warning: variable 'salp_list' set but not used [-Wunused-but-set-variable]
SeqAlignPtr salp_list, salp_last;
^~~~~~~~~
sqnutil3.c: In function 'OrgNameMatchExceptOldName':
sqnutil3.c:13089:28: warning: self-comparison always evaluates to false [-Wtautological-compare]
|| onp2->mgcode != onp2->mgcode
^~
sqnutil3.c: In function 'GetCDSformRNA':
sqnutil3.c:19157:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil3.c: In function 'FindTextInFlatfileEx':
sqnutil3.c:20891:19: warning: variable 'okay' set but not used [-Wunused-but-set-variable]
Boolean okay;
^~~~
sqnutil3.c: In function 'CheckForTitleAuthorConflicts':
sqnutil3.c:21972:14: warning: variable 'author_conflict' set but not used [-Wunused-but-set-variable]
Boolean author_conflict = FALSE;
^~~~~~~~~~~~~~~
sqnutil3.c: In function 'SortVnpByBspProjectId':
sqnutil3.c:25733:31: warning: the comparison will always evaluate as 'true' for the address of 'vnp2' will never be NULL [-Waddress]
if (vnp1 != NULL &&& vnp2 != NULL) {
^~
sqnutil3.c: In function 'GetDiscrepancyItemTextEx':
sqnutil3.c:28202:21: warning: variable 'special_flag' set but not used [-Wunused-but-set-variable]
Boolean special_flag = FALSE;
^~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from sqnutil3.c:62:
sqnutil3.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
sqnutil3.c: In function 'FillInMissingTraces':
sqnutil3.c:31968:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
sqnutil3.c:33544:13: warning: 'TestLatLonFormatting' defined but not used [-Wunused-function]
static void TestLatLonFormatting (FILE *fp)
^~~~~~~~~~~~~~~~~~~~
sqnutil3.c:31404:1: warning: 'BarcodeTestForSeqEntry' defined but not used [-Wunused-function]
BarcodeTestForSeqEntry
^~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:31396:13: warning: 'FindBadGPS' defined but not used [-Wunused-function]
static void FindBadGPS (BioseqPtr bsp, Pointer userdata)
^~~~~~~~~~
sqnutil3.c:23725:13: warning: 'FindSuspectrRNAProductsCallback' defined but not used [-Wunused-function]
static void FindSuspectrRNAProductsCallback (SeqFeatPtr sfp, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:19971:16: warning: 'FeatureCountHasNumFeats' defined but not used [-Wunused-function]
static Boolean FeatureCountHasNumFeats (ValNodePtr vnp, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:18676:24: warning: 'SortVnpByHaplotypeThenSequenceAllowNDiff' defined but not used [-Wunused-function]
static int LIBCALLBACK SortVnpByHaplotypeThenSequenceAllowNDiff (VoidPtr ptr1, VoidPtr ptr2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:16581:24: warning: 'IntervalPairFree' defined but not used [-Wunused-function]
static IntervalPairPtr IntervalPairFree (IntervalPairPtr i)
^~~~~~~~~~~~~~~~
sqnutil3.c:13399:16: warning: 'ContainsBracketsOrParentheses' defined but not used [-Wunused-function]
static Boolean ContainsBracketsOrParentheses (CharPtr pattern, CharPtr search)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:10252:13: warning: 'ExtractVnpByStringSearch' defined but not used [-Wunused-function]
static void ExtractVnpByStringSearch (ValNodePtr PNTR list, CharPtr search)
^~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:9755:13: warning: 'GeneLocusTagDiscrepancyCallback' defined but not used [-Wunused-function]
static void GeneLocusTagDiscrepancyCallback (ValNodePtr item_list, Pointer userdata)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:9672:25: warning: 'InconsistentLocusTagPrefix' defined but not used [-Wunused-function]
static ClickableItemPtr InconsistentLocusTagPrefix (PrefixCheckPtr pcp)
^~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:9621:19: warning: 'FreePrefixCheckList' defined but not used [-Wunused-function]
static ValNodePtr FreePrefixCheckList (ValNodePtr prefix_list)
^~~~~~~~~~~~~~~~~~~
sqnutil3.c: In function 'LinkCDSmRNAbyLabelAndLocationCallback':
sqnutil3.c:889:23: warning: 'best_diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (diff < best_diff) {
^
sqnutil3.c: In function 'ValidateInferenceQualifier':
sqnutil3.c:6030:6: warning: 'rest' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (rest == NULL) return BAD_INFERENCE_BODY;
^
sqnutil3.c:6028:6: warning: 'best' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (best < 0 || inferencePrefix [best] == NULL) return BAD_INFERENCE_PREFIX;
^
sqnutil3.c: In function 'tRNASameStrandBioseqCallback':
sqnutil3.c:16126:8: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (strand == Seq_strand_minus) {
^
sqnutil3.c: In function 'CheckForDivConflicts':
sqnutil3.c:7901:11: warning: 'sdp' may be used uninitialized in this function [-Wmaybe-uninitialized]
else ValNodeAddPointer(&(grp_sdp[i]), OBJ_SEQDESC, sdp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c: In function 'FindMismatchedComments':
sqnutil3.c:25390:47: warning: 'sdp' may be used uninitialized in this function [-Wmaybe-uninitialized]
sprintf (fmt, sub_fmt, (CharPtr) sdp->data.ptrvalue);
~~~~~~~~~^~~~~~~~~
sqnutil3.c: In function 'FixCountryColons':
sqnutil3.c:7523:14: warning: 'biop' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
~~~~^~~~~~~~~~~~~~~
sqnutil3.c: In function 'AddmRNAForCDS':
sqnutil3.c:19565:10: warning: 'rna' may be used uninitialized in this function [-Wmaybe-uninitialized]
return rna;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF sqnutil4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/sqnutils.h:48,
from sqnutil4.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sqnutil4.c: In function 'ListClauses':
sqnutil4.c:8272:43: warning: variable 'twobefore' set but not used [-Wunused-but-set-variable]
FeatureClausePtr thisclause, onebefore, twobefore, oneafter, twoafter;
^~~~~~~~~
sqnutil4.c: In function 'SmashOneTallClause':
sqnutil4.c:9576:20: warning: variable 'subclause_featlist' set but not used [-Wunused-but-set-variable]
ValNodePtr subclause_featlist;
^~~~~~~~~~~~~~~~~~
sqnutil4.c: In function 'GetFeatureClauseForSeg':
sqnutil4.c:10448:21: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start, stop;
^~~~~
sqnutil4.c: In function 'IsAmplifiedMiscFeat':
sqnutil4.c:10701:9: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (sfp != NULL && sfp->idx.subtype == FEATDEF_misc_feature
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&& (StringNICmp (sfp->comment, phrase1, StringLen (phrase1)) == 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil4.c: In function 'ConvertProtToImpFunc':
sqnutil4.c:13849:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil4.c: In function 'ExtraCDSCreationActions':
sqnutil4.c:14728:28: warning: variable 'nsep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr psep, nsep;
^~~~
sqnutil4.c: In function 'TESTDisplayQualCombo':
sqnutil4.c:15752:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Int4 val;
^~~
sqnutil4.c: In function 'ConvertCDSToMatPeptideForOverlappingCDS':
sqnutil4.c:17198:15: warning: variable 'crp' set but not used [-Wunused-but-set-variable]
CdRegionPtr crp;
^~~
sqnutil4.c: In function 'AddNewUniqueAnnotations':
sqnutil4.c:17372:39: warning: variable 'sap_tmp_next' set but not used [-Wunused-but-set-variable]
SeqAnnotPtr sap, sap_next, sap_tmp, sap_tmp_next, sap_copy, last_sap;
^~~~~~~~~~~~
sqnutil4.c: In function 'AssignBioseqToLineageGroup':
sqnutil4.c:18024:27: warning: variable 'vnp_last' set but not used [-Wunused-but-set-variable]
ValNodePtr list, vnp, vnp_last = NULL;
^~~~~~~~
sqnutil4.c: In function 'ImportNucleotideFASTASequencesFromFile':
sqnutil4.c:26442:17: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int4 count;
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from sqnutil4.c:58:
sqnutil4.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/tax3api.h:51:0,
from sqnutil4.c:63:
../include/objtax3.h:183:31: warning: 'Value_valueFree' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr ));
^~~~~~~~~~~~~~~
../include/objtax3.h:184:31: warning: 'Value_valueAsnRead' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~
../include/objtax3.h:185:24: warning: 'Value_valueAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~
sqnutil4.c:15901:13: warning: 'TESTDisplayList' defined but not used [-Wunused-function]
static void TESTDisplayList (ValNodePtr new_list)
^~~~~~~~~~~~~~~
sqnutil4.c:15872:19: warning: 'ExpandOneComboListUsingAllPresentQuals' defined but not used [-Wunused-function]
static ValNodePtr ExpandOneComboListUsingAllPresentQuals (QualComboPtr q)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil4.c:15584:16: warning: 'RemoveFieldFromUniqBioSrcGrpList' defined but not used [-Wunused-function]
static Boolean RemoveFieldFromUniqBioSrcGrpList (ValNodePtr list, FieldTypePtr field)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil4.c:9705:19: warning: 'RemoveAllButLastCDS' defined but not used [-Wunused-function]
static ValNodePtr RemoveAllButLastCDS (
^~~~~~~~~~~~~~~~~~~
sqnutil4.c:9674:13: warning: 'SmashTallClauses' defined but not used [-Wunused-function]
static void SmashTallClauses (
^~~~~~~~~~~~~~~~
sqnutil4.c:9510:13: warning: 'RemoveFeats' defined but not used [-Wunused-function]
static void RemoveFeats (
^~~~~~~~~~~
sqnutil4.c:4945:13: warning: 'CountFeatures' defined but not used [-Wunused-function]
static Int4 CountFeatures (
^~~~~~~~~~~~~
sqnutil4.c: In function 'ConvertProtToImpFunc':
sqnutil4.c:14023:13: warning: 'topOfGbqList' may be used uninitialized in this function [-Wmaybe-uninitialized]
sfp->qual = topOfGbqList;
~~~~~~~~~~^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF subutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/objsub.h:76,
from ../include/subutil.h:50,
from subutil.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
subutil.c: In function 'AddSeqLitToBioseq':
subutil.c:769:16: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
subutil.c: In function 'AddReferenceToSegmentedEntry':
subutil.c:1163:22: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
SeqEntryPtr tmp, prev;
^~~~
subutil.c: In function 'GetDNAConv':
subutil.c:1624:15: warning: array subscript has type 'char' [-Wchar-subscripts]
dnaconv[*ptr] = *ptr;
^
subutil.c: In function 'GetProteinConv':
subutil.c:1646:16: warning: array subscript has type 'char' [-Wchar-subscripts]
protconv[*ptr] = *ptr;
^
subutil.c: In function 'AddBasesToByteStore':
subutil.c:1669:26: warning: array subscript has type 'char' [-Wchar-subscripts]
residue = dnaconv[ch];
^
subutil.c: In function 'AddAAsToByteStore':
subutil.c:1700:25: warning: array subscript has type 'char' [-Wchar-subscripts]
residue = aaconv[ch];
^
subutil.c: In function 'CitArtBuild':
subutil.c:2683:21: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp, tmp;
^~~
At top level:
subutil.c:3546:20: warning: 'TranslateCdRegionNew' defined but not used [-Wunused-function]
static SeqEntryPtr TranslateCdRegionNew (
^~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF edutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from ../include/edutil.h:188,
from edutil.c:365:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
edutil.c: In function 'SeqLocsToDeltaSeqs':
edutil.c:795:14: warning: variable 'sip' set but not used [-Wunused-but-set-variable]
SeqIdPtr sip;
^~~
edutil.c: In function 'SeqLocCopyPart':
edutil.c:2243:13: warning: variable 'done' set but not used [-Wunused-but-set-variable]
Boolean done, started, wasa_null, hada_null;
^~~~
edutil.c: In function 'IndexedSeqFeatsCopy':
edutil.c:2400:16: warning: variable 'region' set but not used [-Wunused-but-set-variable]
ValNodePtr region;
^~~~~~
edutil.c: In function 'SeqFeatsCopy':
edutil.c:2504:16: warning: variable 'region' set but not used [-Wunused-but-set-variable]
ValNodePtr region;
^~~~~~
edutil.c: In function 'SeqLocInsert':
edutil.c:3686:10: warning: variable 'diff' set but not used [-Wunused-but-set-variable]
Int4 diff, numpnt, i, tpos;
^~~~
edutil.c: In function 'SeqEdRecreateDeletedFeats':
edutil.c:4212:19: warning: variable 'sfp' set but not used [-Wunused-but-set-variable]
SeqFeatPtr sfp;
^~~
edutil.c: In function 'SeqEdSeqLocInsert':
edutil.c:4512:8: warning: variable 'diff' set but not used [-Wunused-but-set-variable]
Int4 diff, numpnt, i, tpos;
^~~~
edutil.c: In function 'SeqEdSeqLocDelete':
edutil.c:5069:10: warning: variable 'diff' set but not used [-Wunused-but-set-variable]
Int4 diff;
^~~~
edutil.c: In function 'SeqEdInsertAdjustFeat':
edutil.c:5300:7: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
&& sfp->data.choice == SEQFEAT_CDREGION)
edutil.c: In function 'SeqEdDeleteFromBsp':
edutil.c:6485:11: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
&& sfp->data.choice == SEQFEAT_CDREGION)
edutil.c:6548:11: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
&& sfp->data.choice == SEQFEAT_CDREGION)
edutil.c:6437:21: warning: variable 'merge_mode' set but not used [-Wunused-but-set-variable]
Boolean merge_mode;
^~~~~~~~~~
edutil.c:6428:21: warning: variable 'feats_altered' set but not used [-Wunused-but-set-variable]
Boolean feats_altered = FALSE;
^~~~~~~~~~~~~
edutil.c: In function 'BioseqInsert':
cc1: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
edutil.c: In function 'SeqEdInsert':
cc1: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2ff1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from ../include/seqmgr.h:48,
from asn2ff1.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff1.c: In function 'asn2ff_print':
asn2ff1.c:289:17: warning: unused variable 'dsp' [-Wunused-variable]
DescrStructPtr dsp = NULL;
^~~
asn2ff1.c: In function 'Asn2ffJobCreate':
asn2ff1.c:351:18: warning: unused variable 'itemID' [-Wunused-variable]
Uint4 itemID = 0;
^~~~~~
asn2ff1.c: In function 'SeqEntryToEntrez':
asn2ff1.c:498:15: warning: unused variable 'slp' [-Wunused-variable]
SeqLocPtr slp = NULL;
^~~
asn2ff1.c: In function 'SeqLocToFlat':
asn2ff1.c:1518:19: warning: unused variable 'itemID' [-Wunused-variable]
Uint4 itemID=0;
^~~~~~
asn2ff1.c: In function 'asn2ff_setup':
asn2ff1.c:1579:12: warning: variable 'bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr bsp;
^~~
asn2ff1.c: In function 'PrintStatusLine':
asn2ff1.c:2197:15: warning: unused variable 'ptr' [-Wunused-variable]
CharPtr u, ptr=NULL;
^~~
asn2ff1.c: In function 'asn2gb_setup':
asn2ff1.c:2403:24: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (ajp->genome_view && gbp->map == FALSE || ajp->contig_view) {
At top level:
asn2ff1.c:2189:13: warning: 'PrintStatusLine' defined but not used [-Wunused-function]
static void PrintStatusLine(Asn2ffJobPtr ajp, GBEntryPtr gbp)
^~~~~~~~~~~~~~~
asn2ff1.c:2171:16: warning: 'find_user_object' defined but not used [-Wunused-function]
static Boolean find_user_object(BioseqPtr bsp)
^~~~~~~~~~~~~~~~
asn2ff1.c:816:19: warning: 'SeqEntryToLinkStrEx' defined but not used [-Wunused-function]
static LinkStrPtr SeqEntryToLinkStrEx(Asn2ffJobPtr ajp, SeqEntryPtr sep, LinkStrPtr lsp, Uint1 format)
^~~~~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff1.c:45:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff1.c: In function 'asn2embl_setup':
asn2ff1.c:2754:7: warning: 'max' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (max == index+1) {
^
asn2ff1.c: In function 'asn2gp_setup':
asn2ff1.c:2942:4: warning: 'feat_num' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (index=0; index < feat_num; index++) {
^~~
asn2ff1.c: In function 'SeqEntryToGBFlatNoSeq':
asn2ff1.c:1292:15: warning: 'rsult' may be used uninitialized in this function [-Wmaybe-uninitialized]
Boolean rsult;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2ff2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/gather.h:166,
from asn2ff2.c:216:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff2.c: In function 'GetStrForBankit':
asn2ff2.c:518:9: warning: unused variable 'i' [-Wunused-variable]
Int2 i=0, ptrlen = 0;
^
asn2ff2.c: In function 'GetCommentByChoice':
asn2ff2.c:769:34: warning: unused variable 'string' [-Wunused-variable]
CharPtr buf = NULL, ptr = NULL, string=NULL, new_string=NULL, str=NULL;
^~~~~~
asn2ff2.c: In function 'GP_GetSeqDescrComms':
asn2ff2.c:1163:10: warning: unused variable 'got_comment' [-Wunused-variable]
Boolean got_comment=FALSE;
^~~~~~~~~~~
asn2ff2.c: At top level:
asn2ff2.c:1358:8: warning: return type defaults to 'int' [-Wimplicit-int]
static ChoicePID(SeqIdPtr sid)
^~~~~~~~~
asn2ff2.c: In function 'GetGibbsqCommentLength':
asn2ff2.c:1600:7: warning: unused variable 'gibbsq' [-Wunused-variable]
Int4 gibbsq=0, total;
^~~~~~
asn2ff2.c: In function 'GatherDescrByChoice':
asn2ff2.c:1864:8: warning: variable 'bspID' set but not used [-Wunused-but-set-variable]
Uint2 bspID;
^~~~~
At top level:
asn2ff2.c:1190:16: warning: 'GetSPBlock' defined but not used [-Wunused-function]
static CharPtr GetSPBlock (Asn2ffJobPtr ajp, GBEntryPtr gbp)
^~~~~~~~~~
asn2ff2.c:680:16: warning: 'GetEvidence' defined but not used [-Wunused-function]
static CharPtr GetEvidence(Asn2ffJobPtr ajp, GBEntryPtr gbp)
^~~~~~~~~~~
asn2ff2.c:232:16: warning: 'has_comment' defined but not used [-Wunused-variable]
static Boolean has_comment;
^~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff2.c:218:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff2.c: In function 'GetCommentByChoice':
asn2ff2.c:829:8: warning: 'is_other' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (is_other == TRUE && mfp->completeness) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2ff3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:372,
from asn2ff3.c:628:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff3.c: In function 'PutGeneFirst':
asn2ff3.c:1662:26: warning: unused variable 'qual_temp' [-Wunused-variable]
GBQualPtr gbqual, qual, qual_temp=NULL, qual_gene=NULL;
^~~~~~~~~
asn2ff3.c:1661:10: warning: unused variable 'still_looking' [-Wunused-variable]
Boolean still_looking=TRUE;
^~~~~~~~~~~~~
asn2ff3.c: In function 'mRNAEvidenceComment':
asn2ff3.c:1746:9: warning: unused variable 'Locus_id' [-Wunused-variable]
Int4 Locus_id = 0;
^~~~~~~~
asn2ff3.c: In function 'Add_gene_id':
asn2ff3.c:3306:24: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'Nlm_VoidPtr {aka void *}' [-Wformat=]
sprintf(val, "GeneID:%s", vnp->data.ptrvalue);
^
asn2ff3.c: In function 'Add_trid':
asn2ff3.c:3712:7: warning: unused variable 'gi' [-Wunused-variable]
Int4 gi = -1;
^~
At top level:
asn2ff3.c:3291:13: warning: 'Add_gene_id' defined but not used [-Wunused-function]
static void Add_gene_id (GeneStructPtr gsp, SeqFeatPtr sfp_out)
^~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff3.c:628:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
In file included from ../include/ncbi.h:59:0,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:372,
from asn2ff3.c:628:
asn2ff3.c: In function 'Add_dbxref.isra.0':
../include/ncbimem.h:232:23: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
asn2ff3.c:805:10: note: 'val' was declared here
CharPtr val;
^~~
asn2ff3.c: In function 'GettRNAaa':
asn2ff3.c:2208:9: warning: 'seq_code' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr = Get3LetterSymbol(seq_code, table, trna->aa, error_msgs);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2ff4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:372,
from asn2ff4.c:273:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff4.c: In function 'FlatLocPoint':
asn2ff4.c:437:15: warning: variable 'order' set but not used [-Wunused-but-set-variable]
static Uint1 order[NUM_SEQID];
^~~~~
asn2ff4.c: In function 'do_FlatLoc':
asn2ff4.c:1122:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if ( ! FlatVirtLoc( bsp, slp))
^
asn2ff4.c: At top level:
asn2ff4.c:1347:8: warning: return type defaults to 'int' [-Wimplicit-int]
static CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2)
^~~~~~~~~~
asn2ff4.c: In function 'CreateImpFeatFromProt':
asn2ff4.c:1659:14: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
asn2ff4.c: In function 'MatchNAGeneToFeat':
asn2ff4.c:2196:17: warning: variable 'nsp' set but not used [-Wunused-but-set-variable]
NoteStructPtr nsp; /* UNUSED */
^~~
asn2ff4.c: In function 'MatchAAGeneToFeat':
asn2ff4.c:2367:18: warning: variable 'nsp' set but not used [-Wunused-but-set-variable]
NoteStructPtr nsp; /* UNUSED */
^~~
asn2ff4.c: In function 'SortOrganizeFeat':
asn2ff4.c:2457:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ofp == NULL)
^~
asn2ff4.c:2459:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (ofp->sfpListsize > 0 && ofp->sortListsize < ofp->sfpListsize) {
^~
asn2ff4.c: In function 'OrganizeSeqFeat':
asn2ff4.c:2578:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ajp->ignore_top)
^~
asn2ff4.c:2580:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
gsc.seglevels = 1;
^~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff4.c:273:
At top level:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff4.c: In function 'CheckNewSfpLoc.isra.0':
asn2ff4.c:1767:7: warning: 'slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (SeqLocLen(slp) <= BioseqGetLen(bsp)) {
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2ff5.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:372,
from asn2ff5.c:177:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff5.c: In function 'format_cit_sub':
asn2ff5.c:1023:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
format == EMBLPEPT_FMT && afp->choice == 1)
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
asn2ff5.c:926:41: warning: variable 'need_space' set but not used [-Wunused-but-set-variable]
Boolean need_comma = FALSE, /*UNUSED*/need_space = TRUE;
^~~~~~~~~~
asn2ff5.c: In function 'format_thesis':
asn2ff5.c:1213:20: warning: variable 'embl_format' set but not used [-Wunused-but-set-variable]
Boolean /*UNUSED*/embl_format = FALSE;
^~~~~~~~~~~
asn2ff5.c: In function 'format_book':
asn2ff5.c:1296:10: warning: variable 'embl_format' set but not used [-Wunused-but-set-variable]
Boolean embl_format = FALSE;
^~~~~~~~~~~
asn2ff5.c: In function 'format_jourarticle':
asn2ff5.c:1680:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (ip->pages != NULL)
^
asn2ff5.c: In function 'StripParanthesis':
asn2ff5.c:2124:12: warning: value computed is not used [-Wunused-value]
temp++; *ptr_in++;
^~~~~~~~~
asn2ff5.c: In function 'PostARefErrMessage':
asn2ff5.c:3005:20: warning: variable 'ignore_this' set but not used [-Wunused-but-set-variable]
Boolean /*UNUSED*/ignore_this, submit=FALSE, error;
^~~~~~~~~~~
asn2ff5.c: At top level:
asn2ff5.c:188:26: warning: 'GetSubmitterName' declared 'static' but never defined [-Wunused-function]
static CharPtr /*UNUSED*/GetSubmitterName PROTO ((Uint1 format, ValNodePtr pub));
^~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff5.c:177:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff5.c: In function 'FlatJournal':
asn2ff5.c:1051:11: warning: 'afp' may be used uninitialized in this function [-Wmaybe-uninitialized]
AffilPtr afp;
^~~
asn2ff5.c:2073:10: warning: 'temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
temp = StringMove (temp," ");
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
asn2ff5.c:1946:23: note: 'temp' was declared here
CharPtr affil=NULL, temp, dup_pages=NULL, retval=NULL;
^~~~
asn2ff5.c: In function 'CheckPubs':
asn2ff5.c:2772:5: warning: 'status' may be used uninitialized in this function [-Wmaybe-uninitialized]
PostARefErrMessage (ajp, bsp, psp, NULL, status, NULL);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2ff6.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ff6.h:134,
from asn2ff6.c:347:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff6.c: In function 'AddGBQual':
asn2ff6.c:1327:18: warning: variable 'note' set but not used [-Wunused-but-set-variable]
GBQualPtr curq, note = NULL;
^~~~
asn2ff6.c: In function 'FlatOrganelle':
asn2ff6.c:1483:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! retval )
^~
asn2ff6.c:1486:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
break;
^~~~~
asn2ff6.c: In function 'BioseqGetGBDivCodeEx':
asn2ff6.c:1700:23: warning: variable 'diff' set but not used [-Wunused-but-set-variable]
Int2 tech, /*UNUSED*/diff, retval = 0;
^~~~
asn2ff6.c: In function 'GR_PrintPubs':
asn2ff6.c:2297:41: warning: unused variable 'stop' [-Wunused-variable]
Int4 muid, pmid, pat_seqid=0, start=0, stop=0;
^~~~
asn2ff6.c:2297:32: warning: unused variable 'start' [-Wunused-variable]
Int4 muid, pmid, pat_seqid=0, start=0, stop=0;
^~~~~
asn2ff6.c:2297:13: warning: variable 'pmid' set but not used [-Wunused-but-set-variable]
Int4 muid, pmid, pat_seqid=0, start=0, stop=0;
^~~~
asn2ff6.c:2296:10: warning: unused variable 'descr' [-Wunused-variable]
CharPtr descr = NULL;
^~~~~
asn2ff6.c: In function 'ValidateLocus':
asn2ff6.c:2786:17: warning: variable 'base_locus_max' set but not used [-Wunused-but-set-variable]
Int2 /*UNUSED*/base_locus_max, buf_index, exp, length, num_of_digits;
^~~~~~~~~~~~~~
asn2ff6.c: In function 'ValidateOtherAccession':
asn2ff6.c:2886:29: warning: unused variable 'FiveNum' [-Wunused-variable]
Boolean FirstLetter=FALSE, FiveNum = FALSE;
^~~~~~~
asn2ff6.c:2886:10: warning: unused variable 'FirstLetter' [-Wunused-variable]
Boolean FirstLetter=FALSE, FiveNum = FALSE;
^~~~~~~~~~~
asn2ff6.c: In function 'AddExtraAccessions':
asn2ff6.c:3498:20: warning: variable 'ncbi' set but not used [-Wunused-but-set-variable]
Boolean /*UNUSED*/ncbi = FALSE;
^~~~
At top level:
asn2ff6.c:2883:13: warning: 'ValidateOtherAccession' defined but not used [-Wunused-function]
static Int2 ValidateOtherAccession(CharPtr new_buf, CharPtr orig_buf)
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from asn2ff6.c:347:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff6.c: In function 'ValidateLocus':
asn2ff6.c:2786:44: warning: 'exp' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 /*UNUSED*/base_locus_max, buf_index, exp, length, num_of_digits;
^~~
asn2ff6.c: In function 'MakeBaseLocusAwp':
asn2ff6.c:3070:49: warning: 'num_of_digits' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 index, length, base_locus_max, name_len, num_of_digits, num_seg;
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2gnb1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb1.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb1.c: In function 'IsWholeWordSubstr':
asn2gnb1.c:2092:19: warning: variable 'right' set but not used [-Wunused-but-set-variable]
Boolean left, right;
^~~~~
asn2gnb1.c: In function 's_LocusGetBaseName':
asn2gnb1.c:2240:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
asn2gnb1.c:2242:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
newLength = segNameLen - deleteChars;
^~~~~~~~~
asn2gnb1.c: In function 'DoOneSection':
asn2gnb1.c:2363:24: warning: variable 'iasp' set but not used [-Wunused-but-set-variable]
IntAsn2gbSectPtr iasp;
^~~~
asn2gnb1.c:2357:24: warning: variable 'bkmask' set but not used [-Wunused-but-set-variable]
BlockMask bkmask;
^~~~~~
asn2gnb1.c: In function 'Count2Seg':
asn2gnb1.c:3215:18: warning: variable 'to' set but not used [-Wunused-but-set-variable]
Int4 to;
^~
asn2gnb1.c:3213:18: warning: variable 'parent' set but not used [-Wunused-but-set-variable]
BioseqPtr parent;
^~~~~~
asn2gnb1.c: At top level:
asn2gnb1.c:3492:3: warning: missing braces around initializer [-Wmissing-braces]
{TRUE, TRUE, TRUE, TRUE, TRUE,
^
asn2gnb1.c:3492:3: note: (near initialization for 'flagTable[0]')
asn2gnb1.c:3500:3: warning: missing braces around initializer [-Wmissing-braces]
{FALSE, TRUE, TRUE, TRUE, TRUE,
^
asn2gnb1.c:3500:3: note: (near initialization for 'flagTable[1]')
asn2gnb1.c:3508:3: warning: missing braces around initializer [-Wmissing-braces]
{FALSE, FALSE, FALSE, FALSE, FALSE,
^
asn2gnb1.c:3508:3: note: (near initialization for 'flagTable[2]')
asn2gnb1.c:3516:3: warning: missing braces around initializer [-Wmissing-braces]
{FALSE, FALSE, FALSE, FALSE, FALSE,
^
asn2gnb1.c:3516:3: note: (near initialization for 'flagTable[3]')
asn2gnb1.c:3489:33: warning: missing braces around initializer [-Wmissing-braces]
static ModeFlags flagTable [] = {
^
asn2gnb1.c:3489:33: note: (near initialization for 'flagTable')
asn2gnb1.c: In function 'SeqIdWriteForTable':
asn2gnb1.c:5571:13: warning: variable 'pdb' set but not used [-Wunused-but-set-variable]
pdb = NULL, general = NULL, gi = NULL;
^~~
asn2gnb1.c:5570:40: warning: variable 'patent' set but not used [-Wunused-but-set-variable]
SeqIdPtr accn = NULL, local = NULL, patent = NULL,
^~~~~~
In file included from ../include/ncbi.h:58:0,
from asn2gnb1.c:43:
asn2gnb1.c: In function 'DoImmediateFormat':
../include/ncbistd.h:286:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb1.c:6704:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb1.c:6683:20: warning: variable 'is_www' set but not used [-Wunused-but-set-variable]
Boolean is_www;
^~~~~~
In file included from ../include/ncbi.h:58:0,
from asn2gnb1.c:43:
asn2gnb1.c: In function 'asn2gnbk_format':
../include/ncbistd.h:286:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb1.c:6825:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb1.c: In function 'asn2gnbk_cleanup':
asn2gnb1.c:6871:21: warning: variable 'iasp' set but not used [-Wunused-but-set-variable]
IntAsn2gbSectPtr iasp;
^~~~
asn2gnb1.c: In function 'SeqEntryToGnbk':
asn2gnb1.c:7057:22: warning: variable 'userdata' set but not used [-Wunused-but-set-variable]
Pointer userdata = NULL;
^~~~~~~~
asn2gnb1.c:7052:22: warning: variable 'gbseq' set but not used [-Wunused-but-set-variable]
GBSeqPtr gbseq = NULL;
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb1.c:58:
asn2gnb1.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2gnb2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb2.c: In function 's_LocusAddSuffix':
asn2gnb2.c:206:11: warning: variable 'ch' set but not used [-Wunused-but-set-variable]
Char ch;
^~
asn2gnb2.c: In function 'AddLocusBlock':
asn2gnb2.c:1323:66: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
} else if ((moltype >= 2 && moltype <= 8) || moltype >= 10 && moltype <= 11) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
asn2gnb2.c: In function 'AddDblinkBlock':
asn2gnb2.c:2756:22: warning: variable 'parentID' set but not used [-Wunused-but-set-variable]
Int4 parentID;
^~~~~~~~
asn2gnb2.c: In function 'GetRefsOnBioseq':
asn2gnb2.c:5448:22: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
asn2gnb2.c:5445:22: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb2.c:5439:22: warning: variable 'right' set but not used [-Wunused-but-set-variable]
Int4 right;
^~~~~
asn2gnb2.c:5433:22: warning: variable 'left' set but not used [-Wunused-but-set-variable]
Int4 left;
^~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb2.c:57:
asn2gnb2.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2gnb3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb3.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb3.c: In function 'GetStatusForRefTrack':
asn2gnb3.c:601:22: warning: variable 'urf' set but not used [-Wunused-but-set-variable]
UserFieldPtr ufp, urf = NULL;
^~~
asn2gnb3.c: In function 'GetSourcesOnBioseq':
asn2gnb3.c:4151:22: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
asn2gnb3.c:4149:22: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start;
^~~~~
asn2gnb3.c:4148:22: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb3.c: In function 'GetFeatsOnCdsProduct':
asn2gnb3.c:5007:22: warning: variable 'isRefSeq' set but not used [-Wunused-but-set-variable]
Boolean isRefSeq;
^~~~~~~~
asn2gnb3.c: In function 'GetRemoteFeatsOnCdsProduct':
asn2gnb3.c:5155:20: warning: variable 'lastsfp' set but not used [-Wunused-but-set-variable]
SeqFeatPtr lastsfp;
^~~~~~~
asn2gnb3.c:5154:20: warning: variable 'lastsap' set but not used [-Wunused-but-set-variable]
SeqAnnotPtr lastsap;
^~~~~~~
asn2gnb3.c:5153:20: warning: variable 'lastright' set but not used [-Wunused-but-set-variable]
Int4 lastright;
^~~~~~~~~
asn2gnb3.c:5152:20: warning: variable 'lastleft' set but not used [-Wunused-but-set-variable]
Int4 lastleft;
^~~~~~~~
asn2gnb3.c:5151:20: warning: variable 'isRefSeq' set but not used [-Wunused-but-set-variable]
Boolean isRefSeq;
^~~~~~~~
asn2gnb3.c: In function 'GetFeatsOnBioseq':
asn2gnb3.c:5376:22: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start;
^~~~~
asn2gnb3.c:5349:22: warning: variable 'icp' set but not used [-Wunused-but-set-variable]
IntCdsBlockPtr icp;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb3.c:57:
asn2gnb3.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2gnb4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb4.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb4.c: In function 'FormatFeatureBlockQuals':
asn2gnb4.c:3591:50: warning: "/*" within comment [-Wcomment]
StringChr (str + 1, '(') == NULL /* && StringChr (str, ',') != NULL */) {
asn2gnb4.c:2969:24: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb4.c:2910:24: warning: variable 'at_end' set but not used [-Wunused-but-set-variable]
Boolean at_end = FALSE;
^~~~~~
asn2gnb4.c: In function 'FF_asn2gb_www_featkey':
asn2gnb4.c:5180:16: warning: variable 'prefix' set but not used [-Wunused-but-set-variable]
CharPtr prefix = "?";
^~~~~~
asn2gnb4.c: In function 'FormatFeatureBlockEx':
asn2gnb4.c:6354:22: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
In file included from ../include/ncbi.h:58:0,
from asn2gnb4.c:42:
asn2gnb4.c: In function 'DoImmediateRemoteFeatureFormat':
../include/ncbistd.h:286:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb4.c:8448:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb4.c: In function 'FormatFeatureQuals':
../include/ncbistd.h:286:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb4.c:8521:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb4.c:57:
asn2gnb4.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
asn2gnb4.c: In function 'FormatFeatureBlockEx':
asn2gnb4.c:7398:24: warning: 'sep' may be used uninitialized in this function [-Wmaybe-uninitialized]
oldscope = SeqEntrySetScope (sep);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2gnb5.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb5.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb5.c: In function 'FormatCitBookArt':
asn2gnb5.c:1874:16: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb5.c:57:
asn2gnb5.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2gnb6.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gnb6.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gnb6.c: In function 'FlatLocElement':
asn2gnb6.c:2386:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (sintp->to > 0 &&
~~~~~~~~~~~~~~^~
(sintp->to != sintp->from ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sintp->if_from != NULL ||
~~~~~~~~~~~~~~~~~~~~~~~~~
sintp->if_to != NULL) ||
~~~~~~~~~~~~~~~~~~~~~
asn2gnb6.c: In function 'FormatContigBlock':
asn2gnb6.c:5401:20: warning: variable 'dspnext' set but not used [-Wunused-but-set-variable]
DeltaSeqPtr dspnext;
^~~~~~~
asn2gnb6.c: In function 'FormatSequenceBlock':
asn2gnb6.c:5855:21: warning: variable 'iasp' set but not used [-Wunused-but-set-variable]
IntAsn2gbSectPtr iasp;
^~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2gnb6.c:57:
asn2gnb6.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ftusrstr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ftusrstr.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gbfeat.c
gbfeat.c: In function 'CkLabelType':
gbfeat.c:1529:33: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
for (str = bptr; *str != '\0' && IS_ALPHA(*str) || IS_DIGIT(*str)
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gbftglob.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gbparint.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/parsegb.h:57,
from gbparint.c:99:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gbparint.c: In function 'Nlm_gbparselex':
gbparint.c:2128:24: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (*current_col != '\0')
^
gbparint.c: In function 'Nlm_gbparselex_ver':
gbparint.c:2514:24: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (*current_col != '\0')
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF utilpars.c
utilpars.c:112:39: warning: missing braces around initializer [-Wmissing-braces]
ParFlat_AA_array[ParFlat_TOTAL_AA] = {
^
utilpars.c:112:39: note: (near initialization for 'ParFlat_AA_array')
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF utilpub.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from utilpub.c:13:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
utilpub.c: In function 'FindCit':
utilpub.c:998:24: warning: variable 'ifp' set but not used [-Wunused-but-set-variable]
ImpFeatPtr /*UNUSED*/ifp;
^~~
utilpub.c: In function 'ChangeCitQual':
utilpub.c:1053:53: warning: variable 'pub' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp, pubset = NULL, pub_min, /*UNUSED*/pub;
^~~
utilpub.c:1052:34: warning: variable 'descr' set but not used [-Wunused-but-set-variable]
ValNodePtr PNTR vnpp, /*UNUSED*/descr;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ffprint.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:372,
from ffprint.c:127:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ffprint.c: In function 'FFBSPrint':
ffprint.c:347:19: warning: unused variable 'byte_sp' [-Wunused-variable]
ByteStorePtr byte_sp = NULL;
^~~~~~~
At top level:
ffprint.c:420:16: warning: 'ff_print_insert' defined but not used [-Wunused-function]
static CharPtr ff_print_insert(CharPtr str, CharPtr ins)
^~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from ffprint.c:127:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF wprint.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from wprint.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
wprint.c: In function 'LocPrintGenome':
wprint.c:1696:14: warning: unused variable 'sep' [-Wunused-variable]
SeqEntryPtr sep = NULL;
^~~
wprint.c:1695:25: warning: unused variable 'b' [-Wunused-variable]
BioseqPtr bsp = NULL, b = NULL;
^
wprint.c:1695:13: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp = NULL, b = NULL;
^~~
wprint.c:1692:34: warning: unused variable 'temp' [-Wunused-variable]
static Char buf[14], val[166], temp[166];
^~~~
At top level:
wprint.c:1692:34: warning: 'temp' defined but not used [-Wunused-variable]
wprint.c:79:13: warning: 'link_gdb_map' defined but not used [-Wunused-variable]
static Char link_gdb_map[MAX_WWWBUF];
^~~~~~~~~~~~
wprint.c:77:13: warning: 'link_pir' defined but not used [-Wunused-variable]
static Char link_pir[MAX_WWWBUF];
^~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from wprint.c:51:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
In file included from ../include/ncbi.h:62:0,
from wprint.c:46:
wprint.c: In function 'www_xref':
../include/ncbistr.h:331:19: warning: 'prefix' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringLen Nlm_StringLen
^~~~~~~~~~~~~
wprint.c:1358:19: note: 'prefix' was declared here
CharPtr s, link, prefix, ss;
^~~~~~
In file included from ../include/ncbi.h:62:0,
from wprint.c:46:
../include/ncbistr.h:331:19: warning: 'link' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringLen Nlm_StringLen
^~~~~~~~~~~~~
wprint.c:1358:13: note: 'link' was declared here
CharPtr s, link, prefix, ss;
^~~~
wprint.c: In function 'PrintSPBlock':
wprint.c:1570:6: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
AddLink(s);
^~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF satutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/satutil.h:12,
from satutil.c:87:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
satutil.c: In function 'CopyFeatureFromAlign':
satutil.c:1011:10: warning: variable 'check_gap' set but not used [-Wunused-but-set-variable]
Boolean check_gap;
^~~~~~~~~
At top level:
satutil.c:168:16: warning: 'bk_map_one_location' defined but not used [-Wunused-function]
static Boolean bk_map_one_location(SeqLocPtr source_loc, SeqAlignPtr align, SeqIdPtr target_sip, Boolean check_gap, Int4Ptr r_start, Int4Ptr r_stop, SeqLocPtr PNTR head_slp)
^~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqmgr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from seqmgr.c:55:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqmgr.c: In function 'SeqEntrySetScope':
seqmgr.c:313:13: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
seqmgr.c: In function 'ClearBioseqFindCache':
seqmgr.c:899:14: warning: variable 'smp' set but not used [-Wunused-but-set-variable]
SeqMgrPtr smp;
^~~
seqmgr.c: In function 'GetUniGeneIDForSeqId':
seqmgr.c:3676:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(StringCmp(db_tag->db, "BSNR") == 0)
^~
seqmgr.c:3678:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if(StringCmp(db_tag->db, "HUMGEN") == 0)
^~
seqmgr.c: In function 'SeqMgrGetExtraDataForOmdp':
seqmgr.c:3736:14: warning: variable 'omp' set but not used [-Wunused-but-set-variable]
ObjMgrPtr omp;
^~~
seqmgr.c: In function 'CheckForTransSplice':
seqmgr.c:5644:14: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
SeqLocPtr prev, tmp;
^~~~
seqmgr.c: In function 'SeqEntryAsnOut':
seqmgr.c:11692:41: warning: variable 'aopp_desc' set but not used [-Wunused-but-set-variable]
AsnOptionPtr aopp_feat = NULL, aopp_desc = NULL;
^~~~~~~~~
seqmgr.c:11692:23: warning: variable 'aopp_feat' set but not used [-Wunused-but-set-variable]
AsnOptionPtr aopp_feat = NULL, aopp_desc = NULL;
^~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from seqmgr.c:65:
seqmgr.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
seqmgr.c: In function 'SeqMgrGetNextDescriptor':
seqmgr.c:9580:71: warning: 'bssp' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (omdp->datatype == OBJ_BIOSEQSET && bssp != NULL && bssp->seqentry != NULL) {
~~~~^~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objmgr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from objmgr.c:51:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmgr.c: In function 'ObjMgrReapOne':
objmgr.c:2727:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (omp->reaping) /* protect against recursion caused by ObjMgrSendMsg */
^~
objmgr.c:2730:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
lowest = UINT4_MAX;
^~~~~~
objmgr.c: In function 'ObjMgrDeSelectStructFunc':
objmgr.c:3767:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (next != NULL)
^~
objmgr.c:3770:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ObjMgrSendDeSelMsg (omp, ssp->entityID, ssp->itemID, ssp->itemtype, ssp->regiontype, ssp->region);
^~~~~~~~~~~~~~~~~~
objmgr.c: In function 'ObjMgrSelectFunc2':
objmgr.c:4031:22: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = FALSE;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gather.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/gather.h:166,
from gather.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gather.c: In function 'AttachDataProc':
gather.c:4825:30: warning: variable 'into_seqentry' set but not used [-Wunused-but-set-variable]
Boolean no_good = FALSE, into_seqentry = FALSE;
^~~~~~~~~~~~~
gather.c: In function 'GatherSeqFeat':
gather.c:1570:42: warning: 'newid' may be used uninitialized in this function [-Wmaybe-uninitialized]
tslp = SeqLocReMap(newid, slp, cbp->loc, offset, rev);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gather.c:1530:86: warning: 'max_interval' may be used uninitialized in this function [-Wmaybe-uninitialized]
lrdp = (GatherRangePtr)MemNew((size_t)((max_interval + 20) * sizeof(GatherRange)));
^
gather.c:1537:33: warning: 'offset' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (SeqLocOffset(slp, tslp, &(lrdp[ctr]), offset))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/ncbi.h:59:0,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/gather.h:166,
from gather.c:44:
../include/ncbimem.h:232:23: warning: 'lrdp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
gather.c:1404:38: note: 'lrdp' was declared here
GatherRangePtr rdp = NULL, trdp, lrdp;
^~~~
gather.c: In function 'gather_align_data':
gather.c:2278:11: warning: 'h_stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(!(h_stop < m_start || h_start > m_stop)) /*it is within the range*/
^
gather.c:2278:12: warning: 'h_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(!(h_stop < m_start || h_start > m_stop)) /*it is within the range*/
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gather.c:2468:58: warning: 'master_loc' may be used uninitialized in this function [-Wmaybe-uninitialized]
stop = inverse ? SeqLocLen(master_loc) * mag_val : SeqLocLen(master_loc)/mag_val;
^~~~~~~~~~~~~~~~~~~~~
gather.c:2466:73: warning: 'mag_val' may be used uninitialized in this function [-Wmaybe-uninitialized]
stop = inverse ? (len /mag_val) : (len * mag_val);
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
gather.c: In function 'GatherBioseqFunc':
gather.c:3305:53: warning: 'tlen' may be used uninitialized in this function [-Wmaybe-uninitialized]
rdp->right = offset + tlen - 1;
~~~~~~~^~~~~~
gather.c:3296:40: warning: 'trunc_r' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (trunc_r)
^
gather.c:3291:39: warning: 'trunc_l' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (trunc_l)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF accmmdbs.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from accmmdbs.c:120:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF acccn3ds.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from acccn3ds.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF lsqfetch.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from ../include/seqmgr.h:48,
from ../include/lsqfetch.h:110,
from lsqfetch.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF findrepl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from findrepl.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF codon.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/codon.h:61,
from codon.c:2:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
codon.c: In function 'make_cds_paragraph':
codon.c:262:7: warning: variable 'space_len' set but not used [-Wunused-but-set-variable]
Int4 space_len, i;
^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF jzcoll.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/maputil.h:113,
from ../include/jzcoll.h:123,
from jzcoll.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
jzcoll.c: In function 'load_default_matrix':
jzcoll.c:99:6: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]][pchars[j]] = webb_blosum62[i][j];
^
jzcoll.c:99:17: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]][pchars[j]] = webb_blosum62[i][j];
^
jzcoll.c:101:5: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]]['*'] = ss['*'][pchars[i]] = -4;
^
jzcoll.c:101:31: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]]['*'] = ss['*'][pchars[i]] = -4;
^
jzcoll.c: In function 'GetUseThisGi':
jzcoll.c:143:10: warning: unused variable 'retval' [-Wunused-variable]
Boolean retval=FALSE;
^~~~~~
jzcoll.c: In function 'buffer_for_feature':
jzcoll.c:514:7: warning: unused variable 'i' [-Wunused-variable]
Int2 i=0;
^
jzcoll.c: In function 'ProcessTextInsertion':
jzcoll.c:878:7: warning: variable 'last_ins' set but not used [-Wunused-but-set-variable]
Int4 last_ins;
^~~~~~~~
jzcoll.c: In function 'satcollfunc':
jzcoll.c:1723:12: warning: variable 'head' set but not used [-Wunused-but-set-variable]
SeqLocPtr head;
^~~~
jzcoll.c:1721:8: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
jzcoll.c:1720:7: warning: variable 'current_pos' set but not used [-Wunused-but-set-variable]
Int4 current_pos;
^~~~~~~~~~~
jzcoll.c:1714:12: warning: unused variable 'slp' [-Wunused-variable]
SeqLocPtr slp = NULL;
^~~
jzcoll.c: In function 'collect_anpnode_with_option':
jzcoll.c:3053:13: warning: unused variable 'prev' [-Wunused-variable]
ValNodePtr prev = NULL;
^~~~
jzcoll.c: In function 'ck_seqfeat_extra':
jzcoll.c:3414:10: warning: unused variable 'has_gb' [-Wunused-variable]
Boolean has_gb = FALSE, has_med = FALSE;
^~~~~~
jzcoll.c: In function 'collseqfunc':
jzcoll.c:3768:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(omtp->labelfunc !=NULL)
^~
jzcoll.c:3770:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
fnp->landmark = check_feature_for_landmark(chp->thislabel, chp->gdata, sfp, gcp, chp->priority);
^~~
jzcoll.c: In function 'load_open_close_sts_mark':
jzcoll.c:4010:10: warning: variable 'collected' set but not used [-Wunused-but-set-variable]
Boolean collected = FALSE;
^~~~~~~~~
jzcoll.c: In function 'FeatNodeCompProc':
jzcoll.c:4225:20: warning: variable 'gr2' set but not used [-Wunused-but-set-variable]
GatherRange gr1, gr2;
^~~
jzcoll.c:4225:15: warning: variable 'gr1' set but not used [-Wunused-but-set-variable]
GatherRange gr1, gr2;
^~~
At top level:
jzcoll.c:2316:16: warning: 'stop_collecting_alignment' defined but not used [-Wunused-function]
static Boolean stop_collecting_alignment(ValNodePtr anp_list, Int4 max_num)
^~~~~~~~~~~~~~~~~~~~~~~~~
jzcoll.c:1654:16: warning: 'collect_sequence_label' defined but not used [-Wunused-function]
static Boolean collect_sequence_label(Uint1 format)
^~~~~~~~~~~~~~~~~~~~~~
jzcoll.c: In function 'load_text':
jzcoll.c:421:39: warning: 'smtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
stdaa_res = SeqMapTableConvert(smtp, m_res);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF jzmisc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/jzmisc.h:86,
from jzmisc.c:23:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF maputil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/maputil.h:113,
from maputil.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
maputil.c: In function 'load_gene_list':
maputil.c:690:8: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Uint1 val;
^~~
maputil.c: In function 'gmarkfunc':
maputil.c:985:13: warning: variable 'syn' set but not used [-Wunused-but-set-variable]
ValNodePtr syn = NULL;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mconsist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/mconsist.h:4,
from mconsist.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF macroapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from macroapi.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
macroapi.c: In function 'AdvancedStringCompare':
macroapi.c:4416:23: warning: variable 'init_target_match_len' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, init_target_match_len = 0, target_match_len = 0;
^~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'RemoveGBQualMatch':
macroapi.c:6919:27: warning: variable 'does_match' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE, does_match, do_remove;
^~~~~~~~~~
macroapi.c: In function 'SetNameInPrimerList':
macroapi.c:10517:21: warning: variable 'prev_pp' set but not used [-Wunused-but-set-variable]
PCRPrimerPtr pp, prev_pp = NULL;
^~~~~~~
macroapi.c: In function 'SetSeqInPrimerList':
macroapi.c:10538:21: warning: variable 'prev_pp' set but not used [-Wunused-but-set-variable]
PCRPrimerPtr pp, prev_pp = NULL;
^~~~~~~
macroapi.c: In function 'GetCitListsForSeqEntry':
macroapi.c:15443:19: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
macroapi.c:15441:19: warning: variable 'okay' set but not used [-Wunused-but-set-variable]
Boolean okay;
^~~~
macroapi.c: In function 'GetPubMLStatus':
macroapi.c:17914:14: warning: variable 'csp' set but not used [-Wunused-but-set-variable]
CitSubPtr csp;
^~~
macroapi.c: In function 'ApplyPartial5SetActionToSeqFeat':
macroapi.c:24814:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'ApplyPartial3SetActionToSeqFeat':
macroapi.c:24937:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'ApplyPartialBothSetActionToSeqFeat':
macroapi.c:25004:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'FindPosBeforeFeat':
macroapi.c:25301:15: warning: variable 'regulator' set but not used [-Wunused-but-set-variable]
SeqFeatPtr regulator = NULL, candidate;
^~~~~~~~~
macroapi.c: In function 'PerformAutofixInSeqEntry':
macroapi.c:28058:8: warning: unused variable 'num_created' [-Wunused-variable]
Int4 num_created = 0;
^~~~~~~~~~~
macroapi.c: In function 'AddFileDescriptors':
macroapi.c:28453:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (sdp = SeqDescAsnRead (aip, NULL)) {
^~~~~
macroapi.c: In function 'PreprocessAddDescriptorListMacro':
macroapi.c:30069:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (sdp = SeqDescAsnRead (aip, NULL)) {
^~~~~
macroapi.c: In function 'SummarizeRemoveOutsideAction':
macroapi.c:30940:11: warning: unused variable 'case_insensitive' [-Wunused-variable]
CharPtr case_insensitive = " (case insensitive)";
^~~~~~~~~~~~~~~~
macroapi.c: In function 'GetObjectTableForTabTable':
macroapi.c:35366:63: warning: variable 'last' set but not used [-Wunused-but-set-variable]
ValNodePtr obj_table = NULL, obj_row, last_obj = NULL, tmp, last = NULL;
^~~~
macroapi.c: In function 'CheckObjTableForExistingText':
macroapi.c:35930:14: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
macroapi.c: In function 'FixSuspectProductNamesInEntrezGene':
macroapi.c:38178:18: warning: variable 'prefix' set but not used [-Wunused-but-set-variable]
CharPtr prefix = NULL;
^~~~~~
At top level:
macroapi.c:35102:16: warning: 'IsFieldTypeProteinDesc' defined but not used [-Wunused-function]
static Boolean IsFieldTypeProteinDesc (FieldTypePtr ft)
^~~~~~~~~~~~~~~~~~~~~~
macroapi.c:26150:13: warning: 'GetDescriptorTypeFromDescriptorChoice' defined but not used [-Wunused-function]
static Int4 GetDescriptorTypeFromDescriptorChoice (Uint1 descriptor_choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:20392:13: warning: 'GetFieldsFromAECR' defined but not used [-Wunused-function]
static void GetFieldsFromAECR (AECRActionPtr act, FieldTypePtr PNTR pField, ValNodePtr PNTR pFieldPair)
^~~~~~~~~~~~~~~~~
macroapi.c:15632:13: warning: 'InitBatchExtraForAECRActionAndObjectList' defined but not used [-Wunused-function]
static void InitBatchExtraForAECRActionAndObjectList (BatchExtraPtr batch_extra, AECRActionPtr action, ValNodePtr object_list)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:10224:16: warning: 'HasMultiplePrimerSets' defined but not used [-Wunused-function]
static Boolean HasMultiplePrimerSets (CharPtr value)
^~~~~~~~~~~~~~~~~~~~~
macroapi.c:5435:16: warning: 'DoesLocationMatchConstraint' defined but not used [-Wunused-function]
static Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:4543:13: warning: 'TestAdvancedStringMatch' defined but not used [-Wunused-function]
static void TestAdvancedStringMatch (void)
^~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:2760:13: warning: 'OriginFromOriginName' defined but not used [-Wunused-function]
static Int4 OriginFromOriginName (CharPtr origin_name)
^~~~~~~~~~~~~~~~~~~~
macroapi.c:1189:16: warning: 'IsObjectAppropriateForFieldPair' defined but not used [-Wunused-function]
static Boolean IsObjectAppropriateForFieldPair (Uint1 choice, Pointer data, FieldPairTypePtr fieldpair)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'GetFeatureListForProteinBioseq':
macroapi.c:34248:10: warning: 'sfp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (sfp != NULL)
^
macroapi.c: In function 'ConvertToSite':
macroapi.c:24223:7: warning: 'slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
bsp = GetBioseqGivenSeqLoc (slp, sfp->idx.entityID);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'ConvertToBond':
macroapi.c:24176:7: warning: 'slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
bsp = GetBioseqGivenSeqLoc (slp, sfp->idx.entityID);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'SetAuthorListFromString':
macroapi.c:14074:17: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
name_list = FreeNameList (1, vnp);
^~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'GetSourceQualFromBioSource':
macroapi.c:10861:25: warning: 'subfield' may be used uninitialized in this function [-Wmaybe-uninitialized]
str = GetThreeFieldSubfield (ssp->name, subfield);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'GetMultipleSourceQualsFromBioSource':
macroapi.c:11008:23: warning: 'subfield' may be used uninitialized in this function [-Wmaybe-uninitialized]
str = GetThreeFieldSubfield (ssp->name, subfield);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'RemoveSourceQualFromBioSource':
macroapi.c:11184:25: warning: 'subfield' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp = GetThreeFieldSubfield (ssp->name, subfield);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'CaptureRefBlockSerialNumbers':
macroapi.c:15424:26: warning: 'ppr' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp->data.ptrvalue = ppr;
~~~~~~~~~~~~~~~~~~~^~~~~
macroapi.c: In function 'SetFieldValueForObjectEx':
macroapi.c:13405:29: warning: 'ipp' may be used uninitialized in this function [-Wmaybe-uninitialized]
new_ipp[i] = ipp[i];
~~~^~~
macroapi.c:13352:21: note: 'ipp' was declared here
Int4Ptr ipp, new_ipp;
^~~
macroapi.c:13350:21: warning: 'cpp' may be used uninitialized in this function [-Wmaybe-uninitialized]
CharPtr PNTR cpp;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salpedit.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from salpedit.c:2:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salpedit.c: In function 'SeqAlignInsert':
salpedit.c:162:12: warning: variable 'ssp' set but not used [-Wunused-but-set-variable]
StdSegPtr ssp;
^~~
salpedit.c:161:22: warning: variable 'ddp' set but not used [-Wunused-but-set-variable]
DenseDiagPtr ddp;
^~~
At top level:
salpedit.c:4120:18: warning: 'build_slp_for_gcontig' defined but not used [-Wunused-function]
static SeqLocPtr build_slp_for_gcontig (BioseqPtr gcontig_bsp, SeqIdPtr gcontig_sip)
^~~~~~~~~~~~~~~~~~~~~
salpedit.c:4073:17: warning: 'get_best_id' defined but not used [-Wunused-function]
static SeqIdPtr get_best_id(BioseqPtr bsp)
^~~~~~~~~~~
salpedit.c:4046:16: warning: 'second_seq_has_gap' defined but not used [-Wunused-function]
static Boolean second_seq_has_gap(BioseqPtr s_bsp)
^~~~~~~~~~~~~~~~~~
salpedit.c:4016:18: warning: 'dup_mul_locs' defined but not used [-Wunused-function]
static SeqLocPtr dup_mul_locs(SeqLocPtr slp)
^~~~~~~~~~~~
salpedit.c:3968:18: warning: 'create_fake_bioseq' defined but not used [-Wunused-function]
static BioseqPtr create_fake_bioseq(SeqLocPtr seq_loc, CharPtr fake_name)
^~~~~~~~~~~~~~~~~~
salpedit.c:3937:13: warning: 'reverse_seqloc' defined but not used [-Wunused-function]
static void reverse_seqloc (SeqLocPtr s_loc)
^~~~~~~~~~~~~~
salpedit.c:3850:13: warning: 'save_output' defined but not used [-Wunused-function]
static void save_output (SeqIdPtr sip, CharPtr f_name, SeqAlignPtr align)
^~~~~~~~~~~
salpedit.c:3836:13: warning: 'get_align_list_len' defined but not used [-Wunused-function]
static Int4 get_align_list_len(SeqAlignPtr align)
^~~~~~~~~~~~~~~~~~
salpedit.c:2939:20: warning: 'open_annot' defined but not used [-Wunused-function]
static SeqAnnotPtr open_annot(CharPtr f_name)
^~~~~~~~~~
salpedit.c:2835:13: warning: 'SeqAnnotWrite' defined but not used [-Wunused-function]
static void SeqAnnotWrite(SeqAlignPtr align)
^~~~~~~~~~~~~
salpedit.c:2653:16: warning: 'FigureAlignRange' defined but not used [-Wunused-function]
static Boolean FigureAlignRange(SeqAlignPtr align, SeqLocPtr m_loc, SeqLocPtr s_loc)
^~~~~~~~~~~~~~~~
salpedit.c:1665:16: warning: 'free_diag_in_list' defined but not used [-Wunused-function]
static Boolean free_diag_in_list(ValNodePtr ddp_list, DenseDiagPtr ddp)
^~~~~~~~~~~~~~~~~
salpedit.c:1605:16: warning: 'is_overlap' defined but not used [-Wunused-function]
static Boolean is_overlap(BoolPtr status, Int4 from, Int4 len)
^~~~~~~~~~
salpedit.c:1560:13: warning: 'filter_wrong_orientation' defined but not used [-Wunused-function]
static void filter_wrong_orientation (SeqAlignPtr align, Boolean same_orient)
^~~~~~~~~~~~~~~~~~~~~~~~
salpedit.c:1479:16: warning: 'filter_this_seg' defined but not used [-Wunused-function]
static Boolean filter_this_seg (DenseDiagPtr curr, DenseDiagPtr PNTR h_list, Int2 order)
^~~~~~~~~~~~~~~
salpedit.c:1422:16: warning: 'convert_ddp_to_array' defined but not used [-Wunused-function]
static Int4Ptr convert_ddp_to_array (ValNodePtr ddp_list, Uint1 strand, Int2 s_order, Int4Ptr p_num)
^~~~~~~~~~~~~~~~~~~~
salpedit.c:1387:14: warning: 'has_too_much_overlap' defined but not used [-Wunused-function]
static Uint1 has_too_much_overlap (Int4 start_1, Int4 stop_1, Int4 start_2, Int4 stop_2)
^~~~~~~~~~~~~~~~~~~~
salpedit.c:1281:13: warning: 'attach_new_align' defined but not used [-Wunused-function]
static void attach_new_align(SeqAlignPtr new_salp, SeqAlignPtr PNTR old) {
^~~~~~~~~~~~~~~~
salpedit.c:1169:20: warning: 'JZSeqAlignMerge' defined but not used [-Wunused-function]
static SeqAlignPtr JZSeqAlignMerge(SeqAlignPtr f_align, SeqIdPtr from_id, Int4 from, Int4 to, Uint1 strand, SeqIdPtr to_id, Int4 pos, SeqAlignPtr t_align)
^~~~~~~~~~~~~~~
salpedit.c:254:16: warning: 'is_gap_segment' defined but not used [-Wunused-function]
static Boolean is_gap_segment(Int4Ptr c_starts, Int2 dim)
^~~~~~~~~~~~~~
salpedit.c:158:20: warning: 'SeqAlignInsert' defined but not used [-Wunused-function]
static SeqAlignPtr SeqAlignInsert(SeqIdPtr from_id, Int4 from, Int4 to, Uint1 strand, SeqIdPtr to_id, Int4 pos, SeqAlignPtr head, Boolean merge, Boolean add_insertion)
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salpstat.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from salpstat.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salpstat.c: In function 'DenseSegStats':
salpstat.c:310:10: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if(dsp && (((mmatches || mmismatches) && bsp_1 && bsp_2)) || !(mmatches || mmismatches)) {
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salpstat.c: In function 'SeqAlignScoreFix':
salpstat.c:162:20: warning: 'sp_last' may be used uninitialized in this function [-Wmaybe-uninitialized]
sp_last->next = (ScorePtr) MemNew(sizeof(Score));
salpstat.c: In function 'DenseSegStats':
salpstat.c:382:7: warning: 'spp_2' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqPortFree(spp_2);
^~~~~~~~~~~~~~~~~~
salpstat.c:381:7: warning: 'spp_1' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqPortFree(spp_1);
^~~~~~~~~~~~~~~~~~
salpstat.c: In function 'SeqAlignWindowScoreFN':
salpstat.c:2038:45: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
residue_score[pos]=score;
~~~~~~~~~~~~~~~~~~^~~~~~
salpstat.c:2020:34: warning: 'pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
qgaps_score[last_pos]=-(g_open+len*g_ext);
^
salpstat.c: In function 'SeqAlignWindowScore':
salpstat.c:2214:12: warning: 'scoreptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
return scoreptr;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salpacc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salpacc.h:33,
from salpacc.c:40:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salpacc.c: In function 'SeqAlignStrand':
salpacc.c:334:20: warning: unused variable 'this_strand' [-Wunused-variable]
Uint1Ptr this_strand=Seq_strand_unknown;
^~~~~~~~~~~
salpacc.c: In function 'SeqAlignStop':
salpacc.c:561:13: warning: 'this_stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(this_stop!=-1)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salprop.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from ../include/salprop.h:46,
from salprop.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salprop.c: In function 'CopySeqLocFromSeqAlign':
salprop.c:398:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
salprop.c:401:16: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if(crp != NULL) /*for coding region features*/
^~
salprop.c:291:12: warning: variable 'check_gap' set but not used [-Wunused-but-set-variable]
Boolean check_gap;
^~~~~~~~~
salprop.c: In function 'FeatListToProp':
salprop.c:1336:20: warning: variable 'feat_itemID' set but not used [-Wunused-but-set-variable]
Uint4 feat_itemID;
^~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from salprop.c:46:
salprop.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from salprop.c:42:0:
../include/salprop.h:50:16: warning: 'GBFeat' defined but not used [-Wunused-variable]
static CharPtr GBFeat[number_GBFeat] = {
^~~~~~
salprop.c: In function 'ApplyNewSeqFeat':
salprop.c:620:11: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
j = stop - SeqLocStop(sfp_location);
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salprop.c:514:17: note: 'stop' was declared here
stop,
^~~~
salprop.c:674:17: warning: 'sfp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqFeatPtr sfp;
^~~
salprop.c:733:24: warning: 'ppp.p5' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (!sfp_p5 && ppp.p5)
~~~~~~~~^~~~~~~~~
salprop.c:679:17: note: 'ppp.p5' was declared here
ParTials ppp;
^~~
salprop.c:737:12: warning: 'ppp.p3' may be used uninitialized in this function [-Wmaybe-uninitialized]
SetSeqLocPartial (sfp->location, afp->noLeft, afp->noRight);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salprop.c:679:17: note: 'ppp.p3' was declared here
ParTials ppp;
^~~
salprop.c:861:33: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((val2=is_id_unique (entityID, SeqLocId(sfp->product))))
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salsap.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from ../include/salsap.h:57,
from salsap.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salsap.c: In function 'DenseDiagToDenseSegFunc':
salsap.c:2912:30: warning: variable 'slpstop2' set but not used [-Wunused-but-set-variable]
slpstop1 = 0, slpstop2 = 0;
^~~~~~~~
salsap.c:2912:16: warning: variable 'slpstop1' set but not used [-Wunused-but-set-variable]
slpstop1 = 0, slpstop2 = 0;
^~~~~~~~
salsap.c:2911:31: warning: variable 'slpstart2' set but not used [-Wunused-but-set-variable]
Int4 slpstart1 = 0, slpstart2 = 0,
^~~~~~~~~
salsap.c:2911:16: warning: variable 'slpstart1' set but not used [-Wunused-but-set-variable]
Int4 slpstart1 = 0, slpstart2 = 0,
^~~~~~~~~
salsap.c:2909:28: warning: variable 'start2' set but not used [-Wunused-but-set-variable]
Int4 start1 = 0, start2 = 0,
^~~~~~
salsap.c:2909:16: warning: variable 'start1' set but not used [-Wunused-but-set-variable]
Int4 start1 = 0, start2 = 0,
^~~~~~
In file included from ../include/sqnutils.h:51:0,
from salsap.c:47:
salsap.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
salsap.c:3631:13: warning: 'FindSeqAlignCallback' defined but not used [-Wunused-function]
static void FindSeqAlignCallback (SeqEntryPtr sep, Pointer mydata,
^~~~~~~~~~~~~~~~~~~~
salsap.c:2157:16: warning: 'AreDenseSegSegmentsValid' defined but not used [-Wunused-function]
static Boolean AreDenseSegSegmentsValid (DenseSegPtr dsp, Int4 start, Int4 num)
^~~~~~~~~~~~~~~~~~~~~~~~
salsap.c: In function 'SeqAlignEndExtend':
salsap.c:986:18: warning: 'n_strands' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint1Ptr n_strands;
^~~~~~~~~
salsap.c: In function 'CleanStrandsSeqAlign':
salsap.c:1614:15: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 dim;
^~~
salsap.c:1613:15: warning: 'numseg' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 numseg;
^~~~~~
salsap.c:1611:15: warning: 'startp' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4Ptr startp;
^~~~~~
salsap.c:1610:15: warning: 'lenp' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4Ptr lenp;
^~~~
salsap.c: In function 'LocalAlignToSeqAnnotDimn':
salsap.c:1851:9: warning: 'the_lens' may be used uninitialized in this function [-Wmaybe-uninitialized]
while ( j < lens )
^
salsap.c: In function 'multseqalign_from_pairseqalign':
salsap.c:4394:19: warning: 'strandp' may be used uninitialized in this function [-Wmaybe-uninitialized]
strandp++;
~~~~~~~^~
salsap.c:4245:6: warning: 'ok' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (!ok)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salstruc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from ../include/salstruc.h:56,
from salstruc.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salstruc.c: In function 'data_collect_arrange':
salstruc.c:1338:22: warning: variable 'maxscroll' set but not used [-Wunused-but-set-variable]
Int4 maxscroll;
^~~~~~~~~
salstruc.c: In function 'ShowAlignmentText':
salstruc.c:2203:29: warning: variable 'itemtype' set but not used [-Wunused-but-set-variable]
Uint2 entityID, itemtype;
^~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from salstruc.c:40:
salstruc.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from salstruc.c:41:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
salstruc.c: In function 'prot_to_rputprot':
salstruc.c:707:11: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 j, k;
^
salstruc.c: In function 'data_collect_arrange':
salstruc.c:967:29: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
drawfeat = is_feature_to_buffer(vnpfeat, itemID, entityID, fromseq, length, salp, adp->input_format, adp->sqloc_list);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salstruc.c:872:19: note: 'entityID' was declared here
Uint2 entityID;
^~~~~~~~
salstruc.c:1093:44: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
seq_info->entityID=entityID;
~~~~~~~~~~~~~~~~~~^~~~~~~~~
salstruc.c:1005:17: note: 'entityID' was declared here
Uint2 entityID;
^~~~~~~~
salstruc.c: In function 'ShowAlignmentText':
salstruc.c:2194:19: warning: 'bspsip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqIdPtr bspsip;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from salutil.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salutil.c: In function 'ReadBufferFromSap':
salutil.c:128:24: warning: variable 'buffstart' set but not used [-Wunused-but-set-variable]
Int4 bufflen, buffstart;
^~~~~~~~~
salutil.c:127:15: warning: variable 'sumstart' set but not used [-Wunused-but-set-variable]
Int4 sumstart;
^~~~~~~~
salutil.c: In function 'IS_protSeqLoc':
salutil.c:594:11: warning: variable 'seq' set but not used [-Wunused-but-set-variable]
CharPtr seq;
^~~
salutil.c: In function 'ReplaceSeqIdWithSeqId':
salutil.c:1236:20: warning: variable 'oldscope' set but not used [-Wunused-but-set-variable]
SeqEntryPtr oldscope;
^~~~~~~~
salutil.c: In function 'del_ssp_fromid':
salutil.c:1722:24: warning: variable 'pressp' set but not used [-Wunused-but-set-variable]
SelEdStructPtr ssp, pressp = NULL;
^~~~~~
salutil.c: In function 'checkCDSselect_forprotein':
salutil.c:2510:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (feat != NULL)
^
salutil.c: In function 'NoMoreSegGapForOneAlignment':
salutil.c:3647:8: warning: implicit declaration of function 'AlnMgr2IndexSingleChildSeqAlign' [-Wimplicit-function-declaration]
AlnMgr2IndexSingleChildSeqAlign(salp); /* make sure it's dense-seg */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from salutil.c:53:
salutil.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
salutil.c: In function 'sesp_to_slp':
salutil.c:1976:9: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (k=1; k<j; k++) sesp=sesp->next;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF udvseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from ../include/udvseq.h:100,
from udvseq.c:112:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
udvseq.c: In function 'UDV_EncodeIdxFeat':
udvseq.c:448:2: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return *((Int4Ptr) index_g);
^~~~~~
udvseq.c: In function 'UDV_BigEncodeIdxFeat':
udvseq.c:473:2: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return *((Uint8Ptr) index_g);
^~~~~~
udvseq.c: In function 'UDV_ParaGFTableFeatures':
udvseq.c:947:22: warning: 'nFeatLines' may be used uninitialized in this function [-Wmaybe-uninitialized]
pgp->nFeatLines=nFeatLines/*-decal*/;
~~~~~~~~~~~~~~~^~~~~~~~~~~
udvseq.c:990:9: warning: 'PosFeat' may be used uninitialized in this function [-Wmaybe-uninitialized]
(Uint2)PosFeat-decal,(Uint2)0));
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blocks.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/blocks.h:88,
from blocks.c:93:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blocks.c: In function 'IndexBlocks':
blocks.c:928:19: warning: operation on 'segp_align->to' may be undefined [-Wsequence-point]
segp_align->to = segp_align->to = -1;
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
blocks.c: In function 'IndexNewBlocks':
blocks.c:1084:19: warning: operation on 'segp_align->to' may be undefined [-Wsequence-point]
segp_align->to = segp_align->to = -1;
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
blocks.c: In function 'GetBlockOrientation':
blocks.c:2383:11: warning: 'orient' may be used uninitialized in this function [-Wmaybe-uninitialized]
return orient;
^~~~~~
blocks.c: In function 'SAMergeBlocks':
blocks.c:2165:21: warning: 'tmp2' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp2 = tmp2->next;
~~~~~^~~~~~~~~~~~
blocks.c:1572:28: warning: 'tmp_head' may be used uninitialized in this function [-Wmaybe-uninitialized]
merged->segp_head = tmp_head;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~
blocks.c:1470:27: warning: 'tmp_curr' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp1->prev = tmp_curr;
~~~~~~~~~~~^~~~~~~~~~
blocks.c:1709:27: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp1->prev = prev;
~~~~~~~~~~~^~~~~~
blocks.c:1670:34: warning: 'new_sabp1' may be used uninitialized in this function [-Wmaybe-uninitialized]
new_sabp1->segp_head = tmp_head;
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
blocks.c: In function 'SASplitBlock':
blocks.c:2796:25: warning: 'segp2_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
segp2->prev = segp2_prev;
~~~~~~~~~~~~^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF pgppop.c
pgppop.c:307:2: warning: missing braces around initializer [-Wmissing-braces]
{
^
pgppop.c:307:2: note: (near initialization for 'DDV_PaletteRGB')
pgppop.c: In function 'DDV_WWW_get_CDS_minus':
pgppop.c:578:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
pgppop.c:576:5: warning: variable 'numivals2' set but not used [-Wunused-but-set-variable]
numivals2=0;
^~~~~~~~~
pgppop.c: In function 'DDV_WWW_get_CDS_plus':
pgppop.c:700:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
pgppop.c: In function 'GetClrFromClrGlobal':
pgppop.c:1326:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
if (*((Uint4Ptr)rgb1 )== *((Uint4Ptr)rgb2)){
^~
pgppop.c:1326:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pgppop.c: In function 'DDV_DisplayTopScale':
pgppop.c:1549:7: warning: unused variable 'szBlank' [-Wunused-variable]
Char szBlank[TABLE_LEFT_MARGIN+5]={""};
^~~~~~~
pgppop.c: In function 'DDV_GetBLASTCompLine_1':
pgppop.c:1985:31: warning: array subscript has type 'char' [-Wchar-subscripts]
if (matrix[s][q]>0){
^
pgppop.c:1985:34: warning: array subscript has type 'char' [-Wchar-subscripts]
if (matrix[s][q]>0){
^
pgppop.c: In function 'DDV_DisplayDefaultAlign':
pgppop.c:3417:13: warning: unused variable 'sabp' [-Wunused-variable]
SABlockPtr sabp=NULL;/*indexed SeqAlign*/
^~~~
pgppop.c: In function 'DDV_ShowSeqAlign':
pgppop.c:3760:10: warning: unused variable 'szPopSetAuth' [-Wunused-variable]
Char szPopSetAuth[INFO_SIZE+1]={""};
^~~~~~~~~~~~
pgppop.c:3758:10: warning: unused variable 'szPopSetName' [-Wunused-variable]
Char szPopSetName[INFO_SIZE+1]={""};/*article title of the Pop-Set*/
^~~~~~~~~~~~
pgppop.c: In function 'DDV_PrintPopSetSummary':
pgppop.c:3931:9: warning: variable 'bPairwise' set but not used [-Wunused-but-set-variable]
Boolean bPairwise=TRUE,bPrintTax,bPrintCom;
^~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from pgppop.c:298:
pgppop.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/ddvcreate.h:143,
from pgppop.c:303:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
pgppop.c:2912:13: warning: 'DDV_PrintFastaGappedSequence' defined but not used [-Wunused-function]
static void DDV_PrintFastaGappedSequence(CharPtr szSequence,FILE *fp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pgppop.c:2865:13: warning: 'DDV_GetGappedSequence' defined but not used [-Wunused-function]
static void DDV_GetGappedSequence(SegmentPtr segp,CharPtr szSequence,
^~~~~~~~~~~~~~~~~~~~~
pgppop.c:2090:13: warning: 'DDV_HideMaskedLetters' defined but not used [-Wunused-function]
static void DDV_HideMaskedLetters(CharPtr szSeqMaster,ParaGPtr pgp,ValNodePtr mask)
^~~~~~~~~~~~~~~~~~~~~
pgppop.c:563:13: warning: 'DDV_WWW_get_CDS_minus' defined but not used [-Wunused-function]
static void DDV_WWW_get_CDS_minus(SeqMgrFeatContextPtr context,Int4 start,
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from pgppop.c:300:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
pgppop.c: In function 'DDV_PopDisplay2':
pgppop.c:1246:23: warning: 'pgp2' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (pgp2 && ((pgp2->StopLetter-pgp2->StartLetter+1)>=AbsLengthAli)) {
~~~~^~~~~~~~~~~~
pgppop.c:1253:14: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp->next=NULL;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF samutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/samutil.h:230,
from samutil.c:280:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
samutil.c: In function 'SAM_AlignIdComp':
samutil.c:1034:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((a == NULL) || (b == NULL))
^~
samutil.c:1037:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
choice = a->choice;
^~~~~~
samutil.c: In function 'SAM_AlignIdDup':
samutil.c:1090:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oldid == NULL)
^~
samutil.c:1093:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
newid = ValNodeNew(NULL);
^~~~~
samutil.c: In function 'DDE_FreeStack':
samutil.c:1794:11: warning: operation on 'Index' may be undefined [-Wsequence-point]
Index = ++Index % DDE_STACK_SIZE;
samutil.c: In function 'DDE_Add':
samutil.c:1849:22: warning: operation on 'pStack->StackMin' may be undefined [-Wsequence-point]
pStack->StackMin = ++pStack->StackMin % DDE_STACK_SIZE;
samutil.c:1860:22: warning: operation on 'pStack->StackIndex' may be undefined [-Wsequence-point]
pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE;
samutil.c: In function 'DDE_Prev':
samutil.c:1924:22: warning: operation on 'pStack->StackIndex' may be undefined [-Wsequence-point]
pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE;
samutil.c: In function 'DDE_Next':
samutil.c:1955:22: warning: operation on 'pStack->StackIndex' may be undefined [-Wsequence-point]
pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE;
samutil.c: In function 'DDE_ShowRow':
samutil.c:2222:26: warning: variable 'NumRows' set but not used [-Wunused-but-set-variable]
Int4 i, NumRows, HiRow, LowRow, tmp1, tmp2;
^~~~~~~
samutil.c: In function 'DDE_AddGapToEndOfAllRows':
samutil.c:3344:41: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr ptxtList, last_vnp, vnp;
^~~
samutil.c: In function 'DDE_RightAddNode':
samutil.c:3945:33: warning: variable 'new_vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp, next_vnp, new_vnp;
^~~~~~~
samutil.c: In function 'DDE_LeftMergeAndAddNodeList':
samutil.c:3995:24: warning: variable 'RetVal2' set but not used [-Wunused-but-set-variable]
Boolean RetVal1, RetVal2, IsLeftAlignedGap, NodeDeleted;
^~~~~~~
samutil.c: In function 'DDE_RightMergeAndAddNodeList':
samutil.c:4051:38: warning: variable 'RetVal2' set but not used [-Wunused-but-set-variable]
Boolean RetVal=FALSE, RetVal1, RetVal2, HeadChanged;
^~~~~~~
samutil.c: In function 'DDE_ShiftRightBoundaryLeft1':
samutil.c:4830:41: warning: variable 'Index' set but not used [-Wunused-but-set-variable]
Int4 NumBlocks, i, NumRows, Index, BlockCount=0;
^~~~~
samutil.c: In function 'DDE_CreateArraysForDenseSeg':
samutil.c:5266:22: warning: variable 'NumSegs' set but not used [-Wunused-but-set-variable]
Int4 NumRows, NumSegs, i, StartIndex, StopIndex, ArrayIndex=0;
^~~~~~~
samutil.c: In function 'DDE_GetLastVNP':
samutil.c:3381:9: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return(last_vnp);
^
samutil.c: In function 'DDE_GetNumResidues':
samutil.c:3404:13: warning: 'to' may be used uninitialized in this function [-Wmaybe-uninitialized]
return((to-from) + 1);
~~~^~~~~~
In file included from ../include/ncbi.h:59:0,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/objall.h:64,
from ../include/samutil.h:231,
from samutil.c:280:
samutil.c: In function 'DDE_RemoveGapFromEndOfAllRows':
../include/ncbimem.h:232:23: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
samutil.c:3375:15: note: 'last_vnp' was declared here
ValNodePtr last_vnp;
^~~~~~~~
samutil.c:3272:15: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
last_msap = (MsaTxtDispPtr) last_vnp->data.ptrvalue;
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c: In function 'DDE_AddAGap':
samutil.c:2659:8: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (vnp == pMidtxtList) {
^
samutil.c:3375:15: note: 'last_vnp' was declared here
ValNodePtr last_vnp;
^~~~~~~~
samutil.c: In function 'DDE_AddGapToEndOfAllRows':
samutil.c:3356:9: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp = DDE_AddAGap(pEditInfo, i, last_vnp, FALSE, TRUE);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c: In function 'DDE_ShiftLeftList':
samutil.c:4161:8: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
msap = (MsaTxtDispPtr) last_vnp->data.ptrvalue;
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c: In function 'DDE_ShiftRowLeft1':
samutil.c:2563:13: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
last_msap = (MsaTxtDispPtr) last_vnp->data.ptrvalue;
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c: In function 'DDE_RemoveGap':
samutil.c:3092:8: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
msap = (MsaTxtDispPtr) vnp->data.ptrvalue;
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c: In function 'DDE_ShiftRowRight1':
samutil.c:2594:8: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
msap = (MsaTxtDispPtr) DDE_GetLastVNP(ptxtList)->data.ptrvalue;
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c: In function 'DDE_LastColumnIsAligned':
samutil.c:4448:8: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
msap = (MsaTxtDispPtr) vnp->data.ptrvalue;
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c: In function 'DDE_ShiftRightBoundaryLeft1':
samutil.c:4448:8: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
msap = (MsaTxtDispPtr) vnp->data.ptrvalue;
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c:3375:15: note: 'last_vnp' was declared here
ValNodePtr last_vnp;
^~~~~~~~
samutil.c: In function 'DDE_ShiftRightBoundaryRight1':
samutil.c:4448:8: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
msap = (MsaTxtDispPtr) vnp->data.ptrvalue;
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c:3375:15: note: 'last_vnp' was declared here
ValNodePtr last_vnp;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ddvcolor.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvcolor.c:160:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvcolor.c: In function 'DDV_GetColor':
ddvcolor.c:1422:10: warning: unused variable 'retval' [-Wunused-variable]
Int4 retval = 0;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ddvcolor.c:165:
ddvcolor.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF viewmgr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/viewmgr.h:111,
from viewmgr.c:165:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from viewmgr.c:167:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from viewmgr.c:168:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
viewmgr.c:683:13: warning: 'ViewMgr_Swap' defined but not used [-Wunused-function]
static void ViewMgr_Swap(SeqAlign *salp1, SeqAlign *salp2)
^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ddvcreate.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ddvcreate.h:142,
from ddvcreate.c:245:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvcreate.c:290:2: warning: missing braces around initializer [-Wmissing-braces]
{
^
ddvcreate.c:290:2: note: (near initialization for 'DDV_PaletteRGB')
ddvcreate.c: In function 'DDV_CreateDisplayFromIndex_1':
ddvcreate.c:493:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp))
^~~~~
ddvcreate.c: In function 'DDV_CreateDisplayFromIndex_2':
ddvcreate.c:529:21: warning: variable 'more' set but not used [-Wunused-but-set-variable]
Boolean more;
^~~~
ddvcreate.c: In function 'DDV_CreateDisplayFromIndex_EX2':
ddvcreate.c:779:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp))
^~~~~
ddvcreate.c:690:21: warning: variable 'last' set but not used [-Wunused-but-set-variable]
Boolean last;
^~~~
ddvcreate.c:686:21: warning: variable 'PopulateTo' set but not used [-Wunused-but-set-variable]
Int4 PopulateTo;
^~~~~~~~~~
ddvcreate.c: In function 'DDV_DisplayNewBLAST':
ddvcreate.c:1942:16: warning: variable 'what' set but not used [-Wunused-but-set-variable]
Uint1 what;
^~~~
ddvcreate.c: In function 'UDV_BigEncodeIdxFeat4':
ddvcreate.c:2878:2: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return *((Uint8Ptr) index_g);
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/ddvcreate.h:143,
from ddvcreate.c:245:
ddvcreate.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ddvcreate.c:249:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ddvcreate.c:2362:16: warning: 'DDV_DisplayBlastSAP' defined but not used [-Wunused-function]
static Boolean DDV_DisplayBlastSAP(SeqAlignPtr sap, ValNodePtr mask,
^~~~~~~~~~~~~~~~~~~
ddvcreate.c:525:16: warning: 'DDV_CreateDisplayFromIndex_2' defined but not used [-Wunused-function]
static Boolean DDV_CreateDisplayFromIndex_2(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, Int2 LineSize)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvcreate.c: In function 'UAMgrIntUAMsg':
ddvcreate.c:1141:11: warning: 'stop_middle' may be used uninitialized in this function [-Wmaybe-uninitialized]
ubd->from=Start;
~~~~~~~~~^~~~~~
ddvcreate.c:1158:73: note: 'stop_middle' was declared here
Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
^~~~~~~~~~~
ddvcreate.c:1195:4: warning: 'start_middle' may be used uninitialized in this function [-Wmaybe-uninitialized]
UABitDescrInit(&uamp->ubd[0],0,start_middle-1,TRUE);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvcreate.c:1158:60: note: 'start_middle' was declared here
Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
^~~~~~~~~~~~
ddvcreate.c:1201:60: warning: 'halfBspLengthSeqR' may be used uninitialized in this function [-Wmaybe-uninitialized]
UABitDescrInit(&uamp->ubd[1],halfBspLengthSeqL,MaxLength-halfBspLengthSeqR-1,TRUE);
~~~~~~~~~^~~~~~~~~~~~~~~~~~
ddvcreate.c:1158:24: note: 'halfBspLengthSeqR' was declared here
Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
^~~~~~~~~~~~~~~~~
ddvcreate.c:1200:50: warning: 'halfBspLengthSeqL' may be used uninitialized in this function [-Wmaybe-uninitialized]
UABitDescrInit(&uamp->ubd[0],BspStart,BspStart+halfBspLengthSeqL-1,FALSE);
~~~~~~~~^~~~~~~~~~~~~~~~~~
ddvcreate.c:1158:6: note: 'halfBspLengthSeqL' was declared here
Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
^~~~~~~~~~~~~~~~~
ddvcreate.c: In function 'DDV_PopulateDisplayForDisc':
ddvcreate.c:1048:16: warning: 'vnp_para' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp_list[n-1]=vnp_para;
~~~~~~~~~~~~~^~~~~~~~~
ddvcreate.c: In function 'UABuildDescriptor2':
ddvcreate.c:1541:13: warning: 'stopcopy' may be used uninitialized in this function [-Wmaybe-uninitialized]
*TotLength+=(stopcopy-startcopy);/*to be used for the display coord. system*/
^~
ddvcreate.c: In function 'DDV_DumpSAPInAFile':
ddvcreate.c:1798:2: warning: 'matrix' may be used uninitialized in this function [-Wmaybe-uninitialized]
DDV_AffichageParaG(mpplp,0,0,mpplp->LengthAli-1,mpplp->LengthAli,0,option,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LineSize,hFile,byteSpp,matrix,gclr,NULL);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvcreate.c: In function 'DDV_ReadSeqBin':
ddvcreate.c:2593:9: warning: 'btr' may be used uninitialized in this function [-Wmaybe-uninitialized]
return btr;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF jsavlt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/jsavlt.h:4,
from jsavlt.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF needleman.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/needleman.h:40,
from needleman.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
needleman.c: In function 'NeedlemanWunschQuadraticByLoc':
needleman.c:281:24: warning: variable 'bestDbPos' set but not used [-Wunused-but-set-variable]
Int4 bestQueryPos, bestDbPos; /*position ending best score in
^~~~~~~~~
needleman.c:281:10: warning: variable 'bestQueryPos' set but not used [-Wunused-but-set-variable]
Int4 bestQueryPos, bestDbPos; /*position ending best score in
^~~~~~~~~~~~
needleman.c: In function 'FetchSequenceByLoc':
needleman.c:243:12: warning: 'query' may be used uninitialized in this function [-Wmaybe-uninitialized]
return query;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF txalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/maputil.h:113,
from ../include/jzcoll.h:123,
from ../include/txalign.h:228,
from txalign.c:559:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
txalign.c: In function 'addLinkoutForDefline':
txalign.c:706:13: warning: variable 'hasLinkout' set but not used [-Wunused-but-set-variable]
Boolean hasLinkout=FALSE;
^~~~~~~~~~
txalign.c: In function 'addLinkoutForBioseq':
txalign.c:774:13: warning: variable 'hasLinkout' set but not used [-Wunused-but-set-variable]
Boolean hasLinkout=FALSE;
^~~~~~~~~~
txalign.c: In function 'load_align_sum_for_StdSeg':
txalign.c:2748:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (bsp = BioseqLockById(SeqLocId(ssp->loc->next))) {
^~
txalign.c: In function 'ShowAlignNodeText2Ex':
txalign.c:3548:13: warning: variable 'is_end' set but not used [-Wunused-but-set-variable]
Boolean is_end, strip_semicolon=TRUE;
^~~~~~
txalign.c: In function 'Tx_PrintDefLine':
txalign.c:4597:7: warning: unused variable 'seqid_length' [-Wunused-variable]
Int4 seqid_length = 0, total_length = 0;
^~~~~~~~~~~~
txalign.c: In function 'PrintDefLinesFromSeqAlignWithPath':
txalign.c:5012:39: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
} else if (bestid != NULL && !(options & TXALIGN_NO_DUMPGNL) || (options & TXALIGN_NO_ENTREZ))
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
txalign.c:5016:29: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (bsp = BioseqLockById(bestid)) {
^~
txalign.c:4718:10: warning: unused variable 'ColumnDistance' [-Wunused-variable]
Int2 ColumnDistance=2, extraSpace=0, extraSpace2=0, strLen=0, maxEvalWidth=5, maxNWidth=2;
^~~~~~~~~~~~~~
txalign.c:4710:43: warning: unused variable 'sip_list' [-Wunused-variable]
SeqIdPtr bestid, gi_list, subject_id, sip_list=NULL, last_id;
^~~~~~~~
txalign.c:4706:17: warning: variable 'ptr_start' set but not used [-Wunused-but-set-variable]
Char *ptr, *ptr_start, *eval_buff_ptr, *bit_score_buff_ptr;
^~~~~~~~~
txalign.c: In function 'FormatScoreFromSeqAlignEx':
txalign.c:5335:25: warning: unused variable 't_adj' [-Wunused-variable]
Int4 m_adj = 0, t_adj = 0;
^~~~~
txalign.c:5334:29: warning: unused variable 'last_t_to' [-Wunused-variable]
Int4 last_m_to = 0, last_t_to = 0;
^~~~~~~~~
txalign.c: In function 'FSFPrintOneDefline':
txalign.c:5443:14: warning: variable 'seqid_len' set but not used [-Wunused-but-set-variable]
Int4 gi, seqid_len = 0;
^~~~~~~~~
txalign.c: In function 'FormatScoreFunc':
txalign.c:5660:13: warning: variable 'allocated' set but not used [-Wunused-but-set-variable]
Boolean allocated, first;
^~~~~~~~~
txalign.c: In function 'OOFShowSingleAlignment':
txalign.c:6326:27: warning: array subscript has type 'char' [-Wchar-subscripts]
else if(matrix[line1[line_index]][line2[line_index]] > 0)
^
txalign.c:6326:46: warning: array subscript has type 'char' [-Wchar-subscripts]
else if(matrix[line1[line_index]][line2[line_index]] > 0)
^
txalign.c:6093:13: warning: variable 'lines' set but not used [-Wunused-but-set-variable]
Int4 i, lines, k, shift_info = 0;
^~~~~
txalign.c: In function 'OOFDisplayTraceBack1':
txalign.c:6581:33: warning: unused variable 'st' [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:6581:9: warning: unused variable 'tmp' [-Wunused-variable]
tmp[10] = " ", *st;
^~~
txalign.c: In function 'OOFDisplayTraceBack2':
txalign.c:6655:33: warning: unused variable 'st' [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c: In function 'FDGetTaxNamesFromBioseq':
txalign.c:6757:21: warning: variable 'bdsp' set but not used [-Wunused-but-set-variable]
BlastDefLinePtr bdsp;
^~~~
txalign.c: At top level:
txalign.c:828:19: warning: 'ProcessTextInsertion' declared 'static' but never defined [-Wunused-function]
static ValNodePtr ProcessTextInsertion PROTO((AlignNodePtr anp, Int4 m_left, Int4 m_right, BioseqPtr bsp, Int4 line_len, Int1 frame));
^~~~~~~~~~~~~~~~~~~~
txalign.c:6655:33: warning: 'st' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:6581:9: warning: 'tmp' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~~
txalign.c:6581:33: warning: 'st' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:3433:1: warning: 'get_seq_id' defined but not used [-Wunused-function]
get_seq_id(SeqAlignPtr sap, Int2 index)
^~~~~~~~~~
txalign.c:2338:16: warning: 'has_hit_in_region' defined but not used [-Wunused-function]
static Boolean has_hit_in_region(Uint1Ptr all_frame)
^~~~~~~~~~~~~~~~~
txalign.c:630:16: warning: 'getNameInitials' defined but not used [-Wunused-function]
static CharPtr getNameInitials(CharPtr name){
^~~~~~~~~~~~~~~
In file included from ../include/ncbi.h:62:0,
from ../include/maputil.h:113,
from ../include/jzcoll.h:123,
from ../include/txalign.h:228,
from txalign.c:559:
txalign.c: In function 'DrawTextToBuffer':
../include/ncbistr.h:331:19: warning: 'HTML_buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringLen Nlm_StringLen
^~~~~~~~~~~~~
txalign.c:1612:10: note: 'HTML_buffer' was declared here
CharPtr HTML_buffer;
^~~~~~~~~~~
txalign.c: In function 'OOFShowSingleAlignment.isra.11':
txalign.c:6049:16: warning: 'number' may be used uninitialized in this function [-Wmaybe-uninitialized]
number = number/10;
~~~~~~~^~~~~~~~~~~
txalign.c:6078:16: note: 'number' was declared here
static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
^~~~~~~~~~~~~~~~~~~~~~
txalign.c:6049:16: warning: 'number' may be used uninitialized in this function [-Wmaybe-uninitialized]
number = number/10;
~~~~~~~^~~~~~~~~~~
txalign.c:6078:16: note: 'number' was declared here
static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
^~~~~~~~~~~~~~~~~~~~~~
txalign.c:6049:16: warning: 'number' may be used uninitialized in this function [-Wmaybe-uninitialized]
number = number/10;
~~~~~~~^~~~~~~~~~~
txalign.c:6078:16: note: 'number' was declared here
static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
^~~~~~~~~~~~~~~~~~~~~~
txalign.c:6049:16: warning: 'number' may be used uninitialized in this function [-Wmaybe-uninitialized]
number = number/10;
~~~~~~~^~~~~~~~~~~
txalign.c:6078:16: note: 'number' was declared here
static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
^~~~~~~~~~~~~~~~~~~~~~
txalign.c:6237:12: warning: 'dna_line_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (dna_line_start == 0)
^
txalign.c:6240:11: warning: 'pro_line_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(pro_line_start == 0)
^
txalign.c: In function 'find_score_in_align':
txalign.c:2598:33: warning: 'smtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
stdaa_res = SeqMapTableConvert(smtp, t_res);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
txalign.c:2498:20: note: 'smtp' was declared here
SeqMapTablePtr smtp;
^~~~
txalign.c:2463:13: warning: 't_spp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqPortFree(t_spp);
^~~~~~~~~~~~~~~~~~
txalign.c:2394:23: note: 't_spp' was declared here
SeqPortPtr m_spp, t_spp;
^~~~~
txalign.c:2460:11: warning: 'm_spp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(m_spp == NULL)
^
txalign.c:2394:16: note: 'm_spp' was declared here
SeqPortPtr m_spp, t_spp;
^~~~~
txalign.c: In function 'ShowAlignNodeText2Ex.isra.12':
txalign.c:2284:25: warning: 'm_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
to = MIN(master_len-1, to + 3);
^
txalign.c:3543:10: note: 'm_len' was declared here
Int4 m_len; /*length of the master sequence*/
^~~~~
txalign.c: In function 'ShowTextAlignFromAnnot3':
txalign.c:1467:12: warning: 'retval' may be used uninitialized in this function [-Wmaybe-uninitialized]
return retval;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF fdlobj.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from fdlobj.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
fdlobj.c: In function 'BlastDefLineSetAsnRead':
fdlobj.c:69:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
fdlobj.c: In function 'BlastDefLineAsnRead':
fdlobj.c:202:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF alignmgr2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/alignmgr2.h:110,
from alignmgr2.c:232:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
alignmgr2.c: In function 'AlnMgr2IndexSingleDenseSegSA':
alignmgr2.c:875:13: warning: statement with no effect [-Wunused-value]
for (j; j<dsp->numseg && next == -1; j++)
^~~
alignmgr2.c: In function 'AlnMgr2CopySeg':
alignmgr2.c:2967:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (ldelta = ABS(s->beg - beg)) {
^~
alignmgr2.c: In function 'AlnMgr2AddInNewPairwiseSA':
alignmgr2.c:3204:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (a = AlnMgr2GetNextSeqPiece(a)) {
^~~~~
alignmgr2.c:3206:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (b = AlnMgr2GetNextLimitedSeqPiece(b, a)) {
^~~~~
alignmgr2.c:3216:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (A = AlnMgr2GetNextSeqPiece(A)) {
^~~~~
alignmgr2.c:3220:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (B = AlnMgr2GetNextLimitedSeqPiece(B, A)) {};
^~~~~
alignmgr2.c: In function 'AlnMgr2SetUnaln':
alignmgr2.c:5393:22: warning: variable 'dsp' set but not used [-Wunused-but-set-variable]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2PrintSeqAlign':
alignmgr2.c:5606:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (more = AlnMgr2GetNextAlnBit(sap, amp))
^~~~~
alignmgr2.c: In function 'AlnMgr2GetNextAlnBit':
alignmgr2.c:5702:21: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
alignmgr2.c: In function 'AlnMgr2GetUnalignedInfo':
alignmgr2.c:6068:22: warning: variable 'saip' set but not used [-Wunused-but-set-variable]
SAIndex2Ptr saip;
^~~~
alignmgr2.c: In function 'AlnMgr2GetInterruptInfo':
alignmgr2.c:6314:7: warning: statement with no effect [-Wunused-value]
for (i; i<interrupt->segnum; i++)
^~~
alignmgr2.c: In function 'AlnMgr2ComputeScoreForSeqAlign':
alignmgr2.c:8324:17: warning: variable 'numseqs' set but not used [-Wunused-but-set-variable]
Int4 numseqs;
^~~~~~~
alignmgr2.c:8322:17: warning: variable 'mismatch' set but not used [-Wunused-but-set-variable]
Int4 mismatch;
^~~~~~~~
alignmgr2.c:8321:17: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from alignmgr2.c:232:
alignmgr2.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
alignmgr2.c:3540:13: warning: 'AlnMgr2AddInNewSA' defined but not used [-Wunused-function]
static void AlnMgr2AddInNewSA(SeqAlignPtr parent, SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~
alignmgr2.c:2351:18: warning: 'AlnMgr2GetEdgeList' defined but not used [-Wunused-function]
static AMEdgePtr AlnMgr2GetEdgeList(Int4 vertexnum, AMEdgePtr edge_head, AMEdgePtr already_used)
^~~~~~~~~~~~~~~~~~
alignmgr2.c:2123:13: warning: 'AlnMgr2SortVerticesByNumEdges' defined but not used [-Wunused-function]
static void AlnMgr2SortVerticesByNumEdges(AMVertexPtr PNTR vertexarray, Int4 numvertices)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:1051:13: warning: 'AlnMgr2UnpackSeqAlignChain' defined but not used [-Wunused-function]
static void AlnMgr2UnpackSeqAlignChain(SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetLongestSeqLoc':
alignmgr2.c:10114:15: warning: 'slp_longest' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqLocPtr slp_longest;
^~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2IndexLite':
alignmgr2.c:991:33: warning: 'sap_segs_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap_segs_prev->next = (SeqAlignPtr)(sap_segs->segs);
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:958:17: note: 'sap_segs_prev' was declared here
SeqAlignPtr sap_segs_prev;
^~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetUnalignedInfo':
alignmgr2.c:6105:54: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
*from = dsp->starts[dsp->dim*i+row-1]+dsp->lens[i];
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetMaxUnalignedLength':
alignmgr2.c:7031:22: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAIndex2Ptr saip;
^~~~
alignmgr2.c:7060:19: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (i=0; i<dsp->dim; i++)
~~~^~~~~
alignmgr2.c: In function 'AlnMgr2GetInterruptInfo':
alignmgr2.c:6336:16: warning: 'iip' may be used uninitialized in this function [-Wmaybe-uninitialized]
iip->strand = strand;
~~~~~~~~~~~~^~~~~~~~
alignmgr2.c:6165:19: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
trans = saip->srdp[saip->anchor-1]->sect;
~~~~^~~~~~
alignmgr2.c:6320:48: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
iip->starts[k] = dsp->starts[dsp->dim*i + interrupt->row-1];
~~~^~~~~
alignmgr2.c: In function 'AlnMgr2GetNthSeqRangeInSA':
alignmgr2.c:6461:15: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
srdp = saip->srdp[n-1];
~~~~^~~~~~
alignmgr2.c:6472:57: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
beg = dsp->starts[srdp->sect[srdp->numsect-1]*(dsp->dim) + n-1];
~~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetNthRowSpanInSA':
alignmgr2.c:6533:20: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
*start = saip->aligncoords[i];
~~~~^~~~~~~~~~~~~
alignmgr2.c:6541:41: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
*stop = saip->aligncoords[i] + dsp->lens[srdp->sect[srdp->numsect-1]] - 1;
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetAlnLength':
alignmgr2.c:6772:17: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
len += AlnMgr2GetMaxUnalignedLength(salp, i);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:6764:22: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (saip->aligncoords[saip->numseg-1]+dsp->lens[lastseg]);
~~~~^~~~~~~~~~~~~
alignmgr2.c:6771:20: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
len += dsp->lens[i];
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetNextAlnBit':
alignmgr2.c:6008:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->anchor <= 0)
~~~~^~~~~~~~
alignmgr2.c:6004:59: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
amp->from_row = dsp->starts[trans[start_sect]*dsp->dim+amp->row_num-1] + offset;
~~~^~~~~
alignmgr2.c: In function 'AlnMgr2IsSAPDiscAli':
alignmgr2.c:6796:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->numunaln > 0)
~~~~^~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetNumAlnBlocks':
alignmgr2.c:6819:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->numunaln >= 0)
~~~~^~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetNthBlockRange':
alignmgr2.c:6853:20: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
*start = saip->aligncoords[saip->unaln[n-1]+1];
~~~~^~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetNthUnalignedForNthRow':
alignmgr2.c:6872:22: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAIndex2Ptr saip;
^~~~
alignmgr2.c:6919:65: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
*start = dsp->starts[(saip->srdp[row-1]->unaligned[i])*dsp->dim+row-1] + dsp->lens[(saip->srdp[row-1]->unaligned[i])];
~~~^~~~~
alignmgr2.c: In function 'AlnMgr2GetNextLengthBit':
alignmgr2.c:7002:26: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxseg = saip->unaln[*seg];
~~~~^~~~~~~
alignmgr2.c:6937:22: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2GetNumSegsInRange':
alignmgr2.c:7168:62: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
start = binary_search_on_uint4_list(aligncoords, from, dsp->numseg);
~~~^~~~~~~~
alignmgr2.c:7133:21: warning: 'aligncoords' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint4Ptr aligncoords;
^~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2MapBioseqToSeqAlign':
alignmgr2.c:7635:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->anchor > 0)
~~~~^~~~~~~~
alignmgr2.c:7573:21: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2MapSeqAlignToBioseq':
alignmgr2.c:7671:21: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAIndex2Ptr saip;
^~~~
alignmgr2.c:7713:36: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (dsp->starts[sect*(dsp->dim)+row-1] + dsp->lens[sect] - 1 - offset);
~~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetSubAlign':
alignmgr2.c:7537:26: warning: 'sap_real' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (sap == NULL || sap->saip == NULL)
~~~^~~~~~
alignmgr2.c:7982:21: note: 'sap_real' was declared here
SeqAlignPtr sap_real;
^~~~~~~~
alignmgr2.c: In function 'AlnMgr2FillInUnaligned':
alignmgr2.c:9852:12: warning: 'offset' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr = curr + 1 + offset;
~~~~~^~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF alnread.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF acerdapi.c
acerdapi.c: In function 'DoesSeqStringMatchBsp':
acerdapi.c:201:30: warning: variable 'seq_len' set but not used [-Wunused-but-set-variable]
Int4 ctr, pos = 0, i, len, seq_len;
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from acerdapi.c:40:
acerdapi.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF aceread.c
aceread.c:3308:12: warning: 's_GetUngappedPosition' defined but not used [-Wunused-function]
static int s_GetUngappedPosition (int gapped_pos, char *seq)
^~~~~~~~~~~~~~~~~~~~~
aceread.c:276:13: warning: 'AdjustGapInfoFor3Trim' defined but not used [-Wunused-function]
static void AdjustGapInfoFor3Trim (TGapInfoPtr gap_info, int new_len)
^~~~~~~~~~~~~~~~~~~~~
aceread.c:247:13: warning: 'AdjustGapInfoFor5Trim' defined but not used [-Wunused-function]
static void AdjustGapInfoFor5Trim (TGapInfoPtr gap_info, int trim)
^~~~~~~~~~~~~~~~~~~~~
aceread.c:134:12: warning: 's_IsGapChar' defined but not used [-Wunused-function]
static int s_IsGapChar (char ch, char *gap_chars)
^~~~~~~~~~~
aceread.c: In function 's_ReadContig':
aceread.c:1477:33: warning: 'linestring' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (linestring != NULL) free (linestring);
^~~~~~~~~~~~~~~~~
rm -f libncbiobj.a
ar cru libncbiobj.a objacces.o objalign.o objall.o objbibli.o objfeat.o objgen.o objloc.o objmedli.o objpub.o objres.o objscoremat.o objseq.o objblock.o objcode.o objsset.o objsub.o objprt.o objfdef.o objalignloc.o objtable.o objpubme.o objmdrs.o objproj.o objgbseq.o objtseq.o objinsdseq.o objmacro.o objent2.o ent2api.o pmfapi.o objtax3.o tax3api.o objegkludge.o objentgene.o objmla2.o mla2api.o qblastapi.o vecscnapi.o objmim.o objvalid.o mimapi.o cddapi.o seqport.o sequtil.o prtutil.o simple.o tofasta.o tofile.o tomedlin.o valid.o valapi.o alignmgr.o aliparse.o aliread.o alignval.o sqnutil1.o sqnutil2.o sqnutil3.o sqnutil4.o subutil.o edutil.o asn2ff1.o asn2ff2.o asn2ff3.o asn2ff4.o asn2ff5.o asn2ff6.o asn2gnb1.o asn2gnb2.o asn2gnb3.o asn2gnb4.o asn2gnb5.o asn2gnb6.o ftusrstr.o gbfeat.o gbftglob.o gbparint.o utilpars.o utilpub.o ffprint.o wprint.o satutil.o seqmgr.o objmgr.o gather.o accmmdbs.o acccn3ds.o lsqfetch.o findrepl.o codon.o jzcoll.o jzmisc.o maputil.o mconsist.o macroapi.o salpedit.o salpstat.o salpacc.o salprop.o salsap.o salstruc.o salutil.o udvseq.o blocks.o pgppop.o samutil.o ddvcolor.o viewmgr.o ddvcreate.o jsavlt.o needleman.o txalign.o fdlobj.o alignmgr2.o alnread.o acerdapi.o aceread.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbiobj.a ../lib
ranlib ../lib/libncbiobj.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cdentrez.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from cdentrez.c:162:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cdentrez.c:283:23: warning: 'CdEntMlSumGet' declared 'static' but never defined [-Wunused-function]
static DocSumPtr NEAR CdEntMlSumGet PROTO((Int4 uid));
^~~~~~~~~~~~~
cdentrez.c:310:23: warning: 'CdEntSeqSumGet' declared 'static' but never defined [-Wunused-function]
static DocSumPtr NEAR CdEntSeqSumGet PROTO((Int4 uid, DocType type));
^~~~~~~~~~~~~~
cdentrez.c:2935:23: warning: 'MedSumAsnRead' defined but not used [-Wunused-function]
static DocSumPtr NEAR MedSumAsnRead (AsnIoPtr aip, DocUid uid)
^~~~~~~~~~~~~
cdentrez.c:1616:26: warning: 'FreePostingList' defined but not used [-Wunused-function]
static ByteStorePtr NEAR FreePostingList (ByteStorePtr lst)
^~~~~~~~~~~~~~~
cdentrez.c:307:20: warning: 'BIOSEQ_id_E' defined but not used [-Wunused-variable]
static AsnTypePtr BIOSEQ_id_E = NULL;
^~~~~~~~~~~
cdentrez.c: In function 'CdEntrezMergeTerm':
cdentrez.c:2675:17: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized]
*totl = total;
~~~~~~^~~~~~~
cdentrez.c:2672:17: warning: 'special' may be used uninitialized in this function [-Wmaybe-uninitialized]
*spcl = special;
~~~~~~^~~~~~~~~
cdentrez.c:2640:5: warning: 'termpage' may be used uninitialized in this function [-Wmaybe-uninitialized]
cd3_CdTermScan (db, fld, termpage, (Int4)0, ScanAndFreeProc);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdentrez.c: In function 'CdLinkUidList':
cdentrez.c:938:9: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
return count;
^~~~~
cdentrez.c: In function 'CdTermListByTerm':
cdentrez.c:1036:10: warning: 'first' may be used uninitialized in this function [-Wmaybe-uninitialized]
rsult = cd3_CdTermScan(type,field,first,0,TermListTermScanProc);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdentrez.c: In function 'CdEntTLAddTerm':
cdentrez.c:1895:24: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (scanOk && total > 0) {
~~~~~~~^~~~~~~~~~~~
cdentrez.c:1787:13: note: 'total' was declared here
Int4 total;
^~~~~
cdentrez.c: In function 'CdEntrezFindTerm':
cdentrez.c:1123:3: warning: 'ctp' may be used uninitialized in this function [-Wmaybe-uninitialized]
CdTermFree(ctp);
^~~~~~~~~~~~~~~
cdentrez.c: In function 'CdEntMedlineEntryListGet':
cdentrez.c:2720:6: warning: 'aip' may be used uninitialized in this function [-Wmaybe-uninitialized]
cd3_CdDocAsnClose(aip);
^~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cdromlib.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objacces.h:64,
from ../include/cdromlib.h:71,
from cdromlib.c:73:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cdnewlib.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objacces.h:64,
from ../include/cdromlib.h:71,
from cdnewlib.c:208:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cdnewlib.c:600:27: warning: missing braces around initializer [-Wmissing-braces]
struct CdFInfo _finfo[] = {
^
cdnewlib.c:600:27: note: (near initialization for '_finfo')
cdnewlib.c:614:27: warning: missing braces around initializer [-Wmissing-braces]
struct CdDirInfo _dir[] = {
^
cdnewlib.c:614:27: note: (near initialization for '_dir')
cdnewlib.c: In function 'cd3_CdDocAsnOpen':
cdnewlib.c:1327:9: warning: unused variable 'fdir' [-Wunused-variable]
char *fdir = NULL;
^~~~
cdnewlib.c: In function 'CdDevice_Init':
cdnewlib.c:2739:6: warning: variable 'cd_num' set but not used [-Wunused-but-set-variable]
int cd_num;
^~~~~~
At top level:
cdnewlib.c:3605:13: warning: 'Cache_Purge' defined but not used [-Wunused-function]
static void Cache_Purge (Cache *cache)
^~~~~~~~~~~
cdnewlib.c:3592:14: warning: 'Cache_Peek' defined but not used [-Wunused-function]
static void* Cache_Peek (Cache *cache, long id)
^~~~~~~~~~
cdnewlib.c:3569:12: warning: 'Cache_Touch' defined but not used [-Wunused-function]
static int Cache_Touch (Cache *cache, long id)
^~~~~~~~~~~
cdnewlib.c:3506:12: warning: 'Cache_Delete' defined but not used [-Wunused-function]
static int Cache_Delete (Cache *cache, long id)
^~~~~~~~~~~~
cdnewlib.c:638:18: warning: '_div' defined but not used [-Wunused-variable]
static DivInfo * _div;
^~~~
cdnewlib.c:582:15: warning: '_empty_string' defined but not used [-Wunused-variable]
static char * _empty_string = "";
^~~~~~~~~~~~~
cdnewlib.c: In function 'UnixFileGets':
cdnewlib.c:1509:6: warning: 'ch' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ch == '\0') {
^
cdnewlib.c: In function 'trmncmp':
cdnewlib.c:2379:13: warning: 'c2' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (c1 - c2);
~~~~^~~~~
cdnewlib.c:2379:13: warning: 'c1' may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /usr/include/string.h:635:0,
from ../include/ncbilcl.h:156,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objacces.h:64,
from ../include/cdromlib.h:71,
from cdnewlib.c:208:
In function 'strncat',
inlined from 'CdDevice_FileBuildPath.part.17' at cdnewlib.c:2679:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'CdDevice_Init' at cdnewlib.c:2751:3:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'CdDevice_Init' at cdnewlib.c:2769:6:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdnewlib.c: In function 'TrmIndex_Lookup':
cdnewlib.c:2136:24: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
int lo, hi, mid, len, d;
^
cdnewlib.c:2168:27: warning: 'term' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (d==0 && len == (int)strlen(term))
^~~~~~~~~~~~
cdnewlib.c:2136:14: warning: 'mid' may be used uninitialized in this function [-Wmaybe-uninitialized]
int lo, hi, mid, len, d;
^~~
cdnewlib.c: In function 'UidIndex_Lookup':
cdnewlib.c:1986:20: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
page_num = (uid < *p && mid >0) ? mid-1 : mid;
^~
cdnewlib.c:1986:42: warning: 'mid' may be used uninitialized in this function [-Wmaybe-uninitialized]
page_num = (uid < *p && mid >0) ? mid-1 : mid;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF casn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from casn.c:84:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cdconfig.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cdconfig.c:75:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/ncbi.h:58:0,
from cdconfig.c:75:
cdconfig.c: In function 'ChangeMedia':
../include/ncbistd.h:278:15: warning: statement with no effect [-Wunused-value]
#define FALSE ((Nlm_Boolean)0)
^
../include/ncbifile.h:169:76: note: in expansion of macro 'FALSE'
#define EjectCd(sVolume, deviceName, rawDeviceName, mountPoint, mountCmd) FALSE
^~~~~
cdconfig.c:941:29: note: in expansion of macro 'EjectCd'
EjectCd(toBeEjected->entrez_info->volume_label,
^~~~~~~
../include/ncbistd.h:278:15: warning: statement with no effect [-Wunused-value]
#define FALSE ((Nlm_Boolean)0)
^
../include/ncbifile.h:170:76: note: in expansion of macro 'FALSE'
#define MountCd(sVolume, deviceName, mountPoint, mountCmd) FALSE
^~~~~
cdconfig.c:960:17: note: in expansion of macro 'MountCd'
MountCd(newMedia->entrez_info->volume_label, cdm->device_name,
^~~~~~~
cdconfig.c: At top level:
cdconfig.c:191:17: warning: 'UnMarkLRUineligible' declared 'static' but never defined [-Wunused-function]
static void UnMarkLRUineligible PROTO((void));
^~~~~~~~~~~~~~~~~~~
cdconfig.c: In function 'EntrezInfoMerge':
cdconfig.c:1141:23: warning: 'besttype' may be used uninitialized in this function [-Wmaybe-uninitialized]
EntrezTypeDataPtr besttype;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/cdrom.h:9,
from objentr.c:102:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objentr.c: In function 'CdRomAsnLoad':
objentr.c:170:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (loaded)
^~
objentr.c:172:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
loaded = TRUE;
^~~~~~
objentr.c: In function 'DocSumAsnRead':
objentr.c:970:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentr.c:969:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
At top level:
objentr.c:806:23: warning: 'EntrezDivInfo_Destruct' defined but not used [-Wunused-function]
static EntrezDivInfo* EntrezDivInfo_Destruct (EntrezDivInfo *div)
^~~~~~~~~~~~~~~~~~~~~~
objentr.c:771:16: warning: 'EntrezLinkInfo_AsnWrite' defined but not used [-Wunused-function]
static Boolean EntrezLinkInfo_AsnWrite (const EntrezLinkInfo *link, AsnIo *stream, AsnType *type)
^~~~~~~~~~~~~~~~~~~~~~~
objentr.c: In function 'EntrezInfoAsnRead':
objentr.c:818:5: warning: 'div' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (div == NULL)
^
objentr.c:241:17: note: 'div' was declared here
EntrezDivInfo *div;
^~~
objentr.c:763:17: warning: 'link' may be used uninitialized in this function [-Wmaybe-uninitialized]
link->datasize = (int) val.intvalue;
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
objentr.c:240:18: note: 'link' was declared here
EntrezLinkInfo *link;
^~~~
objentr.c:704:19: warning: 'fld' may be used uninitialized in this function [-Wmaybe-uninitialized]
fld->post_type = (PostType) val.intvalue;
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
objentr.c:239:19: note: 'fld' was declared here
EntrezFieldInfo *fld;
^~~
objentr.c:649:18: warning: 'tinf' may be used uninitialized in this function [-Wmaybe-uninitialized]
tinf->asntype = (char*) val.ptrvalue;
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
objentr.c:238:18: note: 'tinf' was declared here
EntrezTypeInfo *tinf;
^~~~
objentr.c:856:16: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
div->docs[i++] = val.intvalue;
~^~
objentr.c:824:7: note: 'i' was declared here
int i;
^
rm -f libncbicdr.a
ar cru libncbicdr.a cdentrez.o cdromlib.o cdnewlib.o casn.o cdconfig.o objentr.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbicdr.a ../lib
ranlib ../lib/libncbicdr.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibbutns.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibbutns.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibbutns.c: In function 'Nlm_CheckCallback':
vibbutns.c:328:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_RadioCallback':
vibbutns.c:347:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_SetButtonStatus':
vibbutns.c:668:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Nlm_Int2 val;
^~~
vibbutns.c: In function 'Nlm_NewButton.isra.1':
vibbutns.c:1133:3: warning: 'call' may be used uninitialized in this function [-Wmaybe-uninitialized]
XtAddCallback (c, call, Nlm_ButtonCallback, (XtPointer) b);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibextra.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibextra.c:87:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibextra.c: In function 'Nlm_RGB2HSL.constprop':
vibextra.c:1219:13: warning: 'min' may be used uninitialized in this function [-Wmaybe-uninitialized]
i++; if ( i > 2 ) i=0;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibfiles.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibforms.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from vibforms.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibgroup.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibgroup.c:84:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF viblists.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from viblists.c:161:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
viblists.c: In function 'Nlm_SetListPosition':
viblists.c:1118:15: warning: variable 'is_realized' set but not used [-Wunused-but-set-variable]
Nlm_Boolean is_realized;
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibmenus.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibmenus.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibmenus.c: In function 'Nlm_IsMenuItemChecked':
vibmenus.c:563:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CheckMenuItem':
vibmenus.c:591:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableMenuItem':
vibmenus.c:1986:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:1985:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoice':
vibmenus.c:2052:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceGroup':
vibmenus.c:2102:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceItem':
vibmenus.c:2146:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2144:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableMenuItem':
vibmenus.c:2309:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2308:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoice':
vibmenus.c:2375:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoiceItem':
vibmenus.c:2469:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2467:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_RemoveSubMenu':
vibmenus.c:2607:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CountMenuItems':
vibmenus.c:3036:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetMenuItem':
vibmenus.c:3219:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetPopListTitle':
vibmenus.c:3329:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
Nlm_MenU m;
^
vibmenus.c: In function 'Nlm_AppendItems':
vibmenus.c:3948:17: warning: unused variable 'accel' [-Wunused-variable]
Nlm_Char accel;
^~~~~
vibmenus.c: In function 'Nlm_NewPopupList':
vibmenus.c:4939:19: warning: unused variable 'lbl' [-Wunused-variable]
Widget lbl;
^~~
vibmenus.c:4937:19: warning: unused variable 'color' [-Wunused-variable]
Pixel color;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibprmpt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibprmpt.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibsbars.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibsbars.c:128:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibslate.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibslate.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibslate.c: In function 'Nlm_EnableSlate':
vibslate.c:1199:18: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_DisableSlate':
vibslate.c:1254:18: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_SelectSlate':
vibslate.c:1515:5: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:1517:5: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SelectPanel':
vibslate.c:1544:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:1546:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateClick':
vibslate.c:2026:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_SlateClickCallback':
vibslate.c:2157:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2159:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateInputCallback':
vibslate.c:2313:7: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues(w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2315:7: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues(w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateDrawCallback':
vibslate.c:2359:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2361:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibtexts.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibtexts.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibtexts.c: In function 'Nlm_TextCallback':
vibtexts.c:2982:24: warning: unused variable 'cbs' [-Wunused-variable]
XmAnyCallbackStruct *cbs = (XmAnyCallbackStruct *)call_data;
^~~
vibtexts.c: In function 'Nlm_LoseFocusCallback':
vibtexts.c:2999:25: warning: variable 'cbs' set but not used [-Wunused-but-set-variable]
XmAnyCallbackStruct *cbs;
^~~
vibtexts.c: In function 'Nlm_TabCallback':
vibtexts.c:3109:15: warning: variable 'event' set but not used [-Wunused-but-set-variable]
XKeyEvent *event;
^~~~~
vibtexts.c: In function 'Nlm_HiddenReturnCallback':
vibtexts.c:3122:15: warning: variable 'event' set but not used [-Wunused-but-set-variable]
XKeyEvent *event;
^~~~~
vibtexts.c: In function 'Nlm_HiddenActivateCallback':
vibtexts.c:3135:25: warning: variable 'cbs' set but not used [-Wunused-but-set-variable]
XmAnyCallbackStruct *cbs;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibutils.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from vibutils.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibwndws.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibwndws.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibwndws.c: In function 'Nlm_SetColorMap':
vibwndws.c:1060:13: warning: variable 'defaultdepth' set but not used [-Wunused-but-set-variable]
int defaultdepth;
^~~~~~~~~~~~
vibwndws.c: In function 'Nlm_SetWindowTitle':
vibwndws.c:1567:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_GetWindowTitle':
vibwndws.c:1610:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_NewWindow':
vibwndws.c:2155:19: warning: variable 'screen_num' set but not used [-Wunused-but-set-variable]
int screen_num;
^~~~~~~~~~
vibwndws.c: In function 'Nlm_HideWindow':
vibwndws.c:2526:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowNormal':
vibwndws.c:2969:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowModal':
vibwndws.c:3014:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowDocument':
vibwndws.c:3060:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_VibMainPrelude':
vibwndws.c:6771:13: warning: unused variable 'retval' [-Wunused-variable]
Nlm_Int2 retval;
^~~~~~
vibwndws.c: In function 'Nlm_RemoveDyingWindows':
vibwndws.c:6893:20: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibmain.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibmain.c:40:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibmain.c:121:1: warning: return type defaults to 'int' [-Wimplicit-int]
main (int argc, char *argv[])
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbidraw.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ncbidraw.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF drawing.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from drawing.c:128:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mapping.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from mapping.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mapping.c: In function 'Nlm_MapRectToWorldBox':
mapping.c:139:8: warning: variable 'curScale' set but not used [-Wunused-but-set-variable]
Int4 curScale;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF picture.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from picture.c:100:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF viewer.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from viewer.c:120:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF document.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from document.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
document.c: In function 'Nlm_PrintDocument':
document.c:4413:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
document.c:4417:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF table.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/panels.h:68,
from table.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF palette.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/panels.h:68,
from palette.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF diagnost.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from diagnost.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF image.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from image.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
image.c: In function 'ShiftXMask':
image.c:840:26: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
if(!((mask >> hi + low) & (unsigned long)1)) break;
~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF pictur3d.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/pictur3d.h:49,
from ../include/ppict3d.h:49,
from pictur3d.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pictur3d.c: In function 'Nlm_DeleteFromSeg':
pictur3d.c:114:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else seg->first = b->next;
^~~~
pictur3d.c:115:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if ( seg->last == b ) seg->last = bprev;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF prim3d1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d1.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF prim3d2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d2.c:65:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF prim3d3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d3.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF prim3d4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d4.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF prim3d5.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d5.c:66:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF viewer3d.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vibmouse.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from vibmouse.c:67:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF netscape.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from netscape.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netscape.c: In function 'NS_Obtain_lock':
netscape.c:236:10: warning: variable 'waited' set but not used [-Wunused-but-set-variable]
Bool waited = False;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF imagelst.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/imagelst.h:52,
from imagelst.c:61:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF treeview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/treemgr.h:67,
from treeview.c:91:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF shim3d.c
shim3d.c: In function 'Nlm_AddHalfWorm3D':
shim3d.c:3461:46: warning: unused variable 'tmp' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:40: warning: unused variable 'pCz' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:34: warning: unused variable 'pCy' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:28: warning: unused variable 'pCx' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:22: warning: unused variable 'pNz' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:16: warning: unused variable 'pNy' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3461:10: warning: unused variable 'pNx' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3460:47: warning: unused variable 'Cz' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3460:42: warning: unused variable 'Cy' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3460:37: warning: unused variable 'Cx' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3460:32: warning: unused variable 'Nz' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3460:27: warning: unused variable 'Ny' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3460:15: warning: unused variable 'Nx' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3459:21: warning: unused variable 'pi' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~
shim3d.c:3459:15: warning: unused variable 'sinj' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~~~
shim3d.c:3459:9: warning: unused variable 'cosj' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~~~
shim3d.c:3458:33: warning: unused variable 'prevlen' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~~~~~~
shim3d.c:3458:29: warning: unused variable 'Vz' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3458:25: warning: unused variable 'Vy' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3458:21: warning: unused variable 'Vx' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3458:17: warning: unused variable 'Hz' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3458:13: warning: unused variable 'Hy' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3458:9: warning: unused variable 'Hx' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3457:21: warning: unused variable 'dQtz' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3457:15: warning: unused variable 'dQty' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3457:9: warning: unused variable 'dQtx' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3455:14: warning: unused variable 'len' [-Wunused-variable]
GLdouble len, R1x, R1y, R1z, R2x, R2y, R2z, MG[4][3],
^~~
shim3d.c:3454:26: warning: unused variable 'offset' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^~~~~~
shim3d.c:3454:23: warning: unused variable 'm' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^
shim3d.c:3454:20: warning: unused variable 'k' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^
shim3d.c:3454:17: warning: unused variable 'j' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF odlbox.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from odlbox.c:50:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
odlbox.c: In function 'LB_onVScroll':
odlbox.c:424:12: warning: variable 'IsGoUp' set but not used [-Wunused-but-set-variable]
Boolean IsGoUp=FALSE;
^~~~~~
rm -f libvibrant.a
ar cru libvibrant.a vibbutns.o vibextra.o vibfiles.o vibforms.o vibgroup.o viblists.o vibmenus.o vibprmpt.o vibsbars.o vibslate.o vibtexts.o vibutils.o vibwndws.o vibmain.o ncbidraw.o drawing.o mapping.o picture.o viewer.o document.o table.o palette.o diagnost.o image.o pictur3d.o prim3d1.o prim3d2.o prim3d3.o prim3d4.o prim3d5.o viewer3d.o vibmouse.o netscape.o imagelst.o treeview.o shim3d.o odlbox.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libvibrant.a ../lib
ranlib ../lib/libvibrant.a
mv vibbutns.o vibbutns.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibbutns.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibbutns.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibbutns.c: In function 'Nlm_CheckCallback':
vibbutns.c:328:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_RadioCallback':
vibbutns.c:347:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_SetButtonStatus':
vibbutns.c:668:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Nlm_Int2 val;
^~~
vibbutns.c: In function 'Nlm_NewButton.isra.1':
vibbutns.c:1133:3: warning: 'call' may be used uninitialized in this function [-Wmaybe-uninitialized]
XtAddCallback (c, call, Nlm_ButtonCallback, (XtPointer) b);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv vibbutns.o vibbutns.glo
mv vibbutns.tmp vibbutns.o
mv vibextra.o vibextra.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibextra.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibextra.c:87:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibextra.c: In function 'Nlm_RGB2HSL.constprop':
vibextra.c:1219:13: warning: 'min' may be used uninitialized in this function [-Wmaybe-uninitialized]
i++; if ( i > 2 ) i=0;
^
mv vibextra.o vibextra.glo
mv vibextra.tmp vibextra.o
mv vibfiles.o vibfiles.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibfiles.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibfiles.o vibfiles.glo
mv vibfiles.tmp vibfiles.o
mv vibforms.o vibforms.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibforms.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from vibforms.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibforms.o vibforms.glo
mv vibforms.tmp vibforms.o
mv vibgroup.o vibgroup.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibgroup.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibgroup.c:84:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibgroup.o vibgroup.glo
mv vibgroup.tmp vibgroup.o
mv viblists.o viblists.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viblists.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from viblists.c:161:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
viblists.c: In function 'Nlm_SetListPosition':
viblists.c:1118:15: warning: variable 'is_realized' set but not used [-Wunused-but-set-variable]
Nlm_Boolean is_realized;
^~~~~~~~~~~
mv viblists.o viblists.glo
mv viblists.tmp viblists.o
mv vibmenus.o vibmenus.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmenus.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibmenus.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibmenus.c: In function 'Nlm_IsMenuItemChecked':
vibmenus.c:563:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CheckMenuItem':
vibmenus.c:591:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableMenuItem':
vibmenus.c:1986:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:1985:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoice':
vibmenus.c:2052:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceGroup':
vibmenus.c:2102:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceItem':
vibmenus.c:2146:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2144:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableMenuItem':
vibmenus.c:2309:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2308:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoice':
vibmenus.c:2375:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoiceItem':
vibmenus.c:2469:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2467:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_RemoveSubMenu':
vibmenus.c:2607:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CountMenuItems':
vibmenus.c:3036:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetMenuItem':
vibmenus.c:3219:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetPopListTitle':
vibmenus.c:3329:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
Nlm_MenU m;
^
vibmenus.c: In function 'Nlm_AppendItems':
vibmenus.c:3948:17: warning: unused variable 'accel' [-Wunused-variable]
Nlm_Char accel;
^~~~~
vibmenus.c: In function 'Nlm_NewPopupList':
vibmenus.c:4939:19: warning: unused variable 'lbl' [-Wunused-variable]
Widget lbl;
^~~
vibmenus.c:4937:19: warning: unused variable 'color' [-Wunused-variable]
Pixel color;
^~~~~
mv vibmenus.o vibmenus.glo
mv vibmenus.tmp vibmenus.o
mv vibprmpt.o vibprmpt.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibprmpt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibprmpt.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibprmpt.o vibprmpt.glo
mv vibprmpt.tmp vibprmpt.o
mv vibsbars.o vibsbars.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibsbars.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibsbars.c:128:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibsbars.o vibsbars.glo
mv vibsbars.tmp vibsbars.o
mv vibslate.o vibslate.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibslate.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibslate.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibslate.c: In function 'Nlm_EnableSlate':
vibslate.c:1199:18: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_DisableSlate':
vibslate.c:1254:18: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_SelectSlate':
vibslate.c:1515:5: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:1517:5: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SelectPanel':
vibslate.c:1544:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:1546:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (h, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateClick':
vibslate.c:2026:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_SlateTool h;
^
vibslate.c: In function 'Nlm_SlateClickCallback':
vibslate.c:2157:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2159:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateInputCallback':
vibslate.c:2313:7: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues(w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2315:7: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues(w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_SlateDrawCallback':
vibslate.c:2359:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNbackground, &color, 0);
^~~~~~~~~~~~~
vibslate.c:2361:3: warning: missing sentinel in function call [-Wformat=]
XtVaGetValues (w, XmNforeground, &color, 0);
^~~~~~~~~~~~~
vibslate.c: In function 'Nlm_Set3DColorMap':
vibslate.c:2686:17: warning: unused variable 'testvisual' [-Wunused-variable]
Boolean testvisual;
^~~~~~~~~~
vibslate.c:2685:13: warning: variable 'defaultdepth' set but not used [-Wunused-but-set-variable]
int defaultdepth;
^~~~~~~~~~~~
mv vibslate.o vibslate.glo
mv vibslate.tmp vibslate.o
mv vibtexts.o vibtexts.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibtexts.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibtexts.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibtexts.c: In function 'Nlm_TextCallback':
vibtexts.c:2982:24: warning: unused variable 'cbs' [-Wunused-variable]
XmAnyCallbackStruct *cbs = (XmAnyCallbackStruct *)call_data;
^~~
vibtexts.c: In function 'Nlm_LoseFocusCallback':
vibtexts.c:2999:25: warning: variable 'cbs' set but not used [-Wunused-but-set-variable]
XmAnyCallbackStruct *cbs;
^~~
vibtexts.c: In function 'Nlm_TabCallback':
vibtexts.c:3109:15: warning: variable 'event' set but not used [-Wunused-but-set-variable]
XKeyEvent *event;
^~~~~
vibtexts.c: In function 'Nlm_HiddenReturnCallback':
vibtexts.c:3122:15: warning: variable 'event' set but not used [-Wunused-but-set-variable]
XKeyEvent *event;
^~~~~
vibtexts.c: In function 'Nlm_HiddenActivateCallback':
vibtexts.c:3135:25: warning: variable 'cbs' set but not used [-Wunused-but-set-variable]
XmAnyCallbackStruct *cbs;
^~~
mv vibtexts.o vibtexts.glo
mv vibtexts.tmp vibtexts.o
mv vibutils.o vibutils.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibutils.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from vibutils.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibutils.o vibutils.glo
mv vibutils.tmp vibutils.o
mv vibwndws.o vibwndws.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibwndws.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibwndws.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibwndws.c: In function 'Nlm_SetColorMap':
vibwndws.c:1060:13: warning: variable 'defaultdepth' set but not used [-Wunused-but-set-variable]
int defaultdepth;
^~~~~~~~~~~~
vibwndws.c: In function 'Nlm_SetWindowTitle':
vibwndws.c:1567:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_GetWindowTitle':
vibwndws.c:1610:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_NewWindow':
vibwndws.c:2155:19: warning: variable 'screen_num' set but not used [-Wunused-but-set-variable]
int screen_num;
^~~~~~~~~~
vibwndws.c: In function 'Nlm_HideWindow':
vibwndws.c:2526:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowNormal':
vibwndws.c:2969:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowModal':
vibwndws.c:3014:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_ShowDocument':
vibwndws.c:3060:19: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
vibwndws.c: In function 'Nlm_VibMainPrelude':
vibwndws.c:6771:13: warning: unused variable 'retval' [-Wunused-variable]
Nlm_Int2 retval;
^~~~~~
vibwndws.c: In function 'Nlm_RemoveDyingWindows':
vibwndws.c:6893:20: warning: variable 'wptr' set but not used [-Wunused-but-set-variable]
Nlm_WindowTool wptr;
^~~~
At top level:
vibwndws.c:1318:16: warning: 'Nlm_StandardColormap' defined but not used [-Wunused-function]
static Boolean Nlm_StandardColormap(Colormap *cMap,
^~~~~~~~~~~~~~~~~~~~
mv vibwndws.o vibwndws.glo
mv vibwndws.tmp vibwndws.o
mv vibmain.o vibmain.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmain.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibmain.c:40:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibmain.c:121:1: warning: return type defaults to 'int' [-Wimplicit-int]
main (int argc, char *argv[])
^~~~
mv vibmain.o vibmain.glo
mv vibmain.tmp vibmain.o
mv ncbidraw.o ncbidraw.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL ncbidraw.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ncbidraw.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv ncbidraw.o ncbidraw.glo
mv ncbidraw.tmp ncbidraw.o
mv drawing.o drawing.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL drawing.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from drawing.c:128:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv drawing.o drawing.glo
mv drawing.tmp drawing.o
mv mapping.o mapping.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL mapping.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from mapping.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mapping.c: In function 'Nlm_MapRectToWorldBox':
mapping.c:139:8: warning: variable 'curScale' set but not used [-Wunused-but-set-variable]
Int4 curScale;
^~~~~~~~
mv mapping.o mapping.glo
mv mapping.tmp mapping.o
mv picture.o picture.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL picture.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbidraw.h:47,
from picture.c:100:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv picture.o picture.glo
mv picture.tmp picture.o
mv viewer.o viewer.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viewer.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from viewer.c:120:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv viewer.o viewer.glo
mv viewer.tmp viewer.o
mv document.o document.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL document.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from document.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
document.c: In function 'Nlm_PrintDocument':
document.c:4413:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
document.c:4417:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
mv document.o document.glo
mv document.tmp document.o
mv table.o table.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL table.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/panels.h:68,
from table.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv table.o table.glo
mv table.tmp table.o
mv palette.o palette.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL palette.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/panels.h:68,
from palette.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv palette.o palette.glo
mv palette.tmp palette.o
mv diagnost.o diagnost.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL diagnost.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from diagnost.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv diagnost.o diagnost.glo
mv diagnost.tmp diagnost.o
mv image.o image.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL image.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from image.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
image.c: In function 'ShiftXMask':
image.c:840:26: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
if(!((mask >> hi + low) & (unsigned long)1)) break;
~~~^~~~~
mv image.o image.glo
mv image.tmp image.o
mv pictur3d.o pictur3d.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL pictur3d.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/pictur3d.h:49,
from ../include/ppict3d.h:49,
from pictur3d.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pictur3d.c: In function 'Nlm_DeleteFromSeg':
pictur3d.c:114:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else seg->first = b->next;
^~~~
pictur3d.c:115:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if ( seg->last == b ) seg->last = bprev;
^~
mv pictur3d.o pictur3d.glo
mv pictur3d.tmp pictur3d.o
mv prim3d1.o prim3d1.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d1.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv prim3d1.o prim3d1.glo
mv prim3d1.tmp prim3d1.o
mv prim3d2.o prim3d2.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d2.c:65:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv prim3d2.o prim3d2.glo
mv prim3d2.tmp prim3d2.o
mv prim3d3.o prim3d3.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d3.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv prim3d3.o prim3d3.glo
mv prim3d3.tmp prim3d3.o
mv prim3d4.o prim3d4.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d4.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv prim3d4.o prim3d4.glo
mv prim3d4.tmp prim3d4.o
mv prim3d5.o prim3d5.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d5.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from prim3d5.c:66:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv prim3d5.o prim3d5.glo
mv prim3d5.tmp prim3d5.o
mv viewer3d.o viewer3d.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viewer3d.c
mv viewer3d.o viewer3d.glo
mv viewer3d.tmp viewer3d.o
mv vibmouse.o vibmouse.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmouse.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from vibmouse.c:67:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv vibmouse.o vibmouse.glo
mv vibmouse.tmp vibmouse.o
mv netscape.o netscape.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL netscape.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from netscape.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netscape.c: In function 'NS_Obtain_lock':
netscape.c:236:10: warning: variable 'waited' set but not used [-Wunused-but-set-variable]
Bool waited = False;
^~~~~~
mv netscape.o netscape.glo
mv netscape.tmp netscape.o
mv imagelst.o imagelst.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL imagelst.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/imagelst.h:52,
from imagelst.c:61:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv imagelst.o imagelst.glo
mv imagelst.tmp imagelst.o
mv treeview.o treeview.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL treeview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/treemgr.h:67,
from treeview.c:91:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv treeview.o treeview.glo
mv treeview.tmp treeview.o
mv shim3d.o shim3d.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL shim3d.c
shim3d.c: In function 'OGL_AddCylinder3D':
shim3d.c:906:14: warning: unused variable 'iCount' [-Wunused-variable]
Nlm_Int4 iCount;
^~~~~~
shim3d.c: In function 'OGL_AddText3D':
shim3d.c:1198:22: warning: unused variable 'i' [-Wunused-variable]
Nlm_Int4 Length, i;
^
shim3d.c: In function 'OGL_Zoom_DragMA':
shim3d.c:1758:16: warning: unused variable 'OGL_Data' [-Wunused-variable]
TOGL_Data *OGL_Data = MAToOGL(ma);
^~~~~~~~
shim3d.c: In function 'OGL_Hit':
shim3d.c:2053:37: warning: left shift count >= width of type [-Wshift-count-overflow]
ZMinName = ZMinName << (sizeof(GLuint) * 8);
^~
shim3d.c: In function 'write_row_callback':
shim3d.c:2899:15: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
float start, end;
^~~~~
shim3d.c:2899:22: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
float start, end;
^~~
shim3d.c: In function 'SetOGLFont':
shim3d.c:2369:64: warning: 'closest' may be used uninitialized in this function [-Wmaybe-uninitialized]
fontInfo = XLoadQueryFont(Nlm_currentXDisplay, list[closest]);
^
shim3d.c:2364:37: warning: 'mindiff' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ii == 0 || diff < mindiff) {
~~~~~^~~~~~~~~
shim3d.c:2369:64: warning: 'list' may be used uninitialized in this function [-Wmaybe-uninitialized]
fontInfo = XLoadQueryFont(Nlm_currentXDisplay, list[closest]);
^
shim3d.c: In function 'Nlm_AddHalfWorm3D':
shim3d.c:3454:26: warning: 'offset' may be used uninitialized in this function [-Wmaybe-uninitialized]
Nlm_Int4 i, j, k, m, offset;
^~~~~~
mv shim3d.o shim3d.glo
mv shim3d.tmp shim3d.o
mv odlbox.o odlbox.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL odlbox.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from odlbox.c:50:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
odlbox.c: In function 'LB_onVScroll':
odlbox.c:424:12: warning: variable 'IsGoUp' set but not used [-Wunused-but-set-variable]
Boolean IsGoUp=FALSE;
^~~~~~
mv odlbox.o odlbox.glo
mv odlbox.tmp odlbox.o
rm -f libvibrantOGL.a
ar cru libvibrantOGL.a vibbutns.glo vibextra.glo vibfiles.glo vibforms.glo vibgroup.glo viblists.glo vibmenus.glo vibprmpt.glo vibsbars.glo vibslate.glo vibtexts.glo vibutils.glo vibwndws.glo vibmain.glo ncbidraw.glo drawing.glo mapping.glo picture.glo viewer.glo document.glo table.glo palette.glo diagnost.glo image.glo pictur3d.glo prim3d1.glo prim3d2.glo prim3d3.glo prim3d4.glo prim3d5.glo viewer3d.glo vibmouse.glo netscape.glo imagelst.glo treeview.glo shim3d.glo odlbox.glo
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libvibrantOGL.a ../lib
ranlib ../lib/libvibrantOGL.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF accentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from accentr.c:297:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
accentr.c: In function 'EntrezBiostrucGet':
accentr.c:2113:17: warning: unused variable 'retval' [-Wunused-variable]
BiostrucPtr retval = NULL;
^~~~~~
accentr.c: In function 'EntrezGIForSeqIdFunc':
accentr.c:3283:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! gi) return OM_MSG_RET_OK;
^~
accentr.c:3285:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sip2 = ValNodeNew(NULL);
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF accutils.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from ../include/accutils.h:119,
from accutils.c:149:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rm -f libncbiacc.a
ar cru libncbiacc.a accentr.o accutils.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbiacc.a ../lib
ranlib ../lib/libncbiacc.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF drawseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from drawseq.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
drawseq.c: In function 'AddFlatNodeSymbol':
drawseq.c:811:7: warning: unused variable 'symbol_height' [-Wunused-variable]
Int4 symbol_height = 8;
^~~~~~~~~~~~~
drawseq.c: In function 'AddAlignBlocks':
drawseq.c:970:7: warning: variable 'c_num' set but not used [-Wunused-but-set-variable]
Int2 c_num;
^~~~~
drawseq.c: In function 'AddAlignFeature':
drawseq.c:1369:8: warning: unused variable 'ptype' [-Wunused-variable]
Uint1 ptype = 0;
^~~~~
drawseq.c: In function 'AddAlignmentMismatch':
drawseq.c:1523:7: warning: variable 'i_right' set but not used [-Wunused-but-set-variable]
Int4 i_right;
^~~~~~~
drawseq.c: In function 'DrawRestrictionMap':
drawseq.c:1811:10: warning: unused variable 'retval' [-Wunused-variable]
Boolean retval = FALSE;
^~~~~~
drawseq.c:1802:15: warning: variable 'center' set but not used [-Wunused-but-set-variable]
Int4 x1, x2, center;
^~~~~~
drawseq.c: In function 'DrawFeatures':
drawseq.c:2563:7: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Int2 entityID;
^~~~~~~~
drawseq.c: In function 'DrawOneSeqLoc':
drawseq.c:3020:10: warning: variable 'show_seq_label' set but not used [-Wunused-but-set-variable]
Boolean show_seq_label = TRUE; /*show the label of a sequence*/
^~~~~~~~~~~~~~
drawseq.c:3009:10: warning: variable 'ends' set but not used [-Wunused-but-set-variable]
Boolean ends;
^~~~
drawseq.c: In function 'Label_GData':
drawseq.c:3439:10: warning: variable 'success' set but not used [-Wunused-but-set-variable]
Boolean success = FALSE;
^~~~~~~
drawseq.c: In function 'DrawEquivAlign':
drawseq.c:3594:8: warning: unused variable 'my_gray_color' [-Wunused-variable]
Uint1 my_gray_color[]={63, 63, 63};
^~~~~~~~~~~~~
drawseq.c: In function 'load_align_label_rectangle':
drawseq.c:4352:10: warning: variable 'found_it' set but not used [-Wunused-but-set-variable]
Boolean found_it;
^~~~~~~~
drawseq.c: In function 'PicForAlignNode':
drawseq.c:4558:18: warning: variable 'min_scale' set but not used [-Wunused-but-set-variable]
Int4 max_width, min_scale;
^~~~~~~~~
At top level:
drawseq.c:3525:22: warning: 'get_ith_arp' defined but not used [-Wunused-function]
static AlignRangePtr get_ith_arp(AlignRangePtr arp, Int2 i)
^~~~~~~~~~~
drawseq.c:3511:18: warning: 'get_map_pos' defined but not used [-Wunused-function]
static MapPosPtr get_map_pos(MapLayoutPtr mlp, SeqIdPtr sip)
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF dotmatrx.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dotmatrx.h:47,
from dotmatrx.c:32:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF fea2seg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from fea2seg.c:74:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF fstyle.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from fstyle.c:55:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF smdlg1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from smdlg1.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF smdlg2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from smdlg2.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
smdlg2.c: In function 'Nlm_CreateDlgGroup':
smdlg2.c:631:12: warning: variable 'toAlign' set but not used [-Wunused-but-set-variable]
Handle toAlign[3];
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF smdlg3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from smdlg3.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF smtools.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from smtools.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF styleman.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from styleman.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF stylemui.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from stylemui.c:48:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF glbpic.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from glbpic.c:22:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
glbpic.c: In function 'label_linear_mark':
glbpic.c:1295:7: warning: unused variable 'tick_len' [-Wunused-variable]
Int4 tick_len = TICK_LEN;
^~~~~~~~
glbpic.c: In function 'add_alignment_to_global':
glbpic.c:1552:8: warning: variable 'p_val' set but not used [-Wunused-but-set-variable]
Uint1 p_val;
^~~~~
At top level:
glbpic.c:1748:16: warning: 'get_print_score' defined but not used [-Wunused-function]
static Boolean get_print_score(FloatHi min_score, FloatHi max_score, CharPtr label, Uint1 status)
^~~~~~~~~~~~~~~
glbpic.c:584:19: warning: 'extract_align_range' defined but not used [-Wunused-function]
static ValNodePtr extract_align_range(ValNodePtr PNTR arp_list, Uint1 displayOrder)
^~~~~~~~~~~~~~~~~~~
glbpic.c: In function 'get_circle_label_align':
glbpic.c:2349:9: warning: 'align' may be used uninitialized in this function [-Wmaybe-uninitialized]
return align;
^~~~~
glbpic.c: In function 'label_circle_mark':
glbpic.c:2479:6: warning: 'first_align' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(label_align)
^~~~~~
glbpic.c:2450:5: warning: 'p_align' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(label_align)
^~~~~~
glbpic.c:2474:26: warning: 'first_left' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(ABS(first_left - left) < (t_width +3))
^
glbpic.c:2469:28: warning: 'first_width' may be used uninitialized in this function [-Wmaybe-uninitialized]
t_width = (first_width + width)/2;
~~~~~~~~~~~~~^~~~~~~~
glbpic.c:2473:24: warning: 'first_top' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(ABS(first_top - top )< (font_height+3))
^
In file included from ../include/glbpic.h:7:0,
from glbpic.c:23:
glbpic.c: In function 'add_alignment_to_global':
../include/picture.h:520:22: warning: 'g_top' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddTextLabel Nlm_AddTextLabel
^~~~~~~~~~~~~~~~
glbpic.c:1560:7: note: 'g_top' was declared here
Int4 g_top, g_bottom;
^~~~~
glbpic.c: In function 'Draw_Global':
glbpic.c:2177:12: warning: 'seglen' may be used uninitialized in this function [-Wmaybe-uninitialized]
m_stop += seglen;
~~~~~~~^~~~~~~~~
glbpic.c:1943:8: note: 'seglen' was declared here
Int4 seglen;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF layout.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/maputil.h:113,
from ../include/jzcoll.h:123,
from ../include/layout.h:3,
from layout.c:2:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
layout.c: In function 'LayoutNodeFlat':
layout.c:326:24: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp, next, prev;
^~~~
layout.c: In function 'layout_uncompressed_group':
layout.c:1244:20: warning: variable 'group_stop' set but not used [-Wunused-but-set-variable]
Int2 group_start, group_stop;
^~~~~~~~~~
layout.c: In function 'LayoutFeatNode':
layout.c:1365:17: warning: variable 'y_next' set but not used [-Wunused-but-set-variable]
Int4 cur_line, y_next;
^~~~~~
layout.c:1364:17: warning: variable 'labelstyle' set but not used [-Wunused-but-set-variable]
Int4 segstyle, labelstyle;
^~~~~~~~~~
layout.c:1363:10: warning: variable 'show_trunc' set but not used [-Wunused-but-set-variable]
Boolean show_trunc = FALSE;
^~~~~~~~~~
layout.c:1350:10: warning: variable 'k' set but not used [-Wunused-but-set-variable]
Int2 i, k;
^
layout.c: In function 'LayoutAlignNode':
layout.c:2208:7: warning: unused variable 'num' [-Wunused-variable]
Int4 num = 0;
^~~
At top level:
layout.c:1779:16: warning: 'modify_master_line' defined but not used [-Wunused-function]
static Boolean modify_master_line(ValNodePtr vnp, Int4Ptr m_left, Int4Ptr m_right, Int4 maxScale, Uint1 label_align)
^~~~~~~~~~~~~~~~~~
layout.c: In function 'GroupFeatNode':
layout.c:636:14: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
prev->next = new;
~~~~~~~~~~~^~~~~
layout.c:594:35: note: 'prev' was declared here
ValNodePtr my_node = NULL, curr, prev, next;
^~~~
layout.c: In function 'OrderCdsmRNA':
layout.c:963:9: warning: 'm_missed' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(missed < m_missed)
^
layout.c:940:15: note: 'm_missed' was declared here
Int2 missed, m_missed; /*number of exons missed at both end*/
^~~~~~~~
layout.c: In function 'LayoutFeatNode':
layout.c:1503:12: warning: 'p_right' may be used uninitialized in this function [-Wmaybe-uninitialized]
p_right = MAX(right, p_right);
layout.c:1502:11: warning: 'p_left' may be used uninitialized in this function [-Wmaybe-uninitialized]
p_left = MIN(left, p_left);
layout.c:1504:14: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxHeight = MAX(height, maxHeight);
layout.c: In function 'LayoutAlignNode':
layout.c:2215:17: warning: 'next_line' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 cur_line, next_line;
^~~~~~~~~
layout.c:2251:7: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
i = find_align_line_number(anp, vnp->next,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
label_align, &next, &line_status_list, m_right, maxScale);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF saldist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from ../include/saldist.h:48,
from saldist.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
saldist.c: In function 'AAcode':
saldist.c:1003:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='A') return(1); if (car=='B') return(2);
^~
saldist.c:1003:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='A') return(1); if (car=='B') return(2);
^~
saldist.c:1004:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='C') return(3); if (car=='D') return(4);
^~
saldist.c:1004:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='C') return(3); if (car=='D') return(4);
^~
saldist.c:1005:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='E') return(5); if (car=='F') return(6);
^~
saldist.c:1005:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='E') return(5); if (car=='F') return(6);
^~
saldist.c:1006:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='G') return(7); if (car=='H') return(8);
^~
saldist.c:1006:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='G') return(7); if (car=='H') return(8);
^~
saldist.c:1007:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='I') return(9); if (car=='K') return(10);
^~
saldist.c:1007:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='I') return(9); if (car=='K') return(10);
^~
saldist.c:1008:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='L') return(11); if (car=='M') return(12);
^~
saldist.c:1008:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='L') return(11); if (car=='M') return(12);
^~
saldist.c:1009:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='N') return(13); if (car=='P') return(14);
^~
saldist.c:1009:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='N') return(13); if (car=='P') return(14);
^~
saldist.c:1010:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='Q') return(15); if (car=='R') return(16);
^~
saldist.c:1010:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='Q') return(15); if (car=='R') return(16);
^~
saldist.c:1011:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='S') return(17); if (car=='T') return(18);
^~
saldist.c:1011:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='S') return(17); if (car=='T') return(18);
^~
saldist.c:1012:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='V') return(19); if (car=='W') return(20);
^~
saldist.c:1012:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='V') return(19); if (car=='W') return(20);
^~
saldist.c:1013:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='X') return(21); if (car=='Y') return(22);
^~
saldist.c:1013:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='X') return(21); if (car=='Y') return(22);
^~
saldist.c:1014:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (car=='Z') return(23); if (car=='U') return(24);
^~
saldist.c:1014:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (car=='Z') return(23); if (car=='U') return(24);
^~
saldist.c: In function 'copy_string':
saldist.c:1289:12: warning: value computed is not used [-Wunused-value]
*from++;
^~~~~~~
saldist.c:1302:11: warning: value computed is not used [-Wunused-value]
*from++;
^~~~~~~
saldist.c: In function 'nss_ref_complength':
saldist.c:1479:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-')
^
saldist.c:1455:16: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c:1455:12: warning: variable 'c1' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c: In function 'nss_pw_complength':
saldist.c:1572:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-')
^
saldist.c:1547:16: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c:1547:12: warning: variable 'c1' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c: In function 'nss_gp_complength':
saldist.c:1675:21: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-')
^
saldist.c:1640:16: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c:1640:12: warning: variable 'c1' set but not used [-Wunused-but-set-variable]
c1, c2;
^~
saldist.c: In function 'SortbySimProc':
saldist.c:2139:31: warning: variable 'newsalpd' set but not used [-Wunused-but-set-variable]
SeqAlignPtr newsalp, newsalpd;
^~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from saldist.c:49:
saldist.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
saldist.c:1853:22: warning: 'scangp_calcul' defined but not used [-Wunused-function]
static Int4Ptr PNTR scangp_calcul (EditAlignDataPtr adp, Int2 seq1, Int2 seq2, Int4 from, Int4 to, Int2 group, Int2 choice, Int2 win_width)
^~~~~~~~~~~~~
saldist.c:1080:24: warning: 'FloatLomatrix' defined but not used [-Wunused-function]
static FloatLoPtr PNTR FloatLomatrix (Int2 nrows, Int2 ncol)
^~~~~~~~~~~~~
saldist.c:999:13: warning: 'AAcode' defined but not used [-Wunused-function]
static Int2 AAcode(Char car)
^~~~~~
saldist.c:928:16: warning: 'new_matrice' defined but not used [-Wunused-function]
static Boolean new_matrice (Int2 simmatrix, CharPtr path)
^~~~~~~~~~~
saldist.c:910:14: warning: 'matrixlst' defined but not used [-Wunused-variable]
static Char *matrixlst [] = {"", "idmat",
^~~~~~~~~
saldist.c: In function 'writematrixhalf.constprop':
saldist.c:1225:18: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp=vnp->next;
~~~^~~~~~~~~~
saldist.c: In function 'PwDistanceLongItem':
saldist.c:1151:18: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp=vnp->next;
~~~^~~~~~~~~~
saldist.c:1104:19: note: 'vnp' was declared here
ValNodePtr vnp,
^~~
saldist.c: In function 'SortbyLenItem':
saldist.c:2192:11: warning: 'mink' may be used uninitialized in this function [-Wmaybe-uninitialized]
lens [mink] = maxlens + 10;
^
saldist.c:2172:28: note: 'mink' was declared here
Int2 j, k, mink;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF saled.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/saledit.h:48,
from saled.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
saled.c: In function 'ReadAlignmentForSeqEntry':
saled.c:3325:21: warning: unused variable 'dirty' [-Wunused-variable]
dirty = FALSE;
^~~~~
saled.c:3321:21: warning: unused variable 'salp' [-Wunused-variable]
SeqAlignPtr salp=NULL,
^~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from saled.c:49:
saled.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from saled.c:55:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salfiles.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/saledit.h:48,
from ../include/salfiles.h:48,
from salfiles.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salfiles.c: In function 'NewFastaRead':
salfiles.c:315:30: warning: variable 'lastsegsip' set but not used [-Wunused-but-set-variable]
SeqIdPtr segsip=NULL, lastsegsip=NULL;
^~~~~~~~~~
salfiles.c: In function 'ReadAlignmentToStrings':
salfiles.c:664:16: warning: unused variable 'nseq' [-Wunused-variable]
Int2 nseq = 0;
^~~~
salfiles.c: In function 'MacawRead':
salfiles.c:1257:15: warning: unused variable 'vnp' [-Wunused-variable]
vnp = NULL;
^~~
salfiles.c: In function 'ReadLocalAlign':
salfiles.c:1370:14: warning: variable 'tmp1' set but not used [-Wunused-but-set-variable]
tmp1;
^~~~
salfiles.c: In function 'ImportFromFile':
salfiles.c:2072:20: warning: unused variable 'sep' [-Wunused-variable]
SeqEntryPtr sep = NULL;
^~~
salfiles.c:2071:20: warning: unused variable 'sap' [-Wunused-variable]
SeqAnnotPtr sap = NULL;
^~~
salfiles.c: In function 'FindSeqEntryForSeqIdCallback':
salfiles.c:2672:12: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (SeqIdForSameBioseq(cip->sip, sip))
^~
salfiles.c:2674:15: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cip->bsp = bsp;
^~~
salfiles.c: In function 'sesp_to_pept':
salfiles.c:2713:18: warning: unused variable 'bufferPtr' [-Wunused-variable]
bufferPtr = NULL;
^~~~~~~~~
salfiles.c: In function 'SaveFeatProc':
salfiles.c:3387:22: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salfiles.c: In function 'CCReadAnythingLoop':
salfiles.c:3685:16: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from salfiles.c:48:
salfiles.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
salfiles.c:501:19: warning: 'get_lens_fromseqalign' defined but not used [-Wunused-function]
static ValNodePtr get_lens_fromseqalign (SeqAlignPtr salp)
^~~~~~~~~~~~~~~~~~~~~
salfiles.c: In function 'CCDownloadProc':
salfiles.c:2218:7: warning: 'new_sep' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp = SeqEntryToSeqLoc (sep, &n, adp->mol_type);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salfiles.c:2286:15: note: 'new_sep' was declared here
SeqEntryPtr new_sep;
^~~~~~~
salfiles.c: In function 'NewFastaRead.constprop':
salfiles.c:460:6: warning: 'sip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (sip!=NULL)
^
salfiles.c: In function 'GapFastaRead':
salfiles.c:751:19: warning: 'seqstr' may be used uninitialized in this function [-Wmaybe-uninitialized]
seqstr [lgseq] = '\0';
^
salfiles.c:654:16: note: 'seqstr' was declared here
seqstr;
^~~~~~
salfiles.c:724:15: warning: 'startp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (!startp) {
^
salfiles.c:660:16: note: 'startp' was declared here
Boolean startp;
^~~~~~
salfiles.c: In function 'ReadLocalAlignment':
salfiles.c:1287:3: warning: 'seqvnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
ValNodeFree (seqvnp);
^~~~~~~~~~~~~~~~~~~~
salfiles.c:1113:19: note: 'seqvnp' was declared here
ValNodePtr vnp, seqvnp;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salpanel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/saledit.h:48,
from salpanel.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salpanel.c: In function 'go_to_next_to_draw':
salpanel.c:331:17: warning: statement with no effect [-Wunused-value]
offsettmp;
^~~~~~~~~
salpanel.c: In function 'next_to_draw':
salpanel.c:471:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if ( curstr != NULL )
^
salpanel.c: In function 'AssociatePropagatedSubloc':
salpanel.c:3131:16: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
salpanel.c: In function 'FeaturePropagateForm':
salpanel.c:4670:15: warning: variable 'ppt' set but not used [-Wunused-but-set-variable]
PrompT ppt;
^~~
salpanel.c:4665:15: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
salpanel.c: In function 'OkToContinueWithFeatureApply':
salpanel.c:6099:14: warning: unused variable 'num_missing' [-Wunused-variable]
Int4 num_missing = 0, seq_num, start_num;
^~~~~~~~~~~
salpanel.c: In function 'DoApplyFeatureToAlignment':
salpanel.c:6215:31: warning: unused variable 'found_null' [-Wunused-variable]
Boolean found_null = FALSE;
^~~~~~~~~~
salpanel.c: In function 'ApplyFeatureToAlignment':
salpanel.c:6417:31: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from salpanel.c:45:
salpanel.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from salpanel.c:52:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
salpanel.c:5055:13: warning: 'BatchApplyFeatureDetailsMessage' defined but not used [-Wunused-function]
static void BatchApplyFeatureDetailsMessage (DialoG d, Int2 mssg)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salpanel.c:224:13: warning: 'get_client_rectxy' defined but not used [-Wunused-function]
static void get_client_rectxy (PaneL p, RectPtr prc, Int2 x, Int2 y)
^~~~~~~~~~~~~~~~~
salpanel.c:113:14: warning: 'leftOvalFillSym' defined but not used [-Wunused-variable]
static Uint1 leftOvalFillSym [] = {
^~~~~~~~~~~~~~~
salpanel.c:110:14: warning: 'rightOvalFillSym' defined but not used [-Wunused-variable]
static Uint1 rightOvalFillSym [] = {
^~~~~~~~~~~~~~~~
salpanel.c:107:14: warning: 'leftOvalSym' defined but not used [-Wunused-variable]
static Uint1 leftOvalSym [] = {
^~~~~~~~~~~
salpanel.c:104:14: warning: 'rightOvalSym' defined but not used [-Wunused-variable]
static Uint1 rightOvalSym [] = {
^~~~~~~~~~~~
salpanel.c:101:14: warning: 'downTriFillSym' defined but not used [-Wunused-variable]
static Uint1 downTriFillSym [] = {
^~~~~~~~~~~~~~
salpanel.c:98:14: warning: 'upTriFillSym' defined but not used [-Wunused-variable]
static Uint1 upTriFillSym [] = {
^~~~~~~~~~~~
salpanel.c:89:14: warning: 'ovalFillSym' defined but not used [-Wunused-variable]
static Uint1 ovalFillSym [] = {
^~~~~~~~~~~
salpanel.c:86:14: warning: 'diamondFillSym' defined but not used [-Wunused-variable]
static Uint1 diamondFillSym [] = {
^~~~~~~~~~~~~~
salpanel.c:80:14: warning: 'downTriSym' defined but not used [-Wunused-variable]
static Uint1 downTriSym [] = {
^~~~~~~~~~
salpanel.c:77:14: warning: 'upTriSym' defined but not used [-Wunused-variable]
static Uint1 upTriSym [] = {
^~~~~~~~
salpanel.c:68:14: warning: 'ovalSym' defined but not used [-Wunused-variable]
static Uint1 ovalSym [] = {
^~~~~~~
salpanel.c:65:14: warning: 'diamondSym' defined but not used [-Wunused-variable]
static Uint1 diamondSym [] = {
^~~~~~~~~~
salpanel.c: In function 'draw_feat.isra.14.part.15':
salpanel.c:1939:17: warning: 'col1' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 col1;
^~~~
salpanel.c: In function 'on_draw':
salpanel.c:2527:23: warning: 'draw_diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
draw_seq (adp, curssp, from_inseq, drw_width, ptlh, curstr, draw_diff, masterstr, TRUE, itemsubtype, FALSE);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salparam.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from ../include/salparam.h:48,
from salparam.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salparam.c: In function 'mergelst':
salparam.c:1325:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Boolean val;
^~~
salparam.c: In function 'unmergelst':
salparam.c:1340:20: warning: variable 'dbdp' set but not used [-Wunused-but-set-variable]
DialogBoxDataPtr dbdp;
^~~~
salparam.c: In function 'FormulaDialog':
salparam.c:1398:36: warning: variable 'b5' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3, b4, b5;
^~
salparam.c: In function 'JK_NTPattern2Ex':
salparam.c:1596:19: warning: variable 'debug_str' set but not used [-Wunused-but-set-variable]
CharPtr debug_str;
^~~~~~~~~
salparam.c: In function 'DotPlotBtn':
salparam.c:1936:22: warning: variable 'status' set but not used [-Wunused-but-set-variable]
Int2 status;
^~~~~~
salparam.c: In function 'DotPlotDialog':
salparam.c:1973:20: warning: variable 'bt1' set but not used [-Wunused-but-set-variable]
ButtoN bt1, bt2;
^~~
salparam.c: In function 'DotPlotItem':
salparam.c:2004:22: warning: variable 'status' set but not used [-Wunused-but-set-variable]
Int2 status;
^~~~~~
salparam.c: In function 'SelectSeqFunc':
salparam.c:2308:20: warning: variable 'str' set but not used [-Wunused-but-set-variable]
CharPtr str;
^~~
salparam.c: In function 'HighlightSelectionFunc':
salparam.c:2344:22: warning: variable 'wdp' set but not used [-Wunused-but-set-variable]
SeqEditViewFormPtr wdp;
^~~
salparam.c: In function 'PropagateFeatureProc':
salparam.c:2623:25: warning: variable 'iID' set but not used [-Wunused-but-set-variable]
Uint2 eID, iID,
^~~
salparam.c:2614:20: warning: variable 'salp' set but not used [-Wunused-but-set-variable]
SeqAlignPtr salp;
^~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from salparam.c:49:
salparam.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from salparam.c:58:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
salparam.c: In function 'FileInProc':
salparam.c:782:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%d %ld", &n, &lens);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
salparam.c: In function 'DotPlotBtn':
salparam.c:1951:13: warning: 'sep' may be used uninitialized in this function [-Wmaybe-uninitialized]
bsp = (BioseqPtr) sep->data.ptrvalue;
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salsa.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salsa.h:48,
from salsa.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salsa.c: In function 'SelectSubsProc':
salsa.c:2140:23: warning: variable 'svpp' set but not used [-Wunused-but-set-variable]
SeqEditViewProcsPtr svpp=NULL;
^~~~
salsa.c: In function 'SetSeqInfo':
salsa.c:3195:17: warning: unused variable 'vnp' [-Wunused-variable]
ValNodePtr vnp = NULL;
^~~
salsa.c: In function 'SetupAlignDataSap':
salsa.c:3410:16: warning: variable 'entityID_sap' set but not used [-Wunused-but-set-variable]
Uint2 entityID_sap;
^~~~~~~~~~~~
salsa.c: In function 'get_bestpos_formerge':
salsa.c:4304:17: warning: variable 'insert_after' set but not used [-Wunused-but-set-variable]
insert_after=FALSE;
^~~~~~~~~~~~
salsa.c:4303:17: warning: variable 'insert_before' set but not used [-Wunused-but-set-variable]
Boolean insert_before=FALSE,
^~~~~~~~~~~~~
salsa.c: In function 'CreateSeqAlignViewForm':
salsa.c:4689:22: warning: variable 'mergebtn' set but not used [-Wunused-but-set-variable]
ButtoN mergebtn;
^~~~~~~~
salsa.c: In function 'AlgEditFunc':
salsa.c:4988:23: warning: unused variable 'wdp' [-Wunused-variable]
SeqEditViewFormPtr wdp = NULL;
^~~
salsa.c:4986:23: warning: unused variable 'w' [-Wunused-variable]
WindoW w = NULL;
^
salsa.c: In function 'OldAlignmentEditor':
salsa.c:5118:16: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Int2 rval;
^~~~
salsa.c: In function 'LaunchAnnotAlignEditor':
salsa.c:5305:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignEditor':
salsa.c:5322:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignViewer':
salsa.c:5339:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop':
salsa.c:5354:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop2':
salsa.c:5371:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop3':
salsa.c:5390:20: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop4':
salsa.c:5417:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
salsa.c: In function 'InsertSeqProc':
salsa.c:5587:17: warning: variable 'cnclbt' set but not used [-Wunused-but-set-variable]
ButtoN insbt, cnclbt;
^~~~~~
salsa.c:5585:10: warning: variable 'insprt' set but not used [-Wunused-but-set-variable]
PrompT insprt;
^~~~~~
salsa.c: In function 'SeqAlignBestHit':
salsa.c:5654:22: warning: variable 'last' set but not used [-Wunused-but-set-variable]
Int4 last;
^~~~
salsa.c: In function 'SeqAlignStartUpdate':
salsa.c:5839:22: warning: variable 'k' set but not used [-Wunused-but-set-variable]
Int2 index, k, j;
^
salsa.c:5838:15: warning: variable 'start' set but not used [-Wunused-but-set-variable]
start;
^~~~~
salsa.c:5837:15: warning: variable 'len_sum' set but not used [-Wunused-but-set-variable]
Int4 len_sum,
^~~~~~~
salsa.c:5834:15: warning: variable 'lenp' set but not used [-Wunused-but-set-variable]
Int4Ptr lenp,
^~~~
salsa.c:5833:15: warning: variable 'pre' set but not used [-Wunused-but-set-variable]
SeqIdPtr pre, sip, next;
^~~
salsa.c: In function 'CCNormalizeSeqAlignId':
salsa.c:6788:23: warning: unused variable 'gi' [-Wunused-variable]
Int4 gi = 0;
^~
salsa.c:6787:17: warning: unused variable 'missing_fmt' [-Wunused-variable]
CharPtr missing_fmt = "The alignment contains %s that can not be found in GenBank.\nPlease check the accession number.\n";
^~~~~~~~~~~
salsa.c:6786:17: warning: unused variable 'missing_cont_fmt' [-Wunused-variable]
CharPtr missing_cont_fmt = "The alignment contains %s that can not be found in GenBank.\nPlease check the accession number.\nContinue anyway?\n";
^~~~~~~~~~~~~~~~
salsa.c: In function 'ValidateSeqAlignandACCEx':
salsa.c:7145:16: warning: variable 'ans' set but not used [-Wunused-but-set-variable]
MsgAnswer ans;
^~~
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/salpanel.h:53,
from salsa.c:48:
salsa.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from salsa.c:68:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
salsa.c:87:13: warning: 'InsertSequenceDlg' declared 'static' but never defined [-Wunused-function]
static void InsertSequenceDlg (ButtoN b);
^~~~~~~~~~~~~~~~~
salsa.c:6021:13: warning: 'SWPrintFarpointerAln' defined but not used [-Wunused-function]
static void SWPrintFarpointerAln(SeqAlignPtr sap, FILE *fp)
^~~~~~~~~~~~~~~~~~~~
salsa.c:4884:16: warning: 'DeltaLitOnly' defined but not used [-Wunused-function]
static Boolean DeltaLitOnly (BioseqPtr bsp)
^~~~~~~~~~~~
salsa.c:2360:13: warning: 'MakeCdRgnrProc' defined but not used [-Wunused-function]
static void MakeCdRgnrProc (IteM i) {
^~~~~~~~~~~~~~
salsa.c:2356:13: warning: 'MakeCdRgnProc' defined but not used [-Wunused-function]
static void MakeCdRgnProc (IteM i) {
^~~~~~~~~~~~~
salsa.c:1760:13: warning: 'AcceptCloseWindowButton' defined but not used [-Wunused-function]
static void AcceptCloseWindowButton (ButtoN b)
^~~~~~~~~~~~~~~~~~~~~~~
In file included from salsa.c:52:0:
../include/salprop.h:50:16: warning: 'GBFeat' defined but not used [-Wunused-variable]
static CharPtr GBFeat[number_GBFeat] = {
^~~~~~
In file included from ../include/ncbi.h:65:0,
from ../include/salsa.h:48,
from salsa.c:43:
salsa.c: In function 'ExportFASTAForUnselectedUpdates':
../include/ncbifile.h:138:19: warning: 'fp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define FileClose Nlm_FileClose
^~~~~~~~~~~~~
salsa.c:6398:23: note: 'fp' was declared here
FILE *fp;
^~
In file included from ../include/ncbi.h:65:0,
from ../include/salsa.h:48,
from salsa.c:43:
salsa.c: In function 'ExportBadAlignments':
../include/ncbifile.h:138:19: warning: 'fp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define FileClose Nlm_FileClose
^~~~~~~~~~~~~
salsa.c:6366:23: note: 'fp' was declared here
FILE *fp;
^~
salsa.c: In function 'SeqAlignBestHit.isra.13':
salsa.c:5795:23: warning: 'nctr' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = nctr+beg+end;
~~~~^~~~
salsa.c:5795:27: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = nctr+beg+end;
~~~~~~~~^~~~
salsa.c:5795:23: warning: 'beg' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = nctr+beg+end;
~~~~^~~~
salsa.c: In function 'BioseqEditMsgFunc':
salsa.c:912:51: warning: 'anp' may be used uninitialized in this function [-Wmaybe-uninitialized]
ssp = SelStructNew (anp->seq_entityID, anp->bsp_itemID, OBJ_BIOSEQ, from, to, anp->sip, Seq_strand_plus, FALSE);
~~~^~~~~~~~~~~~
salsa.c:890:20: note: 'anp' was declared here
AlignNodePtr anp;
^~~
salsa.c: In function 'DeleteProc':
salsa.c:1955:165: warning: 'sap' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((adp->sap1_original && (FindSeqIdinSeqAlign ((SeqAlignPtr)adp->sap1_original->data, SeqLocId(slp))) > 0) || (FindSeqIdinSeqAlign ((SeqAlignPtr)sap->data, SeqLocId(slp))) > 0)
~~~^~~~~~
salsa.c: In function 'SkipThisWindowProc':
salsa.c:4591:6: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
LaunchAlignViewer(salp);
^~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqfltr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from seqfltr.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqfltr.c: In function 'FilterSeq':
seqfltr.c:259:21: warning: 'fptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
sgp->values = (Pointer) fptr;
~~~~~~~~~~~~^~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqgraph.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from seqgraph.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqgraph.c: In function 'EndPointDialogToEndPointValNode':
seqgraph.c:140:10: warning: 'eplist' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (Pointer) eplist;
^~~~~~~~~~~~~~~~
seqgraph.c: In function 'SeqLocGraphViewProc':
seqgraph.c:1155:17: warning: 'eplist' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (eplist->next == NULL)
~~~~~~^~~~~~
seqgraph.c: In function 'CutOffProc':
seqgraph.c:911:11: warning: 'fval' may be used uninitialized in this function [-Wmaybe-uninitialized]
val = fval/2;
~~~~^~~~~~~~
seqgraph.c:841:14: note: 'fval' was declared here
FloatHi fval;
^~~~
seqgraph.c:1050:20: warning: 'eplist' may be used uninitialized in this function [-Wmaybe-uninitialized]
eplist->next = NULL;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqgrphx.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from seqgrphx.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqgrphx.c:28:25: warning: 'MatrixMsgFunc' defined but not used [-Wunused-function]
static Int2 LIBCALLBACK MatrixMsgFunc (OMMsgStructPtr ommsp)
^~~~~~~~~~~~~
seqgrphx.c: In function 'FilterMsgFunc':
seqgrphx.c:224:12: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (s == NULL)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqmtrx.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from seqmtrx.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqmtrx.c: In function 'MatrixSeq':
seqmtrx.c:304:17: warning: 'matval' may be used uninitialized in this function [-Wmaybe-uninitialized]
*fptr = (FloatHi) matval;
^~~~~~~~~~~~~~~~
seqmtrx.c:284:14: note: 'matval' was declared here
Int4 matval, cutoff = 0;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqpcc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from seqpcc.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqpcc.c: In function 'PCCProc':
seqpcc.c:229:6: warning: 'pbsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((spp = SeqPortNew (pbsp, start, end, 0, Seq_code_iupacaa)) != NULL)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqanal.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from seqanal.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF aacomp.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from aacomp.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
aacomp.c:86:20: warning: 'AACGraph' defined but not used [-Wunused-function]
static SeqGraphPtr AACGraph (SeqPortPtr spp, Int4 start, Int4 end, Int4 window,
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqscrl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from ../include/seqscrl.h:4,
from seqscrl.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF valdlg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/vibforms.h:46,
from valdlg.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
valdlg.c: In function 'ClickRulesDoc':
valdlg.c:373:22: warning: unused variable 'scroll_pos' [-Wunused-variable]
Int2 scroll_pos = 0;
^~~~~~~~~~
valdlg.c:372:22: warning: unused variable 'sb_vert' [-Wunused-variable]
BaR sb_vert = NULL;
^~~~~~~
valdlg.c: In function 'UpdateRuleList':
valdlg.c:479:26: warning: unused variable 'last_cr' [-Wunused-variable]
CommentRulePtr new_cr, last_cr = NULL;
^~~~~~~
valdlg.c: In function 'SaveRuleChanges':
valdlg.c:540:23: warning: variable 'dlg' set but not used [-Wunused-but-set-variable]
CommentSetDlgPtr dlg;
^~~
valdlg.c: In function 'LaunchCommentRulesEditor':
valdlg.c:553:23: warning: unused variable 'm' [-Wunused-variable]
MenU m;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vsm.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/vsmpriv.h:48,
from vsm.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vsm.c: In function 'VSMDrawAbout':
vsm.c:1462:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (vsmp->title != NULL)
^~
vsm.c:1464:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (vsmp->aboutinfo != NULL)
^~
vsm.c: In function 'VSMAboutProc':
vsm.c:1492:8: warning: variable 'p' set but not used [-Wunused-but-set-variable]
PaneL p;
^
vsm.c: In function 'VSeqMgrCreateMainWindow':
vsm.c:1601:12: warning: variable 'omp' set but not used [-Wunused-but-set-variable]
ObjMgrPtr omp;
^~~
vsm.c: In function 'VSeqMgrPopulateMain':
vsm.c:1742:13: warning: variable 'atp' set but not used [-Wunused-but-set-variable]
AsnTypePtr atp;
^~~
vsm.c: In function 'VSMGatherPictProc':
vsm.c:2225:15: warning: variable 'bssp' set but not used [-Wunused-but-set-variable]
BioseqSetPtr bssp;
^~~~
vsm.c:2220:30: warning: variable 'bottom' set but not used [-Wunused-but-set-variable]
Int4 top, lineheight, left, bottom, width, maxwidth;
^~~~~~
vsm.c: In function 'VSMAddPictureToEntity':
vsm.c:2853:10: warning: variable 'ptr' set but not used [-Wunused-but-set-variable]
Pointer ptr;
^~~
vsm.c:2852:13: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vsmfile.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/vsmpriv.h:48,
from vsmfile.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vsmfile.c: In function 'VSMGenericBinAsnOpen':
vsmfile.c:259:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
vsmfile.c: In function 'VSMGenericFastaSave':
vsmfile.c:395:11: warning: variable 'code' set but not used [-Wunused-but-set-variable]
Uint1 code;
^~~~
vsmfile.c: In function 'VSMFastaProtSaveWithProduct':
vsmfile.c:527:11: warning: variable 'code' set but not used [-Wunused-but-set-variable]
Uint1 code;
^~~~
vsmfile.c: In function 'VSMSaveSetsAsFiles':
vsmfile.c:1365:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vsmutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from vsmutil.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vsmutil.c: In function 'GetDocPosForError':
vsmutil.c:1657:18: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Int2 val;
^~~
At top level:
vsmutil.c:1542:16: warning: 'MakeFieldReports' defined but not used [-Wunused-function]
static Boolean MakeFieldReports (ValNodePtr report_list, ValNodePtr field_list, FILE *fp)
^~~~~~~~~~~~~~~~
vsmutil.c:387:20: warning: 'GetSeqDescGivenIDs' defined but not used [-Wunused-function]
static SeqDescrPtr GetSeqDescGivenIDs (Uint2 entityID, Uint4 itemID, Uint2 itemtype)
^~~~~~~~~~~~~~~~~~
vsmutil.c: In function 'ContinueProc':
vsmutil.c:2157:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2156:5: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'RevalidateProc':
vsmutil.c:2124:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2123:5: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'SetVerbosityAndRepopulate':
vsmutil.c:2198:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2197:5: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'ClearValidateWindow':
vsmutil.c:613:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [sev] = 0;
~~~~~~~~~~~~~~~~~~^~~
vsmutil.c:612:7: note: within this loop
for (sev = SEV_NONE; sev <= SEV_MAX; sev++) {
^~~
vsmutil.c: In function 'CreateValidateWindowExExEx':
vsmutil.c:2521:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2520:9: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF udvgraph.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from ../include/udviewer.h:209,
from udvgraph.c:177:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
udvgraph.c: In function 'UDV_click_item':
udvgraph.c:877:9: warning: unused variable 'IsTransNeeded' [-Wunused-variable]
Boolean IsTransNeeded=FALSE;
^~~~~~~~~~~~~
udvgraph.c: In function 'UDV_SendBSPSelectMsg':
udvgraph.c:1230:13: warning: variable 'bDeselectAll' set but not used [-Wunused-but-set-variable]
Boolean bDeselectAll=TRUE;
^~~~~~~~~~~~
udvgraph.c:1226:30: warning: variable 'bsp_coord_old' set but not used [-Wunused-but-set-variable]
Int4 first_bsp_coord, bsp_coord_old,old_pos;
^~~~~~~~~~~~~
udvgraph.c: In function 'UDV_draw_helixDNA':
udvgraph.c:1827:15: warning: variable 'cyChar_2' set but not used [-Wunused-but-set-variable]
Int2 cxChar_2,cyChar_2;
^~~~~~~~
udvgraph.c: In function 'draw_logo':
udvgraph.c:1940:38: warning: variable 'cyGlobal' set but not used [-Wunused-but-set-variable]
Int2 pos,cxChar=7,cyChar=13,cxGlobal,cyGlobal;
^~~~~~~~
udvgraph.c: In function 'UDV_draw_CDS_minus':
udvgraph.c:2337:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
udvgraph.c:2332:5: warning: variable 'numivals2' set but not used [-Wunused-but-set-variable]
numivals2=0,
^~~~~~~~~
udvgraph.c: In function 'UDV_draw_CDS_plus':
udvgraph.c:2461:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
udvgraph.c: In function 'UDV_draw_panel':
udvgraph.c:4111:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(vdp->vgp->MasterViewer == SAMVIEWDDV)
^~
udvgraph.c:4113:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
Row = ViewMgr_GetRow(svpp, vdp->userkey);
^~~
udvgraph.c:4041:21: warning: unused variable 'vnp_seqinfo' [-Wunused-variable]
ValNodePtr vnp_seqinfo=NULL;
^~~~~~~~~~~
udvgraph.c:4035:45: warning: variable 'nLinesDraw' set but not used [-Wunused-but-set-variable]
Int4 decal_haut,from_row,to_row,nTotRow,nLinesDraw;
^~~~~~~~~~
udvgraph.c:4035:37: warning: variable 'nTotRow' set but not used [-Wunused-but-set-variable]
Int4 decal_haut,from_row,to_row,nTotRow,nLinesDraw;
^~~~~~~
At top level:
udvgraph.c:3921:14: warning: 'UDV_calc_decalRC' defined but not used [-Wunused-function]
static Int4 UDV_calc_decalRC(ValNodePtr ParaG,Int4 ScrollPos,
^~~~~~~~~~~~~~~~
udvgraph.c:3433:14: warning: 'UDV_Draw_features_label' defined but not used [-Wunused-function]
static void UDV_Draw_features_label(UnDViewerGraphDataPtr GrData,
^~~~~~~~~~~~~~~~~~~~~~~
udvgraph.c:1298:13: warning: 'UDV_AutoSelectAllSeq' defined but not used [-Wunused-function]
static void UDV_AutoSelectAllSeq(ViewerDialogDataPtr vdp,Boolean bSelect)
^~~~~~~~~~~~~~~~~~~~
udvgraph.c:971:14: warning: 'UDV_draw_horz_cursor' defined but not used [-Wunused-function]
static void UDV_draw_horz_cursor(UnDViewerGraphDataPtr GrData,
^~~~~~~~~~~~~~~~~~~~
udvgraph.c:948:13: warning: 'UDV_draw_vert_cursor' defined but not used [-Wunused-function]
static void UDV_draw_vert_cursor(RecT rcClip,PoinT pos)
^~~~~~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from udvgraph.c:180:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
udvgraph.c: In function 'UDV_GetCurrentDispRange':
udvgraph.c:638:15: warning: 'pgp' may be used uninitialized in this function [-Wmaybe-uninitialized]
*from_bsp=pgp->StartLetter;
~~~^~~~~~~~~~~~~
udvgraph.c: In function 'UDV_Draw_features':
udvgraph.c:3203:58: warning: 'idx6' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_draw_thin_line((Int2)(start_x+idx5),(Int2)(stop_x+idx6),y,
~~~~~~~^~~~~~
udvgraph.c:3203:38: warning: 'idx5' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_draw_thin_line((Int2)(start_x+idx5),(Int2)(stop_x+idx6),y,
~~~~~~~~^~~~~~
udvgraph.c:3196:47: warning: 'idx4' may be used uninitialized in this function [-Wmaybe-uninitialized]
stop2=_min_(pgp->StopLetter,context->ivals[idx4]);
^
udvgraph.c:3189:58: warning: 'idx3' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_draw_thin_line((Int2)(start_x+idx2),(Int2)(stop_x+idx3),y,
~~~~~~~^~~~~~
udvgraph.c:3189:38: warning: 'idx2' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_draw_thin_line((Int2)(start_x+idx2),(Int2)(stop_x+idx3),y,
~~~~~~~~^~~~~~
udvgraph.c:3182:49: warning: 'idx1' may be used uninitialized in this function [-Wmaybe-uninitialized]
start2=_max_(pgp->StartLetter,context->ivals[idx1]);
^
In file included from ../include/udviewer.h:225:0,
from udvgraph.c:177:
../include/udvdef.h:187:40: warning: 'stop_x2' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define _max_(a,b) ((a)>=(b)?(a):(b))
^
udvgraph.c:2803:21: note: 'stop_x2' was declared here
Int2 start_x,stop_x,stop_x2, /*id. but in pixels*/
^~~~~~~
udvgraph.c: In function 'UDV_ClickProc':
udvgraph.c:1461:8: warning: 'vmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_SelectFeatInFeatDlg(vmp,entityID,itemID);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF udvopen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from ../include/udviewer.h:209,
from udvopen.c:101:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
udvopen.c: In function 'UDV_FileOpen':
udvopen.c:875:16: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b,b1,b2;
^~
udvopen.c:875:11: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b,b1,b2;
^
udvopen.c: In function 'UDV_CreateListBioseqDlg':
udvopen.c:1180:9: warning: the address of 'szName' will always evaluate as 'true' [-Waddress]
if (szName){
^~~~~~
udvopen.c: In function 'UDV_FOpenCancelProc':
udvopen.c:792:23: warning: 'vmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_set_PullMenus(&vmp->MainMenu,TRUE);
^~~~~~~~~~~~~~
udvopen.c: In function 'UDV_analyze_SEP_for_open':
udvopen.c:325:15: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
vmp->entityID=entityID;
~~~~~~~~~~~~~^~~~~~~~~
udvopen.c:327:14: warning: 'dataptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
vmp->dataptr=dataptr;
~~~~~~~~~~~~^~~~~~~~
udvopen.c: In function 'UDV_FOpenAcceptProc':
udvopen.c:855:23: warning: 'vmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
UDV_set_PullMenus(&vmp->MainMenu,TRUE);
^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF udvpanel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from ../include/udviewer.h:209,
from udvpanel.c:197:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
udvpanel.c: In function 'UDV_GotoBtnProc':
udvpanel.c:2080:22: warning: variable 'old_ivalue' set but not used [-Wunused-but-set-variable]
Int4 iValue,old_ivalue,line_num,from_bsp,to_bsp,
^~~~~~~~~~
udvpanel.c:2079:15: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
udvpanel.c: In function 'CreateMainControls':
udvpanel.c:2165:8: warning: variable 'cxChar' set but not used [-Wunused-but-set-variable]
Int2 cxChar,cyChar,Margins;
^~~~~~
udvpanel.c: In function 'UDV_SearchFeatForKey':
udvpanel.c:3478:14: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1,b2;
^~
At top level:
udvpanel.c:2773:28: warning: 'FeaturesListBoxScan' defined but not used [-Wunused-function]
static Boolean LIBCALLBACK FeaturesListBoxScan (SeqFeatPtr sfp,
^~~~~~~~~~~~~~~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/udviewer.h:220,
from udvpanel.c:197:
udvpanel.c: In function 'InitFeaturesListDlg':
../include/vibdefns.h:315:19: warning: 'pop' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PopupItem Nlm_PopupItem
^~~~~~~~~~~~~
udvpanel.c:3194:7: note: 'pop' was declared here
PopuP pop;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF dotvibrant.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/dotviewer.h:15,
from dotvibrant.c:84:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dotvibrant.c: In function 'DOT_DisplayHits':
dotvibrant.c:564:18: warning: variable 'ycomp' set but not used [-Wunused-but-set-variable]
Int4 ycomp, xcomp;
^~~~~
dotvibrant.c: In function 'DOT_VscrlProc':
dotvibrant.c:918:16: warning: variable 'visLines' set but not used [-Wunused-but-set-variable]
Int2 visLines, vmargin, hmargin;
^~~~~~~~
dotvibrant.c: In function 'DOT_HscrlProc':
dotvibrant.c:972:20: warning: variable 'visLines' set but not used [-Wunused-but-set-variable]
Int2 dx, visLines, offset, hmargin, vmargin;
^~~~~~~~
dotvibrant.c: In function 'DOT_VCrossHairs':
dotvibrant.c:1402:10: warning: unused variable 'cursor_size' [-Wunused-variable]
Int4 cursor_size =15;
^~~~~~~~~~~
dotvibrant.c: In function 'DOT_HCrossHairs':
dotvibrant.c:1427:9: warning: unused variable 'cursor_size' [-Wunused-variable]
Int4 cursor_size = 15;
^~~~~~~~~~~
dotvibrant.c: In function 'DOT_MoveCrossHairs':
dotvibrant.c:1453:18: warning: variable 'data' set but not used [-Wunused-but-set-variable]
DOTSelDataPtr data;
^~~~
dotvibrant.c:1452:10: warning: unused variable 'cursor_size' [-Wunused-variable]
Int4 cursor_size = 15;
^~~~~~~~~~~
dotvibrant.c: In function 'DOT_DrawXAxis':
dotvibrant.c:1532:38: warning: unused variable 'title' [-Wunused-variable]
Char scale_buf[15] = {""}, title[50]={""}; /*scale value*/
^~~~~
dotvibrant.c: In function 'DOT_DrawYAxis':
dotvibrant.c:1642:38: warning: unused variable 'title' [-Wunused-variable]
Char scale_buf[15] = {""}, title[50]={""}; /*scale value*/
^~~~~
dotvibrant.c:1641:55: warning: variable 'Fh_4' set but not used [-Wunused-but-set-variable]
Int4 pos, ylen, x, y, scale_pos, i, j, Fh_2,Fh_4;
^~~~
dotvibrant.c: In function 'DOT_SVDisplayDiags':
dotvibrant.c:1770:28: warning: variable 'aln_diag' set but not used [-Wunused-but-set-variable]
Int4 diag, aln_diag;
^~~~~~~~
dotvibrant.c:1770:22: warning: variable 'diag' set but not used [-Wunused-but-set-variable]
Int4 diag, aln_diag;
^~~~
dotvibrant.c:1766:22: warning: variable 'width' set but not used [-Wunused-but-set-variable]
Int4 width, height;
^~~~~
dotvibrant.c:1765:31: warning: variable 'p_HFrom' set but not used [-Wunused-but-set-variable]
Int4 p_VFrom, p_HFrom;
^~~~~~~
dotvibrant.c:1765:22: warning: variable 'p_VFrom' set but not used [-Wunused-but-set-variable]
Int4 p_VFrom, p_HFrom;
^~~~~~~
dotvibrant.c:1762:28: warning: unused variable 'cutoff' [-Wunused-variable]
Int4 stop, cutoff=0, q_start, s_start, length;
^~~~~~
dotvibrant.c:1760:34: warning: variable 'seg3' set but not used [-Wunused-but-set-variable]
SegmenT seg1, seg2, seg3, seg4;
^~~~
dotvibrant.c: In function 'DOT_FillNewSeqBufs':
dotvibrant.c:2197:19: warning: unused variable 'alp' [-Wunused-variable]
DOTAlignInfoPtr alp=NULL;
^~~
dotvibrant.c: In function 'DOT_InitCInfo':
dotvibrant.c:2258:14: warning: unused variable 'colBuf' [-Wunused-variable]
Char colBuf[12]={""};
^~~~~~
dotvibrant.c: In function 'DOT_SVDisplaySequence':
dotvibrant.c:2379:16: warning: variable 'matrix' set but not used [-Wunused-but-set-variable]
Int4Ptr PNTR matrix;
^~~~~~
dotvibrant.c:2367:14: warning: variable 'vis_2' set but not used [-Wunused-but-set-variable]
Int4 vis_2, buf_len;
^~~~~
dotvibrant.c:2364:14: warning: unused variable 'prot_threshold' [-Wunused-variable]
Int4 prot_threshold=0, bloc_cntr;
^~~~~~~~~~~~~~
dotvibrant.c:2350:24: warning: variable 'mip2' set but not used [-Wunused-but-set-variable]
DOTMainDataPtr mip1, mip2;
^~~~
dotvibrant.c: In function 'DOT_SVClickProc':
dotvibrant.c:2807:17: warning: unused variable 'handled' [-Wunused-variable]
Int2 handled=0;
^~~~~~~
dotvibrant.c: In function 'DOT_ResizeFeatWindow':
dotvibrant.c:3016:63: warning: variable 'SubjectHeight' set but not used [-Wunused-but-set-variable]
Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw;
^~~~~~~~~~~~~
dotvibrant.c:3016:51: warning: variable 'QueryHeight' set but not used [-Wunused-but-set-variable]
Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw;
^~~~~~~~~~~
dotvibrant.c:3016:37: warning: variable 'gap' set but not used [-Wunused-but-set-variable]
Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw;
^~~
dotvibrant.c: In function 'DOT_ResizeSequenceWindow':
dotvibrant.c:3098:25: warning: variable 'is_visible2' set but not used [-Wunused-but-set-variable]
Boolean is_visible1, is_visible2;
^~~~~~~~~~~
dotvibrant.c:3098:12: warning: variable 'is_visible1' set but not used [-Wunused-but-set-variable]
Boolean is_visible1, is_visible2;
^~~~~~~~~~~
dotvibrant.c:3095:51: warning: variable 'V1Height' set but not used [-Wunused-but-set-variable]
Int2 height,width,gap,vsbWidth,in,hsbHeight,V1Height,V2Height, goHeight;
^~~~~~~~
dotvibrant.c: In function 'DOT_HideFeatDlg':
dotvibrant.c:3745:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
dotvibrant.c: In function 'DOT_SVBuildDiagViewer':
dotvibrant.c:4031:18: warning: variable 'mip' set but not used [-Wunused-but-set-variable]
DOTMainDataPtr mip;
^~~
dotvibrant.c:4029:28: warning: unused variable 'str2' [-Wunused-variable]
Char str1[41]={""}, str2[41]={""};
^~~~
dotvibrant.c:4029:13: warning: unused variable 'str1' [-Wunused-variable]
Char str1[41]={""}, str2[41]={""};
^~~~
dotvibrant.c:4022:18: warning: variable 'pr2' set but not used [-Wunused-but-set-variable]
PrompT pr1, pr2;
^~~
dotvibrant.c:4022:13: warning: variable 'pr1' set but not used [-Wunused-but-set-variable]
PrompT pr1, pr2;
^~~
dotvibrant.c: In function 'DOT_UpdateDataRects':
dotvibrant.c:4166:19: warning: variable 'dy' set but not used [-Wunused-but-set-variable]
Int4 comp, dx, dy, xstart, ystart;
^~
dotvibrant.c:4166:15: warning: variable 'dx' set but not used [-Wunused-but-set-variable]
Int4 comp, dx, dy, xstart, ystart;
^~
dotvibrant.c: In function 'DOT_MsgFunc':
dotvibrant.c:4215:17: warning: variable 'vdp2' set but not used [-Wunused-but-set-variable]
DOTVibDataPtr vdp2 = NULL;
^~~~
dotvibrant.c: In function 'DOT_ReleaseProc':
dotvibrant.c:4373:32: warning: unused variable 'yaxis_incr' [-Wunused-variable]
Boolean xaxis_incr=TRUE, yaxis_incr=TRUE;
^~~~~~~~~~
dotvibrant.c:4373:15: warning: unused variable 'xaxis_incr' [-Wunused-variable]
Boolean xaxis_incr=TRUE, yaxis_incr=TRUE;
^~~~~~~~~~
dotvibrant.c:4371:19: warning: variable 'alp' set but not used [-Wunused-but-set-variable]
DOTAlignInfoPtr alp=NULL;
^~~
dotvibrant.c:4370:18: warning: variable 'mip1' set but not used [-Wunused-but-set-variable]
DOTMainDataPtr mip1=NULL;
^~~~
dotvibrant.c: In function 'DOT_StartDOTPLOT':
dotvibrant.c:4891:23: warning: variable 'vdp' set but not used [-Wunused-but-set-variable]
DOTVibDataPtr vdp;
^~~
dotvibrant.c: In function 'DOT_DoZoom':
dotvibrant.c:5106:18: warning: variable 'data' set but not used [-Wunused-but-set-variable]
DOTSelDataPtr data;
^~~~
dotvibrant.c: In function 'DOT_ZoomProc':
dotvibrant.c:5204:23: warning: variable 'temport' set but not used [-Wunused-but-set-variable]
WindoW temport, w;
^~~~~~~
dotvibrant.c: In function 'AlnMgr2GetNextLine':
dotvibrant.c:5315:3: warning: value computed is not used [-Wunused-value]
*n++;
^~~~
dotvibrant.c: In function 'DOT_GetAlign':
dotvibrant.c:5332:44: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Int4 x1, y1, x2, y2, numlines=0, n=0, i=0;
^
dotvibrant.c: In function 'DOT_FillAlignInfoPointer':
dotvibrant.c:5565:16: warning: unused variable 'i' [-Wunused-variable]
Int4 i=0, n=0;
^
dotvibrant.c: In function 'DOT_Prob_FillAlignInfoPointer':
dotvibrant.c:5681:16: warning: unused variable 'i' [-Wunused-variable]
Int4 i=0, n=0;
^
dotvibrant.c:5680:16: warning: unused variable 'numsaps' [-Wunused-variable]
Int4 numsaps = 0, numlines = 0;
^~~~~~~
dotvibrant.c:5678:37: warning: unused variable 'sap_tmp' [-Wunused-variable]
SeqAlignPtr sap=NULL, salp=NULL, sap_tmp=NULL;
^~~~~~~
dotvibrant.c: In function 'DOT_DoBlast':
dotvibrant.c:5918:23: warning: unused variable 'eval' [-Wunused-variable]
Char eval[11]={""};
^~~~
dotvibrant.c:5917:23: warning: variable 'is_local' set but not used [-Wunused-but-set-variable]
Boolean is_local;
^~~~~~~~
dotvibrant.c:5915:23: warning: unused variable 'entityID' [-Wunused-variable]
Uint2 entityID=0;
^~~~~~~~
dotvibrant.c: In function 'DOT_CreateWindowDetails':
dotvibrant.c:6214:27: warning: variable 'pr2' set but not used [-Wunused-but-set-variable]
PrompT pr1, pr2;
^~~
dotvibrant.c:6214:22: warning: variable 'pr1' set but not used [-Wunused-but-set-variable]
PrompT pr1, pr2;
^~~
dotvibrant.c:6207:21: warning: variable 'g1' set but not used [-Wunused-but-set-variable]
GrouP g, g1, g2;
^~
dotvibrant.c: In function 'DOT_ResizeMainWindow':
dotvibrant.c:6273:35: warning: variable 'gap' set but not used [-Wunused-but-set-variable]
Int2 height, width, in , gap;
^~~
dotvibrant.c: In function 'DOT_FindAlignment':
dotvibrant.c:6662:29: warning: unused variable 'rb_fixed' [-Wunused-variable]
Boolean lt_fixed=FALSE, rb_fixed=FALSE;
^~~~~~~~
dotvibrant.c:6662:13: warning: unused variable 'lt_fixed' [-Wunused-variable]
Boolean lt_fixed=FALSE, rb_fixed=FALSE;
^~~~~~~~
dotvibrant.c:6661:17: warning: variable 'data' set but not used [-Wunused-but-set-variable]
DOTSelDataPtr data;
^~~~
dotvibrant.c: In function 'SCP_CompareOrderOrganizeBioseqs':
dotvibrant.c:6792:25: warning: variable 'itemID' set but not used [-Wunused-but-set-variable]
Uint4 itemID=0;
^~~~~~
dotvibrant.c: In function 'SCP_OrganizeAlnsInSet':
dotvibrant.c:6873:21: warning: variable 'indextype' set but not used [-Wunused-but-set-variable]
Int4 indextype;
^~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/alignmgr2.h:111,
from ../include/actutils.h:105,
from ../include/dotviewer.h:32,
from dotvibrant.c:84:
dotvibrant.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from ../include/dotviewer.h:32,
from dotvibrant.c:84:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
dotvibrant.c:6642:16: warning: 'DOT_DeselectPrim' defined but not used [-Wunused-function]
static Boolean DOT_DeselectPrim (SegmenT seg, PrimitivE prim, Uint2 segID,Uint2 primID, Uint2 primCt, VoidPtr userdata)
^~~~~~~~~~~~~~~~
dotvibrant.c:6346:13: warning: 'DOT_NewAnalysis' defined but not used [-Wunused-function]
static void DOT_NewAnalysis (ButtoN b)
^~~~~~~~~~~~~~~
dotvibrant.c:5894:16: warning: 'DOT_get_eval' defined but not used [-Wunused-function]
static FloatHi DOT_get_eval(Int4 exp)
^~~~~~~~~~~~
dotvibrant.c:5325:16: warning: 'DOT_GetAlign' defined but not used [-Wunused-function]
static Boolean DOT_GetAlign (DOTAlignInfoPtr alp)
^~~~~~~~~~~~
dotvibrant.c:5281:16: warning: 'AlnMgr2GetNextLine' defined but not used [-Wunused-function]
static Boolean AlnMgr2GetNextLine(SeqAlignPtr sap, AlnMsg2Ptr amp1, AlnMsg2Ptr amp2, Int4Ptr x1, Int4Ptr y1, Int4Ptr x2, Int4Ptr y2, Int4Ptr n)
^~~~~~~~~~~~~~~~~~
dotvibrant.c:4767:13: warning: 'DOT_FeatAnalysisProc' defined but not used [-Wunused-function]
static void DOT_FeatAnalysisProc(ButtoN b)
^~~~~~~~~~~~~~~~~~~~
dotvibrant.c:4749:13: warning: 'DOT_GetInfoProc' defined but not used [-Wunused-function]
static void DOT_GetInfoProc (IteM i)
^~~~~~~~~~~~~~~
dotvibrant.c:4213:25: warning: 'DOT_MsgFunc' defined but not used [-Wunused-function]
static Int2 LIBCALLBACK DOT_MsgFunc (OMMsgStructPtr ommsp)
^~~~~~~~~~~
dotvibrant.c:3688:13: warning: 'DOT_HideAcceptProc' defined but not used [-Wunused-function]
static void DOT_HideAcceptProc(ButtoN b)
^~~~~~~~~~~~~~~~~~
dotvibrant.c:3318:13: warning: 'DOT_AddFeatureToSegment' defined but not used [-Wunused-function]
static void DOT_AddFeatureToSegment(SeqMgrFeatContextPtr context,
^~~~~~~~~~~~~~~~~~~~~~~
dotvibrant.c:2954:13: warning: 'DOT_SVChangeLabels' defined but not used [-Wunused-function]
static void DOT_SVChangeLabels (GrouP g)
^~~~~~~~~~~~~~~~~~
dotvibrant.c:2760:16: warning: 'DOT_SVGetDiag' defined but not used [-Wunused-function]
static Boolean DOT_SVGetDiag (Uint2 segID, Uint2 primID, VoidPtr userdata)
^~~~~~~~~~~~~
dotvibrant.c: In function 'DOT_GetNthSeqFromAlign':
dotvibrant.c:5087:3: warning: 'spp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqPortFree(spp);
^~~~~~~~~~~~~~~~
dotvibrant.c: In function 'DOT_SVPopulateSequenceViewer':
dotvibrant.c:2611:19: warning: 'strand2' may be used uninitialized in this function [-Wmaybe-uninitialized]
DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dotvibrant.c:2380:23: note: 'strand2' was declared here
Uint1 strand1, strand2;
^~~~~~~
dotvibrant.c:2611:19: warning: 'strand1' may be used uninitialized in this function [-Wmaybe-uninitialized]
DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dotvibrant.c:2380:14: note: 'strand1' was declared here
Uint1 strand1, strand2;
^~~~~~~
dotvibrant.c:2560:45: warning: 'residue_names' may be used uninitialized in this function [-Wmaybe-uninitialized]
qBuf[c]=*residue_names[(int)*q];
^
dotvibrant.c:2378:16: note: 'residue_names' was declared here
CharPtr PNTR residue_names;
^~~~~~~~~~~~~
dotvibrant.c:2611:19: warning: 's_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dotvibrant.c:2370:42: note: 's_pos' was declared here
Int4 hit_start, hit_stop, q_pos, s_pos;
^~~~~
dotvibrant.c:2611:19: warning: 'q_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dotvibrant.c:2370:35: note: 'q_pos' was declared here
Int4 hit_start, hit_stop, q_pos, s_pos;
^~~~~
dotvibrant.c:2504:11: warning: 'hit_stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
hit_stop+=hit_stop/10;
~~~~~~~~^~~~~~~~~~~~~
dotvibrant.c:2370:25: note: 'hit_stop' was declared here
Int4 hit_start, hit_stop, q_pos, s_pos;
^~~~~~~~
dotvibrant.c:2570:26: warning: 'hit_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (hit_start<=i && i<=(hit_stop+bloc_size))
^
dotvibrant.c:2370:14: note: 'hit_start' was declared here
Int4 hit_start, hit_stop, q_pos, s_pos;
^~~~~~~~~
dotvibrant.c:2503:16: warning: 'buf_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
end=s+buf_len-1;
^
dotvibrant.c:2367:21: note: 'buf_len' was declared here
Int4 vis_2, buf_len;
^~~~~~~
dotvibrant.c:2545:18: warning: 'is_na' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (is_na)
^
dotvibrant.c:2361:27: note: 'is_na' was declared here
Boolean ambig=FALSE, is_na;
^~~~~
dotvibrant.c:2503:6: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
end=s+buf_len-1;
~~~^~~~~~~~~~~~
dotvibrant.c:2357:14: note: 's' was declared here
Uint1Ptr s;
^
dotvibrant.c:2626:16: warning: 'q' may be used uninitialized in this function [-Wmaybe-uninitialized]
q++;
~^~
dotvibrant.c:2356:14: note: 'q' was declared here
Uint1Ptr q;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF dlgutil1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from dlgutil1.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dlgutil1.c: In function 'IsAuthList':
dlgutil1.c:3008:8: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
dlgutil1.c: In function 'TestAuthorDialog':
dlgutil1.c:3357:20: warning: unused variable 'cp' [-Wunused-variable]
CharPtr cp;
^~
dlgutil1.c: In function 'TestIntervalEditor':
dlgutil1.c:5318:20: warning: variable 'fuzz_to' set but not used [-Wunused-but-set-variable]
Int2 fuzz_to;
^~~~~~~
dlgutil1.c:5317:20: warning: variable 'fuzz_from' set but not used [-Wunused-but-set-variable]
Int2 fuzz_from;
^~~~~~~~~
dlgutil1.c:5316:41: warning: variable 'fuzz_before' set but not used [-Wunused-but-set-variable]
Boolean isInterval, isPoint, fuzz_before, fuzz_after;
^~~~~~~~~~~
dlgutil1.c: In function 'CreateStandardEditMenu':
dlgutil1.c:9189:8: warning: variable 'i' set but not used [-Wunused-but-set-variable]
IteM i;
^
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from dlgutil1.c:55:
dlgutil1.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
dlgutil1.c:8378:25: warning: 'GetNthNameValuePair' defined but not used [-Wunused-function]
static NameValuePairPtr GetNthNameValuePair (Int4 n, ValNodePtr list)
^~~~~~~~~~~~~~~~~~~
dlgutil1.c:8061:16: warning: 'ParseSpecimenVoucherOk' defined but not used [-Wunused-function]
static Boolean ParseSpecimenVoucherOk (CharPtr str)
^~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF dlgutil2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from dlgutil2.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dlgutil2.c: In function 'CreateImportFields':
dlgutil2.c:1401:19: warning: variable 'is_gap' set but not used [-Wunused-but-set-variable]
Boolean is_gap = FALSE;
^~~~~~
dlgutil2.c: In function 'UpdateTableDisplayDialogScrollBars':
dlgutil2.c:3532:11: warning: variable 'y' set but not used [-Wunused-but-set-variable]
Int4 x, y;
^
dlgutil2.c:3532:8: warning: variable 'x' set but not used [-Wunused-but-set-variable]
Int4 x, y;
^
dlgutil2.c: In function 'GetTableDisplayCell':
dlgutil2.c:3931:8: warning: variable 'start_row' set but not used [-Wunused-but-set-variable]
Int4 start_row, start_col;
^~~~~~~~~
dlgutil2.c: In function 'NewCreateInferenceDialog':
dlgutil2.c:7600:19: warning: variable 'fnt' set but not used [-Wunused-but-set-variable]
FonT fnt;
^~~
dlgutil2.c: In function 'ClickableListOnKey':
dlgutil2.c:10202:20: warning: variable 'clp' set but not used [-Wunused-but-set-variable]
ClickableListPtr clp;
^~~
dlgutil2.c: In function 'GetSelectedClickableListText':
dlgutil2.c:10874:36: warning: variable 'char_offset' set but not used [-Wunused-but-set-variable]
Int2 item, row, col, char_offset;
^~~~~~~~~~~
dlgutil2.c: In function 'AutomatchFeatures':
dlgutil2.c:13840:36: warning: variable 's3' set but not used [-Wunused-but-set-variable]
SeqIntPtr s1, s2, s3;
^~
At top level:
dlgutil2.c:11993:16: warning: 'ParseMultiListQualOk' defined but not used [-Wunused-function]
static Boolean ParseMultiListQualOk (CharPtr val)
^~~~~~~~~~~~~~~~~~~~
dlgutil2.c:10059:13: warning: 'ClickClickableListItem' defined but not used [-Wunused-function]
static void ClickClickableListItem (DoC d, PoinT pt)
^~~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:10039:13: warning: 'DrawClickableListItem' defined but not used [-Wunused-function]
static void DrawClickableListItem (DoC d, RectPtr r, Int2 item, Int2 firstLine)
^~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:8577:13: warning: 'GetCategoryNumFromName' defined but not used [-Wunused-function]
static Int4 GetCategoryNumFromName (CharPtr category)
^~~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:1672:16: warning: 'GetNameForFeature' defined but not used [-Wunused-function]
static CharPtr GetNameForFeature (SeqFeatPtr sfp)
^~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF e2trmlst.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from e2trmlst.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
e2trmlst.c: In function 'ReadAFew':
e2trmlst.c:2230:61: warning: left-hand operand of comma expression has no effect [-Wunused-value]
for (row = 1, termPtr = e2TermListPtr->list; row <= *count, termPtr != NULL; row++, termPtr = termPtr->next) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF e2docsum.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from e2docsum.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
e2docsum.c: In function 'FormatCdsSeq':
e2docsum.c:1523:22: warning: variable 'gene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr gene = NULL;
^~~~
e2docsum.c: In function 'FetchSequence':
e2docsum.c:1591:16: warning: variable 'currDbName' set but not used [-Wunused-but-set-variable]
CharPtr currDbName;
^~~~~~~~~~
e2docsum.c:1580:16: warning: variable 'group_segs' set but not used [-Wunused-but-set-variable]
Uint1 group_segs = 0;
^~~~~~~~~~
e2docsum.c: In function 'SaveDocsumProject':
e2docsum.c:3606:16: warning: variable 'sfp' set but not used [-Wunused-but-set-variable]
SummFormPtr sfp;
^~~
e2docsum.c: In function 'RetrieveGeneration':
e2docsum.c:4135:19: warning: variable 'e2ip' set but not used [-Wunused-but-set-variable]
Entrez2InfoPtr e2ip;
^~~~
e2docsum.c: In function 'SetupMenus':
e2docsum.c:4849:16: warning: variable 'c' set but not used [-Wunused-but-set-variable]
ChoicE c;
^
In file included from ../include/sqnutils.h:51:0,
from ../include/dlogutil.h:50,
from ../include/bspview.h:48,
from e2docsum.c:53:
e2docsum.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strucapi.h:52:0,
from e2docsum.c:62:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
e2docsum.c: In function 'LaunchStructureViewer':
e2docsum.c:2981:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
e2docsum.c: In function 'LaunchSequin':
e2docsum.c:2838:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
e2docsum.c:2883:13: warning: 'GetBiostrucMaxModels' defined but not used [-Wunused-function]
static Int4 GetBiostrucMaxModels (void)
^~~~~~~~~~~~~~~~~~~~
e2docsum.c:2850:13: warning: 'GetBiostrucComplexity' defined but not used [-Wunused-function]
static Int4 GetBiostrucComplexity (void)
^~~~~~~~~~~~~~~~~~~~~
e2docsum.c:2154:20: warning: 'cddDocProcs' defined but not used [-Wunused-variable]
static DocPrntProc cddDocProcs [] = { Query_FetchDocSum, Query_FetchFields, FetchUid, NULL };
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF asn2graphic.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn2graphic.h:45,
from ../include/asn2graphicp.h:45,
from asn2graphic.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2graphic.c: In function 'ParseFilterItem':
asn2graphic.c:1191:21: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int2 i, j;
^
asn2graphic.c: In function 'GeneProductsLayoutInternal':
asn2graphic.c:3730:36: warning: variable 'featureStart' set but not used [-Wunused-but-set-variable]
Int4 newLeft, featureStart, rowMaxRight;
^~~~~~~~~~~~
asn2graphic.c: In function 'ScaleSntDrawProc':
asn2graphic.c:4401:28: warning: variable 'r' set but not used [-Wunused-but-set-variable]
RecT r;
^
asn2graphic.c: In function 'GphSentProc':
asn2graphic.c:4996:16: warning: variable 'scaleY' set but not used [-Wunused-but-set-variable]
Int4 scaleY;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from asn2graphic.c:46:
asn2graphic.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
asn2graphic.c: In function 'ProcessRows':
asn2graphic.c:4361:13: warning: 'SegmentTreeBot' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (! EnsureFeatureHasSegment (FPSP, featdeftype, SegmentTreeBot)) return 0;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2graphic.c:4353:24: warning: 'SegmentTreeMid' may be used uninitialized in this function [-Wmaybe-uninitialized]
SegmentTreeBot = CreateSegment (SegmentTreeMid, 0, 0);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2graphic.c:4349:24: warning: 'SegmentTreeTop' may be used uninitialized in this function [-Wmaybe-uninitialized]
SegmentTreeMid = CreateSegment (SegmentTreeTop , 0, 0);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF medview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/medview.h:48,
from medview.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
medview.c: In function 'PrintMedlineViewForm':
medview.c:588:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF bspview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from bspview.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from bspview.c:61:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from bspview.c:61:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from bspview.c:61:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from bspview.c:61:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gbfview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from gbfview.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gbfview.c: In function 'RelModeFailText':
gbfview.c:1004:22: warning: variable 'hasPubs' set but not used [-Wunused-but-set-variable]
Boolean hasPubs;
^~~~~~~
gbfview.c: In function 'PopulateFlatFile':
gbfview.c:1289:22: warning: variable 'doColors' set but not used [-Wunused-but-set-variable]
Boolean doColors;
^~~~~~~~
gbfview.c: In function 'PopulateFasta':
gbfview.c:1714:33: warning: left-hand operand of comma expression has no effect [-Wunused-value]
if (ISA_na (bsp->mol)) {TRUE,
^
gbfview.c:1646:20: warning: variable 'group_segs' set but not used [-Wunused-but-set-variable]
Uint1 group_segs;
^~~~~~~~~~
gbfview.c: In function 'PopulateAsnOrXML':
gbfview.c:1969:16: warning: variable 'lookupFar' set but not used [-Wunused-but-set-variable]
Boolean lookupFar = FALSE;
^~~~~~~~~
gbfview.c:1968:16: warning: variable 'lockFar' set but not used [-Wunused-but-set-variable]
Boolean lockFar = FALSE;
^~~~~~~
gbfview.c: In function 'PrintFlatFileFastaOrAsn':
gbfview.c:2491:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
gbfview.c: In function 'ReleaseIcon':
gbfview.c:667:21: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
gbfview.c:1231:13: warning: 'LookForFarProds' defined but not used [-Wunused-function]
static void LookForFarProds (
^~~~~~~~~~~~~~~
gbfview.c:1212:13: warning: 'LookForFarBsp' defined but not used [-Wunused-function]
static void LookForFarBsp (
^~~~~~~~~~~~~
gbfview.c:944:13: warning: 'LookForPubs' defined but not used [-Wunused-function]
static void LookForPubs (BioseqPtr bsp, Pointer userdata)
^~~~~~~~~~~
gbfview.c:289:16: warning: 'ColorIcon' defined but not used [-Wunused-function]
static Boolean ColorIcon (
^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gphview.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from gphview.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gphview.c: In function 'ReleaseAlignment':
gphview.c:1306:18: warning: variable 'slp' set but not used [-Wunused-but-set-variable]
SeqLocPtr slp;
^~~
gphview.c: In function 'DrawAlignOnAllSequences':
gphview.c:1391:10: warning: variable 'vn' set but not used [-Wunused-but-set-variable]
ValNode vn;
^~
gphview.c: In function 'ReleaseDesktop':
gphview.c:1836:18: warning: variable 'seg' set but not used [-Wunused-but-set-variable]
SegmenT seg;
^~~
gphview.c: In function 'AutoScrollGeneName':
gphview.c:2100:21: warning: variable 'num' set but not used [-Wunused-but-set-variable]
Int2 num;
^~~
gphview.c: In function 'DisplayGeneChoiceWindow':
gphview.c:2426:22: warning: variable 'p' set but not used [-Wunused-but-set-variable]
PrompT p;
^
gphview.c: In function 'PrintGraphical':
gphview.c:3268:14: warning: unused variable 'ans' [-Wunused-variable]
MsgAnswer ans;
^~~
gphview.c: In function 'PopulateAsn2GphGraphic':
gphview.c:3868:16: warning: variable 'min' set but not used [-Wunused-but-set-variable]
Int4 min;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gphdraw.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from gphdraw.c:59:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gphdraw.c: In function 'GraphSentProc':
gphdraw.c:195:18: warning: variable 'scaleY' set but not used [-Wunused-but-set-variable]
Int4 scaleY;
^~~~~~
gphdraw.c: In function 'DrawGraphToPanel':
gphdraw.c:453:27: warning: variable 'xp' set but not used [-Wunused-but-set-variable]
Int4Ptr xpoints, xp;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gxydraw.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from gxydraw.c:50:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gxydraw.c: In function 'DotXYPlot':
gxydraw.c:259:19: warning: 'xaxiscount' may be used uninitialized in this function [-Wmaybe-uninitialized]
gsp->xaxiscount = xaxiscount;
~~~~~~~~~~~~~~~~^~~~~~~~~~~~
gxydraw.c:182:19: note: 'xaxiscount' was declared here
Int4 xaxiscount, yaxiscount;
^~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gtrdraw.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from gtrdraw.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/vibrant.h:130:0,
from gtrdraw.c:53:
gtrdraw.c: In function 'TreeSentProc':
../include/vibdefns.h:655:20: warning: 'f' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define DeleteFont Nlm_DeleteFont
^~~~~~~~~~~~~~
gtrdraw.c:82:11: note: 'f' was declared here
FonT f, fx;
^
In file included from ../include/vibrant.h:130:0,
from gtrdraw.c:53:
../include/vibdefns.h:643:20: warning: 'fx' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SelectFont Nlm_SelectFont
^~~~~~~~~~~~~~
gtrdraw.c:82:14: note: 'fx' was declared here
FonT f, fx;
^~
In file included from ../include/vibrant.h:130:0,
from gtrdraw.c:53:
../include/vibdefns.h:623:21: warning: 'curB' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SelectColor Nlm_SelectColor
^~~~~~~~~~~~~~~
gtrdraw.c:83:23: note: 'curB' was declared here
Uint1 curR, curG, curB;
^~~~
In file included from ../include/vibrant.h:130:0,
from gtrdraw.c:53:
../include/vibdefns.h:623:21: warning: 'curG' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SelectColor Nlm_SelectColor
^~~~~~~~~~~~~~~
gtrdraw.c:83:17: note: 'curG' was declared here
Uint1 curR, curG, curB;
^~~~
In file included from ../include/vibrant.h:130:0,
from gtrdraw.c:53:
../include/vibdefns.h:623:21: warning: 'curR' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SelectColor Nlm_SelectColor
^~~~~~~~~~~~~~~
gtrdraw.c:83:11: note: 'curR' was declared here
Uint1 curR, curG, curB;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqpanel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqpanel.c: In function 'FillFeatureInfo':
seqpanel.c:427:18: warning: variable 'stop' set but not used [-Wunused-but-set-variable]
Int4 j, start, stop;
^~~~
seqpanel.c:427:11: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 j, start, stop;
^~~~~
seqpanel.c: In function 'DrawFeatureCodonLines':
seqpanel.c:1897:21: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
Char tmp[2];
^~~
seqpanel.c: In function 'DrawFeature':
seqpanel.c:2127:21: warning: variable 'prot_len' set but not used [-Wunused-but-set-variable]
Int4 prot_len;
^~~~~~~~
seqpanel.c: In function 'GetSeqChapterFeatureInfo':
seqpanel.c:3136:18: warning: variable 'stop' set but not used [-Wunused-but-set-variable]
Int4 j, start, stop;
^~~~
seqpanel.c:3136:11: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 j, start, stop;
^~~~~
seqpanel.c: In function 'onSeqEdVScrollBarSeqPanel':
seqpanel.c:3406:17: warning: variable 'totallines' set but not used [-Wunused-but-set-variable]
Int4 totallines;
^~~~~~~~~~
seqpanel.c: In function 'PrintFeature':
seqpanel.c:3812:28: warning: variable 'fRight' set but not used [-Wunused-but-set-variable]
Int4 fLeft, fRight, swap;
^~~~~~
seqpanel.c:3812:21: warning: variable 'fLeft' set but not used [-Wunused-but-set-variable]
Int4 fLeft, fRight, swap;
^~~~~
seqpanel.c: In function 'PrintTranslatedFrame':
seqpanel.c:3966:17: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
Char tmp[2];
^~~
seqpanel.c: In function 'ExportSequenceText':
seqpanel.c:4372:34: warning: pointer targets in passing argument 1 of 'complement_string' differ in signedness [-Wpointer-sign]
complement_string (file_line + SEQ_ED_PRINT_SEQ_OFFSET);
^~~~~~~~~
In file included from ../include/alignmgr2.h:112:0,
from seqpanel.c:39:
../include/salutil.h:78:20: note: expected 'Nlm_CharPtr {aka char *}' but argument is of type 'Nlm_Uint1Ptr {aka unsigned char *}'
NLM_EXTERN CharPtr complement_string (CharPtr str);
^~~~~~~~~~~~~~~~~
seqpanel.c:4236:17: warning: variable 'curr_para_strings' set but not used [-Wunused-but-set-variable]
ValNodePtr curr_para_strings = NULL;
^~~~~~~~~~~~~~~~~
seqpanel.c:4229:17: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
Uint1Ptr buf;
^~~
seqpanel.c: In function 'SeqEdOnClick':
seqpanel.c:4946:21: warning: variable 'direction' set but not used [-Wunused-but-set-variable]
Int4 direction;
^~~~~~~~~
seqpanel.c: In function 'SeqAlnOnDrag':
seqpanel.c:5685:34: warning: variable 'is_ctrl' set but not used [-Wunused-but-set-variable]
Boolean is_double_click, is_ctrl;
^~~~~~~
seqpanel.c:5685:17: warning: variable 'is_double_click' set but not used [-Wunused-but-set-variable]
Boolean is_double_click, is_ctrl;
^~~~~~~~~~~~~~~
seqpanel.c: In function 'ResizeSeqEdView':
seqpanel.c:5760:8: warning: variable 'sequence_pos' set but not used [-Wunused-but-set-variable]
Int4 sequence_pos = 0;
^~~~~~~~~~~~
seqpanel.c:5755:8: warning: variable 'height' set but not used [-Wunused-but-set-variable]
Int4 height, width;
^~~~~~
seqpanel.c: In function 'WriteAlignmentInterleaveToFileEx':
seqpanel.c:8664:22: warning: passing argument 1 of 'fputs' from incompatible pointer type [-Wincompatible-pointer-types]
fputs (fp, printed_line);
^~
In file included from ../include/ncbilcl.h:154:0,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
/usr/include/stdio.h:689:12: note: expected 'const char * restrict' but argument is of type 'FILE * {aka struct _IO_FILE *}'
extern int fputs (const char *__restrict __s, FILE *__restrict __stream);
^~~~~
seqpanel.c:8664:26: warning: passing argument 2 of 'fputs' from incompatible pointer type [-Wincompatible-pointer-types]
fputs (fp, printed_line);
^~~~~~~~~~~~
In file included from ../include/ncbilcl.h:154:0,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
/usr/include/stdio.h:689:12: note: expected 'FILE * restrict {aka struct _IO_FILE * restrict}' but argument is of type 'Nlm_CharPtr {aka char *}'
extern int fputs (const char *__restrict __s, FILE *__restrict __stream);
^~~~~
seqpanel.c: In function 'WriteAlignmentContiguousToFile':
seqpanel.c:8760:20: warning: passing argument 1 of 'fputs' from incompatible pointer type [-Wincompatible-pointer-types]
fputs (fp, printed_line);
^~
In file included from ../include/ncbilcl.h:154:0,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
/usr/include/stdio.h:689:12: note: expected 'const char * restrict' but argument is of type 'FILE * {aka struct _IO_FILE *}'
extern int fputs (const char *__restrict __s, FILE *__restrict __stream);
^~~~~
seqpanel.c:8760:24: warning: passing argument 2 of 'fputs' from incompatible pointer type [-Wincompatible-pointer-types]
fputs (fp, printed_line);
^~~~~~~~~~~~
In file included from ../include/ncbilcl.h:154:0,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
/usr/include/stdio.h:689:12: note: expected 'FILE * restrict {aka struct _IO_FILE * restrict}' but argument is of type 'Nlm_CharPtr {aka char *}'
extern int fputs (const char *__restrict __s, FILE *__restrict __stream);
^~~~~
seqpanel.c: In function 'ReverseSequenceStrandsInAlignment':
seqpanel.c:9007:17: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from seqpanel.c:39:
seqpanel.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
seqpanel.c:1171:16: warning: 'GetAlignmentColumnPercentIDsForAlignmentSection' defined but not used [-Wunused-function]
static double *GetAlignmentColumnPercentIDsForAlignmentSection (BioseqViewPtr bvp, Int4 line, Int4 aln_idx)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
seqpanel.c: In function 'SeqEdFindPatternDialog':
../include/vibdefns.h:505:22: warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AlignObjects Nlm_AlignObjects
^~~~~~~~~~~~~~~~
seqpanel.c:7632:25: note: 'g1' was declared here
GrouP h, g1, g2;
^~
In file included from ../include/ncbi.h:62:0,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/bspview.h:48,
from seqpanel.c:33:
seqpanel.c: In function 'PrintFeature':
../include/ncbistr.h:331:19: warning: 'str_prot' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringLen Nlm_StringLen
^~~~~~~~~~~~~
seqpanel.c:3810:21: note: 'str_prot' was declared here
CharPtr str_prot;
^~~~~~~~
seqpanel.c: In function 'SeqEdOnClick':
seqpanel.c:5026:10: warning: 'is_left_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (is_left_end)
^
seqpanel.c: In function 'SeqEdExportProc':
seqpanel.c:4353:13: warning: 'seq_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqEdPrintTextLineToFile ((CharPtr)file_line, from, to, seq_pos, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqpanel.c:4233:17: note: 'seq_pos' was declared here
Int4 seq_pos;
^~~~~~~
seqpanel.c: In function 'onDrawSeqPanel':
seqpanel.c:1301:24: warning: 'alnbuf' may be used uninitialized in this function [-Wmaybe-uninitialized]
MemCpy(buf, alnbuf + from, len);
~~~~~~~^~~~~~
seqpanel.c:2466:33: note: 'alnbuf' was declared here
Uint1Ptr buf, seqbuf, alnbuf;
^~~~~~
seqpanel.c:1252:3: warning: 'seqbuf' may be used uninitialized in this function [-Wmaybe-uninitialized]
AlignmentIntervalToString (tmp_salp, row, start, stop, bvp->TargetRow,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bvp->viewWholeEntity, seqbuf, alnbuf, &alnbuf_len,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bvp->showAlnSubstitutions);
~~~~~~~~~~~~~~~~~~~~~~~~~~
seqpanel.c:2466:25: note: 'seqbuf' was declared here
Uint1Ptr buf, seqbuf, alnbuf;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ingengraph.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from ../include/seqmgr.h:48,
from ../include/ingengraph.h:52,
from ingengraph.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ingengraph.c: In function 'Ing_BigEncodeIdxFeat':
ingengraph.c:262:2: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return *((Uint8Ptr) index_g);
^~~~~~
ingengraph.c: In function 'Ing_AddOneAlignToOverviewPage':
ingengraph.c:355:3: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
ingengraph.c:357:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
prim = AddRectangle(seg, start, (row)*(-20), stop, (row)*(-20)+j, NO_ARROW, FALSE,0);
^~~~
ingengraph.c:347:13: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp=NULL;
^~~
ingengraph.c: In function 'Ing_AddAlignsToOverviewPage':
ingengraph.c:372:18: warning: unused variable 'buf' [-Wunused-variable]
Char buf[41]={""};
^~~
ingengraph.c:367:18: warning: variable 'NewLine' set but not used [-Wunused-but-set-variable]
Boolean NewLine=FALSE;
^~~~~~~
ingengraph.c: In function 'Ing_DrawOverviewPage':
ingengraph.c:492:14: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
Int4 offset;
^~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/ingengraph.h:54,
from ingengraph.c:45:
../include/vibdefns.h:438:17: warning: unused variable 'Nlm_Visible' [-Wunused-variable]
#define Visible Nlm_Visible
^
ingengraph.c:488:14: note: in expansion of macro 'Visible'
Boolean Visible=FALSE;
^~~~~~~
ingengraph.c: In function 'Ing_PopOverviewPage':
ingengraph.c:715:16: warning: variable 'margin' set but not used [-Wunused-but-set-variable]
Int4 margin, len;
^~~~~~
ingengraph.c:714:16: warning: unused variable 'buf' [-Wunused-variable]
Char buf[50]={""};
^~~
ingengraph.c:708:16: warning: unused variable 'sanp' [-Wunused-variable]
SeqAnnotPtr sanp=NULL;
^~~~
ingengraph.c: In function 'Ing_AddAlignsToDetailedPage':
ingengraph.c:1097:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((start - offset - (label_len - feat_len)/2)<0)
^~
ingengraph.c:1099:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (bOver_the_edge)
^~
ingengraph.c: In function 'Ing_PopDetailedPage':
ingengraph.c:1437:16: warning: variable 'CurrentSeg' set but not used [-Wunused-but-set-variable]
SegmenT CurrentSeg=NULL;
^~~~~~~~~~
ingengraph.c: In function 'Ing_ExploreSegments':
ingengraph.c:1829:22: warning: unused variable 'isDraft' [-Wunused-variable]
Boolean isDraft = FALSE;
^~~~~~~
ingengraph.c:1827:22: warning: unused variable 'vnp' [-Wunused-variable]
ValNodePtr vnp = NULL;
^~~
ingengraph.c:1826:22: warning: unused variable 'gbp' [-Wunused-variable]
GBBlockPtr gbp = NULL;
^~~
ingengraph.c:1824:33: warning: variable 'black' set but not used [-Wunused-but-set-variable]
Uint1 orange[3], black[3];
^~~~~
ingengraph.c:1823:33: warning: variable 'lime' set but not used [-Wunused-but-set-variable]
Uint1 indigo[3], lime[3];
^~~~
ingengraph.c:1823:22: warning: variable 'indigo' set but not used [-Wunused-but-set-variable]
Uint1 indigo[3], lime[3];
^~~~~~
ingengraph.c: In function 'Ing_AddGCRect':
ingengraph.c:1933:17: warning: variable 'comp2' set but not used [-Wunused-but-set-variable]
FloatHi comp2, comp_prev;
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/ingengraph.h:63,
from ingengraph.c:45:
ingengraph.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
ingengraph.c:71:13: warning: 'Ing_GetNamesZoomedVal' declared 'static' but never defined [-Wunused-function]
static void Ing_GetNamesZoomedVal(VieweR vNames,Int4Ptr from, Int4Ptr to,
^~~~~~~~~~~~~~~~~~~~~
ingengraph.c:602:28: warning: 'Ing_CollectFeatures1' defined but not used [-Wunused-function]
static Boolean LIBCALLBACK Ing_CollectFeatures1(SeqFeatPtr sfp, SeqMgrFeatContextPtr sfc)
^~~~~~~~~~~~~~~~~~~~
ingengraph.c:583:24: warning: 'Ing_SortByChoice' defined but not used [-Wunused-function]
static int LIBCALLBACK Ing_SortByChoice (VoidPtr ptr1, VoidPtr ptr2)
^~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ingenext.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn2ff.h:113,
from ../include/ingenwin.h:58,
from ../include/ingenext.h:53,
from ingenext.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ingenext.c: In function 'Ing_KeepTheBestAlignments':
ingenext.c:167:20: warning: variable 'amaip' set but not used [-Wunused-but-set-variable]
AMAlignIndex2Ptr amaip = NULL;
^~~~~
ingenext.c: In function 'Ing_HandleQBlastResults':
ingenext.c:272:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, TRUE, TRUE, TRUE)){
^~~~~
ingenext.c: In function 'Ing_HandleResults':
ingenext.c:535:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, TRUE, TRUE, TRUE)){
^~~~~
ingenext.c: In function 'Ing_AccepttRNAargsProc':
ingenext.c:739:18: warning: unused variable 'paramlist' [-Wunused-variable]
ValNodePtr paramlist = NULL;
^~~~~~~~~
ingenext.c: In function 'Ing_tRNAscanProc':
ingenext.c:915:22: warning: unused variable 'moveMe' [-Wunused-variable]
ValNodePtr moveMe = NULL;
^~~~~~
ingenext.c:906:22: warning: unused variable 'first' [-Wunused-variable]
TexT first = NULL;
^~~~~
ingenext.c:902:22: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
ingenext.c:896:17: warning: unused variable 'args' [-Wunused-variable]
CharPtr args = NULL;
^~~~
ingenext.c: In function 'Ing_ReadtRNAConfigFile':
ingenext.c:1125:15: warning: variable 'demomode' set but not used [-Wunused-but-set-variable]
Boolean demomode = FALSE;
^~~~~~~~
ingenext.c: In function 'Ing_DoBlast2Seqs':
ingenext.c:1312:23: warning: variable 'is_local' set but not used [-Wunused-but-set-variable]
Boolean is_local, first_bsp=TRUE;
^~~~~~~~
ingenext.c: In function 'Ing_CreateDotMatrixForm':
ingenext.c:1834:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE))
^~~~~
ingenext.c: In function 'Ing_RunSpidey':
ingenext.c:1994:20: warning: unused variable 'sanp' [-Wunused-variable]
SeqAnnotPtr sanp = NULL;
^~~~
ingenext.c:1993:20: warning: unused variable 'spidp_next' [-Wunused-variable]
SPI_mRNAPtr spidp_next = NULL;
^~~~~~~~~~
ingenext.c:1992:20: warning: unused variable 'spidp_head' [-Wunused-variable]
SPI_mRNAPtr spidp_head = NULL;
^~~~~~~~~~
ingenext.c: In function 'Ing_ReadmRNAs_ext':
ingenext.c:2025:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE))
^~~~~
ingenext.c: In function 'Ing_DeleteInsertInGenomic':
ingenext.c:2522:16: warning: unused variable 'newsegs' [-Wunused-variable]
Int2 newsegs = 0, offset = 0;
^~~~~~~
ingenext.c: In function 'Ing_ReplaceAllMismatchedInLocation':
ingenext.c:2777:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (!All)
^~
ingenext.c:2781:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
SeqLocReplace(msip, mmis, mmis, mstrand, gsip, gmis, gmis, gstrand);
^~~~~~~~~~~~~
ingenext.c:2615:21: warning: unused variable 'str' [-Wunused-variable]
Char str[200] = {""};
^~~
ingenext.c:2612:22: warning: unused variable 'amaip' [-Wunused-variable]
AMAlignIndex2Ptr amaip = NULL;
^~~~~
ingenext.c: In function 'Ing_MismatchProc':
ingenext.c:3025:15: warning: unused variable 'sip' [-Wunused-variable]
SeqIdPtr sip = NULL;
^~~
ingenext.c: In function 'Ing_PrintSpideyReport':
ingenext.c:3471:27: warning: variable 'gmis' set but not used [-Wunused-but-set-variable]
Int4 mmis, gmis, miscount = 0;
^~~~
ingenext.c: In function 'Ing_PrintBlastReport':
ingenext.c:3853:18: warning: unused variable 'more' [-Wunused-variable]
Boolean more = FALSE;
^~~~
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/vibdefns.h:622:16: warning: variable 'Nlm_DkGray' set but not used [-Wunused-but-set-variable]
#define DkGray Nlm_DkGray
^
ingenext.c:3850:18: note: in expansion of macro 'DkGray'
Uint1 DkGray[3];
^~~~~~
ingenext.c: In function 'Ing_PopulateReport':
ingenext.c:4328:20: warning: unused variable 'sip' [-Wunused-variable]
SeqIdPtr sip=NULL;
^~~
ingenext.c:4324:20: warning: unused variable 'temp' [-Wunused-variable]
CharPtr temp = NULL;
^~~~
ingenext.c: In function 'Ing_ResizeReportWindow':
ingenext.c:4484:12: warning: variable 'hsb' set but not used [-Wunused-but-set-variable]
BaR hsb;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from ../include/ingenwin.h:60,
from ../include/ingenext.h:53,
from ingenext.c:46:
ingenext.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:135:0,
from ../include/ingenwin.h:62,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/objblst3.h:180:35: warning: 'Cutoff2_cutoff2Free' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr ));
^~~~~~~~~~~~~~~~~~~
../include/objblst3.h:181:35: warning: 'Cutoff2_cutoff2AsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:182:24: warning: 'Cutoff2_cutoff2AsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:199:33: warning: 'Cutoff_cutoffFree' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr ));
^~~~~~~~~~~~~~~~~
../include/objblst3.h:200:33: warning: 'Cutoff_cutoffAsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:201:24: warning: 'Cutoff_cutoffAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ingenext.c:130:13: warning: 'querytimercount' defined but not used [-Wunused-variable]
static Int4 querytimercount = 0;
^~~~~~~~~~~~~~~
ingenext.c:129:13: warning: 'querytimerlimit' defined but not used [-Wunused-variable]
static Int4 querytimerlimit = 100;
^~~~~~~~~~~~~~~
ingenext.c:59:28: warning: 'Ing_BlastCallback' defined but not used [-Wunused-function]
static Boolean LIBCALLBACK Ing_BlastCallback (BlastResponse *brp,
^~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:134:0,
from ../include/ingenwin.h:62,
from ../include/ingenext.h:53,
from ingenext.c:46:
../include/blstspc.h:229:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/blstspc.h:228:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/blstspc.h:227:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/blstspc.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "blstspc.h23";
^~~~~~~~~~~
ingenext.c: In function 'Ing_DoBlast2Seqs':
ingenext.c:1457:17: warning: 'e_head' may be used uninitialized in this function [-Wmaybe-uninitialized]
e_tmp->next=e_head;
~~~~~~~~~~~^~~~~~~
ingenext.c: In function 'Ing_MismatchProc':
ingenext.c:3170:32: warning: 'gstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
gstart = start + (stop - gstart);
~~~~~~^~~~~~~~~
ingenext.c:3206:23: warning: 'mstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
else if (mstart == R1 || mstart == R2 || mstart == R3){
~~~~~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ingenwin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn2ff.h:113,
from ../include/ingenwin.h:58,
from ingenwin.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ingenwin.c: In function 'Ing_PopulateDetailedPage':
ingenwin.c:134:22: warning: unused variable 'bSelected' [-Wunused-variable]
Boolean bSelected = FALSE;
^~~~~~~~~
ingenwin.c: In function 'Ing_DoRange':
ingenwin.c:394:22: warning: variable 'bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr bsp;
^~~
ingenwin.c: In function 'Ing_PopulateCpG':
ingenwin.c:576:19: warning: variable 'nchars' set but not used [-Wunused-but-set-variable]
Int2 cxChar, nchars;
^~~~~~
ingenwin.c: In function 'Ing_ResizeCpGWindow':
ingenwin.c:642:12: warning: variable 'hsb' set but not used [-Wunused-but-set-variable]
BaR hsb;
^~~
ingenwin.c: In function 'Ing_PopulateMotif':
ingenwin.c:718:26: warning: variable 'nchars' set but not used [-Wunused-but-set-variable]
Int2 cxChar, nchars;
^~~~~~
ingenwin.c:717:24: warning: variable 'swidth' set but not used [-Wunused-but-set-variable]
Int4 slen, swidth;
^~~~~~
ingenwin.c:717:18: warning: variable 'slen' set but not used [-Wunused-but-set-variable]
Int4 slen, swidth;
^~~~
ingenwin.c: In function 'Ing_ResizeMotifWindow':
ingenwin.c:785:12: warning: unused variable 'name' [-Wunused-variable]
CharPtr name = NULL;
^~~~
ingenwin.c:783:12: warning: variable 'hsb' set but not used [-Wunused-but-set-variable]
BaR hsb;
^~~
ingenwin.c: In function 'Ing_ShowComplexity':
ingenwin.c:1270:10: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
while ((Boolean)(slp_feat=SeqLocFindNext(slp_dust,slp_feat))){
^
ingenwin.c: In function 'Ing_CreateNewFeature':
ingenwin.c:1301:22: warning: unused variable 'rnatype' [-Wunused-variable]
Uint1 rnatype=0;
^~~~~~~
ingenwin.c: In function 'Ing_GetAlignmentIntervals':
ingenwin.c:1418:20: warning: unused variable 'master' [-Wunused-variable]
SeqIdPtr master = NULL;
^~~~~~
ingenwin.c: In function 'Ing_OldGetAlignmentIntervals':
ingenwin.c:1494:20: warning: unused variable 'master' [-Wunused-variable]
SeqIdPtr master = NULL;
^~~~~~
ingenwin.c: In function 'Ing_OldMakeLocListFromSAP':
ingenwin.c:1613:26: warning: unused variable 'slp2' [-Wunused-variable]
SeqLocPtr slp1 = NULL, slp2 = NULL;
^~~~
ingenwin.c:1613:13: warning: unused variable 'slp1' [-Wunused-variable]
SeqLocPtr slp1 = NULL, slp2 = NULL;
^~~~
ingenwin.c: In function 'Ing_OM_MsgFunc':
ingenwin.c:2380:15: warning: the address of 'sfc' will always evaluate as 'true' [-Waddress]
if (&sfc)
^
ingenwin.c:2284:22: warning: unused variable 'segID' [-Wunused-variable]
Uint2 segID=0;
^~~~~
ingenwin.c:2280:22: warning: unused variable 'sep' [-Wunused-variable]
SeqEntryPtr sep=NULL;
^~~
ingenwin.c:2271:31: warning: unused variable 'number' [-Wunused-variable]
Int4 score=0, number=0;
^~~~~~
ingenwin.c:2271:22: warning: unused variable 'score' [-Wunused-variable]
Int4 score=0, number=0;
^~~~~
ingenwin.c:2270:34: warning: unused variable 'n' [-Wunused-variable]
Int4 s1=0, s2=0, n=1;
^
ingenwin.c:2270:28: warning: unused variable 's2' [-Wunused-variable]
Int4 s1=0, s2=0, n=1;
^~
ingenwin.c:2270:22: warning: unused variable 's1' [-Wunused-variable]
Int4 s1=0, s2=0, n=1;
^~
ingenwin.c: In function 'Ing_MoveCursor':
ingenwin.c:2631:9: warning: variable 'grayClr2' set but not used [-Wunused-but-set-variable]
Uint1 grayClr2[3];
^~~~~~~~
ingenwin.c: In function 'Ing_FeatViewerClickProc':
ingenwin.c:2814:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (subSeg=FindSegPrim(v, pt, NULL, NULL, &prim)){
^~
ingenwin.c:2804:14: warning: unused variable 'slp' [-Wunused-variable]
SeqLocPtr slp=NULL;
^~~
ingenwin.c: In function 'Ing_SequenceClickProc':
ingenwin.c:2908:22: warning: variable 'ssp' set but not used [-Wunused-but-set-variable]
SelStructPtr ssp=NULL;
^~~
ingenwin.c: In function 'Ing_ReadInBlastAsn':
ingenwin.c:3077:19: warning: unused variable 'Report' [-Wunused-variable]
IngReportPtr Report=NULL;
^~~~~~
ingenwin.c:3075:19: warning: unused variable 'sip' [-Wunused-variable]
SeqIdPtr sip=NULL;
^~~
ingenwin.c:3074:19: warning: unused variable 'salp' [-Wunused-variable]
SeqAlignPtr salp=NULL;
^~~~
ingenwin.c:3073:19: warning: unused variable 'n_sap' [-Wunused-variable]
SeqAlignPtr n_sap=NULL;
^~~~~
ingenwin.c: In function 'Ing_ParseSeqIdFile':
ingenwin.c:3142:20: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp=NULL;
^~~
ingenwin.c: In function 'Ing_ReadInFeatureTable':
ingenwin.c:3194:20: warning: variable 'sanp' set but not used [-Wunused-but-set-variable]
SeqAnnotPtr sanp;
^~~~
ingenwin.c: In function 'Ing_AssembleGenscanInfo':
ingenwin.c:3258:17: warning: unused variable 'slp' [-Wunused-variable]
SeqLocPtr slp=NULL;
^~~
ingenwin.c: In function 'Ing_ReadInGenscan':
ingenwin.c:3300:33: warning: unused variable 'str' [-Wunused-variable]
CharPtr letter=NULL, str=NULL;
^~~
ingenwin.c:3300:20: warning: unused variable 'letter' [-Wunused-variable]
CharPtr letter=NULL, str=NULL;
^~~~~~
ingenwin.c:3298:33: warning: unused variable 'first_pass' [-Wunused-variable]
Boolean found=FALSE, first_pass=FALSE;
^~~~~~~~~~
ingenwin.c: In function 'Ing_AssembleTabDelimited':
ingenwin.c:3519:17: warning: variable 'score' set but not used [-Wunused-but-set-variable]
Int4 score;
^~~~~
ingenwin.c:3516:17: warning: unused variable 'tmp' [-Wunused-variable]
CharPtr tmp=NULL;
^~~
ingenwin.c: In function 'Ing_ReadInTabDelimited':
ingenwin.c:3659:40: warning: variable 'label_str' set but not used [-Wunused-but-set-variable]
CharPtr tmp=NULL, str=NULL, label_str=NULL;
^~~~~~~~~
ingenwin.c:3659:20: warning: unused variable 'tmp' [-Wunused-variable]
CharPtr tmp=NULL, str=NULL, label_str=NULL;
^~~
ingenwin.c:3653:20: warning: unused variable 'lip_tmp' [-Wunused-variable]
IngInfoPtr lip_tmp=NULL;
^~~~~~~
ingenwin.c:3650:20: warning: unused variable 'letter' [-Wunused-variable]
CharPtr letter=NULL;
^~~~~~
ingenwin.c: In function 'Ing_FileOpenSpecial':
ingenwin.c:3984:16: warning: unused variable 'Report' [-Wunused-variable]
IngReportPtr Report=NULL;
^~~~~~
ingenwin.c: In function 'Ing_FileOpenMain':
ingenwin.c:4078:21: warning: unused variable 'sep_orig' [-Wunused-variable]
SeqEntryPtr sep_orig=NULL, sep=NULL;
^~~~~~~~
ingenwin.c: In function 'Ing_ResizeMainWindow':
ingenwin.c:4187:25: warning: variable 'InfoHeight' set but not used [-Wunused-but-set-variable]
Int2 RulerHeight, InfoHeight;
^~~~~~~~~~
ingenwin.c: In function 'Ing_OpenFromFileORNetwork':
ingenwin.c:4491:25: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b,b2;
^~
ingenwin.c: In function 'Ing_EditFeature':
ingenwin.c:4640:22: warning: variable 'igvp' set but not used [-Wunused-but-set-variable]
IngGenomeViewerPtr igvp=NULL;
^~~~
ingenwin.c: In function 'Ing_MarkSeqAnnot':
ingenwin.c:4713:16: warning: unused variable 'bNoParent' [-Wunused-variable]
Boolean bNoParent = FALSE;
^~~~~~~~~
ingenwin.c: In function 'Ing_CreateMismatchedDialog':
ingenwin.c:4924:31: warning: 'main' is usually a function [-Wmain]
GrouP g, g1, g2, main;
^~~~
ingenwin.c: In function 'Ing_PropagateClickProc':
ingenwin.c:5064:22: warning: unused variable 'primID' [-Wunused-variable]
Uint2 primID=0;
^~~~~~
ingenwin.c:5063:22: warning: unused variable 'itemtype' [-Wunused-variable]
Uint2 itemtype=0;
^~~~~~~~
ingenwin.c:5062:22: warning: unused variable 'itemID' [-Wunused-variable]
Uint4 itemID=0;
^~~~~~
ingenwin.c:5061:22: warning: unused variable 'entityID' [-Wunused-variable]
Uint2 entityID=0;
^~~~~~~~
ingenwin.c:5060:22: warning: unused variable 'ssp' [-Wunused-variable]
SelStructPtr ssp=NULL;
^~~
ingenwin.c:5059:22: warning: unused variable 'igvp' [-Wunused-variable]
IngGenomeViewerPtr igvp=NULL;
^~~~
ingenwin.c: In function 'Ing_PrintCompProteins':
ingenwin.c:5146:32: warning: unused variable 'str2' [-Wunused-variable]
Char str1[200] = {""}, str2[10] = {""};
^~~~
ingenwin.c: In function 'Ing_PropagateReport':
ingenwin.c:5282:14: warning: variable 'ARROW' set but not used [-Wunused-but-set-variable]
Uint1 ARROW=NO_ARROW;
^~~~~
ingenwin.c:5279:14: warning: unused variable 'stringwidth' [-Wunused-variable]
Int4 stringwidth = 0;
^~~~~~~~~~~
ingenwin.c:5277:14: warning: unused variable 'left' [-Wunused-variable]
Int4 left = 10;
^~~~
ingenwin.c:5276:14: warning: variable 'prim' set but not used [-Wunused-but-set-variable]
PrimitivE prim;
^~~~
ingenwin.c: In function 'Ing_DoPropagate':
ingenwin.c:5596:14: warning: unused variable 'strErr' [-Wunused-variable]
Char strErr[50]={""};
^~~~~~
ingenwin.c: In function 'Ing_GetFromNetwork':
ingenwin.c:7518:11: warning: unused variable 'szAppName' [-Wunused-variable]
Char szAppName [10]={"Ingenue"};
^~~~~~~~~
ingenwin.c: In function 'Ing_SetupMainWindow':
ingenwin.c:7761:16: warning: unused variable 'szAppName' [-Wunused-variable]
Char szAppName [10]={"Ingenue"};
^~~~~~~~~
ingenwin.c:7760:48: warning: unused variable 'str2' [-Wunused-variable]
Char title[100]={""}, str1[20]={""}, str2[20]={""};
^~~~
ingenwin.c:7760:33: warning: unused variable 'str1' [-Wunused-variable]
Char title[100]={""}, str1[20]={""}, str2[20]={""};
^~~~
ingenwin.c:7760:16: warning: unused variable 'title' [-Wunused-variable]
Char title[100]={""}, str1[20]={""}, str2[20]={""};
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from ../include/ingenwin.h:60,
from ingenwin.c:45:
ingenwin.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ingenwin.c:45:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ingenwin.c:45:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ingenwin.c:45:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ingenwin.h:61,
from ingenwin.c:45:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:135:0,
from ../include/ingenwin.h:62,
from ingenwin.c:45:
../include/objblst3.h:180:35: warning: 'Cutoff2_cutoff2Free' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr ));
^~~~~~~~~~~~~~~~~~~
../include/objblst3.h:181:35: warning: 'Cutoff2_cutoff2AsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:182:24: warning: 'Cutoff2_cutoff2AsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:199:33: warning: 'Cutoff_cutoffFree' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr ));
^~~~~~~~~~~~~~~~~
../include/objblst3.h:200:33: warning: 'Cutoff_cutoffAsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:201:24: warning: 'Cutoff_cutoffAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ingenwin.c:7552:13: warning: 'Ing_ItemtoNetwork' defined but not used [-Wunused-function]
static void Ing_ItemtoNetwork(IteM i){
^~~~~~~~~~~~~~~~~
ingenwin.c:6717:13: warning: 'Ing_BspListProc' defined but not used [-Wunused-function]
static void Ing_BspListProc(IteM i)
^~~~~~~~~~~~~~~
ingenwin.c:5535:16: warning: 'Ing_KeywordAlreadyInList' defined but not used [-Wunused-function]
static Boolean Ing_KeywordAlreadyInList (ValNodePtr head, CharPtr kwd)
^~~~~~~~~~~~~~~~~~~~~~~~
ingenwin.c:1869:16: warning: 'Ing_DeSelectPrim' defined but not used [-Wunused-function]
static Boolean Ing_DeSelectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata)
^~~~~~~~~~~~~~~~
ingenwin.c:1610:18: warning: 'Ing_OldMakeLocListFromSAP' defined but not used [-Wunused-function]
static SeqLocPtr Ing_OldMakeLocListFromSAP(SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~~~~~~~~~
ingenwin.c:1487:23: warning: 'Ing_OldGetAlignmentIntervals' defined but not used [-Wunused-function]
static IngIvalInfoPtr Ing_OldGetAlignmentIntervals (SeqAlignPtr sap, Int4 from_row, Int4 to_row, Int4 from, Int4 to, Uint1 strand)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:134:0,
from ../include/ingenwin.h:62,
from ingenwin.c:45:
../include/blstspc.h:229:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/blstspc.h:228:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/blstspc.h:227:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/blstspc.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "blstspc.h23";
^~~~~~~~~~~
ingenwin.c: In function 'Ing_ReplaceMismatchedProc':
ingenwin.c:4902:3: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
Ing_ReplaceAllMismatchedInLocation(igvp, rmp->sap, start, stop, GetStatus(rmp->all), GetStatus(rmp->gaps), GetStatus(rmp->inserts));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ingenwin.c:4902:3: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
ingenwin.c: In function 'Ing_PropagateReport':
ingenwin.c:5224:12: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
last_pos = j;
~~~~~~~~~^~~
ingenwin.c:5137:17: note: 'j' was declared here
Int4 i, j, k, row;
^
ingenwin.c: In function 'Ing_FileOpenSpecial':
ingenwin.c:3290:12: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
slp_list=Ing_MakeSlpList(NULL, n/2, ivals, strand, igvp->bsp->id);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ingenwin.c:3255:17: note: 'strand' was declared here
Uint1 strand;
^~~~~~
ingenwin.c: In function 'Ing_KozakProc':
ingenwin.c:1048:6: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ans == ANS_NO)
^
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ingenwin.c:45:
../include/vibdefns.h:446:16: warning: 'ReportW' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Select Nlm_Select
^~~~~~~~~~
ingenwin.c:1006:22: note: 'ReportW' was declared here
WindoW ReportW;
^~~~~~~
ingenwin.c: In function 'Ing_SignalPeptideProc':
ingenwin.c:1099:6: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ans == ANS_NO)
^
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ingenwin.c:45:
../include/vibdefns.h:446:16: warning: 'ReportW' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Select Nlm_Select
^~~~~~~~~~
ingenwin.c:1057:22: note: 'ReportW' was declared here
WindoW ReportW;
^~~~~~~
ingenwin.c: In function 'Ing_RepeatsProc':
ingenwin.c:997:6: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ans == ANS_NO)
^
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ingenwin.c:45:
../include/vibdefns.h:446:16: warning: 'ReportW' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Select Nlm_Select
^~~~~~~~~~
ingenwin.c:955:22: note: 'ReportW' was declared here
WindoW ReportW;
^~~~~~~
ingenwin.c: In function 'Ing_PolyAProc':
ingenwin.c:946:6: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ans == ANS_NO)
^
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ingenwin.c:45:
../include/vibdefns.h:446:16: warning: 'ReportW' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Select Nlm_Select
^~~~~~~~~~
ingenwin.c:904:22: note: 'ReportW' was declared here
WindoW ReportW;
^~~~~~~
ingenwin.c: In function 'Ing_CpGProc':
ingenwin.c:895:6: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ans == ANS_NO)
^
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from ../include/ingenwin.h:64,
from ingenwin.c:45:
../include/vibdefns.h:446:16: warning: 'ReportW' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Select Nlm_Select
^~~~~~~~~~
ingenwin.c:857:22: note: 'ReportW' was declared here
WindoW ReportW;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF macrodlg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objseq.h:48,
from macrodlg.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
macrodlg.c: In function 'CloseMacroEditorWindowProc':
macrodlg.c:99:11: warning: unused variable 'do_remove' [-Wunused-variable]
Boolean do_remove = FALSE;
^~~~~~~~~
macrodlg.c: In function 'ExistingTextDialog':
macrodlg.c:1908:22: warning: variable 'ppt' set but not used [-Wunused-but-set-variable]
PrompT ppt;
^~~
macrodlg.c: In function 'SourceQualChoiceDialog':
macrodlg.c:3725:48: warning: variable 'b4' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3725:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3725:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3725:29: warning: variable 'b1' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c: In function 'SourceConstraintDialog':
macrodlg.c:3963:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:3963:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:3963:29: warning: variable 'b1' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c: In function 'CDSGeneProtQualConstraintDialog':
macrodlg.c:4277:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:4277:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:4277:29: warning: variable 'b1' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c: In function 'FeatureFieldTypeFromComplexConstraintType':
macrodlg.c:10273:3: warning: enumeration value 'eComplexConstraintType_seqid' not handled in switch [-Wswitch]
switch (constraint_type) {
^~~~~~
macrodlg.c:10273:3: warning: enumeration value 'eComplexConstraintType_string' not handled in switch [-Wswitch]
macrodlg.c:10273:3: warning: enumeration value 'eComplexConstraintType_loc' not handled in switch [-Wswitch]
macrodlg.c: In function 'TestApplyActionDialog':
macrodlg.c:12680:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'TestEditActionDialog':
macrodlg.c:12854:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'TestRemoveOutsideActionDialog':
macrodlg.c:13012:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'AddMacroActions':
macrodlg.c:19633:25: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE;
^~~~
macrodlg.c: In function 'PointerToSampleDialog':
macrodlg.c:19769:19: warning: variable 'max_char_per_line' set but not used [-Wunused-but-set-variable]
Int4 max_char_per_line;
^~~~~~~~~~~~~~~~~
macrodlg.c: In function 'SampleDialogCopy':
macrodlg.c:19889:53: warning: variable 'last_col' set but not used [-Wunused-but-set-variable]
Int2 start_col = 0, end_col = 0, first_col, last_col;
^~~~~~~~
macrodlg.c:19889:42: warning: variable 'first_col' set but not used [-Wunused-but-set-variable]
Int2 start_col = 0, end_col = 0, first_col, last_col;
^~~~~~~~~
macrodlg.c: In function 'SingleMacroAcceptButton':
macrodlg.c:21177:33: warning: variable 'num_features' set but not used [-Wunused-but-set-variable]
Int4 num_fields, num_features;
^~~~~~~~~~~~
macrodlg.c:21177:21: warning: variable 'num_fields' set but not used [-Wunused-but-set-variable]
Int4 num_fields, num_features;
^~~~~~~~~~
macrodlg.c: In function 'LaunchMacroTemplateEditor':
macrodlg.c:22877:23: warning: variable 'bfp' set but not used [-Wunused-but-set-variable]
BaseFormPtr bfp;
^~~
At top level:
macrodlg.c:9778:15: warning: 'LocOrStringConstraintDialog' defined but not used [-Wunused-function]
static DialoG LocOrStringConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
macrodlg.c: In function 'ApplyProductUpdateTableBtn':
macrodlg.c:26278:7: warning: 'lip' may be used uninitialized in this function [-Wmaybe-uninitialized]
FreeLog (lip);
^~~~~~~~~~~~~
macrodlg.c: In function 'RemoveSequencesActionDialog':
macrodlg.c:6490:15: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlg->dialog = (DialoG) p;
~~~~~~~~~~~~^~~~~~~~~~~~
macrodlg.c: In function 'ActionToSingleMacroActionForm':
macrodlg.c:21322:25: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 val, i;
^~~
In file included from ../include/vibrant.h:130:0,
from ../include/vibforms.h:46,
from macrodlg.c:48:
macrodlg.c: In function 'BuildEditMacroActionWindow':
../include/vibdefns.h:505:22: warning: 'indexer_only_group' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AlignObjects Nlm_AlignObjects
^~~~~~~~~~~~~~~~
macrodlg.c:14910:47: note: 'indexer_only_group' was declared here
GrouP p, g, parts_group, x, indexer_only_group;
^~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF biosrc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/biosrc.h:48,
from biosrc.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
biosrc.c: In function 'CreateBioSourceDialog':
biosrc.c:3506:18: warning: variable 'y' set but not used [-Wunused-but-set-variable]
PrompT y;
^
At top level:
biosrc.c:3182:26: warning: 'EnumListFromQualNameAssoc' defined but not used [-Wunused-function]
static EnumFieldAssocPtr EnumListFromQualNameAssoc (Nlm_QualNameAssocPtr qp)
^~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2991:16: warning: 'SubsourceDialogToSubSourcePtr' defined but not used [-Wunused-function]
static Pointer SubsourceDialogToSubSourcePtr (DialoG d)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2568:13: warning: 'SubSourcePtrToSubsourceDialog' defined but not used [-Wunused-function]
static void SubSourcePtrToSubsourceDialog (DialoG d, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2508:16: warning: 'OrgmodDialogToOrgModPtr' defined but not used [-Wunused-function]
static Pointer OrgmodDialogToOrgModPtr (DialoG d)
^~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2459:13: warning: 'OrgModPtrToOrgmodDialog' defined but not used [-Wunused-function]
static void OrgModPtrToOrgmodDialog (DialoG d, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cdrgn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/cdrgn.h:89,
from cdrgn.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cdrgn.c: In function 'ProductToSeqLocPtr':
cdrgn.c:1318:19: warning: variable 'rfp' set but not used [-Wunused-but-set-variable]
RnaFormPtr rfp = NULL;
^~~
cdrgn.c: In function 'CreateCodeBreakAlist':
cdrgn.c:1951:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
cdrgn.c: In function 'CodeBreakPtrToCodeBreakDialog':
cdrgn.c:2002:19: warning: variable 'aa' set but not used [-Wunused-but-set-variable]
Uint1 aa;
^~
cdrgn.c: In function 'PopulateAAPopup':
cdrgn.c:7044:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
At top level:
cdrgn.c:6854:13: warning: 'ConvertRnaRefNameToProductQual' defined but not used [-Wunused-function]
static void ConvertRnaRefNameToProductQual (SeqFeatPtr sfp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdrgn.c:6792:13: warning: 'RemoveQualByName' defined but not used [-Wunused-function]
static void RemoveQualByName (SeqFeatPtr sfp, CharPtr qual_name)
^~~~~~~~~~~~~~~~
cdrgn.c:6773:18: warning: 'FindOrAddQual' defined but not used [-Wunused-function]
static GBQualPtr FindOrAddQual (SeqFeatPtr sfp, CharPtr qual_name)
^~~~~~~~~~~~~
cdrgn.c:6330:15: warning: 'CreateMrnaUserObjectDialog' defined but not used [-Wunused-function]
static DialoG CreateMrnaUserObjectDialog (GrouP h, CharPtr label, SeqEntryPtr sep, BaseFormPtr bfp)
^~~~~~~~~~~~~~~~~~~~~~~~~~
cdrgn.c:6253:14: warning: 'check_rna_type' defined but not used [-Wunused-function]
static Uint1 check_rna_type (Uint1 type)
^~~~~~~~~~~~~~
cdrgn.c:2174:13: warning: 'AccessionToGi' defined but not used [-Wunused-function]
static Int4 AccessionToGi (CharPtr string)
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF import.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/import.h:48,
from import.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF pubdesc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/pubdesc.h:48,
from pubdesc.c:44:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pubdesc.c: In function 'SetPubdescImportExportItems':
pubdesc.c:2859:37: warning: comparison between pointer and integer
&&& pfp->currentPage == 1) {
^~
pubdesc.c: In function 'MakeReplaceAuthorsForm':
pubdesc.c:4289:24: warning: variable 'pepp' set but not used [-Wunused-but-set-variable]
PubdescEditProcsPtr pepp;
^~~~
pubdesc.c: In function 'DisplayDocSum':
pubdesc.c:4851:9: warning: variable 'lineheight' set but not used [-Wunused-but-set-variable]
Int2 lineheight;
^~~~~~~~~~
At top level:
pubdesc.c:5363:13: warning: 'Quit' defined but not used [-Wunused-function]
static void Quit (ButtoN b)
^~~~
pubdesc.c:5099:14: warning: 'AddAll' defined but not used [-Wunused-function]
static void AddAll(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st)
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqsub.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from ../include/seqsub.h:58,
from seqsub.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqsub.c: In function 'SeqSubmitFromTemplateEditor':
seqsub.c:3250:20: warning: variable 'omdp' set but not used [-Wunused-but-set-variable]
ObjMgrDataPtr omdp;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mapgene.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from mapgene.c:2:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mapgene.c: In function 'load_new_align':
mapgene.c:79:17: warning: variable 'match_slp' set but not used [-Wunused-but-set-variable]
SeqLocPtr slp, match_slp, t_slp;
^~~~~~~~~
mapgene.c: In function 'figure_loc_by_position':
mapgene.c:1039:20: warning: variable 'center' set but not used [-Wunused-but-set-variable]
Int4 start, stop, center;
^~~~~~
mapgene.c: In function 'cvt_loc_for_single_gene':
mapgene.c:1958:29: warning: variable 'p_align_offset' set but not used [-Wunused-but-set-variable]
Int4 offset, align_offset, p_align_offset;
^~~~~~~~~~~~~~
mapgene.c:1957:7: warning: unused variable 'shift' [-Wunused-variable]
Int4 shift = 0;
^~~~~
mapgene.c: In function 'print_header_for_center':
mapgene.c:2693:10: warning: variable 'link' set but not used [-Wunused-but-set-variable]
CharPtr link;
^~~~
mapgene.c: In function 'PrintGeneticMarkerForOneMap':
mapgene.c:3635:10: warning: variable 'link' set but not used [-Wunused-but-set-variable]
CharPtr link;
^~~~
At top level:
mapgene.c:3207:16: warning: 'convert_center_name_to_gifname' defined but not used [-Wunused-function]
static Boolean convert_center_name_to_gifname (CharPtr center_name, CharPtr gif_name)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mapgene.c:1788:13: warning: 'adjust_slp_list' defined but not used [-Wunused-function]
static void adjust_slp_list(ValNodePtr slp_list)
^~~~~~~~~~~~~~~
mapgene.c:1748:16: warning: 'merge_slp_list' defined but not used [-Wunused-function]
static Boolean merge_slp_list(ValNodePtr PNTR gene_slp_list, ValNodePtr slp_list)
^~~~~~~~~~~~~~
mapgene.c:1280:13: warning: 'change_anchor_to_front' defined but not used [-Wunused-function]
static void change_anchor_to_front(ValNodePtr msp_list, SeqIdPtr anchor_id)
^~~~~~~~~~~~~~~~~~~~~~
mapgene.c:200:13: warning: 'get_center_pointer' defined but not used [-Wunused-function]
static Int4 get_center_pointer(SeqLocPtr slp)
^~~~~~~~~~~~~~~~~~
mapgene.c:27:13: warning: 'print_this_id' defined but not used [-Wunused-function]
static void print_this_id (SeqIdPtr sip)
^~~~~~~~~~~~~
mapgene.c: In function 'PrintContigForOneMap':
mapgene.c:3181:4: warning: 'yac_num' may be used uninitialized in this function [-Wmaybe-uninitialized]
PrintHTMLContigAlign(band_name, contig_name, anp_list, fp, db, fish_list, yac_list, yac_num);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mapgene.c:3152:7: note: 'yac_num' was declared here
Int4 yac_num;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF prtgene.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/tofile.h:66,
from ../include/prtgene.h:3,
from prtgene.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
prtgene.c: In function 'print_sfp_ext':
prtgene.c:108:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(ufp->choice == 2) /*integer */
^~
prtgene.c:110:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
print_store_buf(temp, buf, buf_size, &len, fp);
^~~~~~~~~~~~~~~
prtgene.c: In function 'print_store_for_html':
prtgene.c:749:7: warning: variable 'white_sp' set but not used [-Wunused-but-set-variable]
Char white_sp;
^~~~~~~~
rm -f libncbidesk.a
ar cru libncbidesk.a drawseq.o dotmatrx.o fea2seg.o fstyle.o smdlg1.o smdlg2.o smdlg3.o smtools.o styleman.o stylemui.o glbpic.o layout.o saldist.o saled.o salfiles.o salpanel.o salparam.o salsa.o seqfltr.o seqgraph.o seqgrphx.o seqmtrx.o seqpcc.o seqanal.o aacomp.o seqscrl.o valdlg.o vsm.o vsmfile.o vsmutil.o udvgraph.o udvopen.o udvpanel.o dotvibrant.o dlgutil1.o dlgutil2.o e2trmlst.o e2docsum.o asn2graphic.o medview.o bspview.o gbfview.o gphview.o gphdraw.o gxydraw.o gtrdraw.o seqpanel.o ingengraph.o ingenext.o ingenwin.o macrodlg.o biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbidesk.a ../lib
ranlib ../lib/libncbidesk.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ddvclick.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvclick.c:248:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvclick.c: In function 'DDV_SendBSPSelectMsg_OLD':
ddvclick.c:979:13: warning: variable 'bDeselectAll' set but not used [-Wunused-but-set-variable]
Boolean bDeselectAll=TRUE;
^~~~~~~~~~~~
ddvclick.c: In function 'DDV_SendBSPSelectMsg':
ddvclick.c:1090:18: warning: variable 'bDeselectAll' set but not used [-Wunused-but-set-variable]
Boolean bDeselectAll=TRUE;
^~~~~~~~~~~~
ddvclick.c: In function 'DDV_DragProc':
ddvclick.c:2013:13: warning: unused variable 'cur_pgp' [-Wunused-variable]
ParaGPtr cur_pgp=NULL;
^~~~~~~
ddvclick.c: In function 'DDV_HoldProc':
ddvclick.c:2494:13: warning: unused variable 'Scroll' [-Wunused-variable]
Boolean Scroll=FALSE;
^~~~~~
ddvclick.c:2490:13: warning: unused variable 'cur_pgp' [-Wunused-variable]
ParaGPtr cur_pgp=NULL;
^~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvclick.c:252:
ddvclick.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvclick.c:252:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvclick.c:252:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvclick.c:252:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ddvclick.c:1823:13: warning: 'EraseOutline' defined but not used [-Wunused-function]
static void EraseOutline(PaneL p) {
^~~~~~~~~~~~
ddvclick.c:1811:16: warning: 'RectanglesAreSame' defined but not used [-Wunused-function]
static Boolean RectanglesAreSame(RecT rc1, RecT rc2) {
^~~~~~~~~~~~~~~~~
ddvclick.c:970:13: warning: 'DDV_SendBSPSelectMsg_OLD' defined but not used [-Wunused-function]
static void DDV_SendBSPSelectMsg_OLD(DdvMainPtr dmp,Int4 bsp_coord,Int4 SeqAlign_coord,
^~~~~~~~~~~~~~~~~~~~~~~~
ddvclick.c:611:13: warning: 'DDV_GetSeqAlignCoordGivenCol' defined but not used [-Wunused-function]
static Int4 DDV_GetSeqAlignCoordGivenCol(DdvMainPtr dmp, Int4 Disp_coord) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvclick.c: In function 'DDV_GetSeqNameGivenRow':
ddvclick.c:956:6: warning: 'sip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (!sip)
^
ddvclick.c: In function 'DDV_ReleaseProc':
ddvclick.c:1127:9: warning: 'pgp' may be used uninitialized in this function [-Wmaybe-uninitialized]
slp = SeqLocIntNew (bsp_coord_start, bsp_coord_stop, direction, pgp->sip);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvclick.c:1091:18: note: 'pgp' was declared here
ParaGPtr pgp;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ddvgraph.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvgraph.c:210:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvgraph.c: In function 'DDV_DrawSequence':
ddvgraph.c:701:31: warning: unused variable 'pos' [-Wunused-variable]
Int2 decal=1,i,x,y,pos=0;
^~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ddvgraph.c:215:
ddvgraph.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ddvgraph.c:215:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ddvgraph.c:215:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ddvgraph.c:215:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ddvopen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvopen.c:372:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvopen.c: In function 'DDV_GetAndCheckSeqAlign':
ddvopen.c:1739:8: warning: variable 'nRet' set but not used [-Wunused-but-set-variable]
Uint2 nRet=DVV_MSG_M_OK;
^~~~
ddvopen.c: In function 'DDV_FOpenAcceptProc':
ddvopen.c:1932:11: warning: variable 'nRet' set but not used [-Wunused-but-set-variable]
Uint2 nRet=DVV_MSG_M_OK,The_entityID;
^~~~
ddvopen.c: In function 'DDV_NetOpen_okProc':
ddvopen.c:2141:8: warning: variable 'AccessType' set but not used [-Wunused-but-set-variable]
Int2 AccessType,procval;
^~~~~~~~~~
ddvopen.c: In function 'DDV_StartMainWin_Slave':
ddvopen.c:2411:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
ddvopen.c:2417:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if (!w) return(NULL);
^~
ddvopen.c: In function 'DDV_ImportBioseqDlg':
ddvopen.c:2819:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
ddvopen.c: In function 'DDV_HideDlg':
ddvopen.c:3135:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
In file included from ../include/sqnutils.h:51:0,
from ../include/udviewer.h:219,
from ddvopen.c:376:
ddvopen.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/udviewer.h:228,
from ddvopen.c:376:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ddvopen.c:377:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ddvopen.c:377:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ddvopen.c:377:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ddvopen.c:377:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ddvopen.c:2111:16: warning: 'DDV_IsInt' defined but not used [-Wunused-function]
static Boolean DDV_IsInt(CharPtr szAccess)
^~~~~~~~~
ddvopen.c:1285:13: warning: 'DDV_NoConvert' defined but not used [-Wunused-function]
static void DDV_NoConvert(ButtoN g) {
^~~~~~~~~~~~~
ddvopen.c:1272:13: warning: 'DDV_Convert' defined but not used [-Wunused-function]
static void DDV_Convert(ButtoN g) {
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ddvpanel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvpanel.c:389:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvpanel.c: In function 'DDV_CreateViewerPanel':
ddvpanel.c:1177:8: warning: variable 'cxChar' set but not used [-Wunused-but-set-variable]
Int2 cxChar,cyChar;
^~~~~~
ddvpanel.c: In function 'DDV_DispStyles_OkProc':
ddvpanel.c:1543:21: warning: unused variable 'szBuf' [-Wunused-variable]
Char szBuf[15]={""};
^~~~~
ddvpanel.c: In function 'DDV_ExportTexte':
ddvpanel.c:2799:40: warning: variable 'browse' set but not used [-Wunused-but-set-variable]
ButtoN chk2,chk3,chk4,chk5,chk6,browse,ok;
^~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvpanel.c:392:
ddvpanel.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvpanel.c:392:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvpanel.c:392:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/ddvopen.h:140,
from ../include/ddvmain.h:202,
from ../include/ddvpanel.h:150,
from ddvpanel.c:392:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
ddvpanel.c:3377:13: warning: 'write_annot' defined but not used [-Wunused-function]
static void write_annot(SeqAlignPtr align)
^~~~~~~~~~~
ddvpanel.c:3296:13: warning: 'DDV_MoveRightBoundaryRight' defined but not used [-Wunused-function]
static void DDV_MoveRightBoundaryRight(IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~~~
ddvpanel.c:3290:13: warning: 'DDV_MoveRightBoundaryLeft' defined but not used [-Wunused-function]
static void DDV_MoveRightBoundaryLeft(IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~~
ddvpanel.c:3284:13: warning: 'DDV_MoveLeftBoundaryRight' defined but not used [-Wunused-function]
static void DDV_MoveLeftBoundaryRight(IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~~
ddvpanel.c:3278:13: warning: 'DDV_MoveLeftBoundaryLeft' defined but not used [-Wunused-function]
static void DDV_MoveLeftBoundaryLeft(IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~
ddvpanel.c:3272:13: warning: 'DDV_MoveRowRight' defined but not used [-Wunused-function]
static void DDV_MoveRowRight(IteM i)
^~~~~~~~~~~~~~~~
ddvpanel.c:3266:13: warning: 'DDV_MoveRowLeft' defined but not used [-Wunused-function]
static void DDV_MoveRowLeft(IteM i)
^~~~~~~~~~~~~~~
ddvpanel.c:3024:13: warning: 'DDV_DeleteRow' defined but not used [-Wunused-function]
static void DDV_DeleteRow(IteM i)
^~~~~~~~~~~~~
ddvpanel.c: In function 'DDVExportTexteOkProc':
ddvpanel.c:2647:5: warning: 'bPrintGap' may be used uninitialized in this function [-Wmaybe-uninitialized]
DDV_DumpSAPInFastaFile(&(dmp->MSA_d.pgp_l),&dob, hFile,bPrintGap);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddvpanel.c: In function 'DDV_SortPGPLineNum':
ddvpanel.c:2441:9: warning: 'pgp' may be used uninitialized in this function [-Wmaybe-uninitialized]
n+=pgp->nLines;
~~~^~~~~~~~
rm -f libddvlib.a
ar cru libddvlib.a ddvclick.o ddvgraph.o ddvopen.o ddvpanel.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libddvlib.a ../lib
ranlib ../lib/libddvlib.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF corematx.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from corematx.c:135:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF dvncode.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from dvncode.c:69:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objmmdb1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmmdb1.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmmdb1.c: In function 'BiostrucAsnRead':
objmmdb1.c:90:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiostrucIdFree':
objmmdb1.c:323:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'BiostrucIdAsnRead':
objmmdb1.c:358:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucSetAsnRead':
objmmdb1.c:547:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiostrucAnnotSetAsnRead':
objmmdb1.c:716:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiostrucResidueGraphSetAsnRead':
objmmdb1.c:885:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiostrucDescrFree':
objmmdb1.c:1015:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'BiostrucDescrAsnRead':
objmmdb1.c:1059:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucHistoryAsnRead':
objmmdb1.c:1270:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:1269:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucReplaceAsnRead':
objmmdb1.c:1450:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:1449:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'VersionOfDatabase_version_of_databaseFree':
objmmdb1.c:1618:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'BiostrucSourceAsnRead':
objmmdb1.c:1652:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'VersionOfDatabase_version_of_databaseAsnRead':
objmmdb1.c:1753:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucGraphAsnRead':
objmmdb1.c:2000:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiomolDescrFree':
objmmdb1.c:2138:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'BiomolDescrAsnRead':
objmmdb1.c:2188:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueGraphAsnRead':
objmmdb1.c:2445:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'MoleculeGraphAsnRead':
objmmdb1.c:2652:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'InterResidueBondAsnRead':
objmmdb1.c:2853:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:2852:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueAsnRead':
objmmdb1.c:3033:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3032:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueGraphPntrFree':
objmmdb1.c:3172:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'ResidueGraphPntrAsnRead':
objmmdb1.c:3207:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucGraphPntrAsnRead':
objmmdb1.c:3394:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3393:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucResidueGraphSetPntrAsnRead':
objmmdb1.c:3559:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3558:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomAsnRead':
objmmdb1.c:3725:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'IntraResidueBondAsnRead':
objmmdb1.c:3916:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3915:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ChiralCenterAsnRead':
objmmdb1.c:4088:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:4087:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomPntrAsnRead':
objmmdb1.c:4276:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:4275:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomPntrSetAsnRead':
objmmdb1.c:4430:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
In file included from ../include/strimprt.h:73:0,
from objmmdb1.c:5:
objmmdb1.c: At top level:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from objmmdb1.c:5:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
objmmdb1.c: In function 'BiostrucDescrAsnRead':
objmmdb1.c:1126:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb1.c: In function 'BiomolDescrAsnRead':
objmmdb1.c:2283:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objmmdb2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmmdb2.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmmdb2.c: In function 'BiostrucModelAsnRead':
objmmdb2.c:88:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'ModelDescrFree':
objmmdb2.c:241:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'ModelDescrAsnRead':
objmmdb2.c:288:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'ModelSpaceAsnRead':
objmmdb2.c:511:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:510:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'Coordinates_coordinatesFree':
objmmdb2.c:707:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'ModelCoordinateSetAsnRead':
objmmdb2.c:741:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'Coordinates_coordinatesAsnRead':
objmmdb2.c:829:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'ReferenceFrameAsnRead':
objmmdb2.c:1060:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:1059:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'CoordinatesFree':
objmmdb2.c:1190:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'CoordinatesAsnRead':
objmmdb2.c:1228:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'AtomicCoordinatesAsnRead':
objmmdb2.c:1417:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'Surface_surfaceFree':
objmmdb2.c:1636:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'SurfaceCoordinatesAsnRead':
objmmdb2.c:1682:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:1681:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'Surface_surfaceAsnRead':
objmmdb2.c:1762:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'DensityCoordinatesAsnRead':
objmmdb2.c:2026:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'ModelSpacePointsAsnRead':
objmmdb2.c:2258:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AtomicTemperatureFactorsFree':
objmmdb2.c:2398:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'AtomicTemperatureFactorsAsnRead':
objmmdb2.c:2433:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'AtomicOccupanciesAsnRead':
objmmdb2.c:2609:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AlternateConformationIdsAsnRead':
objmmdb2.c:2753:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'ConformationEnsembleAsnRead':
objmmdb2.c:2883:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'IsotropicTemperatureFactorsAsnRead':
objmmdb2.c:3046:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AnisotropicTemperatureFactorsAsnRead':
objmmdb2.c:3212:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'TMeshAsnRead':
objmmdb2.c:3416:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'TrianglesAsnRead':
objmmdb2.c:3615:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
In file included from ../include/strimprt.h:72:0,
from objmmdb2.c:5:
objmmdb2.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from objmmdb2.c:5:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from objmmdb2.c:5:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
objmmdb2.c: In function 'ModelDescrAsnRead':
objmmdb2.c:365:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'CoordinatesAsnRead':
objmmdb2.c:1278:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'AtomicTemperatureFactorsAsnRead':
objmmdb2.c:2479:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'ModelCoordinateSetAsnRead':
objmmdb2.c:875:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c:828:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb2.c: In function 'SurfaceCoordinatesAsnRead':
objmmdb2.c:1824:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c:1761:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objmmdb3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmmdb3.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmmdb3.c: In function 'BiostrucFeatureSetAsnRead':
objmmdb3.c:87:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ChemGraphPntrsFree':
objmmdb3.c:219:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'AtomPntrsAsnRead':
objmmdb3.c:442:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ChemGraphAlignmentAsnRead':
objmmdb3.c:624:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ChemGraphInteractionAsnRead':
objmmdb3.c:821:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'SphereAsnRead':
objmmdb3.c:1020:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ConeAsnRead':
objmmdb3.c:1188:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'CylinderAsnRead':
objmmdb3.c:1368:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BrickAsnRead':
objmmdb3.c:1553:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'TransformAsnRead':
objmmdb3.c:1792:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucFeatureSetDescrFree':
objmmdb3.c:1916:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'Location_locationFree':
objmmdb3.c:2156:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'BiostrucFeatureAsnRead':
objmmdb3.c:2201:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'Property_propertyFree':
objmmdb3.c:2716:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'ColorPropAsnRead':
objmmdb3.c:2792:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'CameraAsnRead':
objmmdb3.c:2979:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucScriptAsnRead':
objmmdb3.c:3163:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionPntrsAsnRead':
objmmdb3.c:3322:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionSimilarityAsnRead':
objmmdb3.c:3639:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'OtherFeatureAsnRead':
objmmdb3.c:3815:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucMoleculePntrAsnRead':
objmmdb3.c:3988:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'MoleculePntrsAsnRead':
objmmdb3.c:4330:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ResidueExplicitPntrsAsnRead':
objmmdb3.c:4492:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ResidueIntervalPntrAsnRead':
objmmdb3.c:4659:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionCoordinatesAsnRead':
objmmdb3.c:4830:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionBoundaryFree':
objmmdb3.c:4965:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'AlignStatsAsnRead':
objmmdb3.c:5196:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RealValueAsnRead':
objmmdb3.c:5437:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ModelSpacePointAsnRead':
objmmdb3.c:5597:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'MoveFree':
objmmdb3.c:5740:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'RotMatrixAsnRead':
objmmdb3.c:5948:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'TransMatrixAsnRead':
objmmdb3.c:6180:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'GLMatrixAsnRead':
objmmdb3.c:6358:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucScriptStepAsnRead':
objmmdb3.c:6658:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
In file included from ../include/strimprt.h:72:0,
from objmmdb3.c:5:
objmmdb3.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from objmmdb3.c:5:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from objmmdb3.c:5:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
objmmdb3.c: In function 'ChemGraphPntrsAsnRead':
objmmdb3.c:306:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'BiostrucFeatureSetDescrAsnRead':
objmmdb3.c:2019:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'RegionBoundaryAsnRead':
objmmdb3.c:5059:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'MoveAsnRead':
objmmdb3.c:5820:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'RegionPntrsAsnRead':
objmmdb3.c:3456:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c:3401:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb3.c: In function 'BiostrucFeatureAsnRead':
objmmdb3.c:2365:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c:2303:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objcn3d.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objcn3d.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objcn3d.c: In function 'Cn3dStyleDictionaryAsnRead':
objcn3d.c:87:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dUserAnnotationsAsnRead':
objcn3d.c:251:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dColorAsnRead':
objcn3d.c:415:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:414:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dBackboneStyleAsnRead':
objcn3d.c:604:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:603:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dGeneralStyleAsnRead':
objcn3d.c:787:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:786:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dBackboneLabelStyleAsnRead':
objcn3d.c:969:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:968:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dStyleSettingsAsnRead':
objcn3d.c:1171:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1170:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dStyleSettingsSetAsnRead':
objcn3d.c:1573:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dStyleTableItemAsnRead':
objcn3d.c:1702:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1701:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dResidueRangeAsnRead':
objcn3d.c:1866:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1865:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dMoleculeLocationAsnRead':
objcn3d.c:2028:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dObjectLocationAsnRead':
objcn3d.c:2190:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dUserAnnotationAsnRead':
objcn3d.c:2355:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dGLMatrixAsnRead':
objcn3d.c:2546:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:2545:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dVectorAsnRead':
objcn3d.c:2833:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:2832:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dViewSettingsAsnRead':
objcn3d.c:3005:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:3004:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
In file included from ../include/mapcn3d.h:8:0,
from objcn3d.c:5:
objcn3d.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/mapcn3d.h:8:0,
from objcn3d.c:5:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mmdbapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/mmdbapi1.h:232,
from ../include/mmdbapi.h:92,
from mmdbapi.c:116:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mmdbapi.c: In function 'MakeAModelstruc':
mmdbapi.c:192:11: warning: unused variable 'iCount' [-Wunused-variable]
Int4 iCount = 0;
^~~~~~
mmdbapi.c:189:11: warning: unused variable 'pdnmsCount' [-Wunused-variable]
PDNMS pdnmsCount = NULL;
^~~~~~~~~~
mmdbapi.c: In function 'AddPFBSelect':
mmdbapi.c:532:11: warning: unused variable 'pmsdStruc' [-Wunused-variable]
PMSD pmsdStruc = NULL;
^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mmdbapi1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mmdbapi1.c:294:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mmdbapi1.c: In function 'FreeAtomicModelAsnLists':
mmdbapi1.c:1037:21: warning: unused variable 'pcoThis' [-Wunused-variable]
CoordinatesPtr pcoThis = NULL;
^~~~~~~
mmdbapi1.c: In function 'FetchBS':
mmdbapi1.c:1242:13: warning: unused variable 'bIsNetwork' [-Wunused-variable]
Boolean bIsNetwork = FALSE;
^~~~~~~~~~
mmdbapi1.c: In function 'FreeSurfaceModelAsnList':
mmdbapi1.c:1627:16: warning: variable 'pvnX' set but not used [-Wunused-but-set-variable]
ValNodePtr pvnX = NULL;
^~~~
mmdbapi1.c: In function 'MakeChemGraphNodeList':
mmdbapi1.c:2343:16: warning: variable 'pvnThis' set but not used [-Wunused-but-set-variable]
ValNodePtr pvnThis = NULL;
^~~~~~~
mmdbapi1.c: In function 'DoApplyTransform':
mmdbapi1.c:2573:8: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
mmdbapi1.c: In function 'DoReverseTransform':
mmdbapi1.c:2713:8: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
mmdbapi1.c: In function 'InstBSAnnotSet':
mmdbapi1.c:2860:8: warning: unused variable 'psfsThis' [-Wunused-variable]
PSFS psfsThis = NULL;
^~~~~~~~
mmdbapi1.c:2859:22: warning: unused variable 'pbsfThis' [-Wunused-variable]
BiostrucFeaturePtr pbsfThis = NULL;
^~~~~~~~
mmdbapi1.c:2855:9: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
mmdbapi1.c: In function 'BiosToSeq':
mmdbapi1.c:2978:19: warning: unused variable 'loc1' [-Wunused-variable]
ValNodePtr loc1 = NULL;
^~~~
mmdbapi1.c:2967:22: warning: unused variable 'pbsf' [-Wunused-variable]
BiostrucFeaturePtr pbsf=NULL;
^~~~
mmdbapi1.c: In function 'fnPBSFtoPSA':
mmdbapi1.c:3174:19: warning: unused variable 'loc1' [-Wunused-variable]
ValNodePtr loc1 = NULL;
^~~~
mmdbapi1.c: In function 'BiostrToSeqAnnotSet':
mmdbapi1.c:3408:19: warning: unused variable 'loc1' [-Wunused-variable]
ValNodePtr loc1 = NULL;
^~~~
mmdbapi1.c:3397:22: warning: unused variable 'pbsf' [-Wunused-variable]
BiostrucFeaturePtr pbsf=NULL;
^~~~
mmdbapi1.c: In function 'InstallAlignedSlave':
mmdbapi1.c:3877:9: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest;
^~~~~
mmdbapi1.c:3874:9: warning: unused variable 'psfsThis' [-Wunused-variable]
PSFS psfsThis = NULL;
^~~~~~~~
mmdbapi1.c: In function 'BiostrucAddFeature':
mmdbapi1.c:4184:11: warning: variable 'ncbiVast' set but not used [-Wunused-but-set-variable]
Boolean ncbiVast = FALSE;
^~~~~~~~
mmdbapi1.c:4182:11: warning: variable 'pdbFootnote' set but not used [-Wunused-but-set-variable]
Boolean pdbFootnote = FALSE;
^~~~~~~~~~~
mmdbapi1.c:4181:11: warning: variable 'pdbSite' set but not used [-Wunused-but-set-variable]
Boolean pdbSite = FALSE;
^~~~~~~
mmdbapi1.c:4172:15: warning: unused variable 'pdvnThis' [-Wunused-variable]
DValNodePtr pdvnThis = NULL;
^~~~~~~~
mmdbapi1.c: In function 'BiostrucAsnGet':
mmdbapi1.c:5289:18: warning: variable 'aop' set but not used [-Wunused-but-set-variable]
AsnOptionPtr aop;
^~~
mmdbapi1.c: In function 'BiosToSeq':
mmdbapi1.c:3127:20: warning: 'slavesip' may be used uninitialized in this function [-Wmaybe-uninitialized]
dsp->ids->next = slavesip;
~~~~~~~~~~~~~~~^~~~~~~~~~
mmdbapi1.c: In function 'BiostrToSeqAnnotSet':
mmdbapi1.c:3559:20: warning: 'slavesip' may be used uninitialized in this function [-Wmaybe-uninitialized]
dsp->ids->next = slavesip;
~~~~~~~~~~~~~~~^~~~~~~~~~
mmdbapi1.c: In function 'InstBSAnnotSet':
mmdbapi1.c:2885:13: warning: 'iMMDBId' may be used uninitialized in this function [-Wmaybe-uninitialized]
pdnmsThis = FindLoadedBiostruc(NULL, iMMDBId);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mmdbapi2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mmdbapi2.c:159:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mmdbapi2.c: In function 'GetAtomLocs':
mmdbapi2.c:1471:9: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (pmadThis)
^
mmdbapi2.c: In function 'AssignAtomLocId':
mmdbapi2.c:1537:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest = 0;
^~~~~
mmdbapi2.c: In function 'AssignBackBone':
mmdbapi2.c:1686:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest = 0;
^~~~~
mmdbapi2.c: In function 'AssignVirtual':
mmdbapi2.c:1790:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest = 0;
^~~~~
mmdbapi2.c: In function 'AssignIons':
mmdbapi2.c:1846:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest = 0;
^~~~~
mmdbapi2.c: In function 'MolFromPDBChain':
mmdbapi2.c:1931:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest;
^~~~~
mmdbapi2.c: In function 'SeqStringFromMol':
mmdbapi2.c:1948:9: warning: unused variable 'iTest' [-Wunused-variable]
Int4 iTest =0;
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mmdbapi3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mmdbapi3.c:207:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mmdbapi3.c: In function 'WritePDBHeader':
mmdbapi3.c:840:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(org)
^~
mmdbapi3.c:845:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
src = orgstring;
^~~
mmdbapi3.c:840:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if(org)
^
mmdbapi3.c: In function 'WritePDBRemarks':
mmdbapi3.c:1389:8: warning: unused variable 'len' [-Wunused-variable]
int len;
^~~
mmdbapi3.c:1388:9: warning: unused variable 'pcThis' [-Wunused-variable]
Char pcThis[81];
^~~~~~
mmdbapi3.c:1387:21: warning: unused variable 'pbsdrLast' [-Wunused-variable]
BiostrucDescrPtr pbsdrLast = NULL;
^~~~~~~~~
mmdbapi3.c:1386:21: warning: unused variable 'pbsdrThis' [-Wunused-variable]
BiostrucDescrPtr pbsdrThis = NULL;
^~~~~~~~~
mmdbapi3.c: In function 'WritePDBConnect':
mmdbapi3.c:1610:9: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest;
^~~~~
mmdbapi3.c: In function 'WritePDBModelList':
mmdbapi3.c:1625:10: warning: variable 'iCount' set but not used [-Wunused-but-set-variable]
Int4 iCount;
^~~~~~
mmdbapi3.c: In function 'WriteKinAtom':
mmdbapi3.c:2287:11: warning: unused variable 'pcElName' [-Wunused-variable]
CharPtr pcElName = NULL;
^~~~~~~~
mmdbapi3.c: In function 'WriteFASTAMolecule':
mmdbapi3.c:3537:9: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int4 iTest =0;
^~~~~
mmdbapi3.c: In function 'WriteKinAtom':
mmdbapi3.c:2314:12: warning: 'iTemp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (iTemp < TempsKine[(iIndex-1)]) return; /* too low */
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mmdbapi4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/mmdbapi1.h:232,
from ../include/mmdbapi.h:92,
from mmdbapi4.c:106:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mmdbapi4.c: In function 'RefreshSurface':
mmdbapi4.c:147:10: warning: unused variable 'iVal' [-Wunused-variable]
Int4 iVal = 0;
^~~~
mmdbapi4.c: In function 'FreeCoordinatesAsnLists':
mmdbapi4.c:335:28: warning: variable 'pdcThis' set but not used [-Wunused-but-set-variable]
DensityCoordinatesPtr pdcThis = NULL;
^~~~~~~
mmdbapi4.c: In function 'FreeRedundantAsn':
mmdbapi4.c:371:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
mmdbapi4.c:370:11: warning: unused variable 'pdnmmThis' [-Wunused-variable]
PDNMM pdnmmThis = NULL;
^~~~~~~~~
mmdbapi4.c:367:22: warning: unused variable 'pbsmThis' [-Wunused-variable]
BiostrucModelPtr pbsmThis = NULL;
^~~~~~~~
mmdbapi4.c: In function 'RefreshModelAsnMem':
mmdbapi4.c:474:13: warning: unused variable 'iCoordSets' [-Wunused-variable]
Int4 iCoordSets = 0;
^~~~~~~~~~
mmdbapi4.c:465:20: warning: unused variable 'pappThis' [-Wunused-variable]
AtomPntrsPtr pappThis = NULL;
^~~~~~~~
mmdbapi4.c:464:27: warning: unused variable 'pmspThis' [-Wunused-variable]
ModelSpacePointsPtr pmspThis = NULL;
^~~~~~~~
mmdbapi4.c:463:28: warning: unused variable 'pocThis' [-Wunused-variable]
AtomicOccupanciesPtr pocThis = NULL;
^~~~~~~
mmdbapi4.c:458:34: warning: unused variable 'paciThis' [-Wunused-variable]
AlternateConformationIdsPtr paciThis = NULL;
^~~~~~~~
mmdbapi4.c: In function 'RebuildChemGraphAsn':
mmdbapi4.c:931:15: warning: unused variable 'bOK' [-Wunused-variable]
Boolean bOK = TRUE;
^~~
mmdbapi4.c: In function 'WriteASNChemGraphOnly':
mmdbapi4.c:1192:10: warning: unused variable 'iHash' [-Wunused-variable]
Int4 iHash = 0;
^~~~~
mmdbapi4.c: In function 'FreeSingleModel':
mmdbapi4.c:1336:11: warning: unused variable 'pdnml' [-Wunused-variable]
PDNML pdnml = NULL;
^~~~~
mmdbapi4.c:1332:22: warning: unused variable 'pbsmTemp' [-Wunused-variable]
BiostrucModelPtr pbsmTemp = NULL;
^~~~~~~~
mmdbapi4.c: In function 'WriteAsnModelList':
mmdbapi4.c:1505:14: warning: unused variable 'paioAIP' [-Wunused-variable]
AsnIoPtr paioAIP = NULL;
^~~~~~~
mmdbapi4.c:1502:11: warning: unused variable 'pmldThis' [-Wunused-variable]
PMLD pmldThis = NULL;
^~~~~~~~
mmdbapi4.c:1498:11: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
mmdbapi4.c:1496:22: warning: unused variable 'pbsmThis' [-Wunused-variable]
BiostrucModelPtr pbsmThis = NULL;
^~~~~~~~
mmdbapi4.c:1495:17: warning: unused variable 'pBSThis' [-Wunused-variable]
BiostrucPtr pBSThis = NULL;
^~~~~~~
mmdbapi4.c:1494:13: warning: unused variable 'bFirst' [-Wunused-variable]
Boolean bFirst = TRUE;
^~~~~~
mmdbapi4.c:1493:10: warning: unused variable 'iTest' [-Wunused-variable]
Int2 iTest = 0;
^~~~~
mmdbapi4.c: In function 'BiostrucAnnotSetToSeqAnnot':
mmdbapi4.c:1741:19: warning: unused variable 'loc1' [-Wunused-variable]
ValNodePtr loc1 = NULL;
^~~~
mmdbapi4.c: In function 'WriteAsnModelList':
mmdbapi4.c:1632:13: warning: 'bRet' may be used uninitialized in this function [-Wmaybe-uninitialized]
return bRet;
^~~~
mmdbapi4.c: In function 'BiostrucAnnotSetToSeqAnnot':
mmdbapi4.c:1872:20: warning: 'slavesip' may be used uninitialized in this function [-Wmaybe-uninitialized]
dsp->ids->next = slavesip;
~~~~~~~~~~~~~~~^~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mmdbentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mmdbentr.c:65:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vastsubs.c
vastsubs.c: In function 'LoadSubsetTable':
vastsubs.c:212:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%d", &ndoms);
^~~~~~~~~~~~~~~~~~~~~~~~
vastsubs.c:239:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%d", &nsubs);
^~~~~~~~~~~~~~~~~~~~~~~~
vastsubs.c:258:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%d", &j);
^~~~~~~~~~~~~~~~~~~~
vastsubs.c:287:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%8c", domid);
^~~~~~~~~~~~~~~~~~~~~~~~
vastsubs.c:296:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%d", &n);
^~~~~~~~~~~~~~~~~~~~
vastsubs.c:302:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "%d %d %d", &subset[j], &grps[j], &ranks[j]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vastsubs.c:304:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fd, "\n");
^~~~~~~~~~~~~~~~
vastsubs.c:202:16: warning: 'len' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 i, j, n, len, strindex, ndoms, nsubs;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF prunebsc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/prunebsc.h:10,
from prunebsc.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
prunebsc.c: In function 'PruneFeatureSet':
prunebsc.c:220:22: warning: variable 'bsfpDie' set but not used [-Wunused-but-set-variable]
BiostrucFeaturePtr bsfpDie, bsfp, bsfpnew = NULL;
^~~~~~~
prunebsc.c: In function 'PruneModel':
prunebsc.c:272:30: warning: variable 'mcsDie' set but not used [-Wunused-but-set-variable]
ModelCoordinateSetPtr mcs, mcsDie, mcsnew = NULL;
^~~~~~
prunebsc.c: In function 'PruneBiostruc':
prunebsc.c:559:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (vnp = ValNodeFindNext(currentbp->descr, NULL, BiomolDescr_name))
^~
prunebsc.c:574:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (vnp = ValNodeFindNext(het->descr, NULL, BiomolDescr_name))
^~
prunebsc.c:663:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (vnp = ValNodeFindNext(bsfsp->descr, NULL, BiostrucFeatureSetDescr_name))
^~
In file included from ../include/ncbi.h:62:0,
from ../include/prunebsc.h:10,
from prunebsc.c:34:
../include/ncbistr.h:339:20: warning: 'feature_name' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StringICmp Nlm_StringICmp
^~~~~~~~~~~~~~
prunebsc.c:522:25: note: 'feature_name' was declared here
CharPtr chnid, hetid, feature_name;
^~~~~~~~~~~~
prunebsc.c:649:23: warning: 'pirbnew' may be used uninitialized in this function [-Wmaybe-uninitialized]
pirbnew->next = pirb;
~~~~~~~~~~~~~~^~~~~~
prunebsc.c:591:26: warning: 'currenthet' may be used uninitialized in this function [-Wmaybe-uninitialized]
currenthet->next = het;
~~~~~~~~~~~~~~~~~^~~~~
prunebsc.c:701:24: warning: 'mol_id' may be used uninitialized in this function [-Wmaybe-uninitialized]
bsmpTail->next = PruneModel(bsmp, pvnIds, mol_id);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prunebsc.c:562:9: warning: 'chnid' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*chnid == *chain)
^~~~~~
prunebsc.c:182:7: warning: 'mtype' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(mtype)
^~~~~~
prunebsc.c:173:8: note: 'mtype' was declared here
Int4 mtype, molecule_id;
^~~~~
prunebsc.c:110:7: warning: 'mtype' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(mtype)
^~~~~~
prunebsc.c:102:8: note: 'mtype' was declared here
Int4 mtype;
^~~~~
prunebsc.c:127:25: warning: 'currentbp' may be used uninitialized in this function [-Wmaybe-uninitialized]
currentbp->next = newbp;
~~~~~~~~~~~~~~~~^~~~~~~
prunebsc.c:100:38: note: 'currentbp' was declared here
MoleculeGraphPtr newbp, bp = NULL, currentbp;
^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objcdd.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objcdd.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objcdd.c: In function 'CddIdFree':
objcdd.c:53:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'CddIdAsnRead':
objcdd.c:85:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddIdSetAsnRead':
objcdd.c:248:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:245:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddIdSetAsnWrite':
objcdd.c:301:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddAsnRead':
objcdd.c:401:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddSetAsnRead':
objcdd.c:796:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:793:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddSetAsnWrite':
objcdd.c:849:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddTreeAsnRead':
objcdd.c:932:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:931:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddTreeSetAsnRead':
objcdd.c:1143:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1140:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddTreeSetAsnWrite':
objcdd.c:1196:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddPrefNodesAsnRead':
objcdd.c:1276:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1275:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddPrefNodesAsnWrite':
objcdd.c:1365:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddProjectAsnRead':
objcdd.c:1472:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddOrgRefAsnRead':
objcdd.c:1661:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1660:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddOrgRefSetAsnRead':
objcdd.c:1830:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1827:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddOrgRefSetAsnWrite':
objcdd.c:1883:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddPrefNodeDescrFree':
objcdd.c:1923:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'CddPrefNodeDescrAsnRead':
objcdd.c:1958:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddPrefNodeDescrSetAsnRead':
objcdd.c:2121:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2118:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddPrefNodeDescrSetAsnWrite':
objcdd.c:2174:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'GlobalIdAsnRead':
objcdd.c:2253:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2252:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddRepeatAsnRead':
objcdd.c:2439:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2438:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddBookRefAsnRead':
objcdd.c:2615:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2614:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddDescrSetAsnRead':
objcdd.c:3170:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:3167:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddDescrSetAsnWrite':
objcdd.c:3223:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'MatrixAsnRead':
objcdd.c:3301:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'TriangleAsnRead':
objcdd.c:3489:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'UpdateCommentFree':
objcdd.c:3625:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'UpdateCommentAsnRead':
objcdd.c:3669:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'UpdateAlignAsnRead':
objcdd.c:3873:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'RejectIdAsnRead':
objcdd.c:4047:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'RejectIdAsnWrite':
objcdd.c:4122:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'FeatureEvidenceFree':
objcdd.c:4170:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'FeatureEvidenceAsnRead':
objcdd.c:4214:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'AlignAnnotAsnRead':
objcdd.c:4419:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'AlignAnnotSetAsnRead':
objcdd.c:4587:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4584:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'AlignAnnotSetAsnWrite':
objcdd.c:4640:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'DomainParentAsnRead':
objcdd.c:4718:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4717:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'SequenceTreeAsnRead':
objcdd.c:4898:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4897:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'AlgorithmTypeAsnRead':
objcdd.c:5085:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5084:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'SeqTreeNodeAsnRead':
objcdd.c:5387:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5386:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'Children_footprintAsnRead':
objcdd.c:5572:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5571:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'NodeAnnotationAsnRead':
objcdd.c:5862:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5861:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddViewerRectAsnRead':
objcdd.c:6027:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:6026:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddViewerAsnRead':
objcdd.c:6208:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddScriptAsnRead':
objcdd.c:6382:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:6381:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
In file included from objcdd.c:6:0:
objcdd.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from objcdd.c:6:0:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from objcdd.c:7:0:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
objcdd.c: In function 'CddDescrAsnRead':
objcdd.c:2994:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cddutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cddutil.c:336:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cddutil.c: In function 'CddGetPmIds':
cddutil.c:649:17: warning: unused variable 'bRefOpen' [-Wunused-variable]
Boolean bRefOpen = FALSE;
^~~~~~~~
cddutil.c: In function 'CddGetAnnotNames':
cddutil.c:807:19: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp, vnpHead = NULL;
^~~
cddutil.c: In function 'CddCheckForRepeats':
cddutil.c:1034:7: warning: the address of 'CddHasConsensus' will always evaluate as 'true' [-Waddress]
if (!CddHasConsensus) return FALSE;
^
cddutil.c:1013:23: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddMSLDenDiagToMSLDenSeg':
cddutil.c:1663:30: warning: variable 'lasts' set but not used [-Wunused-but-set-variable]
Int4 lastm, lasts;
^~~~~
cddutil.c:1663:23: warning: variable 'lastm' set but not used [-Wunused-but-set-variable]
Int4 lastm, lasts;
^~~~~
cddutil.c: In function 'SeqAlignInform':
cddutil.c:1938:22: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddAlignInform':
cddutil.c:2125:22: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddPssmInform':
cddutil.c:2248:22: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddPosFreqInform':
cddutil.c:2306:22: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddDenDiagCposComputation':
cddutil.c:2368:33: warning: variable 'RowHead' set but not used [-Wunused-but-set-variable]
ValNodePtr newRow, RowHead;
^~~~~~~
cddutil.c:2365:25: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddCposComputation':
cddutil.c:2571:33: warning: variable 'RowHead' set but not used [-Wunused-but-set-variable]
ValNodePtr newRow, RowHead;
^~~~~~~
cddutil.c:2568:25: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddRetrieveBioseqById':
cddutil.c:3379:15: warning: unused variable 'retcode' [-Wunused-variable]
Int2 retcode = 1;
^~~~~~~
cddutil.c:3377:15: warning: unused variable 'uid' [-Wunused-variable]
Int4 uid = 0;
^~~
cddutil.c: In function 'CddCalculateTriangle':
cddutil.c:3534:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL;
^~
cddutil.c:3534:31: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL;
^~
cddutil.c: In function 'CddCalculateQuerySim':
cddutil.c:3653:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL;
^~
cddutil.c:3653:31: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL;
^~
cddutil.c: In function 'CddConsensus':
cddutil.c:3853:49: warning: variable 'm_end' set but not used [-Wunused-but-set-variable]
Int4 m_last, m_frst, s_insert, m_end;
^~~~~
cddutil.c: In function 'CddCposCompPart1':
cddutil.c:4247:25: warning: variable 'iStatus' set but not used [-Wunused-but-set-variable]
Int2 iStatus;
^~~~~~~
cddutil.c: In function 'CddGetNewIndexForThreading':
cddutil.c:4392:14: warning: unused variable 'Index' [-Wunused-variable]
Int4 i, Index=0;
^~~~~
cddutil.c: In function 'CddCposComp':
cddutil.c:4474:33: warning: variable 'RowHead' set but not used [-Wunused-but-set-variable]
ValNodePtr newRow, RowHead;
^~~~~~~
cddutil.c: In function 'CddDenDiagCposComp2KBP':
cddutil.c:4745:59: warning: variable 'RowHead' set but not used [-Wunused-but-set-variable]
ValNodePtr ColumnHead, LetterHead, newRow, RowHead, newLetter;
^~~~~~~
cddutil.c: In function 'CddDumpTaxLinks':
cddutil.c:5727:16: warning: unused variable 'txid' [-Wunused-variable]
Int4 txid = 0, gi = 0;
^~~~
cddutil.c: At top level:
cddutil.c:6267:1: warning: "/*" within comment [-Wcomment]
/*---------------------------------------------------------------------------*/
In file included from ../include/cddutil.h:205:0,
from cddutil.c:353:
../include/objcdd.h:642:37: warning: 'Children_childrenFree' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:643:37: warning: 'Children_childrenAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:644:24: warning: 'Children_childrenAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:666:38: warning: 'Children_footprintFree' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr ));
^~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:667:38: warning: 'Children_footprintNew' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:668:38: warning: 'Children_footprintAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:669:24: warning: 'Children_footprintAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from cddutil.c:353:0:
../include/cddutil.h:589:25: warning: 'CddFindSeqIdInSeqLoc' declared 'static' but never defined [-Wunused-function]
static SeqIdPtr CddFindSeqIdInSeqLoc(SeqLocPtr location);
^~~~~~~~~~~~~~~~~~~~
cddutil.c:4661:16: warning: 'CddtakeMatrixCheckpoint' defined but not used [-Wunused-function]
static Boolean CddtakeMatrixCheckpoint(compactSearchItems *compactSearch,
^~~~~~~~~~~~~~~~~~~~~~~
In file included from cddutil.c:349:0:
../include/cdd.h:343:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/cdd.h:342:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/cdd.h:341:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/cdd.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "cdd.h24";
^~~~~~~~~~~
cddutil.c: In function 'CddCopyMSLDenDiag':
cddutil.c:3015:25: warning: 'ddpTail' may be used uninitialized in this function [-Wmaybe-uninitialized]
ddpTail->next = ddpNew;
~~~~~~~~~~~~~~^~~~~~~~
cddutil.c: In function 'CddCalculateTriangle':
cddutil.c:3469:22: warning: 'pscTail' may be used uninitialized in this function [-Wmaybe-uninitialized]
pscTail->next = psc; pscTail = psc; psc = NULL;
~~~~~~~~~~~~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cddposutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cddposutil.c:119:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cddposutil.c: In function 'CddfindThreshSequences':
cddposutil.c:359:15: warning: variable 'thisId' set but not used [-Wunused-but-set-variable]
SeqIdPtr thisId; /* Ids of target sequences in current SeqAlign */
^~~~~~
cddposutil.c: In function 'CddfindDenseDiagThreshSequences':
cddposutil.c:386:16: warning: variable 'thisId' set but not used [-Wunused-but-set-variable]
SeqIdPtr thisId; /* Ids of target sequences in current SeqAlign */
^~~~~~
cddposutil.c: In function 'CddposFreqsToMatrix':
cddposutil.c:1038:45: warning: operation on '*(*(posSearch->posPrivateMatrix + (sizetype)((unsigned int)length * 4u)) + (sizetype)((unsigned int)a * 4u))' may be undefined [-Wsequence-point]
posSearch->posPrivateMatrix[length][a] = posSearch->posPrivateMatrix[length][a] = BLAST_SCORE_MIN;
cddposutil.c: In function 'CddposDenseDiagDemographics':
cddposutil.c:1094:17: warning: unused variable 'is_new_id' [-Wunused-variable]
Boolean is_new_id = FALSE;
^~~~~~~~~
cddposutil.c:1093:17: warning: unused variable 'segIndex' [-Wunused-variable]
Int4 segIndex; /*Index for which piece we are at*/
^~~~~~~~
cddposutil.c:1092:25: warning: variable 'startS' set but not used [-Wunused-but-set-variable]
Int4 startQ, startS; /*Indices into array of starting positions*/
^~~~~~
cddposutil.c:1092:17: warning: variable 'startQ' set but not used [-Wunused-but-set-variable]
Int4 startQ, startS; /*Indices into array of starting positions*/
^~~~~~
cddposutil.c:1091:17: warning: unused variable 'curId' [-Wunused-variable]
SeqIdPtr curId; /*Used to compare seq. coming from different SeqAligns*/
^~~~~
cddposutil.c: In function 'CddSetUpSearchInternalByLoc':
cddposutil.c:1246:39: warning: unused variable 'last_length_adjustment' [-Wunused-variable]
index, length, length_adjustment=0, last_length_adjustment, min_query_length;
^~~~~~~~~~~~~~~~~~~~~~
cddposutil.c: In function 'CddSetUpSearchWithReadDb':
cddposutil.c:2040:43: warning: variable 'final_db_seq' set but not used [-Wunused-but-set-variable]
Int4 final_virtual_db_seq=0, final_db_seq=0;
^~~~~~~~~~~~
cddposutil.c:2006:28: warning: unused variable 'virtual_oid_bit' [-Wunused-variable]
Uint4 oid_bit, virtual_oid_bit;
^~~~~~~~~~~~~~~
cddposutil.c:2006:19: warning: unused variable 'oid_bit' [-Wunused-variable]
Uint4 oid_bit, virtual_oid_bit;
^~~~~~~
cddposutil.c:2005:30: warning: unused variable 'virtual_mask_index' [-Wunused-variable]
Int4 mask_index, virtual_mask_index;
^~~~~~~~~~~~~~~~~~
cddposutil.c:2005:18: warning: unused variable 'mask_index' [-Wunused-variable]
Int4 mask_index, virtual_mask_index;
^~~~~~~~~~
cddposutil.c:2004:19: warning: unused variable 'alias_oidlist' [-Wunused-variable]
OIDListPtr alias_oidlist;
^~~~~~~~~~~~~
cddposutil.c:2003:19: warning: unused variable 'use_private_gilist' [-Wunused-variable]
Boolean use_private_gilist = FALSE;
^~~~~~~~~~~~~~~~~~
cddposutil.c:2000:20: warning: unused variable 'vnp' [-Wunused-variable]
ValNodePtr vnp;
^~~
cddposutil.c: In function 'CddposReadAlignment':
cddposutil.c:2226:16: warning: variable 'alignPos' set but not used [-Wunused-but-set-variable]
Int4 alignPos, queryOffset, subjectOffset, matchLength;
^~~~~~~~
In file included from ../include/cddutil.h:205:0,
from cddposutil.c:131:
cddposutil.c: At top level:
../include/objcdd.h:642:37: warning: 'Children_childrenFree' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:643:37: warning: 'Children_childrenAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:644:24: warning: 'Children_childrenAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:666:38: warning: 'Children_footprintFree' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr ));
^~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:667:38: warning: 'Children_footprintNew' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:668:38: warning: 'Children_footprintAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:669:24: warning: 'Children_footprintAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from cddposutil.c:131:0:
../include/cddutil.h:507:27: warning: 'CddReadBlastOptions' declared 'static' but never defined [-Wunused-function]
static PGPBlastOptionsPtr CddReadBlastOptions(BioseqPtr bsp, Int4 iPseudo, CharPtr matrix_name);
^~~~~~~~~~~~~~~~~~~
../include/cddutil.h:512:13: warning: 'BlastKarlinBlkCopy' declared 'static' but never defined [-Wunused-function]
static void BlastKarlinBlkCopy(BLAST_KarlinBlkPtr kbp_in,BLAST_KarlinBlkPtr kbp_out);
^~~~~~~~~~~~~~~~~~
../include/cddutil.h:516:13: warning: 'CddputMatrixKbp' declared 'static' but never defined [-Wunused-function]
static void CddputMatrixKbp(FILE *checkFile, BLAST_KarlinBlkPtr kbp,
^~~~~~~~~~~~~~~
../include/cddutil.h:518:13: warning: 'CddputMatrixMatrix' declared 'static' but never defined [-Wunused-function]
static void CddputMatrixMatrix(FILE *checkFile,
^~~~~~~~~~~~~~~~~~
../include/cddutil.h:522:16: warning: 'CddtakeMatrixCheckpoint' declared 'static' but never defined [-Wunused-function]
static Boolean CddtakeMatrixCheckpoint(compactSearchItems *compactSearch,
^~~~~~~~~~~~~~~~~~~~~~~
../include/cddutil.h:589:25: warning: 'CddFindSeqIdInSeqLoc' declared 'static' but never defined [-Wunused-function]
static SeqIdPtr CddFindSeqIdInSeqLoc(SeqLocPtr location);
^~~~~~~~~~~~~~~~~~~~
../include/cddutil.h:591:25: warning: 'CddRelocateSeqLoc' declared 'static' but never defined [-Wunused-function]
static void CddRelocateSeqLoc(SeqLocPtr location, SeqIdPtr sip, Int4 *ali);
^~~~~~~~~~~~~~~~~
../include/cddutil.h:592:25: warning: 'CddSeqLocInExpAlign' declared 'static' but never defined [-Wunused-function]
static Int4 CddSeqLocInExpAlign(SeqLocPtr location, CddExpAlignPtr eap);
^~~~~~~~~~~~~~~~~~~
../include/cddutil.h:593:25: warning: 'CddFindSeqIdInAlignAnnot' declared 'static' but never defined [-Wunused-function]
static SeqIdPtr CddFindSeqIdInAlignAnnot(AlignAnnotPtr oldannot);
^~~~~~~~~~~~~~~~~~~~~~~~
../include/cddutil.h:623:24: warning: 'HitYet' declared 'static' but never defined [-Wunused-function]
static Boolean HitYet(Int4Ptr retlist, Int4 index, Int4 i);
^~~~~~
../include/cddutil.h:649:16: warning: 'CddFixForXML' declared 'static' but never defined [-Wunused-function]
static CharPtr CddFixForXML(CharPtr pc);
^~~~~~~~~~~~
cddposutil.c:971:13: warning: 'CddfreePosFreqs' defined but not used [-Wunused-function]
static void CddfreePosFreqs(Nlm_FloatHi ** posFreqs, Int4 length)
^~~~~~~~~~~~~~~
cddposutil.c: In function 'CddposComputeSequenceWeights':
cddposutil.c:840:35: warning: 'intervalSigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
posSearch->posSigma[qplace] = intervalSigma;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
cddposutil.c:832:68: warning: 'Sigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
posSearch->posA[thisSeq] = posSearch->posRowSigma[thisSeq]/Sigma;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
cddposutil.c: In function 'CddposDemographics':
cddposutil.c:1199:24: warning: 'retrievalOffset' may be used uninitialized in this function [-Wmaybe-uninitialized]
subjectOffset = curSegs->starts[startS] - retrievalOffset;
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cddposutil.c: In function 'CddSetUpSearchWithReadDb':
cddposutil.c:1740:48: warning: 'min_query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
if( 0 != BlastComputeLengthAdjustment(1/min_query_length,
~^~~~~~~~~~~~~~~~~
cddposutil.c:1246:63: note: 'min_query_length' was declared here
index, length, length_adjustment=0, last_length_adjustment, min_query_length;
^~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF objmime.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmime.c:73:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmime.c: In function 'NcbiMimeAsn1Free':
objmime.c:123:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'NcbiMimeAsn1AsnRead':
objmime.c:170:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'Data_dataFree':
objmime.c:377:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'EntrezGeneralAsnRead':
objmime.c:423:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c:422:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'Data_dataAsnRead':
objmime.c:517:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'BiostrucAlignAsnRead':
objmime.c:791:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucAlignSeqAsnRead':
objmime.c:1016:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucSeqAsnRead':
objmime.c:1208:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucSeqsAsnRead':
objmime.c:1402:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'SeqAlignData_seq_align_dataFree':
objmime.c:1599:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'BiostrucSeqsAlignsCddAsnRead':
objmime.c:1633:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'SeqAlignData_seq_align_dataAsnRead':
objmime.c:1720:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'BundleSeqsAlignsAsnRead':
objmime.c:1954:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
In file included from ../include/mapmime.h:4:0,
from objmime.c:78:
objmime.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/mapmime.h:4:0,
from objmime.c:78:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/mapmime.h:6:0,
from objmime.c:78:
../include/objcdd.h:642:37: warning: 'Children_childrenFree' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:643:37: warning: 'Children_childrenAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:644:24: warning: 'Children_childrenAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:666:38: warning: 'Children_footprintFree' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr ));
^~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:667:38: warning: 'Children_footprintNew' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void ));
^~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:668:38: warning: 'Children_footprintAsnRead' declared 'static' but never defined [-Wunused-function]
static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objcdd.h:669:24: warning: 'Children_footprintAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~
objmime.c: In function 'NcbiMimeAsn1AsnRead':
objmime.c:232:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c: In function 'EntrezGeneralAsnRead':
objmime.c:579:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c:516:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmime.c: In function 'BiostrucSeqsAlignsCddAsnRead':
objmime.c:1766:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c:1719:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF strucapi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from strucapi.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdalgs.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdatd.c
thrdatd.c: In function 'atd':
thrdatd.c:859:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) printf("%d ",sai->al[i]); printf("sai->al\n");
^~~
thrdatd.c:859:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) printf("%d ",sai->al[i]); printf("sai->al\n");
^~~~~~
thrdatd.c:860:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<sai->nmt;i++) printf("%d ",sai->sq[i]); printf("sai->sq\n");
^~~
thrdatd.c:860:51: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<sai->nmt;i++) printf("%d ",sai->sq[i]); printf("sai->sq\n");
^~~~~~
thrdatd.c:862:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) printf("%d ",sli->no[i]); printf("sli->no\n");
^~~
thrdatd.c:862:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) printf("%d ",sli->no[i]); printf("sli->no\n");
^~~~~~
thrdatd.c:863:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) printf("%d ",sli->co[i]); printf("sli->co\n");
^~~
thrdatd.c:863:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) printf("%d ",sli->co[i]); printf("sli->co\n");
^~~~~~
thrdatd.c:864:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<sli->nlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n");
^~~
thrdatd.c:864:51: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<sli->nlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n");
^~~~~~
thrdatd.c:865:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<sli->nmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n");
^~~
thrdatd.c:865:51: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<sli->nmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n");
^~~~~~
thrdatd.c:1014:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(k=0;k<nsc;k++) printf("%d ",sai->al[k]); printf("sai->al\n");
^~~
thrdatd.c:1014:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(k=0;k<nsc;k++) printf("%d ",sai->al[k]); printf("sai->al\n");
^~~~~~
thrdatd.c:1015:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(k=0;k<nmt;k++) printf("%d ",sai->sq[k]); printf("sai->sq\n");
^~~
thrdatd.c:1015:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(k=0;k<nmt;k++) printf("%d ",sai->sq[k]); printf("sai->sq\n");
^~~~~~
thrdatd.c:1017:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) printf("%d ",sli->no[i]); printf("sli->no\n");
^~~
thrdatd.c:1017:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) printf("%d ",sli->no[i]); printf("sli->no\n");
^~~~~~
thrdatd.c:1018:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) printf("%d ",sli->co[i]); printf("sli->co\n");
^~~
thrdatd.c:1018:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) printf("%d ",sli->co[i]); printf("sli->co\n");
^~~~~~
thrdatd.c:1019:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n");
^~~
thrdatd.c:1019:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n");
^~~~~~
thrdatd.c:1020:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n");
^~~
thrdatd.c:1020:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n");
^~~~~~
thrdatd.c:1244:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0;i<nsc;i++) free(spe->gss[i]); free(spe->gss);
^~~
thrdatd.c:1244:39: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0;i<nsc;i++) free(spe->gss[i]); free(spe->gss);
^~~~
thrdatd.c:1251:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<ndi; i++) free(spn->nrr[i]); free(spn->nrr);
^~~
thrdatd.c:1251:41: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<ndi; i++) free(spn->nrr[i]); free(spn->nrr);
^~~~
thrdatd.c:1255:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<ndi; i++) free(spn->nrp[i]); free(spn->nrp);
^~~
thrdatd.c:1255:41: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<ndi; i++) free(spn->nrp[i]); free(spn->nrp);
^~~~
thrdatd.c:1259:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<ndi; i++) free(spn->nrf[i]); free(spn->nrf);
^~~
thrdatd.c:1259:41: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<ndi; i++) free(spn->nrf[i]); free(spn->nrf);
^~~~
thrdatd.c:1260:1: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<ndi; i++) free(spn->frf[i]); free(spn->frf);
^~~
thrdatd.c:1260:41: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<ndi; i++) free(spn->frf[i]); free(spn->frf);
^~~~
thrdatd.c:201:8: warning: variable 'hh' set but not used [-Wunused-but-set-variable]
float hh;
^~
thrdatd.c:198:6: warning: variable 'rf' set but not used [-Wunused-but-set-variable]
int rf; /* Reference position for a core element */
^~
thrdatd.c:188:14: warning: unused variable 'm' [-Wunused-variable]
int i,j,k,l,m,n; /* Counters */
^
thrdatd.c:188:12: warning: unused variable 'l' [-Wunused-variable]
int i,j,k,l,m,n; /* Counters */
^
thrdatd.c:171:6: warning: variable 'nrp' set but not used [-Wunused-but-set-variable]
int nrp; /* Number of residue-peptide contacts in motif */
^~~
thrdatd.c:170:6: warning: variable 'nrr' set but not used [-Wunused-but-set-variable]
int nrr; /* Number of residue-residue contacts in motif */
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdbwfi.c
thrdbwfi.c: In function 'bwfi':
thrdbwfi.c:114:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
thrdbwfi.c:102:13: warning: 'nt' may be used uninitialized in this function [-Wmaybe-uninitialized]
ct=ttb->mx; for(i=0; i<=nt; i++) {
^~~
thrdbwfi.c:89:20: warning: 'nz' may be used uninitialized in this function [-Wmaybe-uninitialized]
cw=0.; ct=ttb->mx; for(i=0; i<=nz; i++) {
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdcpal.c
thrdcpal.c: In function 'cpal':
thrdcpal.c:210:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdcpll.c
thrdcpll.c: In function 'cpll':
thrdcpll.c:74:5: warning: variable 'nrt' set but not used [-Wunused-but-set-variable]
int nrt; /* Number of residue types */
^~~
thrdcpll.c:229:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
thrdcpll.c:220:15: warning: 'r2' may be used uninitialized in this function [-Wmaybe-uninitialized]
cl->rf.t2[k]=r2;
~~~~~~~~~~~~^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdcprl.c
thrdcprl.c: In function 'cprl':
thrdcprl.c:261:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdcxei.c
thrdcxei.c: In function 'cxei':
thrdcxei.c:94:15: warning: variable 'ms' set but not used [-Wunused-but-set-variable]
int ntot, ms;
^~
thrdcxei.c:205:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrddgri.c
thrddgri.c: In function 'g':
thrddgri.c:72:5: warning: variable 's0' set but not used [-Wunused-but-set-variable]
int s0;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdrsmp.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdsal0.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdsalr.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdsalu.c
thrdsalu.c: In function 'salu':
thrdsalu.c:83:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdsgoi.c
thrdsgoi.c: In function 'sgoi':
thrdsgoi.c:98:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<nsc; i++) si[i]=i; break; }
^~~
thrdsgoi.c:98:35: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<nsc; i++) si[i]=i; break; }
^~~~~
thrdsgoi.c:115:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<nsc; i++) to[i]=0; break; }
^~~
thrdsgoi.c:115:33: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<nsc; i++) to[i]=0; break; }
^~~~~
thrdsgoi.c:119:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i=0; i<nsc; i++) to[i]=1; break; }
^~~
thrdsgoi.c:119:33: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'for'
for(i=0; i<nsc; i++) to[i]=1; break; }
^~~~~
thrdsgoi.c:123:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdslo0.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdslor.c
thrdslor.c: In function 'slor':
thrdslor.c:90:6: warning: 'mp' may be used uninitialized in this function [-Wmaybe-uninitialized]
int *mp; /* Motif-derived loop length limits */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdslou.c
thrdslou.c: In function 'slou':
thrdslou.c:114:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdspci.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdspea.c
thrdspea.c: In function 'spea':
thrdspea.c:91:9: warning: variable 'nrt' set but not used [-Wunused-but-set-variable]
int nrt; /* Number of residue types in potential */
^~~
thrdspea.c:189:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdspel.c
thrdspel.c: In function 'spel':
thrdspel.c:88:9: warning: variable 'nrt' set but not used [-Wunused-but-set-variable]
int nrt; /* Number of residue types in potential */
^~~
thrdspel.c:188:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdspni.c
thrdspni.c: In function 'spni':
thrdspni.c:238:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdttb0.c
thrdttb0.c: In function 'ttb0':
thrdttb0.c:75:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdttbi.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF thrdzsc.c
thrdzsc.c: In function 'zsc':
thrdzsc.c:107:7: warning: unused variable 'gs' [-Wunused-variable]
int g,gs;
^~
thrdzsc.c:102:18: warning: unused variable 'zsc' [-Wunused-variable]
float tg,tgp,tgm,zsc; /* Energy of shuffled sequence */
^~~
thrdzsc.c:95:5: warning: unused variable 'ps' [-Wunused-variable]
int ps,ms,cs,
^~
thrdzsc.c:80:5: warning: unused variable 'temp' [-Wunused-variable]
int temp; /* Random index of the query sequence */
^~~~
thrdzsc.c:79:2: warning: unused variable 'kk' [-Wunused-variable]
kk,itr,ii,jj; /* Counters */
^~
thrdzsc.c:369:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
thrdzsc.c:357:39: warning: 'tg_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
ttb->zsc[i_max]=ScalingFactor*(tg_max-avg)/disp;
~~~~~~~^~~~~
rm -f libncbimmdb.a
ar cru libncbimmdb.a corematx.o dvncode.o objmmdb1.o objmmdb2.o objmmdb3.o objcn3d.o mmdbapi.o mmdbapi1.o mmdbapi2.o mmdbapi3.o mmdbapi4.o mmdbentr.o vastsubs.o prunebsc.o objcdd.o cddutil.o cddposutil.o objmime.o strucapi.o thrdalgs.o thrdatd.o thrdbwfi.o thrdcpal.o thrdcpll.o thrdcprl.o thrdcxei.o thrddgri.o thrdrsmp.o thrdsal0.o thrdsalr.o thrdsalu.o thrdsgoi.o thrdslo0.o thrdslor.o thrdslou.o thrdspci.o thrdspea.o thrdspel.o thrdspni.o thrdttb0.o thrdttbi.o thrdzsc.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbimmdb.a ../lib
ranlib ../lib/libncbimmdb.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF csim.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from csim.c:74:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
csim.c: In function 'set_pam_200':
csim.c:163:29: warning: missing braces around initializer [-Wmissing-braces]
static Int2 wgts[23][23] = { /* the PAM200 matrix */
^
csim.c:163:29: note: (near initialization for 'wgts')
csim.c:196:9: warning: array subscript has type 'char' [-Wchar-subscripts]
V[achars[i]][achars[j]]=10*(wgts[i][j]);
^
csim.c:196:20: warning: array subscript has type 'char' [-Wchar-subscripts]
V[achars[i]][achars[j]]=10*(wgts[i][j]);
^
csim.c: In function 'set_pam_file':
csim.c:228:13: warning: array subscript has type 'char' [-Wchar-subscripts]
V[alph[i]][alph[j]]=(Int2)(10*weight);
^
csim.c:228:22: warning: array subscript has type 'char' [-Wchar-subscripts]
V[alph[i]][alph[j]]=(Int2)(10*weight);
^
csim.c: In function 'big_pass':
csim.c:668:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[i]];
^
csim.c:692:23: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i, j, c, p+va[B[j]]) /* diagonal */
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c: In function 'diff1':
csim.c:799:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[1]];
^
csim.c:805:21: warning: array subscript has type 'char' [-Wchar-subscripts]
{ c = va[B[j]] - ( GAP(j-1) + GAP(N-j) );
^
csim.c:849:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[i]];
^
csim.c:853:43: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i+(s_ptr->I), (s_ptr->J)+j, c, s+v[A[i]][B[j]])
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:853:49: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i+(s_ptr->I), (s_ptr->J)+j, c, s+v[A[i]][B[j]])
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:874:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[i+1]];
^
csim.c:878:43: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i+1+s_ptr->I, j+1+s_ptr->J, c, s+v[A[i+1]][B[j+1]])
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:878:51: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i+1+s_ptr->I, j+1+s_ptr->J, c, s+v[A[i+1]][B[j+1]])
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:893:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (c > midc || CC[j] != DD[j] && RR[j] == SS[j])
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
csim.c: In function 'locate':
csim.c:974:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[i]];
^
csim.c:991:23: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i, j, c, p+va[B[j]]) /* diagonal */
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:1030:14: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[(plist->m1)]];
^
csim.c:1043:33: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG((plist->m1), j, c, p+va[B[j]]) /* diagonal */
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:1061:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~~~~~~^~~~~~~~~~
csim.c:1062:44: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| fi > rl && fj > cl ) )
~~~~~~~~^~~~~~~~~~
csim.c:1071:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~~~~~~^~~~~~~~~~
csim.c:1072:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| fi > rl && fj > cl ) )
~~~~~~~~^~~~~~~~~~
csim.c:1084:14: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[B[(plist->n1)]];
^
csim.c:1110:40: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i, (plist->n1), c, p+va[A[i]])
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c:1128:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~~~~~~^~~~~~~~~~
csim.c:1129:29: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| fi > rl && fj > cl ) )
~~~~~~~~^~~~~~~~~~
csim.c:1138:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~~~~~~^~~~~~~~~~
csim.c:1139:47: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| fi > rl && fj > cl ) )
~~~~~~~~^~~~~~~~~~
csim.c:1144:29: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ( (plist->m1) == 1 && (plist->n1) == 1 || no_cross(flag, plist, &rl, &cl) )
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
csim.c: In function 'small_pass':
csim.c:1186:13: warning: array subscript has type 'char' [-Wchar-subscripts]
va = v[A[i]];
^
csim.c:1212:23: warning: array subscript has type 'char' [-Wchar-subscripts]
DIAG(i, j, c, p+va[B[j]]) /* diagonal */
^
csim.c:440:11: note: in definition of macro 'DIAG'
x = ( pvalue ); \
^~~~~~
csim.c: In function 'display':
csim.c:1360:5: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (i < M || j < N)
^
csim.c: In function 'set_pam_file':
csim.c:227:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%f", &weight); /**get the matrix**/
^~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
csim.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: csim.c,v 6.2 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
csim.c: In function 'SIM':
csim.c:1071:62: warning: 'dj' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~^~~~
csim.c:928:23: note: 'dj' was declared here
register Int4 di, dj; /* end-point associated with d */
^~
csim.c:1071:51: warning: 'di' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~^~~~
csim.c:928:19: note: 'di' was declared here
register Int4 di, dj; /* end-point associated with d */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF db_slist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/list.h:56,
from db_slist.c:97:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
db_slist.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: db_slist.c,v 6.2 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF dust.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from dust.c:102:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dust.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: dust.c,v 6.5 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_dust.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from blast_dust.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_dust.c:39:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF falign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from falign.c:92:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
falign.c: In function 'fbld_table':
falign.c:490:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*++q];
^
falign.c:494:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'bbld_table':
falign.c:517:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*--q];
^
falign.c:521:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'rcbld_table':
falign.c:544:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*--q];
^
falign.c:548:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'ex_table':
falign.c:567:42: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'free_all':
falign.c:668:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = cdiag_prev[l]) {
^~
falign.c: In function 'scan':
falign.c:688:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*++q];
^
falign.c:694:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c:710:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = diag_prev[len1+len2-1-pos]) {
^~
falign.c:719:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df=diag_prev[l]) {
^~
falign.c: In function 'fscan':
falign.c:763:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*++q];
^
falign.c:769:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'bscan':
falign.c:794:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*--q];
^
falign.c:800:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'rfscan':
falign.c:870:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*++q];
^
falign.c:876:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c:881:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = diag_prev[len1+se2-pos]) {
^~
falign.c:889:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = diag_prev[len1+se2-pos]) {
^~
falign.c: In function 'trcscan':
falign.c:1476:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*--q];
^
falign.c:1482:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*q];
^
falign.c: In function 'rclocal':
falign.c:1547:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = diag_prev[ocur_diag]) {
^~
falign.c: In function 'enterS':
falign.c:1897:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (s = findS(f->bgf)) {
^~
falign.c: In function 'local':
falign.c:1958:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = diag_prev[cur_diag]) {
^~
falign.c: In function 'align':
falign.c:1999:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = cdiag_prev[cur_diag]) {
^~
falign.c: In function 'calign':
falign.c:2054:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = cdiag_prev[cur_diag]) {
^~
falign.c: In function 'malign':
falign.c:2109:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = cdiag_prev[cur_diag]) {
^~
At top level:
falign.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: falign.c,v 6.3 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF g_any.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from g_any.c:89:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
g_any.c: In function 'k_align':
g_any.c:212:10: warning: array subscript has type 'char' [-Wchar-subscripts]
va = vv[A[i+1]];
^
g_any.c:229:26: warning: array subscript has type 'char' [-Wchar-subscripts]
if (j < J2) c = s + va[B[j+1]];
^
g_any.c:319:10: warning: array subscript has type 'char' [-Wchar-subscripts]
b2 = PP[t1][b1];
^
g_any.c:322:10: warning: array subscript has type 'char' [-Wchar-subscripts]
t2 = PT[t1][b1];
^
g_any.c: In function 'z_ALIGN':
g_any.c:367:7: warning: variable 'check_score' set but not used [-Wunused-but-set-variable]
Int4 check_score;
^~~~~~~~~~~
g_any.c: In function 'CHECK_SCORE':
g_any.c:492:13: warning: array subscript has type 'char' [-Wchar-subscripts]
score = vv[A[++i]][B[++j]] + score;
^
g_any.c:492:21: warning: array subscript has type 'char' [-Wchar-subscripts]
score = vv[A[++i]][B[++j]] + score;
^
At top level:
g_any.c:428:35: warning: 'CLINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:428:24: warning: 'BLINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:428:13: warning: 'ALINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: g_any.c,v 6.5 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF sim2.c
sim2.c: In function 'SIM2':
sim2.c:19:16: warning: unused variable 'compB' [-Wunused-variable]
CharPtr A, B, compB = NULL;
^~~~~
sim2.c:17:26: warning: unused variable 'sapC' [-Wunused-variable]
SeqAlignPtr sap = NULL, sapC=NULL, out_sap, out_sapC;
^~~~
At top level:
sim2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: sim2.c,v 6.1 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF sim3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from sim3.c:28:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sim3.c: In function 'locate':
sim3.c:103:34: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*p++];
^
sim3.c:105:43: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*p++];
^
sim3.c:113:48: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*p++];
^
sim3.c:115:57: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*p++];
^
sim3.c:129:48: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = (ecode << 2) + encoding[*p++];
^
sim3.c:133:57: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*p++];
^
sim3.c:152:45: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode1 = ((ecode1 & mask) << 2) + encoding[*q++];
^
sim3.c:155:57: warning: array subscript has type 'char' [-Wchar-subscripts]
ecode = ((ecode & mask) << 2) + encoding[*p++];
^
At top level:
sim3.c:1067:16: warning: 'is_end_seg' defined but not used [-Wunused-function]
static Boolean is_end_seg(EditScriptPtr curr, EditScriptPtr head)
^~~~~~~~~~
sim3.c:1056:13: warning: 'get_current_pos' defined but not used [-Wunused-function]
static Int4 get_current_pos(Int4Ptr pos, Int4 length)
^~~~~~~~~~~~~~~
sim3.c:1048:13: warning: 'get_start_pos' defined but not used [-Wunused-function]
static Int4 get_start_pos(SeqLocPtr slp)
^~~~~~~~~~~~~
sim3.c:806:13: warning: 'Print_Script' defined but not used [-Wunused-function]
static void Print_Script(EditScriptPtr head, Int4 M, Int4 N, CharPtr A, CharPtr B)
^~~~~~~~~~~~
sim3.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: sim3.c,v 6.2 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
sim3.c: In function 'locate':
sim3.c:230:17: warning: 'paired_bj' may be used uninitialized in this function [-Wmaybe-uninitialized]
*j2 = paired_bj+1;
~~~~~~~~~^~
sim3.c:229:6: warning: 'paired_fj' may be used uninitialized in this function [-Wmaybe-uninitialized]
*j1 = paired_fj;
~~~~^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF sim4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from sim4.c:18:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sim4.c: In function 'sim4x':
sim4.c:630:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while(i1 = sgp->Blist[i].next) {
^~~~~
sim4.c: In function 'greedy':
sim4.c:1770:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (row == 0 && col == 0)
^
sim4.c:1794:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (row == 0)
^
sim4.c:1838:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (col == 0)
^
sim4.c:1962:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (row == m && col == n)
^
sim4.c:1991:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (row == m)
^
sim4.c:2037:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (col == n)
^
sim4.c: In function 'DISPLAY':
sim4.c:2625:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (a >= ALINE+50 || i >= M && j >= N)
~~~~~~~^~~~~~~~~
At top level:
sim4.c:2592:13: warning: 'DISPLAY' defined but not used [-Wunused-function]
static void DISPLAY(Int1 A[], Int1 B[], Int4 M, Int4 N, Int4 S[], Int4 AP, Int4 BP)
^~~~~~~
sim4.c:2563:13: warning: 'S2A' defined but not used [-Wunused-function]
static void S2A(EditScriptPtr head, Int4Ptr S)
^~~
sim4.c:2499:13: warning: 'Print_Script' defined but not used [-Wunused-function]
static void Print_Script(EditScriptPtr head, Int4 M, Int4 N, data_t *data)
^~~~~~~~~~~~
sim4.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: sim4.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
sim4.c: In function 'locate':
sim4.c:2919:19: warning: 'paired_bj' may be used uninitialized in this function [-Wmaybe-uninitialized]
*j2 = paired_bj + 1;
~~~~~~~~~~^~~
sim4.c:2918:7: warning: 'paired_fj' may be used uninitialized in this function [-Wmaybe-uninitialized]
*j1 = paired_fj;
~~~~^~~~~~~~~~~
sim4.c: In function 'greedy.isra.12':
sim4.c:2112:37: warning: 'forth' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (m-min_row[back]>=max_row[forth]) {
^
sim4.c:2112:22: warning: 'back' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (m-min_row[back]>=max_row[forth]) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF simutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from simutil.c:103:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
simutil.c: In function 'make_align':
simutil.c:495:9: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
At top level:
simutil.c:848:16: warning: 'is_alu_seq' defined but not used [-Wunused-function]
static Boolean is_alu_seq(CharPtr name)
^~~~~~~~~~
simutil.c:814:16: warning: 're_cal_score' defined but not used [-Wunused-function]
static FloatHi re_cal_score(RecordEndsPtr o_rep, RecordEndsPtr n_rep)
^~~~~~~~~~~~
simutil.c:344:17: warning: 'convert' defined but not used [-Wunused-function]
static ScorePtr convert(Int4Ptr x, Int4Ptr y, Int4Ptr start, Int4Ptr length, Int4 n, SeqLocPtr locx, SeqLocPtr locy, Int2Ptr numseg, FloatHiPtr SegScores)
^~~~~~~
simutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: simutil.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
simutil.c: In function 'sort_align_list':
simutil.c:602:20: warning: 'score2' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (score2 > score1) { /* swap */
^
simutil.c:602:20: warning: 'score1' may be used uninitialized in this function [-Wmaybe-uninitialized]
simutil.c: In function 'get_top_K_alignment':
simutil.c:659:16: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (score < cut_off) break;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF slist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/list.h:56,
from slist.c:101:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
slist.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: slist.c,v 6.2 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF sec.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from sec.c:67:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sec.c: In function 'Region':
sec.c:268:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:268:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:292:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:292:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:321:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:321:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:345:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:345:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:428:35: warning: array subscript has type 'char' [-Wchar-subscripts]
diag_score = diag_score + V[seq1[i]][seq2[j]];
^
sec.c:428:44: warning: array subscript has type 'char' [-Wchar-subscripts]
diag_score = diag_score + V[seq1[i]][seq2[j]];
^
At top level:
sec.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: sec.c,v 6.1 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
sec.c: In function 'Region':
sec.c:504:11: warning: 'old_l' may be used uninitialized in this function [-Wmaybe-uninitialized]
LB[i] = old_l;
~~~~~~^~~~~~~
sec.c:72:37: warning: 'ppj' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Min(x,y) ((x) <= (y) ? (x) : (y))
^
sec.c:172:20: note: 'ppj' was declared here
Int4 pi, pj, ppi, ppj;
^~~
sec.c:172:15: warning: 'ppi' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 pi, pj, ppi, ppj;
^~~
sec.c:172:7: warning: 'pi' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 pi, pj, ppi, ppj;
^~
sec.c:502:10: warning: 'ej' may be used uninitialized in this function [-Wmaybe-uninitialized]
tr = Min(cj + Width, ej);
^
sec.c:163:15: warning: 'ei' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 bi, bj, ei, ej, t;
^~
sec.c:71:37: warning: 'bj' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Max(x,y) ((x) >= (y) ? (x) : (y))
^
sec.c:163:11: note: 'bj' was declared here
Int4 bi, bj, ei, ej, t;
^~
sec.c:462:16: warning: 'bi' may be used uninitialized in this function [-Wmaybe-uninitialized]
MemFree(LB+bi);
^
sec.c:463:16: warning: 'RB' may be used uninitialized in this function [-Wmaybe-uninitialized]
MemFree(RB+bi);
~~^~~
sec.c:462:16: warning: 'LB' may be used uninitialized in this function [-Wmaybe-uninitialized]
MemFree(LB+bi);
~~^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF tfuns.c
tfuns.c: In function 'find_orf':
tfuns.c:846:26: warning: unused variable 'into' [-Wunused-variable]
IntFuzzPtr infrom=NULL, into=NULL;
^~~~
tfuns.c:846:13: warning: unused variable 'infrom' [-Wunused-variable]
IntFuzzPtr infrom=NULL, into=NULL;
^~~~~~
At top level:
tfuns.c:956:13: warning: 'find_orf_from_circle' defined but not used [-Wunused-function]
static void find_orf_from_circle (SeqPortPtr spp, Boolean flagIsCircle,
^~~~~~~~~~~~~~~~~~~~
tfuns.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: tfuns.c,v 6.14 2007/10/10 16:10:17 bollin Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF toasn3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/gather.h:166,
from toasn3.c:10:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
toasn3.c: In function 'FindOrg':
toasn3.c:1311:17: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
toasn3.c: In function 'CheckQualsWithComm':
toasn3.c:1592:18: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toasn3.c: In function 'CheckQuals':
toasn3.c:1629:18: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toasn3.c: In function 'CountSourceFeat':
toasn3.c:2415:13: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
toasn3.c:2406:19: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
toasn3.c: In function 'TASNTrimInternalSemicolons':
toasn3.c:3986:12: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
CharPtr tmp;
^~~
toasn3.c: In function 'ImpFeatToProtRef':
toasn3.c:4672:13: warning: variable 'lfree' set but not used [-Wunused-but-set-variable]
Boolean lfree = FALSE, partial5, partial3;
^~~~~
toasn3.c: In function 'RemovePeptideImpFeats':
toasn3.c:4967:24: warning: variable 'ifp' set but not used [-Wunused-but-set-variable]
ImpFeatPtr ifp;
^~~
At top level:
toasn3.c:1572:16: warning: 'GetQualValue' defined but not used [-Wunused-function]
static CharPtr GetQualValue(GBQualPtr gbqual, CharPtr qual)
^~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from toasn3.c:19:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
toasn3.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: toasn3.c,v 6.133 2012/06/04 20:04:10 kans Exp $";
^~~~~
toasn3.c: In function 'GetOriginalBeforeAdjustment':
toasn3.c:4185:29: warning: 'last' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (last != NULL && last->choice != SEQLOC_INT) /* this is too weird */
~~~~^~~~~~~~
toasn3.c: In function 'FixNucProtSet':
toasn3.c:2057:21: warning: 'bseg' may be used uninitialized in this function [-Wmaybe-uninitialized]
bseg->descr = descr;
~~~~~~~~~~~~^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF toporg.c
toporg.c: In function 'ChkSegset':
toporg.c:62:51: warning: variable 'is_title' set but not used [-Wunused-but-set-variable]
Boolean is_org = FALSE, is_modif = FALSE, is_title = FALSE;
^~~~~~~~
toporg.c:61:17: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toporg.c:58:17: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
toporg.c:53:17: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp = NULL, set_vnp = NULL, upd_date_vnp = NULL;
^~~
toporg.c: In function 'ChkNucProt':
toporg.c:594:51: warning: variable 'is_title' set but not used [-Wunused-but-set-variable]
Boolean is_org = FALSE, is_modif = FALSE, is_title = FALSE;
^~~~~~~~
toporg.c: In function 'StripBSfromParts':
toporg.c:1280:17: warning: variable 'empty' set but not used [-Wunused-but-set-variable]
Boolean empty;
^~~~~
toporg.c:1279:17: warning: variable 'bsmp' set but not used [-Wunused-but-set-variable]
BSMapPtr bsmp;
^~~~
toporg.c:1278:29: warning: variable 'set_vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr descr, vnp, set_vnp;
^~~~~~~
toporg.c: In function 'MapsToGenref':
toporg.c:1944:17: warning: variable 'loc' set but not used [-Wunused-but-set-variable]
SeqLocPtr loc;
^~~
toporg.c:1939:17: warning: variable 'descr' set but not used [-Wunused-but-set-variable]
ValNodePtr descr = NULL, head, last, vnp;
^~~~~
toporg.c: In function 'FindOldLineage':
toporg.c:2521:17: warning: variable 'lineage' set but not used [-Wunused-but-set-variable]
CharPtr lineage;
^~~~~~~
toporg.c: In function 'ArePubsMergeableForFig':
toporg.c:4461:36: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
|| !cgp_fig->serial_number != cgp_nofig->serial_number) {
^~
toporg.c: In function 'StripBadTitleFromProteinProducts':
toporg.c:4968:22: warning: variable 'tech' set but not used [-Wunused-but-set-variable]
Uint1 tech;
^~~~
At top level:
toporg.c:3010:13: warning: 'BarCodeTechToKeyword' defined but not used [-Wunused-function]
static void BarCodeTechToKeyword (BioseqPtr bsp, Pointer userdata)
^~~~~~~~~~~~~~~~~~~~
toporg.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: toporg.c,v 6.197 2012/05/10 21:20:48 kans Exp $";
^~~~~
toporg.c: In function 'MergeEquivCitSubs':
toporg.c:3782:7: warning: 'csp1' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (DateMatch (csp1->date, csp2->date, FALSE) != 0) return FALSE;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
toporg.c:3802:18: note: 'csp1' was declared here
CitSubPtr csp1, csp2;
^~~~
toporg.c: In function 'CheckMaps':
toporg.c:1715:11: warning: 'to' may be used uninitialized in this function [-Wmaybe-uninitialized]
sip->to = to;
~~~~~~~~^~~~
toporg.c:1696:24: note: 'to' was declared here
Int4 from, to;
^~
toporg.c:1714:13: warning: 'from' may be used uninitialized in this function [-Wmaybe-uninitialized]
sip->from = from;
~~~~~~~~~~^~~~~~
toporg.c:1696:18: note: 'from' was declared here
Int4 from, to;
^~~~
toporg.c: In function 'ConvertSegSetToDeltaSeq':
toporg.c:6566:3: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqMgrClearFeatureIndexes (entityID, NULL);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF pobutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from ../include/pobutil.h:7,
from pobutil.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pobutil.c: In function 'build_repeat_feat':
pobutil.c:187:7: warning: unused variable 'c' [-Wunused-variable]
Char c='%';
^
pobutil.c: In function 'merge_StdSeg':
pobutil.c:1033:7: warning: variable 'start_1' set but not used [-Wunused-but-set-variable]
Int4 start_1, stop_1, start_2, stop_2;
^~~~~~~
pobutil.c:1031:7: warning: unused variable 'overlap' [-Wunused-variable]
Int4 overlap = -1;
^~~~~~~
In file included from ../include/ncbi.h:59:0,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from ../include/pobutil.h:7,
from pobutil.c:3:
pobutil.c: In function 'FindHumanRepeats':
../include/ncbimem.h:191:21: warning: 'memset' used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args]
#define Nlm_MemSet memset
^
../include/ncbimem.h:210:17: note: in expansion of macro 'Nlm_MemSet'
#define MemSet Nlm_MemSet
^~~~~~~~~~
pobutil.c:2380:2: note: in expansion of macro 'MemSet'
MemSet((Pointer) (&tmp), sizeof(ValNode), 0);
^~~~~~
../include/ncbimem.h:191:21: warning: 'memset' used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args]
#define Nlm_MemSet memset
^
../include/ncbimem.h:210:17: note: in expansion of macro 'Nlm_MemSet'
#define MemSet Nlm_MemSet
^~~~~~~~~~
pobutil.c:2381:2: note: in expansion of macro 'MemSet'
MemSet((Pointer) (&si), sizeof(SeqInt), 0);
^~~~~~
pobutil.c: In function 'AluFeat':
pobutil.c:2431:10: warning: variable 'my_userdata' set but not used [-Wunused-but-set-variable]
Pointer my_userdata;
^~~~~~~~~~~
At top level:
pobutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: pobutil.c,v 6.10 2007/05/07 13:30:54 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF stsutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from stsutil.c:88:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
stsutil.c: In function 'InitSTSSearch_r':
stsutil.c:270:10: warning: unused variable 'StsCount' [-Wunused-variable]
Int4 StsCount=0;
^~~~~~~~
stsutil.c: In function 'GetSTSEntry':
stsutil.c:635:13: warning: variable 'p' set but not used [-Wunused-but-set-variable]
CharPtr p;
^
stsutil.c: In function 'STSCalculateHash':
stsutil.c:753:26: warning: array subscript has type 'char' [-Wchar-subscripts]
if ((j = HashCode[*p++]) < 0)
^
stsutil.c: In function 'STSReverse':
stsutil.c:771:28: warning: array subscript has type 'char' [-Wchar-subscripts]
if ((*t = ComplCode[*s]) == 0)
^
stsutil.c: In function 'InitHashTable':
stsutil.c:910:21: warning: variable 'sts_uid' set but not used [-Wunused-but-set-variable]
CharPtr gb_uid, sts_uid;
^~~~~~~
stsutil.c:910:13: warning: variable 'gb_uid' set but not used [-Wunused-but-set-variable]
CharPtr gb_uid, sts_uid;
^~~~~~
stsutil.c:908:23: warning: variable 'gi' set but not used [-Wunused-but-set-variable]
Int4 id_sts, len, gi, StsCount = 0, StsInvalid =0;
^~
stsutil.c:908:10: warning: variable 'id_sts' set but not used [-Wunused-but-set-variable]
Int4 id_sts, len, gi, StsCount = 0, StsInvalid =0;
^~~~~~
stsutil.c:907:23: warning: unused variable 'error' [-Wunused-variable]
Int4 LineLength, error= FALSE;
^~~~~
At top level:
stsutil.c:892:13: warning: 'STSHashInitFree' defined but not used [-Wunused-function]
static void STSHashInitFree(STSHashInitPtr sts)
^~~~~~~~~~~~~~~
stsutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: stsutil.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF suggadj.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from suggadj.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
suggadj.c: In function 'score_possible_splice_sites':
suggadj.c:874:13: warning: array subscript has type 'char' [-Wchar-subscripts]
score = ( vx[seq_or_rev[putative_donor]]==3) ?10:0;
^
suggadj.c:875:13: warning: array subscript has type 'char' [-Wchar-subscripts]
score += (vx[seq_or_rev[putative_acceptor]]==3 )?10:0;
^
suggadj.c:878:14: warning: array subscript has type 'char' [-Wchar-subscripts]
score += ( vx[seq_or_rev[putative_donor+1]]==0 )?3:0;
^
suggadj.c:879:14: warning: array subscript has type 'char' [-Wchar-subscripts]
score += ( vx[seq_or_rev[putative_acceptor-1]]==2 )?3:0;
^
suggadj.c: In function 'check_split_codon':
suggadj.c:985:29: warning: array subscript has type 'char' [-Wchar-subscripts]
val_assuming_1_from_left= vx[seq_or_rev[left_ends+1]] * 16 +
^
suggadj.c:986:4: warning: array subscript has type 'char' [-Wchar-subscripts]
vx[seq_or_rev[right_starts-2]]*4+
^
suggadj.c:987:4: warning: array subscript has type 'char' [-Wchar-subscripts]
vx[seq_or_rev[right_starts-1]];
^
suggadj.c:998:29: warning: array subscript has type 'char' [-Wchar-subscripts]
val_assuming_2_from_left= vx[seq_or_rev[left_ends+1]] * 16 +
^
suggadj.c:999:4: warning: array subscript has type 'char' [-Wchar-subscripts]
vx[seq_or_rev[left_ends+2]] * 4 +
^
suggadj.c:1000:4: warning: array subscript has type 'char' [-Wchar-subscripts]
vx[seq_or_rev[right_starts-1]];
^
suggadj.c: In function 'overlapping_fixer':
suggadj.c:1370:18: warning: array subscript has type 'char' [-Wchar-subscripts]
test_val = vx[seq_or_rev[left_exon_ends]]*16 +
^
suggadj.c:1371:8: warning: array subscript has type 'char' [-Wchar-subscripts]
vx[seq_or_rev[right_exon_starts-1]];
^
suggadj.c:1373:20: warning: array subscript has type 'char' [-Wchar-subscripts]
test_val += vx[seq_or_rev[right_exon_starts-2]]*4;
^
suggadj.c:1375:20: warning: array subscript has type 'char' [-Wchar-subscripts]
test_val += vx[seq_or_rev[left_exon_ends+1]]*4;
^
At top level:
suggadj.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: suggadj.c,v 6.3 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF suggest.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from suggest.c:199:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
suggest.c: In function 'get_frames':
suggest.c:458:12: warning: array subscript has type 'char' [-Wchar-subscripts]
val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]];
^
suggest.c:458:26: warning: array subscript has type 'char' [-Wchar-subscripts]
val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]];
^
At top level:
suggest.c:1331:13: warning: 'ReportSuggestIntervalsError' defined but not used [-Wunused-function]
static void ReportSuggestIntervalsError (SeqRecPtr srp, CharPtr gen_txt)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
suggest.c:1222:1: warning: 'fprintf_m_stk_entry' defined but not used [-Wunused-function]
fprintf_m_stk_entry(FILE *fp, Int4 index, char *msg)
^~~~~~~~~~~~~~~~~~~
suggest.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: suggest.c,v 6.14 2009/04/10 17:22:14 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF suggslp.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from suggslp.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
suggslp.c: In function 'MakeReverseSequence':
suggslp.c:190:11: warning: array subscript has type 'char' [-Wchar-subscripts]
*t++ = r[*--s];
^
At top level:
suggslp.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: suggslp.c,v 6.6 2009/04/16 18:35:41 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blast.c:2572:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast.c: In function 'BlastReevaluateWithAmbiguities':
blast.c:2954:24: warning: variable 'query_end' set but not used [-Wunused-but-set-variable]
Uint1Ptr query_start, query_end, subject_real_start=NULL;
^~~~~~~~~
blast.c:2949:16: warning: variable 'hspcnt' set but not used [-Wunused-but-set-variable]
Int4 context, hspcnt, hspcnt_max, index, index1, status;
^~~~~~
blast.c: In function 'BlastGetVirtualOIDList':
blast.c:3179:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (virtual_oidlist = rdfp_chain->oidlist) {
^~
blast.c: In function 'BlastGetDbChunk':
blast.c:3210:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) {
^~
blast.c: In function 'BlastCreateQueryDNAP':
blast.c:4100:11: warning: variable 'strand_option' set but not used [-Wunused-but-set-variable]
Uint1 strand_option;
^~~~~~~~~~~~~
blast.c: In function 'BlastReapPartialHitlistByEvalue':
blast.c:6486:10: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
blast.c:6490:6: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if( !search->mult_queries )
^~
blast.c: In function 'BlastWordFinder_contig':
blast.c:7094:16: warning: variable 'bits_to_shift' set but not used [-Wunused-but-set-variable]
register Int4 bits_to_shift, min_diag_length, min_diag_mask;
^~~~~~~~~~~~~
blast.c: In function 'BlastWordExtend':
blast.c:7835:46: warning: variable 'leftscore' set but not used [-Wunused-but-set-variable]
BLAST_Score leftsum, rightsum, rightscore, leftscore;
^~~~~~~~~
blast.c: In function 'BlastNewWordExtend':
blast.c:7982:46: warning: variable 'leftscore' set but not used [-Wunused-but-set-variable]
BLAST_Score leftsum, rightsum, rightscore, leftscore;
^~~~~~~~~
blast.c: In function 'BlastNtWordFinder_mh':
blast.c:8843:23: warning: variable 'bits_to_shift' set but not used [-Wunused-but-set-variable]
register Int4 bits_to_shift, min_diag_length, min_diag_mask;
^~~~~~~~~~~~~
blast.c:8842:103: warning: variable 'compression_factor' set but not used [-Wunused-but-set-variable]
Int4 s_pos, q_off, s_off, offset, virtual_wordsize, wordsize, compressed_wordsize, compression_factor;
^~~~~~~~~~~~~~~~~~
blast.c: In function 'BlastNtWordFinder':
blast.c:9076:14: warning: variable 'bits_to_shift' set but not used [-Wunused-but-set-variable]
Int4 bits_to_shift, min_diag_length, min_diag_mask;
^~~~~~~~~~~~~
blast.c: In function 'BlastSaveCurrentHitlist':
blast.c:10115:11: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if( hitlist_max > 1 )
^
blast.c:9785:7: warning: variable 'query_length' set but not used [-Wunused-but-set-variable]
Int4 query_length;
^~~~~~~~~~~~
blast.c: In function 'SumHSPEvalue':
blast.c:10588:9: warning: variable 'gap_size' set but not used [-Wunused-but-set-variable]
Int4 gap_size, num, subject_length;
^~~~~~~~
blast.c: In function 'link_hsps':
blast.c:11267:10: warning: variable 'frame_change' set but not used [-Wunused-but-set-variable]
Boolean frame_change, linked_set, ignore_small_gaps;
^~~~~~~~~~~~
At top level:
blast.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast.c,v 6.451 2008/01/25 21:15:22 bealer Exp $";
^~~~~
blast.c: In function 'BLASTMergeHitLists.isra.4':
blast.c:6256:24: warning: 'op_type' may be used uninitialized in this function [-Wmaybe-uninitialized]
esp2->op_type = op_type;
~~~~~~~~~~~~~~^~~~~~~~~
blast.c:6058:10: note: 'op_type' was declared here
Uint1 op_type;
^~~~~~~
In file included from ../include/ncbi.h:59:0,
from blast.c:2572:
blast.c: In function 'blastMergeFilterLocs':
../include/ncbimem.h:232:23: warning: 'dup_slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
blast.c:3933:20: note: 'dup_slp' was declared here
SeqLocPtr slp, dup_slp, dup_head;
^~~~~~~
blast.c: In function 'BlastLinkHsps':
blast.c:10455:41: warning: 'orig_hitlist' may be used uninitialized in this function [-Wmaybe-uninitialized]
search->current_hitlist = orig_hitlist;
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blastutl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastutl.c:1836:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastutl.c: In function 'BlastSeqLocFilterEx':
blastutl.c:7554:11: warning: statement with no effect [-Wunused-value]
stop_timer("after repeat filtering");
^
blastutl.c: In function 'BlastPreliminaryGappedScore':
blastutl.c:9853:30: warning: variable 'query_length' set but not used [-Wunused-but-set-variable]
Int4 index, max_offset = 0, query_length, min_score;
^~~~~~~~~~~~
blastutl.c: In function 'BlastGetGappedScore':
blastutl.c:10282:11: warning: statement with no effect [-Wunused-value]
stop_timer("after BlastGappedScoreInternal");
^
At top level:
blastutl.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastutl.c,v 6.472 2010/12/10 18:47:12 madden Exp $";
^~~~~
blastutl.c: In function 'BlastNtFindWords':
blastutl.c:11445:10: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
end = MIN(end, len-initial_wordsize);
blastutl.c: In function 'BlastFindWords':
blastutl.c:11623:8: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
stop = MIN(stop, len);
blastutl.c:11711:18: warning: 'start_score2' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score2 += matrix[(Int4) *(str+index2)][*(words+index2)];
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:11717:15: warning: 'start_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
score += matrix[(Int4) *(str+wordsize-1)][index2];
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:11704:17: warning: 'first_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score = second_score+first_score;
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:11695:11: warning: 'diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
diff2 += diff;
~~~~~~^~~~~~~
blastutl.c: In function 'BlastNewFindWords_Old':
blastutl.c:11931:18: warning: 'start_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score2 += MtrxScorePosSearch(search->sbp,
blastutl.c:11924:17: warning: 'first_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score = second_score+first_score;
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:11915:11: warning: 'diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
diff2 += diff;
~~~~~~^~~~~~~
blastutl.c: In function 'BlastNewFindWordsEx':
blastutl.c:12124:30: warning: 'start_score2' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score2 += posMatrix[offset+index2][*(words+index2)];
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:12129:23: warning: 'start_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
score += posMatrix[offset+wordsize-1][index2];
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:12118:29: warning: 'first_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score = second_score + first_score;
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:12110:23: warning: 'diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
diff2 += diff;
~~~~~~^~~~~~~
blastutl.c: In function 'RealBlastGetGappedAlignmentTraceback':
blastutl.c:9008:42: warning: 'seqalign_array' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAlignPtr seqalign, seqalign_var, *seqalign_array;
^~~~~~~~~~~~~~
blastutl.c: In function 'SumBlastGetGappedAlignmentEx':
blastutl.c:9670:33: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
HeapSort(hsp_array+start,(stop-start),sizeof(BLAST_HSPPtr), score_compare_hsps);
~~~~~^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blastool.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastool.c:946:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastool.c: In function 'BlastScaleMatrix':
blastool.c:3032:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
blastool.c:3035:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if (new_lambda > lambda)
^~
blastool.c: In function 'OOFBlastHSPGetNumIdentical':
blastool.c:6081:9: warning: variable 'context' set but not used [-Wunused-but-set-variable]
Int2 context;
^~~~~~~
At top level:
blastool.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastool.c,v 6.292 2007/03/15 20:39:17 madden Exp $";
^~~~~
blastool.c: In function 'BlastCreateVirtualOIDList':
blastool.c:2556:24: warning: 'gilist' may be used uninitialized in this function [-Wmaybe-uninitialized]
BlastDoubleInt4Ptr gilist, real_gilist = NULL, *real_gilist_ptrs = NULL;
^~~~~~
blastool.c: In function 'BlastInsertList2Heap':
blastool.c:3595:31: warning: 'query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
context = hsp->query_offset / query_length;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
blastool.c: In function 'BlastFreeHeap':
blastool.c:3687:31: warning: 'query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
context = hsp->query_offset / query_length;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
blastool.c: In function 'BLASTFilterOverlapRegions':
blastool.c:4531:24: warning: 'next_tail' may be used uninitialized in this function [-Wmaybe-uninitialized]
tail->next = seqalign;
~~~~~~~~~~~^~~~~~~~~~
blastool.c: In function 'BlastPrintAlignInfo':
blastool.c:4800:23: warning: 'sap' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap->next = SeqAlignNew();
~~~~~~~~~~^~~~~~~~~~~~~~~
blastool.c: In function 'MegaBlastPrintAlignInfo':
blastool.c:963:17: warning: 'subject_seq_buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define fprintf blastool_fprintf
^~~~~~~~~~~~~~~~
blastool.c:5046:30: note: 'subject_seq_buffer' was declared here
CharPtr query_seq_buffer, subject_seq_buffer;
^~~~~~~~~~~~~~~~~~
blastool.c:963:17: warning: 'query_seq_buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define fprintf blastool_fprintf
^~~~~~~~~~~~~~~~
blastool.c:5046:12: note: 'query_seq_buffer' was declared here
CharPtr query_seq_buffer, subject_seq_buffer;
^~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blastconcat.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastconcat.c:89:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastconcat.c: In function 'BlastMakeFakeBspConcat':
blastconcat.c:648:12: warning: variable 'slp' set but not used [-Wunused-but-set-variable]
SeqLocPtr slp = NULL;
^~~
At top level:
blastconcat.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastconcat.c,v 1.14 2007/05/07 13:30:54 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF splutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from splutil.c:52:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
splutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: splutil.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gapxdrop.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/gapxdrop.h:150,
from gapxdrop.c:368:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gapxdrop.c: In function 'ALIGN_EX':
gapxdrop.c:864:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (s == 1)
^
gapxdrop.c:867:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (s == 2)
^
At top level:
gapxdrop.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: gapxdrop.c,v 6.76 2003/11/07 21:52:52 dondosha Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF bandalg0.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg0.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg0.c: In function 'g_band0_align':
bandalg0.c:273:9: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if(leftd >= 1)
^
At top level:
bandalg0.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg0.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF bandalg1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg1.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg1.c: In function 'gband_quadratic':
bandalg1.c:54:14: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int4 c, i, j;
^
bandalg1.c: In function 'g_band1_align':
bandalg1.c:205:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if(leftd >= 1)
^
At top level:
bandalg1.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg1.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF bandalg2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg2.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg2.c: In function 'gb_linear_align':
bandalg2.c:208:24: warning: variable 'misma' set but not used [-Wunused-but-set-variable]
register Int4 match, misma;
^~~~~
bandalg2.c:208:17: warning: variable 'match' set but not used [-Wunused-but-set-variable]
register Int4 match, misma;
^~~~~
bandalg2.c:207:18: warning: variable 'AA' set but not used [-Wunused-but-set-variable]
register Uint1 AA;
^~
At top level:
bandalg2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg2.c,v 6.5 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
bandalg2.c: In function 'gb_linear_align':
bandalg2.c:577:12: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
_INS(N - Y);
^
bandalg2.c:575:10: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
_DEL(M - X)
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF bandalg3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg3.c:37:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg3.c: In function 'gband_linear_qgap':
bandalg3.c:54:14: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int4 c, i, j;
^
At top level:
bandalg3.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg3.c,v 6.4 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
bandalg3.c: In function 'gband_linear_qgap':
bandalg3.c:314:16: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
else if(Y != rightd) _INS(rightd-Y)
^
bandalg3.c:185:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
bandalg3.c:313:21: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(X != M) _DEL(M - X)
^
bandalg3.c:185:25: note: 'X' was declared here
Int4 ib, best=MININT, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF bandalg4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg4.c:37:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg4.c: In function 'g_band4_align_small':
bandalg4.c:826:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (e == 1)
^
bandalg4.c:829:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (e == 2)
^
bandalg4.c:630:8: warning: variable 'band' set but not used [-Wunused-but-set-variable]
Int4 band, j;
^~~~
At top level:
bandalg4.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg4.c,v 6.4 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
bandalg4.c: In function 'g_band4_align':
bandalg4.c:534:22: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(X != M || Y != N) regA = regB = 1;
~~^~~~
bandalg4.c:534:12: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(X != M || Y != N) regA = regB = 1;
~~^~~~
bandalg4.c:569:7: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
g_band4_align(A, B, r, r + rmid - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MAX(-r, low), rmid - 1, tb, 2, legA, legB, 1, 1, data);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bandalg4.c:857:37: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
else if (Y != rightd) _INS(rightd - Y);
^
bandalg4.c:640:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
In file included from bandalg4.c:37:0:
../include/bandalgn.h:140:76: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
data->last = (data->last < 0) ? (data->sapp[-1] -= (k)) : (*data->sapp++ = -(k));
^
bandalg4.c:640:25: note: 'X' was declared here
Int4 ib, best=MININT, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF bandalg5.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg5.c:36:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg5.c: In function 'gband_q3gap':
bandalg5.c:56:14: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int4 c, i, j;
^
bandalg5.c: In function 'g_band5_align':
bandalg5.c:292:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (e == 1)
^
bandalg5.c:295:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (e == 2)
^
At top level:
bandalg5.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg5.c,v 6.3 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
bandalg5.c: In function 'gband_q3gap':
bandalg5.c:320:6: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (Y != rightd) _INS(rightd - Y);
^
bandalg5.c:146:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
bandalg5.c:319:22: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (X != M) _DEL(M - X);
^
bandalg5.c:146:25: note: 'X' was declared here
Int4 ib, best=MININT, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF bandalgn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from bandalgn.c:118:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalgn.c: In function 'ExtendSeqAlign':
bandalgn.c:1113:22: warning: variable 'ddp' set but not used [-Wunused-but-set-variable]
DenseDiagPtr ddp;
^~~
bandalgn.c: In function 'CC_ExtendSeqAlign':
bandalgn.c:1188:22: warning: variable 'ddp' set but not used [-Wunused-but-set-variable]
DenseDiagPtr ddp;
^~~
At top level:
bandalgn.c:699:14: warning: 'HSblastna_to_ncbi4na' defined but not used [-Wunused-variable]
static Uint1 HSblastna_to_ncbi4na[] = { 1, /* A, 0 */
^~~~~~~~~~~~~~~~~~~~
bandalgn.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalgn.c,v 6.17 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
bandalgn.c: In function 'LocalBandToEditBlock':
bandalgn.c:463:20: warning: 'edit_block' may be used uninitialized in this function [-Wmaybe-uninitialized]
lbsp->edit_block = edit_block;
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
bandalgn.c: In function 'SetLowUpFromBlast':
bandalgn.c:1053:7: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (maxsc < val) {
^
bandalgn.c:1060:7: warning: 'alnlen' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (maxlen < alnlen) {
^
bandalgn.c:1070:9: warning: 'maxdi_up' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxy = MAX(maxy,maxdi_up);
bandalgn.c:1069:9: warning: 'mindi_low' may be used uninitialized in this function [-Wmaybe-uninitialized]
miny = MIN(miny,mindi_low);
bandalgn.c:1062:10: warning: 'maxdi' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxy = maxdi + width;
~~~~~^~~~~~~~~~~~~~~
bandalgn.c:1063:10: warning: 'mindi' may be used uninitialized in this function [-Wmaybe-uninitialized]
miny = mindi - width;
~~~~~^~~~~~~~~~~~~~~
bandalgn.c: In function 'GetAlignExtremes':
bandalgn.c:1309:7: warning: 'y2' may be used uninitialized in this function [-Wmaybe-uninitialized]
*yy2 = y2;
~~~~~^~~~
bandalgn.c:1308:7: warning: 'y1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*yy1 = y1;
~~~~~^~~~
bandalgn.c:1307:7: warning: 'x2' may be used uninitialized in this function [-Wmaybe-uninitialized]
*xx2 = x2;
~~~~~^~~~
bandalgn.c:1306:7: warning: 'x1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*xx1 = x1;
~~~~~^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blastkar.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastkar.c:648:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastkar.c:2373:25: warning: 'Altschul_prob' defined but not used [-Wunused-variable]
static BLAST_LetterProb Altschul_prob[] = {
^~~~~~~~~~~~~
blastkar.c:2347:25: warning: 'Dayhoff_prob' defined but not used [-Wunused-variable]
static BLAST_LetterProb Dayhoff_prob[] = {
^~~~~~~~~~~~
blastkar.c:1121:13: warning: 'blosum62_20_prefs' defined but not used [-Wunused-variable]
static Int4 blosum62_20_prefs[BLOSUM62_20_VALUES_MAX] = {
^~~~~~~~~~~~~~~~~
blastkar.c:1053:21: warning: 'blosum62_20_values' defined but not used [-Wunused-variable]
static Nlm_FloatHi blosum62_20_values[BLOSUM62_20_VALUES_MAX][8] = {
^~~~~~~~~~~~~~~~~~
blastkar.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastkar.c,v 6.115 2006/12/14 17:08:19 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF actutils.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/actutils.h:103,
from actutils.c:232:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
actutils.c: In function 'SlideToHit':
actutils.c:346:23: warning: variable 'done' set but not used [-Wunused-but-set-variable]
Boolean inIsland, done;
^~~~
actutils.c:346:13: warning: variable 'inIsland' set but not used [-Wunused-but-set-variable]
Boolean inIsland, done;
^~~~~~~~
actutils.c: In function 'ResolveSpinConflict':
actutils.c:1484:35: warning: unused variable 'row2_conflict' [-Wunused-variable]
Boolean row1_conflict = FALSE, row2_conflict = FALSE;
^~~~~~~~~~~~~
actutils.c:1484:12: warning: unused variable 'row1_conflict' [-Wunused-variable]
Boolean row1_conflict = FALSE, row2_conflict = FALSE;
^~~~~~~~~~~~~
actutils.c: In function 'ACT_FindBestAlnByDotPlot':
actutils.c:2002:20: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
actutils.c:2001:20: warning: variable 'start2' set but not used [-Wunused-but-set-variable]
Int4 start2;
^~~~~~
actutils.c:2000:20: warning: variable 'start1' set but not used [-Wunused-but-set-variable]
Int4 start1;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from actutils.c:232:
actutils.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
actutils.c:3132:13: warning: 'DumpAlignments' defined but not used [-Wunused-function]
static void DumpAlignments (SeqAlignPtr salp)
^~~~~~~~~~~~~~
actutils.c:2927:13: warning: 'MapBioseqToBioseqSpecial' defined but not used [-Wunused-function]
static Int4 MapBioseqToBioseqSpecial(SeqAlignPtr sap, Int4 begin, Int4 fin, Int4 pos, Int4 which_end)
^~~~~~~~~~~~~~~~~~~~~~~~
actutils.c:1654:16: warning: 'SpinsConflict' defined but not used [-Wunused-function]
static Boolean SpinsConflict (SQN_nPtr spin1, SQN_nPtr spin2, Int4 fuzz, Int4 strand)
^~~~~~~~~~~~~
actutils.c:1392:13: warning: 'am_fix_strand' defined but not used [-Wunused-function]
static void am_fix_strand(SeqAlignPtr sap, Uint1 strand1, Uint1 strand2)
^~~~~~~~~~~~~
actutils.c:1375:16: warning: 'am_isa_gap' defined but not used [-Wunused-function]
static Boolean am_isa_gap(Int4 start, Int4 prevstop, Uint1 strand)
^~~~~~~~~~
actutils.c:749:13: warning: 'StateTableSearch' defined but not used [-Wunused-function]
static void StateTableSearch (TextFsaPtr tbl, CharPtr txt, Int4Ptr state, Int4 pos, ACT_sitelistPtr PNTR asp_prev, ACT_sitelistPtr PNTR asp_head)
^~~~~~~~~~~~~~~~
actutils.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: actutils.c,v 6.56 2008/10/22 17:19:22 bollin Exp $";
^~~~~
In file included from ../include/ncbi.h:59:0,
from ../include/actutils.h:103,
from actutils.c:232:
actutils.c: In function 'GetOldBlastAlignmentPiece':
../include/ncbimem.h:232:23: warning: 'program' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
actutils.c:3089:25: note: 'program' was declared here
CharPtr program;
^~~~~~~
actutils.c: In function 'ACT_FindPeakScores':
actutils.c:1342:31: warning: 'ats_newprev' may be used uninitialized in this function [-Wmaybe-uninitialized]
ats_newprev->next = ats_new;
~~~~~~~~~~~~~~~~~~^~~~~~~~~
actutils.c:1321:28: warning: 'ats_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
ats_prev->next = ats;
~~~~~~~~~~~~~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF posit.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from posit.c:402:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
posit.c: In function 'posDemographics':
posit.c:1110:17: warning: variable 'numSeqAligns' set but not used [-Wunused-but-set-variable]
Int4 numseq, numSeqAligns; /*number of matching sequences and SeqAligns*/
^~~~~~~~~~~~
posit.c: In function 'posFreqsToMatrix':
posit.c:1679:45: warning: operation on '*(*(posSearch->posPrivateMatrix + (sizetype)((unsigned int)length * 4u)) + (sizetype)((unsigned int)a * 4u))' may be undefined [-Wsequence-point]
posSearch->posPrivateMatrix[length][a] = posSearch->posPrivateMatrix[length][a] = BLAST_SCORE_MIN;
posit.c: In function 'posComputePseudoFreqs':
posit.c:1840:16: warning: variable 'lambda' set but not used [-Wunused-but-set-variable]
Nlm_FloatHi lambda; /*Karlin-Altschul parameter*/
^~~~~~
posit.c: In function 'WposComputation':
posit.c:1988:13: warning: variable 'numSeqAligns' set but not used [-Wunused-but-set-variable]
Int4 i, numSeqAligns, numseq, qlength;
^~~~~~~~~~~~
posit.c: In function 'posPrintInformation':
posit.c:2319:8: warning: variable 'querySize' set but not used [-Wunused-but-set-variable]
Int4 querySize;
^~~~~~~~~
posit.c: In function 'posFindAlignmentDimensions':
posit.c:3064:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c:3070:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c:3079:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c:3086:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c: In function 'posPreprocessAlignment':
posit.c:3137:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c:3152:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextLine, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
posit.c: In function 'posReadAlignment':
posit.c:3253:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(nextline, ALIGN_LINE_LENGTH,checkFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
posit.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: posit.c,v 6.88 2011/10/25 14:33:16 boratyng Exp $";
^~~~~
posit.c: In function 'posFindAlignmentDimensions':
posit.c:3090:20: warning: 'testCountSeqs' may be used uninitialized in this function [-Wmaybe-uninitialized]
testCountSeqs++;
~~~~~~~~~~~~~^~
posit.c: In function 'posComputeSequenceWeights':
posit.c:1447:36: warning: 'intervalSigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
posSearch->posSigma[qplace] = intervalSigma;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
posit.c:1424:11: warning: 'Sigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (Sigma > 0) {
^
posit.c: In function 'posReadCheckpoint':
posit.c:2873:28: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (i < pssm->numColumns || j < pssm->numRows) {
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
posit.c:2702:11: note: 'j' was declared here
Int4 i, j, c;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF lookup.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from lookup.c:308:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
lookup.c: In function 'lookup_get_memory':
lookup.c:555:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
Uint8 extra = ((Uint8)mem_struct->current) & ((Uint8) 63);
^
In file included from ../include/blastdef.h:922:0,
from ../include/blast.h:470,
from lookup.c:309:
lookup.c: In function 'MegaBlastBuildLookupTable':
../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
#define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT
^
lookup.c:1047:35: note: in expansion of macro 'GET_EXTRA_CODE_18_OPT'
GET_EXTRA_CODE_18_OPT(seq)) & no_bit0;
^~~~~~~~~~~~~~~~~~~~~
../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
#define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT
^
lookup.c:1051:35: note: in expansion of macro 'GET_EXTRA_CODE_18_OPT'
GET_EXTRA_CODE_18_OPT(seq)) & no_bit0;
^~~~~~~~~~~~~~~~~~~~~
../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
#define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT
^
lookup.c:1078:31: note: in expansion of macro 'GET_EXTRA_CODE_18_OPT'
GET_EXTRA_CODE_18_OPT(seq) | bit0;
^~~~~~~~~~~~~~~~~~~~~
../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
#define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT
^
lookup.c:1082:31: note: in expansion of macro 'GET_EXTRA_CODE_18_OPT'
GET_EXTRA_CODE_18_OPT(seq) | bit0;
^~~~~~~~~~~~~~~~~~~~~
lookup.c:914:25: warning: variable 'extra_code' set but not used [-Wunused-but-set-variable]
register Int4 ecode, extra_code;
^~~~~~~~~~
At top level:
lookup.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: lookup.c,v 6.59 2005/07/28 14:57:10 coulouri Exp $";
^~~~~
lookup.c: In function 'MegaBlastBuildLookupTable':
lookup.c:975:10: warning: 'word_weight' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (word_weight >= 12) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF readdb.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2052:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
readdb.c: In function 'readdb_parse_db_names':
readdb.c:2498:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (**filenames == '"')
^
readdb.c: In function 's_GetBlastDirInfo':
readdb.c:2729:32: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess]
memset(blast_dir, 0, sizeof(blast_dir));
^
readdb.c: In function 'IndexFileExists':
readdb.c:3315:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (rdfp->cih)
^~
readdb.c:3321:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (rdbap->first_oid > 0) {
^~
readdb.c:3395:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (rdfp->cih && rdfp->aliasfilebit == 0)
^~
readdb.c:3401:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (rdbap->first_oid > 0) {
^~
readdb.c: In function 'FindBlastDBFileEx':
readdb.c:3475:33: warning: unused variable 'envp' [-Wunused-variable]
CharPtr buffer, buffer1, envp = NULL;
^~~~
readdb.c: In function 'readdb_new_internalEx':
readdb.c:3553:25: warning: unused variable 'envp' [-Wunused-variable]
CharPtr charptr, envp = NULL;
^~~~
readdb.c: In function 'readdb_get_link':
readdb.c:4747:12: warning: variable 'loaded_new' set but not used [-Wunused-but-set-variable]
Boolean loaded_new = FALSE;
^~~~~~~~~~
readdb.c:4746:24: warning: variable 'last_used' set but not used [-Wunused-but-set-variable]
ReadDBFILEPtr last, last_used, rdfp_var;
^~~~~~~~~
readdb.c: In function 'readdb_check_oid':
readdb.c:4891:38: warning: comparisons like 'X<=Y<=Z' do not have their mathematical meaning [-Wparentheses]
if (rdfp_var->start <= oid <= rdfp_var->stop)
~~~~~~~~~~~~~~~~^~~~~~
readdb.c: In function 'readdb_seqid2fasta':
readdb.c:5231:22: warning: unused variable 'dummy_gi' [-Wunused-variable]
Int4 dummy_gi = 0; /* Not used, should have been handled above. */
^~~~~~~~
readdb.c:5175:13: warning: unused variable 'chptr' [-Wunused-variable]
CharPtr chptr = NULL;
^~~~~
readdb.c: In function 'FDBuildOldStyleDefline':
readdb.c:6361:33: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess]
MemSet(defline, '\0', sizeof(defline));
^
readdb.c: In function 'FDBLoadMembershipsTable':
readdb.c:8260:21: warning: variable 'fn_name' set but not used [-Wunused-but-set-variable]
const char* fn_name = NULL;
^~~~~~~
readdb.c: In function 'SeqIdE2Index':
readdb.c:8608:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((tsip->version > 0) && (tsip->release == NULL))
^~
readdb.c:8610:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
break;
^~~~~
readdb.c:8613:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (tsip->version > 0)
^~
readdb.c:8615:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
break;
^~~~~
readdb.c:8572:13: warning: unused variable 'tmp' [-Wunused-variable]
CharPtr tmp, ptr=NULL;
^~~
readdb.c:8571:11: warning: unused variable 'tmptype' [-Wunused-variable]
Uint1 tmptype;
^~~~~~~
readdb.c: In function 'SeqIdSetE2Index':
readdb.c:8876:14: warning: variable 'oldanp' set but not used [-Wunused-but-set-variable]
SeqIdPtr oldanp;
^~~~~~
readdb.c: In function 'FindDBbyGI':
readdb.c:11392:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (gi > cih->maxgi)
^~
readdb.c:11395:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
cigi = cih->ci + gi;
^~~~
readdb.c: In function 'Fastacmd_Search_ex':
readdb.c:12075:22: warning: variable 'guess_gi' set but not used [-Wunused-but-set-variable]
Int4 guess_gi = -1;
^~~~~~~~
readdb.c: In function 'DumpOneSequence':
readdb.c:12412:14: warning: unused variable 'numeric_id' [-Wunused-variable]
Boolean numeric_id = GetAccessionVersionFromSeqId(accn, &gi, &id, TRUE);
^~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from readdb.c:2062:
readdb.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
readdb.c:12824:1: warning: 'readdb_preload_index' defined but not used [-Wunused-function]
readdb_preload_index (ReadDBFILEPtr rdfp, Int4 first_db_seq,
^~~~~~~~~~~~~~~~~~~~
In file included from readdb.c:2055:0:
../include/ncbisami.h:191:14: warning: 'OneBit' defined but not used [-Wunused-variable]
static Uint1 OneBit[] = {0x80 , 0x40, 0x20, 0x10, 0x8, 0x4, 0x2, 0x1};
^~~~~~
../include/ncbisami.h:183:14: warning: 'PowersOfTwo' defined but not used [-Wunused-variable]
static Uint4 PowersOfTwo[] = {01,02,04,010,020,040,0100,0200,0400,01000,
^~~~~~~~~~~
readdb.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: readdb.c,v 6.548 2012/03/14 20:09:35 camacho Exp $";
^~~~~
readdb.c: In function 'readdb_get_taxonomy_names':
readdb.c:5674:28: warning: 'ufp_last' may be used uninitialized in this function [-Wmaybe-uninitialized]
ufp_last->next = ufp;
~~~~~~~~~~~~~~~^~~~~
readdb.c: In function 'readdb_get_descriptor':
readdb.c:6663:44: warning: 'new_defline_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
new_defline_length += StringLen(defline) + StringLen(id_buf);
^~
readdb.c: In function 'GetAccList':
readdb.c:11816:29: warning: 'AccListLast' may be used uninitialized in this function [-Wmaybe-uninitialized]
AccListLast->next = AccListTmp;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbisam.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbisam.c:198:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbisam.c: In function 'ISAMMakeStringIndex':
ncbisam.c:842:22: warning: unused variable 'file_pos' [-Wunused-variable]
Int4 file_pos = ftell(data->db_fd);
^~~~~~~~
ncbisam.c: In function 'ISAMInitSearch':
ncbisam.c:1399:10: warning: variable 'reserved2' set but not used [-Wunused-but-set-variable]
Int4 reserved2;
^~~~~~~~~
At top level:
ncbisam.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: ncbisam.c,v 6.34 2007/11/06 19:20:06 coulouri Exp $";
^~~~~
In file included from ../include/ncbi.h:59:0,
from ncbisam.c:198:
ncbisam.c: In function 'ISAMMakeIndex':
../include/ncbimem.h:232:23: warning: 'KeySamples' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
ncbisam.c:983:23: note: 'KeySamples' was declared here
Uint4Ptr KeyInfo, KeySamples;
^~~~~~~~~~
In file included from ../include/ncbi.h:59:0,
from ncbisam.c:198:
../include/ncbimem.h:232:23: warning: 'KeyDataSamples' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
ncbisam.c:984:34: note: 'KeyDataSamples' was declared here
NISAMKeyDataPtr KeyDataInfo, KeyDataSamples;
^~~~~~~~~~~~~~
ncbisam.c:984:21: warning: 'KeyDataInfo' may be used uninitialized in this function [-Wmaybe-uninitialized]
NISAMKeyDataPtr KeyDataInfo, KeyDataSamples;
^~~~~~~~~~~
ncbisam.c:983:14: warning: 'KeyInfo' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint4Ptr KeyInfo, KeySamples;
^~~~~~~
In file included from ../include/ncbi.h:59:0,
from ncbisam.c:198:
ncbisam.c: In function 'ISAMCreateDatabase':
../include/ncbimem.h:232:23: warning: 'prevterm' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
ncbisam.c:1181:13: note: 'prevterm' was declared here
CharPtr prevterm;
^~~~~~~~
In file included from ../include/ncbimsg.h:78:0,
from ../include/ncbi.h:60,
from ncbisam.c:198:
../include/ncbierr.h:246:23: warning: 'field_in' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define ErrLogPrintf Nlm_ErrLogPrintf
^~~~~~~~~~~~~~~~
ncbisam.c:1177:37: note: 'field_in' was declared here
unsigned long uid_in, uid_last, field_in;
^~~~~~~~
ncbisam.c: In function 'NISAMSearch':
ncbisam.c:1814:32: warning: 'KeyDataPageStart' may be used uninitialized in this function [-Wmaybe-uninitialized]
KeyDataPageStart = MemFree(KeyDataPageStart);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbisam.c:1812:28: warning: 'KeyPageStart' may be used uninitialized in this function [-Wmaybe-uninitialized]
KeyPageStart = MemFree(KeyPageStart);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
ncbisam.c:1750:36: warning: 'KeyPage' may be used uninitialized in this function [-Wmaybe-uninitialized]
Key = SwapUint4(KeyPage[current]);
^
ncbisam.c:1593:24: warning: 'SampleNum' may be used uninitialized in this function [-Wmaybe-uninitialized]
*Start = SampleNum * data->PageSize;
~~~~~~~~~~^~~~~~~~~~~~~~~~
ncbisam.c:1618:27: note: 'SampleNum' was declared here
Int4 Start = 0, Stop, SampleNum;
^~~~~~~~~
ncbisam.c: In function 'SISAMSearch':
ncbisam.c:2373:8: warning: 'SampleNum' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ( (SampleNum < 0) || (SampleNum >= data->NumSamples)) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbisort.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbisort.h:62,
from ../include/ncbisrti.h:60,
from ncbisort.c:83:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbisort.c: In function 'SORTFracCompare':
ncbisort.c:692:12: warning: type defaults to 'int' in declaration of 'tmpa' [-Wimplicit-int]
register tmpa = UCHAR(*a), tmpb = UCHAR(*b);
^~~~
ncbisort.c:692:30: warning: type defaults to 'int' in declaration of 'tmpb' [-Wimplicit-int]
register tmpa = UCHAR(*a), tmpb = UCHAR(*b);
^~~~
In file included from ncbisort.c:83:0:
ncbisort.c: At top level:
../include/ncbisrti.h:213:13: warning: 'inthandler' declared 'static' but never defined [-Wunused-function]
static void inthandler(int i);
^~~~~~~~~~
ncbisort.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: ncbisort.c,v 6.8 2006/05/10 20:47:17 camacho Exp $";
^~~~~
ncbisort.c: In function 'SORTMergeFPS':
ncbisort.c:1110:10: warning: 'savealloc' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (savealloc < lines[ord[0]].lines[cur[ord[0]]].length + 1) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salign.h:10,
from salign.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salign.c: In function 'BandAlignTwoSeqLocsFunc':
salign.c:173:13: warning: variable 'is_prot' set but not used [-Wunused-but-set-variable]
Boolean is_prot;
^~~~~~~
salign.c: In function 'SortBlastHits':
salign.c:391:15: warning: variable 'totalvalmax' set but not used [-Wunused-but-set-variable]
totalvalmax = INT4_MAX,
^~~~~~~~~~~
salign.c: In function 'link_solution':
salign.c:1188:15: warning: unused variable 'first' [-Wunused-variable]
Boolean first = TRUE;
^~~~~
At top level:
salign.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: salign.c,v 6.11 2009/01/21 17:09:18 bollin Exp $";
^~~~~
salign.c: In function 'SortBlastHits':
salign.c:454:6: warning: 'salpdup' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (salpdup!=NULL)
^
salign.c: In function 'TranslateSeqLoc.constprop':
salign.c:660:10: warning: 'slpp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return slpp;
^~~~
salign.c: In function 'BlastTwoSeqLocs':
salign.c:591:18: warning: 'strand2' may be used uninitialized in this function [-Wmaybe-uninitialized]
sit->strand = strand2;
~~~~~~~~~~~~^~~~~~~~~
salign.c:589:18: warning: 'strand1' may be used uninitialized in this function [-Wmaybe-uninitialized]
sit->strand = strand1;
~~~~~~~~~~~~^~~~~~~~~
salign.c: In function 'BlastBandAlignTwoSeqLocs.isra.4':
salign.c:1433:17: warning: 'tail' may be used uninitialized in this function [-Wmaybe-uninitialized]
tail->next = salptmp;
~~~~~~~~~~~^~~~~~~~~
salign.c:1408:15: note: 'tail' was declared here
tail,
^~~~
salign.c:1348:38: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
intronlg = (float)(abs(stop - start1) - alignlens)/(float)(j-1);
~~~~~^~~~~~~~
salign.c:1301:30: note: 'stop' was declared here
Int4 start, start1, stop;
^~~~
salign.c:1348:38: warning: 'start1' may be used uninitialized in this function [-Wmaybe-uninitialized]
intronlg = (float)(abs(stop - start1) - alignlens)/(float)(j-1);
~~~~~^~~~~~~~
salign.c:1301:22: note: 'start1' was declared here
Int4 start, start1, stop;
^~~~~~
salign.c:1270:38: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
intronlg = (float)(abs(stop - start1) - alignlen)/(float)(j-1);
~~~~~^~~~~~~~
salign.c:1229:30: note: 'stop' was declared here
Int4 start, start1, stop;
^~~~
salign.c:1270:38: warning: 'start1' may be used uninitialized in this function [-Wmaybe-uninitialized]
intronlg = (float)(abs(stop - start1) - alignlen)/(float)(j-1);
~~~~~^~~~~~~~
salign.c:1229:22: note: 'start1' was declared here
Int4 start, start1, stop;
^~~~~~
salign.c: In function 'SeqLocListToSeqAlign':
salign.c:1670:22: warning: 'master_slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
salpblast = BlastTwoSeqLocs (master_slp, slp, is_prot, msp);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF salptool.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from salptool.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salptool.c: In function 'MergeTwoDspBySIM4':
salptool.c:285:10: warning: variable 'has_overlap' set but not used [-Wunused-but-set-variable]
Boolean has_overlap;
^~~~~~~~~~~
salptool.c:281:7: warning: variable 'gap' set but not used [-Wunused-but-set-variable]
Int4 gap=0,gap_1, gap_2;
^~~
salptool.c: In function 'extend_dsp_ends':
salptool.c:1329:21: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
salptool.c:1331:4: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if(extend_len > 0)
^~
salptool.c:1346:21: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
salptool.c:1348:4: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if(extend_len > 0)
^~
salptool.c:1363:21: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
salptool.c:1365:4: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if(extend_len > 0)
^~
salptool.c:1380:21: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
salptool.c:1382:4: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
if(extend_len > 0)
^~
In file included from ../include/sqnutils.h:51:0,
from salptool.c:12:
salptool.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from salptool.c:14:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
salptool.c:1518:24: warning: 'OrderBestHits' defined but not used [-Wunused-function]
static int LIBCALLBACK OrderBestHits(Pointer ptr1, Pointer ptr2)
^~~~~~~~~~~~~
salptool.c:1468:13: warning: 'showtextalign_fromalign' defined but not used [-Wunused-function]
static void showtextalign_fromalign (SeqAlignPtr salp, CharPtr path, FILE *fp)
^~~~~~~~~~~~~~~~~~~~~~~
salptool.c:1453:13: warning: 'getlengthforid' defined but not used [-Wunused-function]
static Int4 getlengthforid (SeqIdPtr sip)
^~~~~~~~~~~~~~
salptool.c:1267:16: warning: 'need_recompute' defined but not used [-Wunused-function]
static Boolean need_recompute(SeqAlignPtr align, Int4 m_len, Int4 s_len)
^~~~~~~~~~~~~~
salptool.c:838:13: warning: 'SeqLocTrimPolyATail' defined but not used [-Wunused-function]
static void SeqLocTrimPolyATail(SeqLocPtr loc_2, BioseqPtr bsp_2) {
^~~~~~~~~~~~~~~~~~~
salptool.c:46:13: warning: 'SeqAnnotWrite' defined but not used [-Wunused-function]
static void SeqAnnotWrite(SeqAlignPtr align)
^~~~~~~~~~~~~
salptool.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: salptool.c,v 6.57 2008/07/07 18:52:31 bollin Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urkutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from urkutil.c:59:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkutil.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urkpcc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkpcc.h:54,
from urkpcc.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkpcc.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkpcc.c,v 6.13 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urkptpf.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from urkptpf.c:65:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkptpf.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkptpf.c,v 6.33 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urkepi.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkepi.h:54,
from urkepi.c:59:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkepi.c: In function 'PredictEpiI0':
urkepi.c:214:21: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[*seq] += 1;
^
urkepi.c:239:58: warning: array subscript has type 'char' [-Wchar-subscripts]
episcore = DownArrayScore (episcore, epip->epiarray[*seq]);
^
urkepi.c:240:21: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[*seq] += 1;
^
urkepi.c:241:56: warning: array subscript has type 'char' [-Wchar-subscripts]
episcore = UpArrayScore (episcore, epip->epiarray[*seq]);
^
urkepi.c:263:58: warning: array subscript has type 'char' [-Wchar-subscripts]
episcore = DownArrayScore (episcore, epip->epiarray[*(seq-window)]);
^
urkepi.c:264:21: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[*(seq-window)] -= 1;
^
urkepi.c:265:56: warning: array subscript has type 'char' [-Wchar-subscripts]
episcore = UpArrayScore (episcore, epip->epiarray[*(seq-window)]);
^
urkepi.c: In function 'OptimizeEpiComp':
urkepi.c:605:14: warning: array subscript has type 'char' [-Wchar-subscripts]
bin[seq[i]] += 1;
^
urkepi.c:621:14: warning: array subscript has type 'char' [-Wchar-subscripts]
bin[seq[i]] += 1;
^
urkepi.c:651:15: warning: array subscript has type 'char' [-Wchar-subscripts]
if (fbin[seq[i]] > expect)
^
urkepi.c:657:15: warning: array subscript has type 'char' [-Wchar-subscripts]
if (fbin[seq[i]] > expect)
^
urkepi.c: In function 'OptimizeEpiHP':
urkepi.c:782:27: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[seq[j]] += 1;
^
urkepi.c:797:27: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[seq[j]] += 1;
^
urkepi.c:837:25: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[seq[n]] -= 1;
^
urkepi.c: In function 'OptimizeEpiProbFunc':
urkepi.c:982:27: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[seq[n]] += 1;
^
urkepi.c:994:27: warning: array subscript has type 'char' [-Wchar-subscripts]
epip->epiarray[seq[n]] += 1;
^
At top level:
urkepi.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkepi.c,v 6.19 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
urkepi.c: In function 'FilterEpi':
urkepi.c:1053:21: warning: 'right' may be used uninitialized in this function [-Wmaybe-uninitialized]
cfap->right = right;
~~~~~~~~~~~~^~~~~~~
urkepi.c:936:56: note: 'right' was declared here
Int4 i, n, j, k, start, stop, loop, fact, left, right;
^~~~~
urkepi.c:1052:20: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized]
cfap->left = left;
~~~~~~~~~~~^~~~~~
urkepi.c:936:50: note: 'left' was declared here
Int4 i, n, j, k, start, stop, loop, fact, left, right;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urkfltr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkfltr.h:51,
from urkfltr.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkfltr.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkfltr.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urkdust.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkdust.h:51,
from urkdust.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkdust.c: In function 'DustMe_h':
urkdust.c:196:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(dcvp->curlevel <= newlevel) && dcvp->curend == loop+1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
urkdust.c: In function 'DustForGraph':
urkdust.c:776:17: warning: variable 'drphead' set but not used [-Wunused-but-set-variable]
DustRegionPtr drphead;
^~~~~~~
At top level:
urkdust.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkdust.c,v 6.10 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urksigu.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urksigu.h:57,
from urksigu.c:59:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urksigu.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urksigu.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seg.c
seg.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seg.c,v 6.19 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
seg.c: In function 'getprob':
seg.c:935:15: warning: 'ans2' may be used uninitialized in this function [-Wmaybe-uninitialized]
ans = ans1 + ans2 - totseq;
~~~~~^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urkbias.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from urkbias.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkbias.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkbias.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urkcnsrt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkcnsrt.h:60,
from urkcnsrt.c:80:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkcnsrt.c:1203:13: warning: 'ScanFrame' defined but not used [-Wunused-function]
static void ScanFrame (BioseqPtr bsp, SeqLocPtr slp, Int4 frame,
^~~~~~~~~
urkcnsrt.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkcnsrt.c,v 6.21 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
urkcnsrt.c: In function 'Scan3Frames':
urkcnsrt.c:1312:34: warning: 'length' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 i, n, start, stop, length, chunk;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF urktree.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urktree.h:51,
from urktree.c:53:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urktree.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urktree.c,v 6.6 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF pseed3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from pseed3.c:176:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pseed3.c: In function 'SeedPruneHitsFromSeedReturn':
pseed3.c:230:17: warning: variable 'curSegs' set but not used [-Wunused-but-set-variable]
DenseSegPtr curSegs, testSegs; /*Used to extract ids from curSeqAlign, testSeqAlign*/
^~~~~~~
pseed3.c: In function 'seedEngineCore':
pseed3.c:507:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, &numPatOccur, &effectiveOccurrences, program_flag, unfilter_query, query, search->sbp->query_length, is_dna, patternSearch, seedSearch, showDiagnostics, &(search->error_return), info_vnp, hitArraySz)) {
^~~~~
pseed3.c: In function 'output_hits':
pseed3.c:1202:10: warning: variable 'posBaseIndex' set but not used [-Wunused-but-set-variable]
Int4 posBaseIndex; /*loop index for copying pos results arrays*/
^~~~~~~~~~~~
pseed3.c: In function 'init_order':
pseed3.c:1483:38: warning: array subscript has type 'char' [-Wchar-subscripts]
seedSearch->order[seedSearch->pchars[i]] = i;
^
pseed3.c:1483:19: warning: array subscript has type 'char' [-Wchar-subscripts]
seedSearch->order[seedSearch->pchars[i]] = i;
^
pseed3.c:1487:33: warning: array subscript has type 'char' [-Wchar-subscripts]
seedSearch->charMultiple[i] = 0;
^
pseed3.c:1489:30: warning: array subscript has type 'char' [-Wchar-subscripts]
if (seedSearch->standardProb[i] > seedepsilon) {
^
pseed3.c:1490:22: warning: array subscript has type 'char' [-Wchar-subscripts]
matrixRow = matrix[i];
^
pseed3.c:1493:34: warning: array subscript has type 'char' [-Wchar-subscripts]
if (seedSearch->standardProb[j] > seedepsilon)
^
pseed3.c:1494:42: warning: array subscript has type 'char' [-Wchar-subscripts]
rowSum += seedSearch->standardProb[j]*exp(-(seedSearch->paramLambda)*matrixRow[j]);
^
pseed3.c:1494:86: warning: array subscript has type 'char' [-Wchar-subscripts]
rowSum += seedSearch->standardProb[j]*exp(-(seedSearch->paramLambda)*matrixRow[j]);
^
pseed3.c:1496:28: warning: array subscript has type 'char' [-Wchar-subscripts]
seedSearch->charMultiple[i] = rowSum;
^
At top level:
pseed3.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: pseed3.c,v 6.54 2008/10/31 18:51:07 madden Exp $";
^~~~~
pseed3.c: In function 'seedParallelFill':
pseed3.c:712:68: warning: iteration 100 invokes undefined behavior [-Waggressive-loop-optimizations]
returnData->seedSearch->name_space[i] = seedSearch->name_space[i];
~~~~~~~~~~~~~~~~~~~~~~^~~
pseed3.c:711:4: note: within this loop
for( i = 0; i <= BUF_SIZE; i++)
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF pattern1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from pattern1.c:80:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
pattern1.c: In function 'init_pattern':
pattern1.c:286:52: warning: array subscript has type 'char' [-Wchar-subscripts]
positionProbability = seedSearch->standardProb[seedSearch->order[c]];
^
pattern1.c:303:53: warning: array subscript has type 'char' [-Wchar-subscripts]
positionProbability += seedSearch->standardProb[seedSearch->order[c]];
^
pattern1.c:317:53: warning: array subscript has type 'char' [-Wchar-subscripts]
positionProbability -= seedSearch->standardProb[seedSearch->order[c]];
^
pattern1.c: In function 'find_hitsS_DNA':
pattern1.c:534:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) {
^~
pattern1.c:547:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) {
^~
pattern1.c: At top level:
pattern1.c:744:8: warning: return type defaults to 'int' [-Wimplicit-int]
static and(Int4 *result, Int4 *a, Int4 *b, patternSearchItems *patternSearch)
^~~
pattern1.c: In function 'and':
pattern1.c:750:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (result[i] = (a[i] & b[i]))
^~
pattern1.c: In function 'align':
pattern1.c:1102:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (leftd >= 1)
^
pattern1.c: In function 'pat_output':
pattern1.c:1637:2: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
pattern1.c:1639:11: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
ValNodeCopyStr(info_vnp, 0, buffer);
^~~~~~~~~~~~~~
At top level:
pattern1.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: pattern1.c,v 6.22 2006/08/04 21:11:17 papadopo Exp $";
^~~~~
pattern1.c: In function 'get_patL':
pattern1.c:1348:42: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
*end = wordIndex*BITS_PACKED_PER_WORD+j;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
pattern1.c: In function 'align':
pattern1.c:1158:8: warning: 'CDrow' may be used uninitialized in this function [-Wmaybe-uninitialized]
score = (CDrow-1)->CC;
~~~~~~^~~~~~~~~~~~~~~
pattern1.c: In function 'get_patLL':
pattern1.c:1393:5: warning: 'pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j = 0; j < pos; j+= wordIndex) {
^~~
pattern1.c: In function 'init_pattern':
pattern1.c:192:11: warning: 'tj' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 tj; /*temporary copy of j*/
^~
pattern1.c: In function 'align_of_pattern':
pattern1.c:1562:19: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized]
local_score += ALIGN_B(querySeq-1, dbSeq-1, queryMatchOffset, dbMatchOffset,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BAND_LOW, BAND_HIGH, matrix, gap_open, gap_extend, alignScript, data);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF impatool.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from impatool.c:73:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
impatool.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: impatool.c,v 6.16 2006/06/30 18:44:40 camacho Exp $";
^~~~~
impatool.c: In function 'IMPALAPrintHelp':
impatool.c:301:20: warning: 'ret_buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
ret_buffer = MemFree(ret_buffer);
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF posit2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from posit2.c:78:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
posit2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: posit2.c,v 6.12 2006/09/18 20:54:27 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mbalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/mbalign.h:4,
from mbalign.c:176:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mbalign.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: mbalign.c,v 6.43 2006/02/02 17:57:34 papadopo Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF vecscrn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vecscrn.h:74,
from vecscrn.c:103:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vecscrn.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: vecscrn.c,v 6.137 2005/12/27 14:46:44 madden Exp $";
^~~~~
vecscrn.c: In function 'VSPrintOverviewFromSeqLocs':
vecscrn.c:1085:8: warning: 'tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp = tmp->next;
~~~~^~~~~~~~~~~
vecscrn.c: In function 'VSPrintListFromSeqLocs':
vecscrn.c:1191:8: warning: 'tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
tmp = tmp->next;
~~~~^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF mblast.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from mblast.c:710:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mblast.c: In function 'BioseqMegaBlastEngineCore':
mblast.c:961:12: warning: statement with no effect [-Wunused-value]
stop_timer("BioseqBlastEngineCore: before do_the_blast_run()");
^
mblast.c:987:12: warning: statement with no effect [-Wunused-value]
stop_timer("MegaBlastEngineCore: after do_the_blast_run()");
^
mblast.c:942:14: warning: variable 'seqalign' set but not used [-Wunused-but-set-variable]
SeqAlignPtr seqalign, PNTR seqalignp;
^~~~~~~~
mblast.c: In function 'MegaBlastSetUpSearchInternalByLoc':
mblast.c:1167:16: warning: variable 'avglen' set but not used [-Wunused-but-set-variable]
Nlm_FloatHi avglen;
^~~~~~
mblast.c: In function 'MegaBlastPackAlignmentsByQuery':
mblast.c:1829:14: warning: variable 'slp' set but not used [-Wunused-but-set-variable]
SeqLocPtr slp;
^~~
mblast.c: In function 'MegaBlastWordFinder_disc_1b':
mblast.c:2372:32: warning: variable 'mask' set but not used [-Wunused-but-set-variable]
register Int4 s_off, ecode, mask, q_off, extra_code;
^~~~
At top level:
mblast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: mblast.c,v 6.215 2006/09/21 13:42:37 madden Exp $";
^~~~~
mblast.c: In function 'MegaBlastPackAlignmentsByQuery':
mblast.c:1864:19: warning: 'sap' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap->next = seqalign_var;
~~~~~~~~~~^~~~~~~~~~~~~~
mblast.c: In function 'MegaBlastWordFinder_disc':
mblast.c:2250:53: warning: 'ecode2' may be used uninitialized in this function [-Wmaybe-uninitialized]
(((PV_ARRAY_TYPE) 1)<<(ecode2&PV_ARRAY_MASK))) == 0))) {
~~~~~~~^~~~~~~~~~~~~~~
mblast.c:2151:47: warning: 'ecode1' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (q_off = lookup->mb_lt->hashtable[ecode1]; q_off>0;
^
mblast.c: In function 'MegaBlastWordFinder':
mblast.c:2711:51: warning: 'ecode2' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (q_off = lookup->mb_lt->hashtable2[ecode2]; q_off>0;
^
mblast.c:2373:17: note: 'ecode2' was declared here
Int4 ecode1, ecode2;
^~~~~~
mblast.c:2475:52: warning: 'ecode1' may be used uninitialized in this function [-Wmaybe-uninitialized]
(((PV_ARRAY_TYPE) 1)<<(ecode1&PV_ARRAY_MASK))) == 0)
~~~~~~~^~~~~~~~~~~~~~~
mblast.c:2373:9: note: 'ecode1' was declared here
Int4 ecode1, ecode2;
^~~~~~
mblast.c: In function 'MegaBlastGapInfoToSeqAlign':
mblast.c:3504:16: warning: 'seqalign' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAlignPtr seqalign, seqalign_var, sap;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF rpsutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/rpsutil.h:128,
from rpsutil.c:281:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rpsutil.c: In function 'RPSBlastSearchLight':
rpsutil.c:1838:10: warning: variable 'status' set but not used [-Wunused-but-set-variable]
Int2 status;
^~~~~~
rpsutil.c: In function 'RPSBgetCddHits':
rpsutil.c:2210:21: warning: variable 'found_score' set but not used [-Wunused-but-set-variable]
Boolean found_score = FALSE;
^~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from rpsutil.c:282:
rpsutil.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
rpsutil.c: In function 'getAuxInformation':
rpsutil.c:398:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%s",underlyingMatrixName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:404:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%d\n", gap_open);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:405:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%d\n", gap_extend);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:406:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Kungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:407:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Hungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:408:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &maxLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:409:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &dbLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:410:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%lf", &privateScalingFactor);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:415:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &maxLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:416:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &(rpsinfo->karlinK[index]));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
rpsutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: rpsutil.c,v 6.76 2007/05/07 13:30:54 kans Exp $";
^~~~~
rpsutil.c: In function 'RPSAlignTraceBack':
rpsutil.c:1444:32: warning: 'posMatrix' may be used uninitialized in this function [-Wmaybe-uninitialized]
search->sbp->posMatrix = posMatrix;
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
rpsutil.c:1433:22: warning: 'rev_subject_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
seqalign = BlastGetGapAlgnTbck (search, 0, TRUE, FALSE,
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
subject, subject_length,
~~~~~~~~~~~~~~~~~~~~~~~~
rev_subject, rev_subject_length);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c: In function 'RPSCalcEValue':
rpsutil.c:1269:30: warning: 'posMatrix' may be used uninitialized in this function [-Wmaybe-uninitialized]
search->sbp->posMatrix = posMatrix;
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF kappa.c
kappa.c: In function 'Kappa_SequenceGetProteinRange':
kappa.c:1399:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
kappa.c: At top level:
kappa.c:2203:5: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
Kappa_SequenceGetRange,
^~~~~~~~~~~~~~~~~~~~~~
kappa.c:2203:5: note: (near initialization for 'redo_align_callbacks.get_range')
kappa.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: kappa.c,v 6.93 2012/04/30 12:45:01 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF xmlblast.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/xmlblast.h:89,
from xmlblast.c:171:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
xmlblast.c: In function 'PSIXmlInit':
xmlblast.c:1239:13: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = FALSE;
^~~~~~
At top level:
xmlblast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: xmlblast.c,v 6.41 2007/05/07 13:30:54 kans Exp $";
^~~~~
xmlblast.c: In function 'BXMLGetSeqLineForStdSeg':
xmlblast.c:373:28: warning: 'genetic_code2' may be used uninitialized in this function [-Wmaybe-uninitialized]
CharPtr genetic_code1, genetic_code2;
^~~~~~~~~~~~~
xmlblast.c: In function 'BXMLSeqAlignToHits':
xmlblast.c:867:36: warning: 'hspp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if((hspp->next = BXMLGetHspFromSeqAlign(sap2, is_aa, chain,
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
is_ooframe, mask_loc)) == NULL)
~~~~~~~~~~~~~~~~~~~~~~
xmlblast.c: In function 'SeqAlignToHits':
xmlblast.c:1646:24: warning: 'hspp' may be used uninitialized in this function [-Wmaybe-uninitialized]
hspp->next = GetHspFromSeqAlign(sap2, ungapped, &hsp_count);
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF bxmlobj.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from bxmlobj.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bxmlobj.c: In function 'BlastOutputAsnRead':
bxmlobj.c:96:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c: In function 'ParametersAsnRead':
bxmlobj.c:361:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c:360:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
bxmlobj.c: In function 'IterationAsnRead':
bxmlobj.c:613:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c: In function 'StatisticsAsnRead':
bxmlobj.c:829:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c:828:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
bxmlobj.c: In function 'HitAsnRead':
bxmlobj.c:1039:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c: In function 'HspAsnRead':
bxmlobj.c:1244:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
bxmlobj.c:1243:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
At top level:
bxmlobj.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bxmlobj.c,v 6.11 2006/09/18 15:20:39 bealer Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF dotseq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from ../include/tofasta.h:47,
from ../include/dotseq.h:63,
from dotseq.c:86:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dotseq.c:96:36: warning: missing braces around initializer [-Wmissing-braces]
static Int4 DOTblosum62[24][24] = {
^
dotseq.c:96:36: note: (near initialization for 'DOTblosum62')
dotseq.c: In function 'DOT_BuildPLookup':
dotseq.c:887:31: warning: variable 'found_ambig' set but not used [-Wunused-but-set-variable]
Boolean EXACTMATCH, found_ambig, saved_index = FALSE;
^~~~~~~~~~~
dotseq.c:885:19: warning: unused variable 'threshold' [-Wunused-variable]
Int4 threshold=13; /* one-hit heuristics T must be at least 13*/
^~~~~~~~~
dotseq.c:883:19: warning: unused variable 'index' [-Wunused-variable]
Int4 index = 0;
^~~~~
dotseq.c: In function 'DOT_ComputeHits':
dotseq.c:1043:47: warning: variable 'q_end' set but not used [-Wunused-but-set-variable]
Uint1Ptr s, subject0, s_end, q_end;
^~~~~
dotseq.c:1041:19: warning: unused variable 'saved_index' [-Wunused-variable]
Boolean saved_index = FALSE;
^~~~~~~~~~~
dotseq.c:1039:19: warning: unused variable 'threshold' [-Wunused-variable]
Int4 threshold=13;
^~~~~~~~~
dotseq.c: In function 'DOT_SPI_FindBestAlnByDotPlot':
dotseq.c:2016:20: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
dotseq.c:2015:20: warning: variable 'start2' set but not used [-Wunused-but-set-variable]
Int4 start2;
^~~~~~
dotseq.c:2014:20: warning: variable 'start1' set but not used [-Wunused-but-set-variable]
Int4 start1;
^~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from dotseq.c:87:
dotseq.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
dotseq.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: dotseq.c,v 6.14 2006/07/13 17:16:20 bollin Exp $";
^~~~~
dotseq.c: In function 'DOT_BuildHitList':
dotseq.c:1310:19: warning: 'index' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 index;
^~~~~
dotseq.c:1309:19: warning: 'hitlist' may be used uninitialized in this function [-Wmaybe-uninitialized]
DOTDiagPtr PNTR hitlist;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF spidey.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/spidey.h:102,
from spidey.c:259:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
spidey.c: In function 'SPI_PrintResult':
spidey.c:1736:21: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
Int4 offset;
^~~~~~
spidey.c: In function 'SPI_AlnSinglemRNAToPieces':
spidey.c:2850:19: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if (spot->from == spot->to == 0)
~~~~~~~~~~~^~~~~~~~~~~
spidey.c: In function 'SPI_FillInLastmRNAHoles':
spidey.c:6295:21: warning: variable 'internal' set but not used [-Wunused-but-set-variable]
Boolean internal;
^~~~~~~~
spidey.c: In function 'SPI_FindBestAlnByDotPlot':
spidey.c:6441:20: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
spidey.c:6440:20: warning: variable 'start2' set but not used [-Wunused-but-set-variable]
Int4 start2;
^~~~~~
spidey.c:6439:20: warning: variable 'start1' set but not used [-Wunused-but-set-variable]
Int4 start1;
^~~~~~
spidey.c: In function 'SPI_ConnectAlnPieces':
spidey.c:7810:30: warning: variable 'tmparray' set but not used [-Wunused-but-set-variable]
SPI_FragPtr PNTR tmparray;
^~~~~~~~
spidey.c:7796:25: warning: variable 'sfpprev' set but not used [-Wunused-but-set-variable]
SPI_FragPtr sfpprev;
^~~~~~~
spidey.c: In function 'SPI_AdjustSplicesInPieces':
spidey.c:8444:23: warning: variable 'minus' set but not used [-Wunused-but-set-variable]
Boolean minus;
^~~~~
spidey.c: In function 'SPI_CheckMrnaOrder':
spidey.c:10292:35: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if ((ival->strand == Seq_strand_plus == ival2->strand
spidey.c:10296:38: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
|| (ival->strand == Seq_strand_minus == ival2->strand
spidey.c:10309:35: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if ((ival->strand == Seq_strand_plus == ival2->strand
spidey.c:10311:38: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
|| (ival->strand == Seq_strand_plus == ival2->strand
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/spidey.h:103,
from spidey.c:259:
spidey.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
spidey.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: spidey.c,v 6.73 2006/06/01 14:55:31 kskatz Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF motif.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/motif.h:45,
from motif.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
motif.c: In function 'MOT_FindPolyA':
motif.c:86:18: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
Uint1 buf[MOT_WINSIZE];
^~~
motif.c: In function 'MOT_FindKozak':
motif.c:216:18: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
Uint1 buf[MOT_WINSIZE];
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from ../include/motif.h:48,
from motif.c:47:
motif.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
motif.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: motif.c,v 6.7 2007/05/07 13:30:54 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blfmtutl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blfmtutl.c:172:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blfmtutl.c: In function 'CBStatisticsGetReference':
blfmtutl.c:590:4: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
} else
^~~~
blfmtutl.c:592:4: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
add_string_to_bufferEx("Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,", &ret_buffer, &ret_buffer_length, TRUE);
^~~~~~~~~~~~~~~~~~~~~~
At top level:
blfmtutl.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blfmtutl.c,v 1.43 2011/10/28 14:24:13 coulouri Exp $";
^~~~~
blfmtutl.c: In function 'BlastPrintTabularResults':
blfmtutl.c:1113:13: warning: 'alignments_count' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (--alignments_count < 0)
^
blfmtutl.c:1331:19: warning: 's_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
s_end += s_shift;
~~~~~~^~~~~~~~~~
blfmtutl.c:1330:21: warning: 's_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
s_start += s_shift;
~~~~~~~~^~~~~~~~~~
blfmtutl.c:1329:19: warning: 'q_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
q_end += q_shift;
~~~~~~^~~~~~~~~~
blfmtutl.c:1328:21: warning: 'q_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
q_start += q_shift;
~~~~~~~~^~~~~~~~~~
blfmtutl.c:1077:24: warning: 'query_id' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (slp && SeqIdComp(query_id, SeqLocId(slp)) != SIC_YES)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blfmtutl.c: In function 'BlastSetUserErrorString':
blfmtutl.c:1392:26: warning: 'title' may be used uninitialized in this function [-Wmaybe-uninitialized]
CharPtr buf_start, ptr, title;
^~~~~
rm -f libncbitool.a
ar cru libncbitool.a csim.o db_slist.o dust.o blast_dust.o falign.o g_any.o sim2.o sim3.o sim4.o simutil.o slist.o sec.o tfuns.o toasn3.o toporg.o pobutil.o stsutil.o suggadj.o suggest.o suggslp.o blast.o blastutl.o blastool.o blastconcat.o splutil.o gapxdrop.o bandalg0.o bandalg1.o bandalg2.o bandalg3.o bandalg4.o bandalg5.o bandalgn.o blastkar.o actutils.o posit.o lookup.o readdb.o ncbisam.o ncbisort.o salign.o salptool.o urkutil.o urkpcc.o urkptpf.o urkepi.o urkfltr.o urkdust.o urksigu.o seg.o urkbias.o urkcnsrt.o urktree.o pseed3.o pattern1.o impatool.o posit2.o mbalign.o vecscrn.o mblast.o rpsutil.o kappa.o xmlblast.o bxmlobj.o dotseq.o spidey.o motif.o blfmtutl.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbitool.a ../lib
ranlib ../lib/libncbitool.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF matrix_frequency_data.c
matrix_frequency_data.c:31:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF compo_mode_condition.c
compo_mode_condition.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF composition_adjustment.c
composition_adjustment.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF nlm_linear_algebra.c
nlm_linear_algebra.c:31:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF optimize_target_freq.c
optimize_target_freq.c:86:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF compo_heap.c
compo_heap.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF smith_waterman.c
smith_waterman.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF redo_alignment.c
redo_alignment.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF unified_pvalues.c
unified_pvalues.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
rm -f libblastcompadj.a
ar cru libblastcompadj.a matrix_frequency_data.o compo_mode_condition.o composition_adjustment.o nlm_linear_algebra.o optimize_target_freq.o compo_heap.o smith_waterman.o redo_alignment.o unified_pvalues.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libblastcompadj.a ../lib
ranlib ../lib/libblastcompadj.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gdfontg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/gifgen.h:115,
from gdfontg.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gdfontmb.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/gifgen.h:115,
from gdfontmb.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gdfontt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/gifgen.h:115,
from gdfontt.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF pictogif.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from pictogif.c:50:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gdfontl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/gifgen.h:115,
from gdfontl.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gdfonts.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/gifgen.h:115,
from gdfonts.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -DWIN_GIF -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbidrwg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ncbidrwg.c:43:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbidrwg.c: In function 'Nlm_ClearRgn':
ncbidrwg.c:6081:16: warning: variable 'ntool' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool;
^~~~~
ncbidrwg.c: In function 'Nlm_DiffRgn':
ncbidrwg.c:6273:16: warning: variable 'ntool3' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool3;
^~~~~~
ncbidrwg.c:6272:16: warning: variable 'ntool2' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool2;
^~~~~~
ncbidrwg.c:6271:16: warning: variable 'ntool1' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool1;
^~~~~~
ncbidrwg.c: In function 'Nlm_XorRgn':
ncbidrwg.c:6324:16: warning: variable 'ntool3' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool3;
^~~~~~
ncbidrwg.c:6323:16: warning: variable 'ntool2' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool2;
^~~~~~
ncbidrwg.c:6322:16: warning: variable 'ntool1' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool1;
^~~~~~
ncbidrwg.c: In function 'Nlm_EqualRgn':
ncbidrwg.c:6353:16: warning: variable 'ntool2' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool2;
^~~~~~
ncbidrwg.c:6352:16: warning: variable 'ntool1' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool1;
^~~~~~
ncbidrwg.c: In function 'Nlm_EmptyRgn':
ncbidrwg.c:6381:17: warning: variable 'ntool' set but not used [-Wunused-but-set-variable]
Nlm_RgnTool ntool;
^~~~~
ncbidrwg.c: In function 'Nlm_CopyPixmap':
ncbidrwg.c:7040:25: warning: variable 'height' set but not used [-Wunused-but-set-variable]
Nlm_Int2 height;
^~~~~~
ncbidrwg.c:7039:25: warning: variable 'width' set but not used [-Wunused-but-set-variable]
Nlm_Int2 width;
^~~~~
ncbidrwg.c: In function 'Nlm_GetColorRGB':
ncbidrwg.c:1373:10: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
return (Nlm_Uint4)i;
^~~~~~~~~~~~
rm -f libvibgif.a
ar cru libvibgif.a gdfontg.o gdfontmb.o gdfontt.o pictogif.o gdfontl.o gdfonts.o ncbidrwg.o drawing.o mapping.o picture.o ncbimain.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libvibgif.a ../lib
ranlib ../lib/libvibgif.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF algorend.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/viewer3d.h:125,
from algorend.c:584:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
algorend.c: In function 'ColorFromSS':
algorend.c:893:10: warning: unused variable 'rsult' [-Wunused-variable]
Int2 rsult = 0;
^~~~~
algorend.c: In function 'Cn3D_RenWire':
algorend.c:1400:10: warning: unused variable 'pmldThis' [-Wunused-variable]
PMLD pmldThis = NULL;
^~~~~~~~
algorend.c:1399:11: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
algorend.c:1398:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
algorend.c: In function 'Cn3D_ColSeqCons':
algorend.c:1795:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
pars->ConsColAlg = (Nlm_Int2) GetObjectExtra(i);
^
algorend.c: In function 'RenderObject':
algorend.c:3135:25: warning: variable 'fZTo' set but not used [-Wunused-but-set-variable]
FloatLo fXTo, fYTo, fZTo;
^~~~
algorend.c:3135:19: warning: variable 'fYTo' set but not used [-Wunused-but-set-variable]
FloatLo fXTo, fYTo, fZTo;
^~~~
algorend.c:3135:13: warning: variable 'fXTo' set but not used [-Wunused-but-set-variable]
FloatLo fXTo, fYTo, fZTo;
^~~~
algorend.c:3134:29: warning: variable 'fZFrom' set but not used [-Wunused-but-set-variable]
FloatLo fXFrom, fYFrom, fZFrom;
^~~~~~
algorend.c:3134:21: warning: variable 'fYFrom' set but not used [-Wunused-but-set-variable]
FloatLo fXFrom, fYFrom, fZFrom;
^~~~~~
algorend.c:3134:13: warning: variable 'fXFrom' set but not used [-Wunused-but-set-variable]
FloatLo fXFrom, fYFrom, fZFrom;
^~~~~~
algorend.c: In function 'RenderLabel':
algorend.c:3393:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
algorend.c: In function 'RenderBond':
algorend.c:3554:10: warning: variable 'pmsdParent' set but not used [-Wunused-but-set-variable]
PMSD pmsdParent = NULL;
^~~~~~~~~~
algorend.c: In function 'RenderHalfWormBond':
algorend.c:3673:10: warning: variable 'pmsdParent' set but not used [-Wunused-but-set-variable]
PMSD pmsdParent;
^~~~~~~~~~
algorend.c:3671:24: warning: variable 'pmad2' set but not used [-Wunused-but-set-variable]
PMAD pmad0, pmad1, pmad2, pmad3;
^~~~~
algorend.c: In function 'RenderAnAtom':
algorend.c:3758:10: warning: unused variable 'pmadFrom' [-Wunused-variable]
PMAD pmadFrom = NULL;
^~~~~~~~
algorend.c:3757:10: warning: variable 'pmsdParent' set but not used [-Wunused-but-set-variable]
PMSD pmsdParent = NULL;
^~~~~~~~~~
algorend.c: In function 'RenderAllAtom':
algorend.c:3829:9: warning: variable 'iMenu' set but not used [-Wunused-but-set-variable]
int iMenu;
^~~~~
algorend.c:3815:11: warning: unused variable 'pvnmbThis' [-Wunused-variable]
PVNMB pvnmbThis = NULL;
^~~~~~~~~
algorend.c:3811:11: warning: unused variable 'pvnmaThis' [-Wunused-variable]
PVNMA pvnmaThis = NULL;
^~~~~~~~~
algorend.c: In function 'RenderGraph':
algorend.c:4498:10: warning: unused variable 'bReservedThis' [-Wunused-variable]
Byte bReservedThis = 0;
^~~~~~~~~~~~~
algorend.c: In function 'LabelChainTermini':
algorend.c:4772:14: warning: unused variable 'pmbdThis' [-Wunused-variable]
PMBD pmbdThis = NULL;
^~~~~~~~
algorend.c:4771:15: warning: unused variable 'pvnmbThis' [-Wunused-variable]
PVNMB pvnmbThis = NULL;
^~~~~~~~~
algorend.c: In function 'RenderMolecule':
algorend.c:4871:11: warning: variable 'pdnmmThis' set but not used [-Wunused-but-set-variable]
PDNMM pdnmmThis = NULL;
^~~~~~~~~
algorend.c: In function 'fnARLoop':
algorend.c:5556:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest;
^~~~~
algorend.c: In function 'AlgorithmicRendering':
algorend.c:5684:10: warning: unused variable 'i' [-Wunused-variable]
Int2 i = 0;
^
algorend.c:5683:10: warning: unused variable 'Cn3d_LayerNow_sofar' [-Wunused-variable]
Int2 Cn3d_LayerNow_sofar = 0;
^~~~~~~~~~~~~~~~~~~
algorend.c: In function 'Do3DOrigin':
algorend.c:5756:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
algorend.c:5751:13: warning: variable 'fTo' set but not used [-Wunused-but-set-variable]
FloatLo fTo[3];
^~~
algorend.c:5750:13: warning: variable 'fFrom' set but not used [-Wunused-but-set-variable]
FloatLo fFrom[3];
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from algorend.c:598:
algorend.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
algorend.c:2265:13: warning: 'LabelGroupOnOffProc' defined but not used [-Wunused-function]
static void LabelGroupOnOffProc(GrouP g)
^~~~~~~~~~~~~~~~~~~
algorend.c:717:16: warning: 'Cn3d_CopyToNode' defined but not used [-Wunused-variable]
static Boolean Cn3d_CopyToNode = FALSE;
^~~~~~~~~~~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
algorend.c: In function 'RenderLabel':
../include/pictur3d.h:235:27: warning: 'iX' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddText3D Nlm_AddText3D
^~~~~~~~~~~~~
algorend.c:3389:10: note: 'iX' was declared here
Int4 iX, iY, iZ;
^~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:235:27: warning: 'iY' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddText3D Nlm_AddText3D
^~~~~~~~~~~~~
algorend.c:3389:14: note: 'iY' was declared here
Int4 iX, iY, iZ;
^~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:235:27: warning: 'iZ' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddText3D Nlm_AddText3D
^~~~~~~~~~~~~
algorend.c:3389:18: note: 'iZ' was declared here
Int4 iX, iY, iZ;
^~
algorend.c:3444:41: warning: 'fZCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fZt = (fZCen - fZFrom) + (fZCen - fZTo);
~~~~~~~^~~~~~~
algorend.c:3443:41: warning: 'fYCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~
algorend.c:3442:41: warning: 'fXCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~
algorend.c:3444:41: warning: 'fZTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fZt = (fZCen - fZFrom) + (fZCen - fZTo);
~~~~~~~^~~~~~~
algorend.c:3443:41: warning: 'fYTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~
algorend.c:3442:41: warning: 'fXTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~
algorend.c:3444:22: warning: 'fZFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fZt = (fZCen - fZFrom) + (fZCen - fZTo);
~~~~~~~^~~~~~~~~
algorend.c:3443:22: warning: 'fYFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~~~
algorend.c:3442:22: warning: 'fXFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~~~
algorend.c: In function 'MasterChangeRenderProc.isra.1':
algorend.c:1316:33: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
pars->SolventRender = k;
~~~~~~~~~~~~~~~~~~~~^~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
algorend.c: In function 'RenderObject':
../include/pictur3d.h:234:27: warning: 'iXFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3136:10: note: 'iXFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:234:27: warning: 'iYFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3136:18: note: 'iYFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:234:27: warning: 'iZFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3136:26: note: 'iZFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:234:27: warning: 'iXTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3137:10: note: 'iXTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:234:27: warning: 'iYTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3137:16: note: 'iYTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:234:27: warning: 'iZTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddCylinder3D Nlm_AddCylinder3D
^~~~~~~~~~~~~~~~~
algorend.c:3137:22: note: 'iZTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
algorend.c: In function 'Do3DOrigin':
../include/pictur3d.h:232:27: warning: 'iXFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5752:10: note: 'iXFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:232:27: warning: 'iYFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5752:18: note: 'iYFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:232:27: warning: 'iZFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5752:26: note: 'iZFrom' was declared here
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:232:27: warning: 'iXTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5753:10: note: 'iXTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:232:27: warning: 'iYTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5753:16: note: 'iYTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
In file included from ../include/viewer3d.h:129:0,
from algorend.c:584:
../include/pictur3d.h:232:27: warning: 'iZTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AddLine3D Nlm_AddLine3D
^~~~~~~~~~~~~
algorend.c:5753:22: note: 'iZTo' was declared here
Int4 iXTo, iYTo, iZTo;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dmsel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmsel.c:60:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dopen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dopen.c:394:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dopen.c: In function 'Cn3D_OpenStart':
cn3dopen.c:722:10: warning: unused variable 'iBioseq' [-Wunused-variable]
Int4 iBioseq = 0;
^~~~~~~
cn3dopen.c: In function 'MMDB_ReadMime':
cn3dopen.c:1000:19: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
cn3dopen.c:989:25: warning: unused variable 'pbsasThis' [-Wunused-variable]
BiostrucAlignSeqPtr pbsasThis = NULL;
^~~~~~~~~
cn3dopen.c: In function 'Cn3D_NetOpenBiostruc':
cn3dopen.c:1310:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dopen.c:412:
cn3dopen.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from cn3dopen.c:413:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
cn3dopen.c:431:15: warning: 'Cn3D_bOpenBrowse' defined but not used [-Wunused-variable]
static ButtoN Cn3D_bOpenBrowse;
^~~~~~~~~~~~~~~~
cn3dopen.c:430:15: warning: 'Cn3D_wOpen' defined but not used [-Wunused-variable]
static WindoW Cn3D_wOpen;
^~~~~~~~~~
cn3dopen.c: In function 'MMDB_ReadMime':
cn3dopen.c:529:9: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAM_ReplaceGI(salp);
^~~~~~~~~~~~~~~~~~~
cn3dopen.c:513:15: note: 'salp' was declared here
SeqAlign *salp;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dsave.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dsave.c:157:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dsave.c: In function 'Cn3D_ExportAsnNow':
cn3dsave.c:375:11: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
cn3dsave.c:372:24: warning: variable 'pbsfThis' set but not used [-Wunused-but-set-variable]
BiostrucFeaturePtr pbsfThis;
^~~~~~~~
cn3dsave.c:366:10: warning: unused variable 'pmsdSlave' [-Wunused-variable]
PMSD pmsdSlave = NULL, pmsdMaster = NULL;
^~~~~~~~~
cn3dsave.c:362:27: warning: variable 'FirstSlave' set but not used [-Wunused-but-set-variable]
Boolean iCn3d = TRUE, FirstSlave = FALSE;
^~~~~~~~~~
cn3dsave.c:357:13: warning: unused variable 'pcSave' [-Wunused-variable]
CharPtr pcSave = NULL;
^~~~~~
cn3dsave.c: In function 'Cn3D_SaveBiostruc':
cn3dsave.c:524:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dsave.c:523:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dsave.c:518:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dsave.c: In function 'Cn3D_ExportDictNow':
cn3dsave.c:598:13: warning: unused variable 'pcSave' [-Wunused-variable]
CharPtr pcSave = NULL;
^~~~~~
cn3dsave.c:596:10: warning: unused variable 'iCount' [-Wunused-variable]
Int4 iCount = 0;
^~~~~~
cn3dsave.c: In function 'Cn3D_SaveDictionary':
cn3dsave.c:629:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dsave.c:624:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dsave.c: In function 'Cn3D_SaveSub':
cn3dsave.c:688:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
IteM i;
^
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dsave.c:171:
cn3dsave.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
cn3dsave.c:184:15: warning: 'Cn3D_bFeatOn' defined but not used [-Wunused-variable]
static ButtoN Cn3D_bFeatOn;
^~~~~~~~~~~~
In file included from cn3dsave.c:165:0:
../include/asnmime.h:119:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnmime.h:118:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnmime.h:117:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/asnmime.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnmime.h12";
^~~~~~~~~~~
cn3dsave.c: In function 'Cn3D_GetSubSet.isra.1':
cn3dsave.c:289:24: warning: 'isep' may be used uninitialized in this function [-Wmaybe-uninitialized]
isep->next = SeqEntryNew();
~~~~~~~~~~~^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dxprt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dxprt.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportPDB':
cn3dxprt.c:209:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dxprt.c:208:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dxprt.c:203:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportKin':
cn3dxprt.c:381:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dxprt.c:380:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dxprt.c:375:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportSub':
cn3dxprt.c:513:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
IteM i;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dwin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dwin.c:647:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dwin.c:733:1: warning: missing braces around initializer [-Wmissing-braces]
{
^
cn3dwin.c:733:1: note: (near initialization for 'Cn3d_PaletteRGB')
cn3dwin.c: In function 'Viewer3DGroups':
cn3dwin.c:1728:10: warning: unused variable 'groups' [-Wunused-variable]
Int2 groups = 0;
^~~~~~
cn3dwin.c: In function 'Viewer3DViewer':
cn3dwin.c:1784:10: warning: unused variable 'groups' [-Wunused-variable]
Int2 groups = 0;
^~~~~~
cn3dwin.c: In function 'Cn3D_AlignEdit':
cn3dwin.c:1936:10: warning: unused variable 'iCount' [-Wunused-variable]
Int2 iCount = 0;
^~~~~~
cn3dwin.c:1935:10: warning: variable 'pmmdThis' set but not used [-Wunused-but-set-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dwin.c:1933:17: warning: unused variable 'salp' [-Wunused-variable]
SeqAlignPtr salp = NULL;
^~~~
cn3dwin.c:1931:29: warning: variable 'pmsdSlave' set but not used [-Wunused-but-set-variable]
PMSD pmsdMaster = NULL, pmsdSlave = NULL;
^~~~~~~~~
cn3dwin.c:1930:11: warning: unused variable 'pdnmsSlave' [-Wunused-variable]
PDNMS pdnmsSlave = NULL;
^~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/udviewer.h:219,
from cn3dwin.c:665:
cn3dwin.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/udviewer.h:228,
from cn3dwin.c:665:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
cn3dwin.c:1626:13: warning: 'HLmolecule_MA' defined but not used [-Wunused-function]
static void HLmolecule_MA(MAPtr ma,
^~~~~~~~~~~~~
cn3dwin.c:1428:13: warning: 'HLatom_MA' defined but not used [-Wunused-function]
static void HLatom_MA(MAPtr ma,
^~~~~~~~~
cn3dwin.c:929:13: warning: 'Cn3D_MoveCB' defined but not used [-Wunused-function]
static void Cn3D_MoveCB(IteM i)
^~~~~~~~~~~
cn3dwin.c:922:13: warning: 'Cn3D_ZoomCB' defined but not used [-Wunused-function]
static void Cn3D_ZoomCB(IteM i)
^~~~~~~~~~~
cn3dwin.c:688:13: warning: 'Cn3D_iModelCtrl' defined but not used [-Wunused-variable]
static IteM Cn3D_iModelCtrl = NULL;
^~~~~~~~~~~~~~~
cn3dwin.c:682:13: warning: 'Cn3D_iLabelCtrl' defined but not used [-Wunused-variable]
static IteM Cn3D_iLabelCtrl = NULL;
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/cn3dmain.h:182,
from cn3dentr.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dmsg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmsg.c:254:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmsg.c: In function 'SeqStrucMediaMsgFunc':
cn3dmsg.c:593:19: warning: variable 'omudp' set but not used [-Wunused-but-set-variable]
OMUserDataPtr omudp = NULL;
^~~~~
In file included from ../include/sqnutils.h:51:0,
from cn3dmsg.c:267:
cn3dmsg.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dmsg.c:271:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dmatn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmatn.c:173:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmatn.c: In function 'FindMM':
cn3dmatn.c:217:29: warning: unused variable 'pdnmsThisSlave' [-Wunused-variable]
PDNMS pdnmsThis = NULL, pdnmsThisSlave = NULL;
^~~~~~~~~~~~~~
cn3dmatn.c: In function 'DoMediaHL':
cn3dmatn.c:249:10: warning: variable 'MainAtom' set but not used [-Wunused-but-set-variable]
Byte MainAtom = 0;
^~~~~~~~
cn3dmatn.c:247:10: warning: unused variable 'paldThis' [-Wunused-variable]
PALD paldThis = NULL;
^~~~~~~~
cn3dmatn.c:246:11: warning: unused variable 'pvnalThis' [-Wunused-variable]
PVNAL pvnalThis = NULL;
^~~~~~~~~
cn3dmatn.c:245:10: warning: unused variable 'pmadThis' [-Wunused-variable]
PMAD pmadThis = NULL;
^~~~~~~~
cn3dmatn.c:244:11: warning: unused variable 'pvnmaThis' [-Wunused-variable]
PVNMA pvnmaThis = NULL;
^~~~~~~~~
cn3dmatn.c: In function 'Cn3DCheckAndDoHighlight':
cn3dmatn.c:372:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dmatn.c:371:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dmodl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmodl.c: In function 'Cn3DCheckNoSingleHighlight':
cn3dmodl.c:353:11: warning: unused variable 'pdnmgThis' [-Wunused-variable]
PDNMG pdnmgThis = NULL;
^~~~~~~~~
cn3dmodl.c: In function 'Cn3DCheckHighlighted':
cn3dmodl.c:364:29: warning: unused variable 'pmsdSlave' [-Wunused-variable]
PMSD pmsdMaster = NULL, pmsdSlave = NULL;
^~~~~~~~~
cn3dmodl.c: In function 'Cn3D_ReSetVisibleStatus':
cn3dmodl.c:508:10: warning: unused variable 'pmgd' [-Wunused-variable]
PMGD pmgd = NULL;
^~~~
cn3dmodl.c:507:11: warning: unused variable 'pdnmg' [-Wunused-variable]
PDNMG pdnmg = NULL;
^~~~~
cn3dmodl.c:506:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'fnAlignList':
cn3dmodl.c:996:25: warning: unused variable 'itemtype' [-Wunused-variable]
Uint2 entityID = 0, itemtype = 0;
^~~~~~~~
cn3dmodl.c:996:11: warning: unused variable 'entityID' [-Wunused-variable]
Uint2 entityID = 0, itemtype = 0;
^~~~~~~~
cn3dmodl.c:995:14: warning: unused variable 'sipThis' [-Wunused-variable]
SeqIdPtr sipThis = NULL;
^~~~~~~
cn3dmodl.c:993:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'SynchronizeModVisibleStatus':
cn3dmodl.c:1065:11: warning: unused variable 'pdnmg' [-Wunused-variable]
PDNMG pdnmg = NULL;
^~~~~
cn3dmodl.c:1064:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'SetResidueVisibilities':
cn3dmodl.c:1201:11: warning: unused variable 'pvnmoThis' [-Wunused-variable]
PVNMO pvnmoThis = NULL;
^~~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dmodl.c:319:
cn3dmodl.c: At top level:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dmodl.c:323:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dshim.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/cn3dmain.h:182,
from cn3dshim.c:131:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dmesh.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmesh.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmesh.c: In function 'Cn3D_MeshAcceptProc':
cn3dmesh.c:103:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dmesh.c: In function 'Cn3D_OpenMesh':
cn3dmesh.c:151:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dmesh.c: In function 'Cn3D_MeshAcceptProc':
cn3dmesh.c:111:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d", &(Mesh.NumVert), &(Mesh.NumEdge),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.NumTri));
~~~~~~~~~~~~~~~
cn3dmesh.c:119:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%lf %lf %lf %lf %lf %lf %f %f %f %d %d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[0]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[1]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[2]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[0]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[1]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[2]), &fDummy, &fDummy, &fDummy,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&lDummy, &lDummy, &lDummy);
~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmesh.c:129:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d %d %d", &Mesh.Edges[i].Vertex[0],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Edges[i].Vertex[1], &lDummy, &lDummy, &lDummy);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmesh.c:133:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d %d %d %d %d %d %d", &Mesh.Tri[i].Edge[0],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Edge[1], &Mesh.Tri[i].Edge[2],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Vertex[0], &Mesh.Tri[i].Vertex[1],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Vertex[2], &lDummy, &Mesh.Tri[i].Atom,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&lDummy);
~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF cn3dstyl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dstyl.c:72:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dstyl.c: In function 'GetThisSpecialAlgorRenderSet':
cn3dstyl.c:459:27: warning: unused variable 'sfipThis' [-Wunused-variable]
SpecialFeatureInfoPtr sfipThis = NULL;
^~~~~~~~
cn3dstyl.c: In function 'GetSpecialAlgorRenderSet':
cn3dstyl.c:641:10: warning: unused variable 'parsThis' [-Wunused-variable]
PARS parsThis = NULL;
^~~~~~~~
cn3dstyl.c:640:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'ChangeSpecialLabelsProc':
cn3dstyl.c:866:44: warning: unused variable 'PDBOn' [-Wunused-variable]
Boolean NumOn = FALSE, NameOn = FALSE, PDBOn = FALSE, WhiteOn =
^~~~~
cn3dstyl.c: In function 'lFeatureEditedAction':
cn3dstyl.c:1136:10: warning: unused variable 'val' [-Wunused-variable]
Int4 val = 0;
^~~
cn3dstyl.c: In function 'bFeatureMoveAction':
cn3dstyl.c:1153:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'bFeatureEditAction':
cn3dstyl.c:1176:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'ModelControls':
cn3dstyl.c:1364:19: warning: variable 'ppt13' set but not used [-Wunused-but-set-variable]
PrompT ppt12, ppt13, ppt14;
^~~~~
cn3dstyl.c:1362:36: warning: variable 'ppt5' set but not used [-Wunused-but-set-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10,
^~~~
cn3dstyl.c:1362:12: warning: variable 'ppt1' set but not used [-Wunused-but-set-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10,
^~~~
cn3dstyl.c: In function 'GetBiostrucFeatureLocationForHihglightedResidues':
cn3dstyl.c:1728:30: warning: variable 'SingleInterval' set but not used [-Wunused-but-set-variable]
Boolean Started = FALSE, SingleInterval, UserDefinedFeatureFound =
^~~~~~~~~~~~~~
cn3dstyl.c:1725:20: warning: variable 'iMolCurrent' set but not used [-Wunused-but-set-variable]
Int2 iMol = 0, iMolCurrent = 0;
^~~~~~~~~~~
cn3dstyl.c: In function 'MakeBiostrucFeatureSetForUserDefinedFeature':
cn3dstyl.c:2122:60: warning: unused variable 'bsfsp_tail' [-Wunused-variable]
BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail =
^~~~~~~~~~
cn3dstyl.c:2122:41: warning: unused variable 'bsfsp_head' [-Wunused-variable]
BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail =
^~~~~~~~~~
cn3dstyl.c: In function 'GetUserDefinedFeature':
cn3dstyl.c:2196:27: warning: unused variable 'sfipThis' [-Wunused-variable]
SpecialFeatureInfoPtr sfipThis = NULL;
^~~~~~~~
cn3dstyl.c: In function 'Cn3DIndexUserDefinedFeature':
cn3dstyl.c:2551:23: warning: variable 'sfpThis' set but not used [-Wunused-but-set-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c:2549:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dstyl.c:2548:11: warning: unused variable 'pdnmmHead' [-Wunused-variable]
PDNMM pdnmmHead = NULL;
^~~~~~~~~
cn3dstyl.c:2547:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dstyl.c:89:
cn3dstyl.c: At top level:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c:456:30: warning: 'GetThisSpecialAlgorRenderSet' defined but not used [-Wunused-function]
static SpecialFeatureInfoPtr GetThisSpecialAlgorRenderSet(Int2 id)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c:149:15: warning: 'bResetFeatureTitle' defined but not used [-Wunused-variable]
static ButtoN bResetFeatureTitle;
^~~~~~~~~~~~~~~~~~
cn3dstyl.c:144:14: warning: 'Cn3D_pupModelStyleItem' defined but not used [-Wunused-variable]
static PopuP Cn3D_pupModelStyleItem;
^~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c: In function 'CopyLocation':
cn3dstyl.c:496:27: warning: 'rsipNewHead' may be used uninitialized in this function [-Wmaybe-uninitialized]
rspNew->data.ptrvalue = (VoidPtr) rsipNewHead;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqcons.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from seqcons.c:112:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from seqcons.c:115:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/alignmgr2.h:111,
from ../include/actutils.h:105,
from seqcons.c:116:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
seqcons.c:263:19: warning: 'CSC_Blosum62Fields' defined but not used [-Wunused-const-variable=]
static const char CSC_Blosum62Fields[CSC_BLOSUMSIZE] =
^~~~~~~~~~~~~~~~~~
seqcons.c: In function 'CSC_Algorithm_ByBlosum62':
seqcons.c:402:43: warning: 'minScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
scale = 1.0 - 1.0 * (score[i] - minScore) / (maxScore - minScore);
~~~~~~~~~~^~~~~~~~~~~
seqcons.c:402:67: warning: 'maxScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
scale = 1.0 - 1.0 * (score[i] - minScore) / (maxScore - minScore);
~~~~~~~~~~^~~~~~~~~~~
rm -f libncbicn3d.a
ar cru libncbicn3d.a algorend.o cn3dmsel.o cn3dopen.o cn3dsave.o cn3dxprt.o cn3dwin.o cn3dentr.o cn3dmsg.o cn3dmatn.o cn3dmodl.o cn3dshim.o cn3dmesh.o cn3dstyl.o seqcons.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbicn3d.a ../lib
ranlib ../lib/libncbicn3d.a
mv algorend.o algorend.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL algorend.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/shim3d.h:153,
from algorend.c:582:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
algorend.c: In function 'Cn3D_SetOGLFont':
algorend.c:791:24: warning: unused variable 'currentUnderlined' [-Wunused-variable]
currentUnderlined = FALSE;
^~~~~~~~~~~~~~~~~
algorend.c:790:45: warning: unused variable 'currentItalic' [-Wunused-variable]
static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE,
^~~~~~~~~~~~~
algorend.c:790:24: warning: unused variable 'currentBold' [-Wunused-variable]
static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE,
^~~~~~~~~~~
algorend.c:789:40: warning: unused variable 'currentSize' [-Wunused-variable]
static Nlm_Int2 currentIndex = -1, currentSize = -1;
^~~~~~~~~~~
algorend.c:789:21: warning: unused variable 'currentIndex' [-Wunused-variable]
static Nlm_Int2 currentIndex = -1, currentSize = -1;
^~~~~~~~~~~~
algorend.c: In function 'ColorFromSS':
algorend.c:893:10: warning: unused variable 'rsult' [-Wunused-variable]
Int2 rsult = 0;
^~~~~
algorend.c: In function 'Cn3D_RenWire':
algorend.c:1400:10: warning: unused variable 'pmldThis' [-Wunused-variable]
PMLD pmldThis = NULL;
^~~~~~~~
algorend.c:1399:11: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
algorend.c:1398:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
algorend.c: In function 'Cn3D_ColSeqCons':
algorend.c:1795:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
pars->ConsColAlg = (Nlm_Int2) GetObjectExtra(i);
^
algorend.c: In function 'MasterChangeLabelsProc':
algorend.c:2075:44: warning: unused variable 'TopOn' [-Wunused-variable]
Boolean NumOn, NameOn, PDBOn, WhiteOn, TopOn;
^~~~~
algorend.c:2073:13: warning: unused variable 'k' [-Wunused-variable]
Int2 i, k, nameval;
^
algorend.c: In function 'ResetLabelCtrls':
algorend.c:2272:25: warning: variable 'size' set but not used [-Wunused-but-set-variable]
Int2 i, val, style, size, termStyle;
^~~~
algorend.c: In function 'LabelControls':
algorend.c:2434:19: warning: variable 'ppt11' set but not used [-Wunused-but-set-variable]
PrompT ppt10, ppt11;
^~~~~
algorend.c:2431:36: warning: unused variable 'ppt7' [-Wunused-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt7, ppt8, ppt9;
^~~~
algorend.c: In function 'Cn3D_SetQualityFromAppParams':
algorend.c:2649:9: warning: unused variable 'i' [-Wunused-variable]
int i;
^
algorend.c: In function 'OGL_Quality':
algorend.c:2769:23: warning: unused variable 'q' [-Wunused-variable]
Nlm_PrompT bp, p, q;
^
algorend.c:2769:20: warning: variable 'p' set but not used [-Wunused-but-set-variable]
Nlm_PrompT bp, p, q;
^
algorend.c:2769:16: warning: variable 'bp' set but not used [-Wunused-but-set-variable]
Nlm_PrompT bp, p, q;
^~
algorend.c: In function 'RenderControls':
algorend.c:2893:12: warning: variable 'ppt5' set but not used [-Wunused-but-set-variable]
PrompT ppt5;
^~~~
algorend.c: In function 'RenderObject':
algorend.c:3138:10: warning: unused variable 'iCylRadius' [-Wunused-variable]
Int4 iCylRadius;
^~~~~~~~~~
algorend.c:3137:22: warning: unused variable 'iZTo' [-Wunused-variable]
Int4 iXTo, iYTo, iZTo;
^~~~
algorend.c:3137:16: warning: unused variable 'iYTo' [-Wunused-variable]
Int4 iXTo, iYTo, iZTo;
^~~~
algorend.c:3137:10: warning: unused variable 'iXTo' [-Wunused-variable]
Int4 iXTo, iYTo, iZTo;
^~~~
algorend.c:3136:26: warning: unused variable 'iZFrom' [-Wunused-variable]
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
algorend.c:3136:18: warning: unused variable 'iYFrom' [-Wunused-variable]
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
algorend.c:3136:10: warning: unused variable 'iXFrom' [-Wunused-variable]
Int4 iXFrom, iYFrom, iZFrom;
^~~~~~
algorend.c:3133:10: warning: unused variable 'i' [-Wunused-variable]
Int4 i = 0;
^
algorend.c: In function 'RenderLabel':
algorend.c:3394:10: warning: variable 'paldPrim' set but not used [-Wunused-but-set-variable]
PALD paldPrim = NULL;
^~~~~~~~
algorend.c:3393:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
algorend.c:3389:18: warning: unused variable 'iZ' [-Wunused-variable]
Int4 iX, iY, iZ;
^~
algorend.c:3389:14: warning: unused variable 'iY' [-Wunused-variable]
Int4 iX, iY, iZ;
^~
algorend.c:3389:10: warning: unused variable 'iX' [-Wunused-variable]
Int4 iX, iY, iZ;
^~
algorend.c: In function 'RenderBond':
algorend.c:3554:10: warning: variable 'pmsdParent' set but not used [-Wunused-but-set-variable]
PMSD pmsdParent = NULL;
^~~~~~~~~~
algorend.c: In function 'RenderHalfWormBond':
algorend.c:3673:10: warning: variable 'pmsdParent' set but not used [-Wunused-but-set-variable]
PMSD pmsdParent;
^~~~~~~~~~
algorend.c:3671:24: warning: variable 'pmad2' set but not used [-Wunused-but-set-variable]
PMAD pmad0, pmad1, pmad2, pmad3;
^~~~~
algorend.c: In function 'RenderAnAtom':
algorend.c:3758:10: warning: unused variable 'pmadFrom' [-Wunused-variable]
PMAD pmadFrom = NULL;
^~~~~~~~
algorend.c: In function 'RenderAllAtom':
algorend.c:3829:9: warning: variable 'iMenu' set but not used [-Wunused-but-set-variable]
int iMenu;
^~~~~
algorend.c:3815:11: warning: unused variable 'pvnmbThis' [-Wunused-variable]
PVNMB pvnmbThis = NULL;
^~~~~~~~~
algorend.c:3811:11: warning: unused variable 'pvnmaThis' [-Wunused-variable]
PVNMA pvnmaThis = NULL;
^~~~~~~~~
algorend.c: In function 'RenderGraph':
algorend.c:4498:10: warning: unused variable 'bReservedThis' [-Wunused-variable]
Byte bReservedThis = 0;
^~~~~~~~~~~~~
algorend.c: In function 'LabelChainTermini':
algorend.c:4772:14: warning: unused variable 'pmbdThis' [-Wunused-variable]
PMBD pmbdThis = NULL;
^~~~~~~~
algorend.c:4771:15: warning: unused variable 'pvnmbThis' [-Wunused-variable]
PVNMB pvnmbThis = NULL;
^~~~~~~~~
algorend.c: In function 'RenderMolecule':
algorend.c:4871:11: warning: variable 'pdnmmThis' set but not used [-Wunused-but-set-variable]
PDNMM pdnmmThis = NULL;
^~~~~~~~~
algorend.c: In function 'fnARLoop':
algorend.c:5556:10: warning: variable 'iTest' set but not used [-Wunused-but-set-variable]
Int2 iTest;
^~~~~
algorend.c: In function 'AlgorithmicRendering':
algorend.c:5684:10: warning: unused variable 'i' [-Wunused-variable]
Int2 i = 0;
^
algorend.c:5683:10: warning: unused variable 'Cn3d_LayerNow_sofar' [-Wunused-variable]
Int2 Cn3d_LayerNow_sofar = 0;
^~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from algorend.c:598:
algorend.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
algorend.c:789:21: warning: 'currentIndex' defined but not used [-Wunused-variable]
static Nlm_Int2 currentIndex = -1, currentSize = -1;
^~~~~~~~~~~~
algorend.c:789:40: warning: 'currentSize' defined but not used [-Wunused-variable]
static Nlm_Int2 currentIndex = -1, currentSize = -1;
^~~~~~~~~~~
algorend.c:790:24: warning: 'currentBold' defined but not used [-Wunused-variable]
static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE,
^~~~~~~~~~~
algorend.c:790:45: warning: 'currentItalic' defined but not used [-Wunused-variable]
static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE,
^~~~~~~~~~~~~
algorend.c:791:24: warning: 'currentUnderlined' defined but not used [-Wunused-variable]
currentUnderlined = FALSE;
^~~~~~~~~~~~~~~~~
algorend.c:2265:13: warning: 'LabelGroupOnOffProc' defined but not used [-Wunused-function]
static void LabelGroupOnOffProc(GrouP g)
^~~~~~~~~~~~~~~~~~~
algorend.c:717:16: warning: 'Cn3d_CopyToNode' defined but not used [-Wunused-variable]
static Boolean Cn3d_CopyToNode = FALSE;
^~~~~~~~~~~~~~~
algorend.c: In function 'MasterChangeRenderProc':
algorend.c:1316:33: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
pars->SolventRender = k;
~~~~~~~~~~~~~~~~~~~~^~~
algorend.c: In function 'RenderLabel':
algorend.c:3448:15: warning: 'fZCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fZCen += fZt / l;
~~~~~~^~~~~~~~~~
algorend.c:3443:41: warning: 'fYCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~
algorend.c:3442:41: warning: 'fXCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~
algorend.c:3449:41: warning: 'fZTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fYCen - fYFrom) * (fZCen - fZTo) - (fZCen - fZFrom) * (fYCen - fYTo);
~~~~~~~^~~~~~~
algorend.c:3443:41: warning: 'fYTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~
algorend.c:3442:41: warning: 'fXTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~
algorend.c:3449:58: warning: 'fZFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fYCen - fYFrom) * (fZCen - fZTo) - (fZCen - fZFrom) * (fYCen - fYTo);
~~~~~~~^~~~~~~~~
algorend.c:3443:22: warning: 'fYFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYt = (fYCen - fYFrom) + (fYCen - fYTo);
~~~~~~~^~~~~~~~~
algorend.c:3442:22: warning: 'fXFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fXCen - fXFrom) + (fXCen - fXTo);
~~~~~~~^~~~~~~~~
mv algorend.o algorend.glo
mv algorend.tmp algorend.o
mv cn3dmsel.o cn3dmsel.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmsel.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmsel.c:60:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv cn3dmsel.o cn3dmsel.glo
mv cn3dmsel.tmp cn3dmsel.o
mv cn3dopen.o cn3dopen.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dopen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dopen.c:394:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dopen.c: In function 'Cn3D_OpenStart':
cn3dopen.c:722:10: warning: unused variable 'iBioseq' [-Wunused-variable]
Int4 iBioseq = 0;
^~~~~~~
cn3dopen.c: In function 'MMDB_ReadMime':
cn3dopen.c:1000:19: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
cn3dopen.c:989:25: warning: unused variable 'pbsasThis' [-Wunused-variable]
BiostrucAlignSeqPtr pbsasThis = NULL;
^~~~~~~~~
cn3dopen.c: In function 'Cn3D_NetOpenBiostruc':
cn3dopen.c:1310:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dopen.c:412:
cn3dopen.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from cn3dopen.c:413:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
cn3dopen.c:431:15: warning: 'Cn3D_bOpenBrowse' defined but not used [-Wunused-variable]
static ButtoN Cn3D_bOpenBrowse;
^~~~~~~~~~~~~~~~
cn3dopen.c:430:15: warning: 'Cn3D_wOpen' defined but not used [-Wunused-variable]
static WindoW Cn3D_wOpen;
^~~~~~~~~~
cn3dopen.c: In function 'MMDB_ReadMime':
cn3dopen.c:529:9: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAM_ReplaceGI(salp);
^~~~~~~~~~~~~~~~~~~
cn3dopen.c:513:15: note: 'salp' was declared here
SeqAlign *salp;
^~~~
mv cn3dopen.o cn3dopen.glo
mv cn3dopen.tmp cn3dopen.o
mv cn3dsave.o cn3dsave.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dsave.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dsave.c:157:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dsave.c: In function 'Cn3D_AddMatrix':
cn3dsave.c:206:41: warning: unused variable 'bsfsp_new' [-Wunused-variable]
BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_new = NULL;
^~~~~~~~~
cn3dsave.c: In function 'Cn3D_ExportAsnNow':
cn3dsave.c:375:11: warning: unused variable 'pdnmlThis' [-Wunused-variable]
PDNML pdnmlThis = NULL;
^~~~~~~~~
cn3dsave.c:372:24: warning: variable 'pbsfThis' set but not used [-Wunused-but-set-variable]
BiostrucFeaturePtr pbsfThis;
^~~~~~~~
cn3dsave.c:366:10: warning: unused variable 'pmsdSlave' [-Wunused-variable]
PMSD pmsdSlave = NULL, pmsdMaster = NULL;
^~~~~~~~~
cn3dsave.c:362:27: warning: variable 'FirstSlave' set but not used [-Wunused-but-set-variable]
Boolean iCn3d = TRUE, FirstSlave = FALSE;
^~~~~~~~~~
cn3dsave.c:357:13: warning: unused variable 'pcSave' [-Wunused-variable]
CharPtr pcSave = NULL;
^~~~~~
cn3dsave.c: In function 'Cn3D_SaveBiostruc':
cn3dsave.c:524:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dsave.c:523:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dsave.c:518:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dsave.c: In function 'Cn3D_ExportDictNow':
cn3dsave.c:598:13: warning: unused variable 'pcSave' [-Wunused-variable]
CharPtr pcSave = NULL;
^~~~~~
cn3dsave.c:596:10: warning: unused variable 'iCount' [-Wunused-variable]
Int4 iCount = 0;
^~~~~~
cn3dsave.c: In function 'Cn3D_SaveDictionary':
cn3dsave.c:629:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dsave.c:624:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dsave.c: In function 'Cn3D_SaveSub':
cn3dsave.c:688:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
IteM i;
^
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dsave.c:171:
cn3dsave.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
cn3dsave.c:184:15: warning: 'Cn3D_bFeatOn' defined but not used [-Wunused-variable]
static ButtoN Cn3D_bFeatOn;
^~~~~~~~~~~~
In file included from cn3dsave.c:165:0:
../include/asnmime.h:119:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnmime.h:118:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnmime.h:117:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/asnmime.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnmime.h12";
^~~~~~~~~~~
cn3dsave.c: In function 'Cn3D_GetSubSet.isra.1':
cn3dsave.c:289:24: warning: 'isep' may be used uninitialized in this function [-Wmaybe-uninitialized]
isep->next = SeqEntryNew();
~~~~~~~~~~~^~~~~~~~~~~~~~~
mv cn3dsave.o cn3dsave.glo
mv cn3dsave.tmp cn3dsave.o
mv cn3dxprt.o cn3dxprt.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dxprt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dxprt.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportPDB':
cn3dxprt.c:209:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dxprt.c:208:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dxprt.c:203:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportKin':
cn3dxprt.c:381:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dxprt.c:380:11: warning: variable 'gMS' set but not used [-Wunused-but-set-variable]
GrouP gMS;
^~~
cn3dxprt.c:375:10: warning: variable 'pmsdThis' set but not used [-Wunused-but-set-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dxprt.c: In function 'Cn3D_ExportSub':
cn3dxprt.c:513:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
IteM i;
^
mv cn3dxprt.o cn3dxprt.glo
mv cn3dxprt.tmp cn3dxprt.o
mv cn3dwin.o cn3dwin.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dwin.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dwin.c:647:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dwin.c:733:1: warning: missing braces around initializer [-Wmissing-braces]
{
^
cn3dwin.c:733:1: note: (near initialization for 'Cn3d_PaletteRGB')
cn3dwin.c: In function 'Cn3D_Default_HLColor':
cn3dwin.c:982:27: warning: variable 'colorB' set but not used [-Wunused-but-set-variable]
Uint1 colorR, colorG, colorB;
^~~~~~
cn3dwin.c:982:19: warning: variable 'colorG' set but not used [-Wunused-but-set-variable]
Uint1 colorR, colorG, colorB;
^~~~~~
cn3dwin.c:982:11: warning: variable 'colorR' set but not used [-Wunused-but-set-variable]
Uint1 colorR, colorG, colorB;
^~~~~~
cn3dwin.c: In function 'Cn3D_RedrawEx':
cn3dwin.c:1251:19: warning: unused variable 'iColor' [-Wunused-variable]
DDV_ColorCell iColor;
^~~~~~
cn3dwin.c: In function 'fnPreCHLresidue':
cn3dwin.c:1543:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dwin.c: In function 'Viewer3DGroups':
cn3dwin.c:1728:10: warning: unused variable 'groups' [-Wunused-variable]
Int2 groups = 0;
^~~~~~
cn3dwin.c: In function 'Cn3D_AlignEdit':
cn3dwin.c:1936:10: warning: unused variable 'iCount' [-Wunused-variable]
Int2 iCount = 0;
^~~~~~
cn3dwin.c:1935:10: warning: variable 'pmmdThis' set but not used [-Wunused-but-set-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dwin.c:1933:17: warning: unused variable 'salp' [-Wunused-variable]
SeqAlignPtr salp = NULL;
^~~~
cn3dwin.c:1931:29: warning: variable 'pmsdSlave' set but not used [-Wunused-but-set-variable]
PMSD pmsdMaster = NULL, pmsdSlave = NULL;
^~~~~~~~~
cn3dwin.c:1930:11: warning: unused variable 'pdnmsSlave' [-Wunused-variable]
PDNMS pdnmsSlave = NULL;
^~~~~~~~~~
cn3dwin.c: In function 'Cn3DWin':
cn3dwin.c:2364:5: warning: implicit declaration of function 'Nlm_SetOGLContext' [-Wimplicit-function-declaration]
Nlm_SetOGLContext(NULL, NULL, NULL, NULL);
^~~~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/udviewer.h:219,
from cn3dwin.c:665:
cn3dwin.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/udviewer.h:228,
from cn3dwin.c:665:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
cn3dwin.c:1626:13: warning: 'HLmolecule_MA' defined but not used [-Wunused-function]
static void HLmolecule_MA(MAPtr ma,
^~~~~~~~~~~~~
cn3dwin.c:1428:13: warning: 'HLatom_MA' defined but not used [-Wunused-function]
static void HLatom_MA(MAPtr ma,
^~~~~~~~~
cn3dwin.c:1349:25: warning: 'DoHighlightSeg' defined but not used [-Wunused-function]
static void LIBCALLBACK DoHighlightSeg(PFB pfbThis,
^~~~~~~~~~~~~~
cn3dwin.c:979:13: warning: 'Cn3D_Default_HLColor' defined but not used [-Wunused-function]
static void Cn3D_Default_HLColor(IteM i)
^~~~~~~~~~~~~~~~~~~~
cn3dwin.c:953:13: warning: 'Cn3D_BgColor' defined but not used [-Wunused-function]
static void Cn3D_BgColor(IteM i)
^~~~~~~~~~~~
cn3dwin.c:936:13: warning: 'Cn3D_Default_BgColor' defined but not used [-Wunused-function]
static void Cn3D_Default_BgColor(IteM i)
^~~~~~~~~~~~~~~~~~~~
cn3dwin.c:929:13: warning: 'Cn3D_MoveCB' defined but not used [-Wunused-function]
static void Cn3D_MoveCB(IteM i)
^~~~~~~~~~~
cn3dwin.c:922:13: warning: 'Cn3D_ZoomCB' defined but not used [-Wunused-function]
static void Cn3D_ZoomCB(IteM i)
^~~~~~~~~~~
cn3dwin.c:719:14: warning: 'Cn3D_gViewCtrl' defined but not used [-Wunused-variable]
static GrouP Cn3D_gViewCtrl;
^~~~~~~~~~~~~~
cn3dwin.c:713:14: warning: 'Cn3D_gViewer' defined but not used [-Wunused-variable]
static GrouP Cn3D_gViewer;
^~~~~~~~~~~~
cn3dwin.c:688:13: warning: 'Cn3D_iModelCtrl' defined but not used [-Wunused-variable]
static IteM Cn3D_iModelCtrl = NULL;
^~~~~~~~~~~~~~~
cn3dwin.c:682:13: warning: 'Cn3D_iLabelCtrl' defined but not used [-Wunused-variable]
static IteM Cn3D_iLabelCtrl = NULL;
^~~~~~~~~~~~~~~
cn3dwin.c:676:14: warning: 'Cn3D_Vy' defined but not used [-Wunused-variable]
static Uint2 Cn3D_Vy, Cn3D_Rx;
^~~~~~~
mv cn3dwin.o cn3dwin.glo
mv cn3dwin.tmp cn3dwin.o
mv cn3dentr.o cn3dentr.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/cn3dmain.h:182,
from cn3dentr.c:81:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mv cn3dentr.o cn3dentr.glo
mv cn3dentr.tmp cn3dentr.o
mv cn3dmsg.o cn3dmsg.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmsg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmsg.c:254:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmsg.c: In function 'SeqStrucMediaMsgFunc':
cn3dmsg.c:593:19: warning: variable 'omudp' set but not used [-Wunused-but-set-variable]
OMUserDataPtr omudp = NULL;
^~~~~
In file included from ../include/sqnutils.h:51:0,
from cn3dmsg.c:267:
cn3dmsg.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dmsg.c:271:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv cn3dmsg.o cn3dmsg.glo
mv cn3dmsg.tmp cn3dmsg.o
mv cn3dmatn.o cn3dmatn.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmatn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmatn.c:173:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmatn.c: In function 'FindMM':
cn3dmatn.c:217:29: warning: unused variable 'pdnmsThisSlave' [-Wunused-variable]
PDNMS pdnmsThis = NULL, pdnmsThisSlave = NULL;
^~~~~~~~~~~~~~
cn3dmatn.c: In function 'DoMediaHL':
cn3dmatn.c:249:10: warning: variable 'MainAtom' set but not used [-Wunused-but-set-variable]
Byte MainAtom = 0;
^~~~~~~~
cn3dmatn.c:247:10: warning: unused variable 'paldThis' [-Wunused-variable]
PALD paldThis = NULL;
^~~~~~~~
cn3dmatn.c:246:11: warning: unused variable 'pvnalThis' [-Wunused-variable]
PVNAL pvnalThis = NULL;
^~~~~~~~~
cn3dmatn.c:245:10: warning: unused variable 'pmadThis' [-Wunused-variable]
PMAD pmadThis = NULL;
^~~~~~~~
cn3dmatn.c:244:11: warning: unused variable 'pvnmaThis' [-Wunused-variable]
PVNMA pvnmaThis = NULL;
^~~~~~~~~
cn3dmatn.c: In function 'Cn3DCheckAndDoHighlight':
cn3dmatn.c:372:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dmatn.c:371:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
mv cn3dmatn.o cn3dmatn.glo
mv cn3dmatn.tmp cn3dmatn.o
mv cn3dmodl.o cn3dmodl.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmodl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmodl.c: In function 'Cn3DCheckNoSingleHighlight':
cn3dmodl.c:353:11: warning: unused variable 'pdnmgThis' [-Wunused-variable]
PDNMG pdnmgThis = NULL;
^~~~~~~~~
cn3dmodl.c: In function 'Cn3DCheckHighlighted':
cn3dmodl.c:364:29: warning: unused variable 'pmsdSlave' [-Wunused-variable]
PMSD pmsdMaster = NULL, pmsdSlave = NULL;
^~~~~~~~~
cn3dmodl.c: In function 'Cn3D_ReSetVisibleStatus':
cn3dmodl.c:508:10: warning: unused variable 'pmgd' [-Wunused-variable]
PMGD pmgd = NULL;
^~~~
cn3dmodl.c:507:11: warning: unused variable 'pdnmg' [-Wunused-variable]
PDNMG pdnmg = NULL;
^~~~~
cn3dmodl.c:506:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'fnAlignList':
cn3dmodl.c:996:25: warning: unused variable 'itemtype' [-Wunused-variable]
Uint2 entityID = 0, itemtype = 0;
^~~~~~~~
cn3dmodl.c:996:11: warning: unused variable 'entityID' [-Wunused-variable]
Uint2 entityID = 0, itemtype = 0;
^~~~~~~~
cn3dmodl.c:995:14: warning: unused variable 'sipThis' [-Wunused-variable]
SeqIdPtr sipThis = NULL;
^~~~~~~
cn3dmodl.c:993:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'SynchronizeModVisibleStatus':
cn3dmodl.c:1065:11: warning: unused variable 'pdnmg' [-Wunused-variable]
PDNMG pdnmg = NULL;
^~~~~
cn3dmodl.c:1064:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dmodl.c: In function 'SetResidueVisibilities':
cn3dmodl.c:1201:11: warning: unused variable 'pvnmoThis' [-Wunused-variable]
PVNMO pvnmoThis = NULL;
^~~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dmodl.c:319:
cn3dmodl.c: At top level:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from cn3dmodl.c:323:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
mv cn3dmodl.o cn3dmodl.glo
mv cn3dmodl.tmp cn3dmodl.o
mv cn3dshim.o cn3dshim.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dshim.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/cn3dmain.h:182,
from cn3dshim.c:131:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dshim.c: In function 'Cn3D_Size':
cn3dshim.c:413:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis;
^~~~~~~~
cn3dshim.c:412:11: warning: unused variable 'pdnmsSlave' [-Wunused-variable]
PDNMS pdnmsSlave;
^~~~~~~~~~
cn3dshim.c: In function 'Cn3D_SizeCB':
cn3dshim.c:391:36: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations]
BoundBox->x[i] = pflvDataThis[i / (int) 2];
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dshim.c:390:17: note: within this loop
for (i = 0; i < 6; i++) {
^~~
cn3dshim.c:399:36: warning: iteration 1 invokes undefined behavior [-Waggressive-loop-optimizations]
BoundBox->x[i + 1]) BoundBox->x[i + 1] =
~~~~~~~~~~~^~~~~~~
cn3dshim.c:395:17: note: within this loop
for (i = 0; i < 6; i += 2) { /* check to see if the atom lies outside the bound box */
^~~
mv cn3dshim.o cn3dshim.glo
mv cn3dshim.tmp cn3dshim.o
mv cn3dmesh.o cn3dmesh.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmesh.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from cn3dmesh.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmesh.c: In function 'Cn3D_MeshAcceptProc':
cn3dmesh.c:103:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
cn3dmesh.c: In function 'Cn3D_OpenMesh':
cn3dmesh.c:151:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
cn3dmesh.c: In function 'Cn3D_MeshAcceptProc':
cn3dmesh.c:111:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d", &(Mesh.NumVert), &(Mesh.NumEdge),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.NumTri));
~~~~~~~~~~~~~~~
cn3dmesh.c:119:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%lf %lf %lf %lf %lf %lf %f %f %f %d %d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[0]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[1]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Vertex[2]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[0]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[1]),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&(Mesh.Vertices[i].Normal[2]), &fDummy, &fDummy, &fDummy,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&lDummy, &lDummy, &lDummy);
~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmesh.c:129:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d %d %d", &Mesh.Edges[i].Vertex[0],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Edges[i].Vertex[1], &lDummy, &lDummy, &lDummy);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmesh.c:133:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(hFile, "%d %d %d %d %d %d %d %d %d", &Mesh.Tri[i].Edge[0],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Edge[1], &Mesh.Tri[i].Edge[2],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Vertex[0], &Mesh.Tri[i].Vertex[1],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&Mesh.Tri[i].Vertex[2], &lDummy, &Mesh.Tri[i].Atom,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&lDummy);
~~~~~~~~
mv cn3dmesh.o cn3dmesh.glo
mv cn3dmesh.tmp cn3dmesh.o
mv cn3dstyl.o cn3dstyl.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dstyl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dstyl.c:72:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dstyl.c: In function 'GetThisSpecialAlgorRenderSet':
cn3dstyl.c:459:27: warning: unused variable 'sfipThis' [-Wunused-variable]
SpecialFeatureInfoPtr sfipThis = NULL;
^~~~~~~~
cn3dstyl.c: In function 'GetSpecialAlgorRenderSet':
cn3dstyl.c:641:10: warning: unused variable 'parsThis' [-Wunused-variable]
PARS parsThis = NULL;
^~~~~~~~
cn3dstyl.c:640:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'ChangeSpecialLabelsProc':
cn3dstyl.c:867:16: warning: unused variable 'TopOn' [-Wunused-variable]
FALSE, TopOn = FALSE;
^~~~~
cn3dstyl.c:866:44: warning: unused variable 'PDBOn' [-Wunused-variable]
Boolean NumOn = FALSE, NameOn = FALSE, PDBOn = FALSE, WhiteOn =
^~~~~
cn3dstyl.c:864:17: warning: unused variable 'k' [-Wunused-variable]
Int2 i = 0, k = 0, nameval = 0;
^
cn3dstyl.c: In function 'ModelSetLabelCtrls':
cn3dstyl.c:1059:37: warning: variable 'size' set but not used [-Wunused-but-set-variable]
Int2 i = 0, val = 0, style = 0, size = 0;
^~~~
cn3dstyl.c: In function 'lFeatureEditedAction':
cn3dstyl.c:1136:10: warning: unused variable 'val' [-Wunused-variable]
Int4 val = 0;
^~~
cn3dstyl.c: In function 'bFeatureMoveAction':
cn3dstyl.c:1153:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'bFeatureEditAction':
cn3dstyl.c:1176:23: warning: unused variable 'sfpThis' [-Wunused-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c: In function 'ModelControls':
cn3dstyl.c:1364:19: warning: variable 'ppt13' set but not used [-Wunused-but-set-variable]
PrompT ppt12, ppt13, ppt14;
^~~~~
cn3dstyl.c:1363:9: warning: unused variable 'ppt11' [-Wunused-variable]
ppt11;
^~~~~
cn3dstyl.c:1362:60: warning: unused variable 'ppt9' [-Wunused-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10,
^~~~
cn3dstyl.c:1362:36: warning: variable 'ppt5' set but not used [-Wunused-but-set-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10,
^~~~
cn3dstyl.c:1362:12: warning: variable 'ppt1' set but not used [-Wunused-but-set-variable]
PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10,
^~~~
cn3dstyl.c: In function 'GetBiostrucFeatureLocationForHihglightedResidues':
cn3dstyl.c:1728:30: warning: variable 'SingleInterval' set but not used [-Wunused-but-set-variable]
Boolean Started = FALSE, SingleInterval, UserDefinedFeatureFound =
^~~~~~~~~~~~~~
cn3dstyl.c:1725:20: warning: variable 'iMolCurrent' set but not used [-Wunused-but-set-variable]
Int2 iMol = 0, iMolCurrent = 0;
^~~~~~~~~~~
cn3dstyl.c: In function 'MakeBiostrucFeatureSetForUserDefinedFeature':
cn3dstyl.c:2122:60: warning: unused variable 'bsfsp_tail' [-Wunused-variable]
BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail =
^~~~~~~~~~
cn3dstyl.c:2122:41: warning: unused variable 'bsfsp_head' [-Wunused-variable]
BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail =
^~~~~~~~~~
cn3dstyl.c: In function 'GetUserDefinedFeature':
cn3dstyl.c:2196:27: warning: unused variable 'sfipThis' [-Wunused-variable]
SpecialFeatureInfoPtr sfipThis = NULL;
^~~~~~~~
cn3dstyl.c: In function 'Cn3DIndexUserDefinedFeature':
cn3dstyl.c:2551:23: warning: variable 'sfpThis' set but not used [-Wunused-but-set-variable]
SpecialFeaturePtr sfpThis = NULL;
^~~~~~~
cn3dstyl.c:2549:10: warning: unused variable 'pmmdThis' [-Wunused-variable]
PMMD pmmdThis = NULL;
^~~~~~~~
cn3dstyl.c:2548:11: warning: unused variable 'pdnmmHead' [-Wunused-variable]
PDNMM pdnmmHead = NULL;
^~~~~~~~~
cn3dstyl.c:2547:10: warning: unused variable 'pmsdThis' [-Wunused-variable]
PMSD pmsdThis = NULL;
^~~~~~~~
In file included from ../include/cn3dopen.h:111:0,
from cn3dstyl.c:89:
cn3dstyl.c: At top level:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c:456:30: warning: 'GetThisSpecialAlgorRenderSet' defined but not used [-Wunused-function]
static SpecialFeatureInfoPtr GetThisSpecialAlgorRenderSet(Int2 id)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c:149:15: warning: 'bResetFeatureTitle' defined but not used [-Wunused-variable]
static ButtoN bResetFeatureTitle;
^~~~~~~~~~~~~~~~~~
cn3dstyl.c:144:14: warning: 'Cn3D_pupModelStyleItem' defined but not used [-Wunused-variable]
static PopuP Cn3D_pupModelStyleItem;
^~~~~~~~~~~~~~~~~~~~~~
cn3dstyl.c: In function 'CopyLocation':
cn3dstyl.c:496:27: warning: 'rsipNewHead' may be used uninitialized in this function [-Wmaybe-uninitialized]
rspNew->data.ptrvalue = (VoidPtr) rsipNewHead;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
mv cn3dstyl.o cn3dstyl.glo
mv cn3dstyl.tmp cn3dstyl.o
mv seqcons.o seqcons.tmp
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF -D_OPENGL seqcons.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from seqcons.c:112:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from seqcons.c:115:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/alignmgr2.h:111,
from ../include/actutils.h:105,
from seqcons.c:116:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
seqcons.c:263:19: warning: 'CSC_Blosum62Fields' defined but not used [-Wunused-const-variable=]
static const char CSC_Blosum62Fields[CSC_BLOSUMSIZE] =
^~~~~~~~~~~~~~~~~~
seqcons.c: In function 'CSC_Algorithm_ByBlosum62':
seqcons.c:402:43: warning: 'minScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
scale = 1.0 - 1.0 * (score[i] - minScore) / (maxScore - minScore);
~~~~~~~~~~^~~~~~~~~~~
seqcons.c:402:67: warning: 'maxScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
scale = 1.0 - 1.0 * (score[i] - minScore) / (maxScore - minScore);
~~~~~~~~~~^~~~~~~~~~~
mv seqcons.o seqcons.glo
mv seqcons.tmp seqcons.o
rm -f libncbicn3dOGL.a
ar cru libncbicn3dOGL.a algorend.glo cn3dmsel.glo cn3dopen.glo cn3dsave.glo cn3dxprt.glo cn3dwin.glo cn3dentr.glo cn3dmsg.glo cn3dmatn.glo cn3dmodl.glo cn3dshim.glo cn3dmesh.glo cn3dstyl.glo seqcons.glo
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbicn3dOGL.a ../lib
ranlib ../lib/libncbicn3dOGL.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF aa_ungapped.c
aa_ungapped.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_diagnostics.c
blast_diagnostics.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_engine.c
blast_engine.c:57:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_extend.c
blast_extend.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_filter.c
blast_filter.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_gapalign.c
blast_gapalign.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_hits.c
blast_hits.c: In function 'Blast_HSPResultsFromHSPStreamWithLimitEx':
blast_hits.c:3499:13: warning: variable 'rm_hsps' set but not used [-Wunused-but-set-variable]
Boolean rm_hsps = FALSE;
^~~~~~~
At top level:
blast_hits.c:3212:12: warning: 's_SortHspWrapEvalue' defined but not used [-Wunused-function]
static int s_SortHspWrapEvalue(const void *x, const void *y)
^~~~~~~~~~~~~~~~~~~
blast_hits.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_itree.c
blast_itree.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_lookup.c
blast_lookup.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_message.c
blast_message.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_options.c
blast_options.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_seg.c
blast_seg.c:38:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_seqsrc.c
blast_seqsrc.c:38:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_sw.c
blast_sw.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_setup.c
blast_setup.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_stat.c
blast_stat.c: In function 's_BlastGumbelBlkNew':
blast_stat.c:818:21: warning: unused variable 'retv' [-Wunused-variable]
Blast_GumbelBlk* retv;
^~~~
At top level:
blast_stat.c:5081:15: warning: 's_CalculateNormalProbability' defined but not used [-Wunused-function]
static double s_CalculateNormalProbability(double x_, double eps_)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_stat.c:52:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_traceback.c
blast_traceback.c:52:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
blast_traceback.c: In function 'Blast_TracebackFromHSPList':
blast_traceback.c:393:25: warning: 'qe' may be used uninitialized in this function [-Wmaybe-uninitialized]
Blast_HSPInit(qs, qe, ss, se, qs, ss,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hsp->context, hsp->query.frame,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hsp->subject.frame, 0, &new_esp, &new_hsp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_traceback.c:365:22: note: 'qe' was declared here
Int4 qs, qe, ss, se, es, ee, os;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_util.c
blast_util.c: In function 'BlastProgram2Number':
blast_util.c:309:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (strcasecmp("phiblastp", program) == 0)
^~
blast_util.c:312:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
return 0;
^~~~~~
At top level:
blast_util.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gapinfo.c
gapinfo.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF greedy_align.c
greedy_align.c:38:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF link_hsps.c
link_hsps.c: In function 's_FwdCompareHSPs':
link_hsps.c:138:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (h1->context > h2->context)
^~
link_hsps.c:141:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (h1->query.offset < h2->query.offset)
^~
At top level:
link_hsps.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF lookup_wrap.c
lookup_wrap.c:39:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF na_ungapped.c
na_ungapped.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_math.c
ncbi_math.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF ncbi_std.c
ncbi_std.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF pattern.c
pattern.c:58:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF phi_extend.c
phi_extend.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF phi_lookup.c
phi_lookup.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF lookup_util.c
lookup_util.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_encoding.c
blast_encoding.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_psi.c
blast_psi.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_psi_priv.c
blast_psi_priv.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_kappa.c
blast_kappa.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF matrix_freq_ratios.c
matrix_freq_ratios.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_hspstream.c
blast_hspstream.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_parameters.c
blast_parameters.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_posit.c
blast_posit.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF phi_gapalign.c
phi_gapalign.c:57:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_program.c
blast_program.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_query_info.c
blast_query_info.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_tune.c
blast_tune.c:37:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_aalookup.c
blast_aalookup.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_nalookup.c
blast_nalookup.c:38:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_aascan.c
blast_aascan.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_nascan.c
blast_nascan.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_dynarray.c
blast_dynarray.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF split_query.c
split_query.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF gencode_singleton.c
gencode_singleton.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF index_ungapped.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF hspfilter_collector.c
hspfilter_collector.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
rm -f libblast.a
ar cru libblast.a aa_ungapped.o blast_diagnostics.o blast_engine.o blast_extend.o blast_filter.o blast_gapalign.o blast_hits.o blast_itree.o blast_lookup.o blast_message.o blast_options.o blast_seg.o blast_seqsrc.o blast_sw.o blast_setup.o blast_stat.o blast_traceback.o blast_util.o gapinfo.o greedy_align.o link_hsps.o lookup_wrap.o na_ungapped.o ncbi_math.o ncbi_std.o pattern.o phi_extend.o phi_lookup.o lookup_util.o blast_encoding.o blast_psi.o blast_psi_priv.o blast_kappa.o matrix_freq_ratios.o blast_hspstream.o blast_parameters.o blast_posit.o phi_gapalign.o blast_program.o blast_query_info.o blast_tune.o blast_aalookup.o blast_nalookup.o blast_aascan.o blast_nascan.o blast_dynarray.o split_query.o gencode_singleton.o index_ungapped.o hspfilter_collector.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libblast.a ../lib
ranlib ../lib/libblast.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_api.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/algo/blast/api/blast_tabular.h:42,
from ../include/algo/blast/api/blast_api.h:47,
from blast_api.c:38:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_api.c: In function 's_BlastRPSInfoInit':
blast_api.c:149:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%s", buffer);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:151:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%d", &info->aux_info.gap_open_penalty);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:152:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%d", &info->aux_info.gap_extend_penalty);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:153:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%le", &info->aux_info.ungapped_k);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:154:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%le", &info->aux_info.ungapped_h);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:155:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%d", &info->aux_info.max_db_seq_length);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:156:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%d", &info->aux_info.db_length);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:157:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%lf", &info->aux_info.scale_factor);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:161:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%d", &seq_size); /* not used */
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_api.c:162:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(auxfile, "%le", &info->aux_info.karlin_k[i]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_input.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:85,
from blast_input.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_input.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_input.c,v 1.32 2008/06/09 17:28:41 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_format.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/algo/blast/api/blast_format.h:45,
from blast_format.c:38:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_format.c: In function 's_MBXmlInit':
blast_format.c:255:13: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = FALSE;
^~~~~~
blast_format.c: In function 's_LoadMatrix':
blast_format.c:673:20: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]][pchars[j]] = pack_matrix->scores[(i*dim)+j];
^
blast_format.c:673:31: warning: array subscript has type 'char' [-Wchar-subscripts]
ss[pchars[i]][pchars[j]] = pack_matrix->scores[(i*dim)+j];
^
At top level:
blast_format.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_format.c,v 1.119 2011/05/26 20:59:45 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_mtlock.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/ncbithr.h:87,
from blast_mtlock.c:39:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_mtlock.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_options_api.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_prelim.c
blast_prelim.c: In function 'Blast_PrelimSearchThreadRun':
blast_prelim.c:100:9: warning: variable 'status' set but not used [-Wunused-but-set-variable]
Int2 status = 0;
^~~~~~
At top level:
blast_prelim.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_prelim.c,v 1.8 2006/05/24 21:17:50 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_returns.c
blast_returns.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_returns.c,v 1.39 2010/06/10 13:44:46 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_seq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from blast_seq.c:34:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_seq.c: In function 's_SeqLocFillSequenceBuffer':
blast_seq.c:529:10: warning: variable 'seq_code' set but not used [-Wunused-but-set-variable]
Uint1 seq_code, strand;
^~~~~~~~
At top level:
blast_seq.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_seq.c,v 1.89 2008/06/09 17:29:14 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_seqalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from ../include/algo/blast/api/blast_seqalign.h:42,
from blast_seqalign.c:35:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_seqalign.c: In function 's_HSPListToSeqAlignUngapped':
blast_seqalign.c:343:26: warning: variable 'hspset_cnt_old' set but not used [-Wunused-but-set-variable]
Int4 hsp_cnt, index2, hspset_cnt_old;
^~~~~~~~~~~~~~
At top level:
blast_seqalign.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_seqalign.c,v 1.64 2010/02/12 20:54:54 maning Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_tabular.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/algo/blast/api/blast_tabular.h:42,
from blast_tabular.c:35:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_tabular.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_tabular.c,v 1.41 2009/06/01 14:33:38 maning Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF repeats_filter.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:85,
from ../include/algo/blast/api/repeats_filter.h:41,
from repeats_filter.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
repeats_filter.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: repeats_filter.c,v 1.19 2007/12/19 21:56:48 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqsrc_multiseq.c
seqsrc_multiseq.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seqsrc_multiseq.c,v 1.28 2011/05/26 20:59:45 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF seqsrc_readdb.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from ../include/algo/blast/api/seqsrc_readdb.h:38,
from seqsrc_readdb.c:35:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqsrc_readdb.c: In function 's_ReaddbGetNextChunk':
seqsrc_readdb.c:375:11: warning: variable 'real_readdb_entries' set but not used [-Wunused-but-set-variable]
Uint4 real_readdb_entries;
^~~~~~~~~~~~~~~~~~~
At top level:
seqsrc_readdb.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seqsrc_readdb.c,v 1.60 2011/05/26 20:59:45 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF twoseq_api.c
twoseq_api.c: In function 's_TwoSeqBasicFillOptions':
twoseq_api.c:100:10: warning: unused variable 'status' [-Wunused-variable]
Int2 status = 0;
^~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/algo/blast/api/twoseq_api.h:41,
from twoseq_api.c:45:
twoseq_api.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF dust_filter.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:85,
from ../include/algo/blast/api/dust_filter.h:41,
from dust_filter.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dust_filter.c: In function 's_GetFilteringLocations':
dust_filter.c:171:32: warning: unused variable 'filter_slp_rev' [-Wunused-variable]
BlastSeqLoc* filter_slp_rev = NULL;
^~~~~~~~~~~~~~
At top level:
dust_filter.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: dust_filter.c,v 1.12 2007/12/19 22:05:56 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF blast_message_api.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from blast_message_api.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -D_PNG -I../include -DWIN_MOTIF hspfilter_queue.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:103,
from ../include/ncbithr.h:87,
from hspfilter_queue.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
hspfilter_queue.c: In function 's_BlastHSPQueueInit':
hspfilter_queue.c:65:24: warning: unused variable 'q_data' [-Wunused-variable]
BlastHSPQueueData * q_data = data;
^~~~~~
At top level:
hspfilter_queue.c:36:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
rm -f libblastapi.a
ar cru libblastapi.a blast_api.o blast_input.o blast_format.o blast_mtlock.o blast_options_api.o blast_prelim.o blast_returns.o blast_seq.o blast_seqalign.o blast_tabular.o repeats_filter.o seqsrc_multiseq.o seqsrc_readdb.o twoseq_api.o dust_filter.o blast_message_api.o hspfilter_queue.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libblastapi.a ../lib
ranlib ../lib/libblastapi.a
gcc -o asntool -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -DWIN_MOTIF -L../shlib asntool.c asncode.c ../lib/libncbi.a -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asntool.c:64:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from asnbuild.h:70,
from asncode.c:52:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asncode.c: In function 'AsnCode_SETOF_base_or_user':
asncode.c:1518:20: warning: variable 'real_type' set but not used [-Wunused-but-set-variable]
Int2 real_type;
^~~~~~~~~
asncode.c:1517:20: warning: variable 'valslot' set but not used [-Wunused-but-set-variable]
CharPtr valslot;
^~~~~~~
asncode.c: In function 'userobj_and_basetype_SETOF':
asncode.c:2472:20: warning: variable 'valslot' set but not used [-Wunused-but-set-variable]
CharPtr valslot;
^~~~~~~
asncode.c: In function 'AsnCodeIsReallyChoice':
asncode.c:3201:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (now_atp)
^
asncode.c: In function 'AsnCodeFunctionWriteFuncChoiceStart':
asncode.c:3623:20: warning: variable 'obj_use' set but not used [-Wunused-but-set-variable]
CharPtr obj_use = which_node->obj_name;
^~~~~~~
asncode.c: In function 'AsnCodeIter':
asncode.c:4237:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (iter->atp != NULL)
^
asncode.c: In function 'AsnCode':
asncode.c:4316:48: warning: variable 'objnamety' set but not used [-Wunused-but-set-variable]
CharPtr objnameuc = NULL, objnamemc = NULL, objnamety = NULL;
^~~~~~~~~
At top level:
asncode.c:291:17: warning: 'defbyte' defined but not used [-Wunused-variable]
static CharPtr defbyte = "ASNCODE_BYTEVAL_SLOT";
^~~~~~~
asncode.c:290:17: warning: 'defbool' defined but not used [-Wunused-variable]
static CharPtr defbool = "ASNCODE_BOOLVAL_SLOT";
^~~~~~~
asncode.c:289:17: warning: 'defreal' defined but not used [-Wunused-variable]
static CharPtr defreal = "ASNCODE_REALVAL_SLOT";
^~~~~~~
asncode.c:288:17: warning: 'defbigint' defined but not used [-Wunused-variable]
static CharPtr defbigint = "ASNCODE_BIGINTVAL_SLOT";
^~~~~~~~~
asncode.c:286:17: warning: 'defptr' defined but not used [-Wunused-variable]
static CharPtr defptr = "ASNCODE_PTRVAL_SLOT";
^~~~~~
../lib/libncbi.a(ncbifile.o): In function `Nlm_TmpNam':
./build/ncbifile.c:1209: warning: the use of `tempnam' is dangerous, better use `mkstemp'
cp -p asntool ../bin
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -C build -f makedemo.unx LCL=lnx CC="gcc " LDFLAGS1="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"' -fPIE -pie -Wl,-z,relro -Wl,-z,now" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" NCBI_LINKINGLIBDIR="../shlib" \
CFLAGS1="-c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"'" VIBLIBS= VIBFLAG= LIB50=-lpcre
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
./ln-if-absent ../demo/*.* .
./ln-if-absent ../regexp/test/*.* .
./ln-if-absent ../regexp/demo/*.* .
./ln-if-absent ../internal/*.* .
set: No match.
makedemo.unx:156: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
chmod -R ug+rw,o+r .
echo Waiting...go
Waiting...go
gcc -o testcore -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib testcore.c -lncbi -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from testcore.c:42:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
testcore.c:337:13: warning: 'TestStrings' defined but not used [-Wunused-function]
static void TestStrings (void)
^~~~~~~~~~~
gcc -o makeset -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib makeset.c -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/all.h:9,
from makeset.c:9:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from makeset.c:9:0:
../include/all.h:7192:0: warning: "RNA_QUAL" redefined
#define RNA_QUAL &at[2231]
../include/all.h:5745:0: note: this is the location of the previous definition
#define RNA_QUAL &at[1023]
makeset.c: In function 'Nlm_Main':
makeset.c:27:26: warning: unused variable 'uid' [-Wunused-variable]
Int4 seekptr, tempseek, uid;
^~~
makeset.c:27:16: warning: unused variable 'tempseek' [-Wunused-variable]
Int4 seekptr, tempseek, uid;
^~~~~~~~
makeset.c:27:7: warning: unused variable 'seekptr' [-Wunused-variable]
Int4 seekptr, tempseek, uid;
^~~~~~~
gcc -o getmesh -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib getmesh.c -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/allpub.h:9,
from getmesh.c:8:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o indexpub -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib indexpub.c -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/allpub.h:9,
from indexpub.c:7:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o getpub -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib getpub.c -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/allpub.h:9,
from getpub.c:7:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o testobj -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib testobj.c -lncbiobj -lncbi -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmedli.h:80,
from testobj.c:8:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o seqtest -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib seqtest.c -lncbiobj -lncbi -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from seqtest.c:8:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o dosimple -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib dosimple.c -lncbiobj -lncbi -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/simple.h:63,
from dosimple.c:7:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o asn2ff -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib asn2ff.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from asn2ff.c:7:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2ff.c: In function 'Nlm_Main':
asn2ff.c:129:10: warning: unused variable 'good' [-Wunused-variable]
Boolean good = FALSE;
^~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from asn2ff.c:9:
At top level:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
asn2ff.c: In function 'Nlm_Main':
asn2ff.c:404:7: warning: 'atp2' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (atp == atp2) { /* top level Seq-entry */
^
asn2ff.c:351:7: warning: 'atp1' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (atp == atp1) {
^
gcc -o checksub -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib checksub.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/objsub.h:76,
from checksub.c:8:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o asndhuff -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib asndhuff.c -lncbicdr -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/casn.h:96,
from asndhuff.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asndhuff.c: In function 'do_medline':
asndhuff.c:182:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
for (count=0; entry=CASN_NextMedlineEntry(casnh); ++count)
^~~
asndhuff.c: In function 'do_sequence':
asndhuff.c:221:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
for (count=0; entry=CASN_NextSeqEntry(casnh); ++count)
^~~
asndhuff.c:200:10: warning: unused variable 'val' [-Wunused-variable]
DataVal val;
^~~
gcc -o entrcmd -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib entrcmd.c -lncbiacc -lncbicdr -lncbiobj -lncbi -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from entrcmd.c:113:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
entrcmd.c: In function 'PrintDSPMwww':
entrcmd.c:373:21: warning: unused variable 'lsp' [-Wunused-variable]
LocalLinkSetPtr lsp;
^~~
entrcmd.c: In function 'PrintDSPNwww':
entrcmd.c:465:21: warning: unused variable 'lsp' [-Wunused-variable]
LocalLinkSetPtr lsp;
^~~
entrcmd.c: In function 'PrintDSPPwww':
entrcmd.c:569:21: warning: unused variable 'lsp' [-Wunused-variable]
LocalLinkSetPtr lsp;
^~~
entrcmd.c: In function 'TermProcessing':
entrcmd.c:1297:13: warning: variable 'inclusive' set but not used [-Wunused-but-set-variable]
Boolean inclusive;
^~~~~~~~~
entrcmd.c:1296:13: warning: variable 'endWithTerm' set but not used [-Wunused-but-set-variable]
Boolean endWithTerm = FALSE;
^~~~~~~~~~~
entrcmd.c:1295:13: warning: variable 'beginWithTerm' set but not used [-Wunused-but-set-variable]
Boolean beginWithTerm = FALSE;
^~~~~~~~~~~~~
At top level:
entrcmd.c:284:16: warning: 'IsGenBank' defined but not used [-Wunused-function]
static Boolean IsGenBank (SeqEntryPtr sep)
^~~~~~~~~
entrcmd.c: In function 'LinkSetToLocalLinkSet':
entrcmd.c:212:12: warning: 'lsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return lsp;
^~~
entrcmd.c: In function 'TermProcessing':
entrcmd.c:1387:43: warning: 'ratio' may be used uninitialized in this function [-Wmaybe-uninitialized]
termsBefore = (Int2) (numTerms / ((float) ratio / 2));
^~~~~~~~~~~~~
entrcmd.c: In function 'Nlm_Main':
entrcmd.c:1548:17: warning: 'db' may be used uninitialized in this function [-Wmaybe-uninitialized]
slp->db = db;
~~~~~~~~^~~~
entrcmd.c:1476:13: note: 'db' was declared here
DocType db;
^~
entrcmd.c:2207:24: warning: 'neighborFile' may be used uninitialized in this function [-Wmaybe-uninitialized]
neighborFp = FileOpen(neighborFile, "r");
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/ncbi.h:62:0,
from entrcmd.c:113:
../include/ncbistr.h:312:18: warning: 'taxString' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define StrICmp Nlm_StrICmp
^~~~~~~~~~~
entrcmd.c:1917:13: note: 'taxString' was declared here
CharPtr taxString;
^~~~~~~~~
entrcmd.c:2231:9: warning: 'termString' may be used uninitialized in this function [-Wmaybe-uninitialized]
TermProcessing(programStr, termString, db, FALSE);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
entrcmd.c:2137:12: warning: 'boolString' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((bsp = EntrezTLEvalXString(boolString, db, -1, NULL, NULL)) != NULL)
^
gcc -o errhdr -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib errhdr.c -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from errhdr.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/string.h:635:0,
from ../include/ncbilcl.h:156,
from ../include/ncbi.h:57,
from errhdr.c:1:
In function 'strncat',
inlined from 'main' at errhdr.c:44:4:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -o cdscan -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib cdscan.c -lncbiacc -lncbicdr -lncbiobj -lncbi -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cdscan.c:83:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cdscan.c:576:13: warning: 'SeqEntryToFeat' defined but not used [-Wunused-function]
static void SeqEntryToFeat (SeqEntryPtr sep, FILE *fp)
^~~~~~~~~~~~~~
cdscan.c:392:13: warning: 'GenBankPubs' defined but not used [-Wunused-function]
static void GenBankPubs (SeqEntryPtr sep, FILE * fp)
^~~~~~~~~~~
cdscan.c:133:13: warning: 'root' defined but not used [-Wunused-variable]
static Char root [PATH_MAX];
^~~~
gcc -o findspl -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib findspl.c -lncbiacc -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from findspl.c:62:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o ncbisort -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib sortcmd.c -lncbitool -lblastcompadj \
-lncbi -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ncbisort.h:62,
from sortcmd.c:64:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o fa2htgs -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib fa2htgs.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/objsub.h:76,
from ../include/subutil.h:50,
from fa2htgs.c:30:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
fa2htgs.c: In function 'Nlm_Main':
fa2htgs.c:475:10: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
litp = (SeqLitPtr) dsp->data.ptrvalue;
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fa2htgs.c:448:16: note: 'dsp' was declared here
DeltaSeqPtr dsp;
^~~
gcc -o fastacmd -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib fastacmd.c -lncbitool -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from fastacmd.c:164:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
fastacmd.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: fastacmd.c,v 6.36 2005/06/22 13:55:22 coulouri Exp $";
^~~~~
gcc -o formatdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib formatdb.c -lncbitool -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from formatdb.c:417:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/sqnutils.h:51:0,
from formatdb.c:421:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
formatdb.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: formatdb.c,v 6.104 2007/08/21 20:07:49 kans Exp $";
^~~~~
gcc -o formatrpsdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib formatrpsdb.c -lncbitool \
-lblast -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from formatrpsdb.c:142:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/sqnutils.h:51:0,
from formatrpsdb.c:145:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
formatrpsdb.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: formatrpsdb.c,v 1.29 2010/10/20 13:09:42 madden Exp $";
^~~~~
formatrpsdb.c: In function 'RPSUpdateStatistics':
formatrpsdb.c:440:43: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (freq_list != NULL || i < seq_size || j < alphabet_size)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
formatrpsdb.c: In function 'RPSUpdatePSSM':
formatrpsdb.c:575:27: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (i < seq_size || j < alphabet_size) {
~~^~~~~~~~~~~~~~~
gcc -o blastall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib blastall.c -lblastapi \
-lblast -lncbitool -lncbiobj -lncbi
blastall.c: In function 'Main_old':
blastall.c:1812:26: warning: variable 'nuc_concat' set but not used [-Wunused-but-set-variable]
Boolean concat_done, nuc_concat;
^~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from blastall.c:727:
blastall.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
blastall.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastall.c,v 6.206 2011/12/19 18:40:17 gouriano Exp $";
^~~~~
blastall.c: In function 'Main_old':
blastall.c:2410:74: warning: 'fake_bsp_arr' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr_bsp = (num_queries>0) ? *(fake_bsp_arr + bsp_iter) : query_bsp;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
blastall.c:1808:22: warning: 'seq_annot_arr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAnnotPtrArray seq_annot_arr;
^~~~~~~~~~~~~
blastall.c:2742:84: warning: 'sap_array' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr_seqalign = (num_queries > 0) ? *(sap_array + sap_iter) : seqalign;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
blastall.c:1795:10: warning: 'num_bsps' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 num_bsps, index;
^~~~~~~~
blastall.c:2618:18: warning: 'next_seqalign' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (seqalign) {
^
blastall.c:2895:12: warning: 'err_ticket' may be used uninitialized in this function [-Wmaybe-uninitialized]
BlastDeleteUserErrorString(err_ticket);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastall.c:2812:18: warning: 'xml_aip' may be used uninitialized in this function [-Wmaybe-uninitialized]
BXMLPrintOutput(xml_aip, NULL, options, blast_program,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_database, fake_bsp, other_returns, 0,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
message, mask_loc);
~~~~~~~~~~~~~~~~~~
gcc -o blastpgp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib blastpgp.c -lncbitool \
-lncbiobj -lncbi
blastpgp.c: In function 'PGPFormatFooter':
blastpgp.c:1290:32: warning: variable 'dbinfo_head' set but not used [-Wunused-but-set-variable]
TxDfDbInfoPtr dbinfo=NULL, dbinfo_head;
^~~~~~~~~~~
blastpgp.c: In function 'Nlm_Main':
blastpgp.c:1685:14: warning: variable 'alignCheckpoint' set but not used [-Wunused-but-set-variable]
Boolean alignCheckpoint = FALSE;
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from blastpgp.c:561:
blastpgp.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/ddvcreate.h:143,
from blastpgp.c:563:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
blastpgp.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastpgp.c,v 6.140 2008/03/31 13:35:18 madden Exp $";
^~~~~
gcc -o testval -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib testval.c -lncbiobj -lncbi -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/objsub.h:76,
from testval.c:9:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
testval.c: In function 'Nlm_Main':
testval.c:186:7: warning: 'atp2' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (atp == atp2) /* top level Seq-entry */
^
testval.c:183:9: warning: 'atp' may be used uninitialized in this function [-Wmaybe-uninitialized]
while ((atp = AsnReadId(aip, amp, atp)) != NULL)
^
gcc -o seedtop -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib seedtop.c -lncbitool \
-lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from seedtop.c:88:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seedtop.c: In function 'Nlm_Main':
seedtop.c:363:36: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
&error_returns, &info_vnp,hitArraySz)) {
^
At top level:
seedtop.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seedtop.c,v 6.19 2008/01/09 19:17:49 merezhuk Exp $";
^~~~~
gcc -o makemat -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib makemat.c -lncbitool \
-lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from makemat.c:40:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/sqnutils.h:51:0,
from makemat.c:52:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
makemat.c: In function 'convertToMatrices':
makemat.c:277:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(profilesFile,"%s", profileFileName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makemat.c:279:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(profilesFile,"%s", relativeProfileFileName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makemat.c:290:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(sequencesFile,"%s", sequenceFileName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makemat.c:292:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(sequencesFile,"%s", relativeSequenceFileName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
makemat.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: makemat.c,v 6.17 2005/07/28 14:52:22 coulouri Exp $";
^~~~~
makemat.c: In function 'makeMatrixName':
makemat.c:97:15: warning: 'lastc' may be used uninitialized in this function [-Wmaybe-uninitialized]
returnName[lastc] = '.';
^
makemat.c: In function 'Nlm_Main':
makemat.c:437:5: warning: 'sbp' may be used uninitialized in this function [-Wmaybe-uninitialized]
BLAST_ScoreBlkDestruct(sbp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
makemat.c:244:23: note: 'sbp' was declared here
BLAST_ScoreBlkPtr sbp;
^~~
In file included from ../include/ncbi.h:59:0,
from makemat.c:40:
../include/ncbimem.h:232:23: warning: 'relativeMatrixFileName' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
makemat.c:230:29: note: 'relativeMatrixFileName' was declared here
Char * matrixFileName, *relativeMatrixFileName; /*file name for corresponding matrix file*/
^~~~~~~~~~~~~~~~~~~~~~
makemat.c:232:10: warning: 'prefixLength' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 prefixLength; /*length of directoryPrefix*/
^~~~~~~~~~~~
gcc -o copymat -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib copymat.c -lblast -lncbitool \
-lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from copymat.c:181:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
copymat.c: In function 'RPSCreateLookupFile':
copymat.c:622:10: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start, i, header_size, all_length, magicNumber;
^~~~~
copymat.c: In function 'findTotalLength':
copymat.c:429:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%s",underlyingMatrixName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:430:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%d\n", &gap_open);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:431:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%d\n", &gap_extend);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:432:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Kungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:433:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Hungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:434:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &maxLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:435:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &dbLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:436:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%lf", scalingFactor);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:439:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &thisLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:440:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Kungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c: In function 'readAllMatrices':
copymat.c:383:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixnamefp,"%s", oneMatrixFileName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:385:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixnamefp,"%s", relativeMatrixFileName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c: In function 'readNextMatrix':
copymat.c:299:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile, "%d", &lengthInFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:301:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%s",sequence);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:304:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkLambda);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:305:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkK);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:306:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junklogK);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:307:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkH);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:309:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkLambda);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:310:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkK);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:311:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junklogK);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:312:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkH);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:314:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkLambda);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:315:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkK);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:316:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junklogK);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:317:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le\n", &junkH);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
copymat.c:319:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(rowOfScores, MAXLINELEN, thisMatrixFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
copymat.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: copymat.c,v 6.49 2008/11/04 16:44:38 maning Exp $";
^~~~~
copymat.c: In function 'Nlm_Main':
copymat.c:371:10: warning: 'prefixLength' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 prefixLength; /*length of directoryPrefix*/
^~~~~~~~~~~~
gcc -o impala -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib profiles.c -lncbitool \
-lncbiobj -lncbi -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from profiles.c:85:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
profiles.c: In function 'Nlm_Main':
profiles.c:1692:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (myargs[ARG_ALIGN_VIEW].intvalue == 1 ||
^~
profiles.c:1695:3: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if (myargs[ARG_ALIGN_VIEW].intvalue == 3 ||
^~
profiles.c:1430:16: warning: variable 'spp' set but not used [-Wunused-but-set-variable]
SeqPortPtr spp=NULL; /*used for filtering*/
^~~
In file included from ../include/sqnutils.h:51:0,
from profiles.c:105:
profiles.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
profiles.c: In function 'findMatchingProfiles':
profiles.c:1104:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(sequencesFile,"%s", oneSequenceFileName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:1106:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(sequencesFile,"%s", relativeSequenceFileName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:1117:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matricesFile,"%s", oneMatrixFileName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:1119:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matricesFile,"%s", relativeMatrixFileName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c: In function 'computeL':
profiles.c:379:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%s",underlyingMatrixName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:380:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%d\n", &gap_open);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:381:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%d\n", &gap_extend);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:382:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Kungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:383:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Hungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:397:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &maxLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:398:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &sequenceDbLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:399:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%lf", &scalingFactor);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:412:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &(dbSeqLengths[profileIndex]));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:414:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &(gappedKArray[profileIndex]));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c: In function 'readkbp':
profiles.c:267:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile, "%d", &lengthInFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:273:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%s",sequence);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:276:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkLambda);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:277:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkK);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:278:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junklogK);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:279:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &junkH);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:281:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &(kbp->Lambda));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:282:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &(kbp->K));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:283:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &(kbp->logK));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:284:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(thisMatrixFile,"%le", &(kbp->H));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c: In function 'readSequence':
profiles.c:204:6: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets((CharPtr) descr, MAXLINELEN, sequenceFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:206:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(sequenceFile, "%*[^\n]");
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:235:6: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets((CharPtr) lineOfQuery, MAXLINELEN, sequenceFile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:237:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(sequenceFile, "%*[^\n]");
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c: In function 'findProfileParams':
profiles.c:461:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%s",underlyingMatrixName);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:462:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%d\n", &local_gap_open);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:463:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile,"%d\n", &local_gap_extend);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:464:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Kungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:465:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Hungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:466:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &maxLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:467:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &sequenceDbSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:468:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%lf\n", &scalingFactor);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:471:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%d", &thisLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:472:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(matrixAuxiliaryFile, "%le", &Kungapped);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
profiles.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: profiles.c,v 6.38 2005/07/28 14:52:22 coulouri Exp $";
^~~~~
profiles.c: In function 'findMatchingProfiles':
profiles.c:192:11: warning: 'query' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint1 * query; /*sequence read in*/
^~~~~
profiles.c:1251:27: warning: 'subject_id' may be used uninitialized in this function [-Wmaybe-uninitialized]
newSW->subject_id = subject_id;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
profiles.c:1244:22: warning: 'bestScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
newSW->score = bestScore;
~~~~~~~~~~~~~^~~~~~~~~~~
profiles.c:1246:23: warning: 'bestEvalue' may be used uninitialized in this function [-Wmaybe-uninitialized]
newSW->eValue = bestEvalue;
~~~~~~~~~~~~~~^~~~~~~~~~~~
profiles.c:983:9: warning: 'prefixLength' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 prefixLength; /*length of directoryPrefix*/
^~~~~~~~~~~~
profiles.c: In function 'Nlm_Main':
profiles.c:1769:16: warning: 'txmatrix' may be used uninitialized in this function [-Wmaybe-uninitialized]
txmatrix = TxMatrixDestruct(txmatrix);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:1767:11: warning: 'matrix' may be used uninitialized in this function [-Wmaybe-uninitialized]
matrix = BLAST_MatrixDestruct(matrix);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:1775:11: warning: 'search' may be used uninitialized in this function [-Wmaybe-uninitialized]
search = BlastSearchBlkDestruct(search);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:1773:12: warning: 'options' may be used uninitialized in this function [-Wmaybe-uninitialized]
options = BLASTOptionDelete(options);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
profiles.c:1779:25: warning: 'fake_bsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
fake_bsp->length = 0;
~~~~~~~~~~~~~~~~~^~~
gcc -o megablast -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib megablast.c -lblastapi \
-lblast -lncbitool -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from megablast.c:656:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
megablast.c: In function 'Main_old':
megablast.c:1439:4: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else if (myargs[ARG_OUTTYPE].intvalue == MBLAST_DELAYED_TRACEBACK)
^~~~
megablast.c:1444:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
options->megablast_full_deflines = (Boolean) myargs[ARG_FULLID].intvalue;
^~~~~~~
megablast.c: In function 'BLAST_FillOptions':
megablast.c:1908:9: warning: unused variable 'windows' [-Wunused-variable]
Int4 windows = 0;
^~~~~~~
In file included from ../include/sqnutils.h:51:0,
from megablast.c:661:
megablast.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
megablast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: megablast.c,v 6.203 2009/06/01 14:33:38 maning Exp $";
^~~~~
gcc -o vecscreen -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib vecscreen.c -lncbitool \
-lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from vecscreen.c:57:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/sqnutils.h:51:0,
from vecscreen.c:68:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
gcc -o gil2bin -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib gil2bin.c -lncbitool -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from gil2bin.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gil2bin.c: In function 'Nlm_Main':
gil2bin.c:90:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
gil2bin.c:93:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
return 0;
^~~~~~
gcc -o blastclust -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib blastclust.c -lncbitool \
-lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastclust.c:189:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastclust.c: In function 'Nlm_Main':
blastclust.c:1067:8: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tmpdir = getenv("TMPDIR")) {
^~
blastclust.c:1278:25: warning: variable 'head' set but not used [-Wunused-but-set-variable]
SeqAlignPtr PNTR head; /* Will not be used */
^~~~
blastclust.c:961:11: warning: variable 'align_type' set but not used [-Wunused-but-set-variable]
Uint1 align_type;
^~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from blastclust.c:200:
blastclust.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
blastclust.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastclust.c,v 6.50 2011/12/19 18:40:17 gouriano Exp $";
^~~~~
blastclust.c: In function 'PrintNeighbors':
blastclust.c:808:40: warning: 'context' may be used uninitialized in this function [-Wmaybe-uninitialized]
query = search->context[context].query->sequence;
^
blastclust.c:776:59: warning: 'query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
length_coverage = MIN(((FloatHi)q_length) / query_length,
^
blastclust.c:668:31: warning: 'hsp_info_array' may be used uninitialized in this function [-Wmaybe-uninitialized]
BlastClustHspInfoPtr PNTR hsp_info_array;
^~~~~~~~~~~~~~
blastclust.c:809:26: warning: 'hsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
esp = hsp->gap_info->esp;
~~~^~~~~~~~~~
gcc -o rpsblast -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib rpsblast.c -lblastapi \
-lblast -lncbitool -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from rpsblast.c:328:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rpsblast.c: In function 'Nlm_Main':
rpsblast.c:567:22: warning: variable 'program_number' set but not used [-Wunused-but-set-variable]
EBlastProgramType program_number;
^~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/algo/blast/api/twoseq_api.h:41,
from ../include/algo/blast/api/blast_format.h:51,
from rpsblast.c:330:
rpsblast.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
rpsblast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: rpsblast.c,v 6.93 2008/07/23 14:06:57 madden Exp $";
^~~~~
gcc -o asn2xml -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib asn2xml.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from asn2xml.c:21:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o debruijn -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib debruijn.c -lblast -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from debruijn.c:38:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
debruijn.c: In function 'Nlm_Main':
debruijn.c:72:12: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
alphabet = myargs[1].strvalue;
^
debruijn.c:80:14: warning: pointer targets in passing argument 1 of 'strlen' differ in signedness [-Wpointer-sign]
k = strlen(alphabet);
^~~~~~~~
In file included from ../include/ncbilcl.h:156:0,
from ../include/ncbi.h:57,
from debruijn.c:38:
/usr/include/string.h:394:15: note: expected 'const char *' but argument is of type 'Nlm_Uint1 * {aka unsigned char *}'
extern size_t strlen (const char *__s)
^~~~~~
debruijn.c:89:10: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
output = (char *) malloc(outputsize + 1);
^
debruijn.c:106:8: warning: pointer targets in passing argument 1 of 'puts' differ in signedness [-Wpointer-sign]
puts(output);
^~~~~~
In file included from ../include/ncbilcl.h:154:0,
from ../include/ncbi.h:57,
from debruijn.c:38:
/usr/include/stdio.h:695:12: note: expected 'const char *' but argument is of type 'Nlm_Uint1 * {aka unsigned char *}'
extern int puts (const char *__s);
^~~~
debruijn.c:109:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
At top level:
debruijn.c:29:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: debruijn.c,v 1.4 2004/02/09 21:24:59 ucko Exp $";
^~~~~
gcc -o asn2idx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib asn2idx.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2idx.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o sortbyquote -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib sortbyquote.c -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from sortbyquote.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o subfuse -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib subfuse.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from subfuse.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o test_regexp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib pcretest.c -lpcre
gcc -o demo_regexp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib pcredemo.c -lpcre
gcc -o demo_regexp_grep -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib pcregrep.c -lpcre
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
cd build && rm -f blast blastall blastall_old blastpgp seedtop megablast rpsblast blastclust
/usr/bin/make -C build -f makedemo.unx LCL=lnx CC="gcc " LDFLAGS1="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"' -fPIE -pie -Wl,-z,relro -Wl,-z,now" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" NCBI_LINKINGLIBDIR="../shlib" \
CFLAGS1="-c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"'" VIBLIBS= VIBFLAG= THREAD_OBJ="ncbithr.o" \
THREAD_OTHERLIBS="-lpthread" blast blastall blastall_old blastpgp seedtop megablast rpsblast blastclust
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
./ln-if-absent ../demo/*.* .
./ln-if-absent ../regexp/test/*.* .
./ln-if-absent ../regexp/demo/*.* .
./ln-if-absent ../internal/*.* .
set: No match.
makedemo.unx:156: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
chmod -R ug+rw,o+r .
gcc -o blast -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib blast_driver.c ncbithr.o -lblastapi \
-lblast -lncbitool -lncbiobj -lncbi -lpthread
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blast_driver.c:40:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_driver.c:38:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_driver.c,v 1.129 2007/10/23 16:03:23 madden Exp $";
^~~~~
gcc -o blastall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib blastall.c ncbithr.o -lblastapi \
-lblast -lncbitool -lncbiobj -lncbi -lpthread
blastall.c: In function 'Main_old':
blastall.c:1812:26: warning: variable 'nuc_concat' set but not used [-Wunused-but-set-variable]
Boolean concat_done, nuc_concat;
^~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from blastall.c:727:
blastall.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
blastall.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastall.c,v 6.206 2011/12/19 18:40:17 gouriano Exp $";
^~~~~
blastall.c: In function 'Main_old':
blastall.c:2410:74: warning: 'fake_bsp_arr' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr_bsp = (num_queries>0) ? *(fake_bsp_arr + bsp_iter) : query_bsp;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
blastall.c:1808:22: warning: 'seq_annot_arr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAnnotPtrArray seq_annot_arr;
^~~~~~~~~~~~~
blastall.c:2742:84: warning: 'sap_array' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr_seqalign = (num_queries > 0) ? *(sap_array + sap_iter) : seqalign;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
blastall.c:1795:10: warning: 'num_bsps' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 num_bsps, index;
^~~~~~~~
blastall.c:2618:18: warning: 'next_seqalign' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (seqalign) {
^
blastall.c:2895:12: warning: 'err_ticket' may be used uninitialized in this function [-Wmaybe-uninitialized]
BlastDeleteUserErrorString(err_ticket);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastall.c:2812:18: warning: 'xml_aip' may be used uninitialized in this function [-Wmaybe-uninitialized]
BXMLPrintOutput(xml_aip, NULL, options, blast_program,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_database, fake_bsp, other_returns, 0,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
message, mask_loc);
~~~~~~~~~~~~~~~~~~
gcc -o blastall_old -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DBLASTALL_TOOLS_ONLY blastall.c \
ncbithr.o -lncbitool -lncbiobj -lncbi -lpthread
blastall.c: In function 'Main_old':
blastall.c:1812:26: warning: variable 'nuc_concat' set but not used [-Wunused-but-set-variable]
Boolean concat_done, nuc_concat;
^~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from blastall.c:727:
blastall.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
blastall.c:2931:1: warning: 'readdb_use_new_blast' defined but not used [-Wunused-function]
readdb_use_new_blast(char* dbname)
^~~~~~~~~~~~~~~~~~~~
blastall.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastall.c,v 6.206 2011/12/19 18:40:17 gouriano Exp $";
^~~~~
blastall.c: In function 'Main_old':
blastall.c:2410:74: warning: 'fake_bsp_arr' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr_bsp = (num_queries>0) ? *(fake_bsp_arr + bsp_iter) : query_bsp;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
blastall.c:1808:22: warning: 'seq_annot_arr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAnnotPtrArray seq_annot_arr;
^~~~~~~~~~~~~
blastall.c:2742:84: warning: 'sap_array' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr_seqalign = (num_queries > 0) ? *(sap_array + sap_iter) : seqalign;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
blastall.c:1795:10: warning: 'num_bsps' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 num_bsps, index;
^~~~~~~~
blastall.c:2618:18: warning: 'next_seqalign' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (seqalign) {
^
blastall.c:2895:12: warning: 'err_ticket' may be used uninitialized in this function [-Wmaybe-uninitialized]
BlastDeleteUserErrorString(err_ticket);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastall.c:2812:18: warning: 'xml_aip' may be used uninitialized in this function [-Wmaybe-uninitialized]
BXMLPrintOutput(xml_aip, NULL, options, blast_program,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_database, fake_bsp, other_returns, 0,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
message, mask_loc);
~~~~~~~~~~~~~~~~~~
gcc -o blastpgp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib blastpgp.c ncbithr.o -lncbitool \
-lncbiobj -lncbi -lpthread
blastpgp.c: In function 'PGPFormatFooter':
blastpgp.c:1290:32: warning: variable 'dbinfo_head' set but not used [-Wunused-but-set-variable]
TxDfDbInfoPtr dbinfo=NULL, dbinfo_head;
^~~~~~~~~~~
blastpgp.c: In function 'Nlm_Main':
blastpgp.c:1685:14: warning: variable 'alignCheckpoint' set but not used [-Wunused-but-set-variable]
Boolean alignCheckpoint = FALSE;
^~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from blastpgp.c:561:
blastpgp.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/ddvcreate.h:143,
from blastpgp.c:563:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
blastpgp.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastpgp.c,v 6.140 2008/03/31 13:35:18 madden Exp $";
^~~~~
gcc -o seedtop -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib seedtop.c ncbithr.o -lncbitool \
-lncbiobj -lncbi -lpthread
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from seedtop.c:88:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seedtop.c: In function 'Nlm_Main':
seedtop.c:363:36: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
&error_returns, &info_vnp,hitArraySz)) {
^
At top level:
seedtop.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seedtop.c,v 6.19 2008/01/09 19:17:49 merezhuk Exp $";
^~~~~
gcc -o megablast -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib megablast.c ncbithr.o -lblastapi \
-lblast -lncbitool -lncbiobj -lncbi -lpthread
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from megablast.c:656:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
megablast.c: In function 'Main_old':
megablast.c:1439:4: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else if (myargs[ARG_OUTTYPE].intvalue == MBLAST_DELAYED_TRACEBACK)
^~~~
megablast.c:1444:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'else'
options->megablast_full_deflines = (Boolean) myargs[ARG_FULLID].intvalue;
^~~~~~~
megablast.c: In function 'BLAST_FillOptions':
megablast.c:1908:9: warning: unused variable 'windows' [-Wunused-variable]
Int4 windows = 0;
^~~~~~~
In file included from ../include/sqnutils.h:51:0,
from megablast.c:661:
megablast.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
megablast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: megablast.c,v 6.203 2009/06/01 14:33:38 maning Exp $";
^~~~~
gcc -o rpsblast -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib rpsblast.c ncbithr.o -lblastapi \
-lblast -lncbitool -lncbiobj -lncbi -lpthread
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from rpsblast.c:328:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rpsblast.c: In function 'Nlm_Main':
rpsblast.c:567:22: warning: variable 'program_number' set but not used [-Wunused-but-set-variable]
EBlastProgramType program_number;
^~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/algo/blast/api/twoseq_api.h:41,
from ../include/algo/blast/api/blast_format.h:51,
from rpsblast.c:330:
rpsblast.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
rpsblast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: rpsblast.c,v 6.93 2008/07/23 14:06:57 madden Exp $";
^~~~~
gcc -o blastclust -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib blastclust.c ncbithr.o -lncbitool \
-lncbiobj -lncbi -lpthread
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastclust.c:189:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastclust.c: In function 'Nlm_Main':
blastclust.c:1067:8: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tmpdir = getenv("TMPDIR")) {
^~
blastclust.c:1278:25: warning: variable 'head' set but not used [-Wunused-but-set-variable]
SeqAlignPtr PNTR head; /* Will not be used */
^~~~
blastclust.c:961:11: warning: variable 'align_type' set but not used [-Wunused-but-set-variable]
Uint1 align_type;
^~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from blastclust.c:200:
blastclust.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
blastclust.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastclust.c,v 6.50 2011/12/19 18:40:17 gouriano Exp $";
^~~~~
blastclust.c: In function 'PrintNeighbors':
blastclust.c:808:40: warning: 'context' may be used uninitialized in this function [-Wmaybe-uninitialized]
query = search->context[context].query->sequence;
^
blastclust.c:776:59: warning: 'query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
length_coverage = MIN(((FloatHi)q_length) / query_length,
^
blastclust.c:668:31: warning: 'hsp_info_array' may be used uninitialized in this function [-Wmaybe-uninitialized]
BlastClustHspInfoPtr PNTR hsp_info_array;
^~~~~~~~~~~~~~
blastclust.c:809:26: warning: 'hsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
esp = hsp->gap_info->esp;
~~~^~~~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -C build -f makenet.unx LCL=lnx CC="gcc " LDFLAGS1="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"' -fPIE -pie -Wl,-z,relro -Wl,-z,now" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" NCBI_LINKINGLIBDIR="../shlib" \
CFLAGS1="-c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='\"Aug 20 2016\"' -DBUILD_TIME='\"07:20:38\"'" THREAD_OBJ="ncbithr.o" \
THREAD_OTHERLIBS="-lpthread" \
NETENTREZVERSION="2.02c2ASN1SPEC6" BLIB31=libvibnet.a \
OGLLIBS= VIBLIBS= VIB="Psequin sbtedit udv ddv blastcl3 taxblast idfetch bl2seq asn2gb tbl2asn gene2xml entrez2 gbseqget asn2all asn2asn asn2fsa asn2xml asndisc asnmacro asnval cleanasn insdseqget nps2gps spidey trna2sap trna2tbl Cn3D"
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
./ln-if-absent ../connect/test/*.c .
./ln-if-absent ../network/entrez/client/*.h ../include
./ln-if-absent ../network/entrez/client/*.c .
./ln-if-absent ../network/medarch/client/*.h ../include
./ln-if-absent ../network/medarch/client/*.c .
./ln-if-absent ../network/taxonomy/client/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/taxonomy/client/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/taxon1/common/*.h ../include
./ln-if-absent ../network/taxon1/common/*.c .
./ln-if-absent ../network/taxon1/taxon2/*.h ../include
./ln-if-absent ../network/taxon1/taxon2/*.c .
./ln-if-absent ../network/id0arch/client/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/id0arch/client/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/id1arch/*.h ../include
./ln-if-absent ../network/id1arch/*.c .
./ln-if-absent ../network/id2arch/*.h ../include
./ln-if-absent ../network/id2arch/*.c .
./ln-if-absent ../network/spell/client/*.h ../include
./ln-if-absent ../network/spell/client/*.c .
./ln-if-absent ../network/suggest/client/*.h ../include
./ln-if-absent ../network/suggest/client/*.c .
./ln-if-absent ../network/blast3/client/*.h ../include
./ln-if-absent ../network/blast3/client/*.c .
./ln-if-absent ../tools/taxblast.h ../include
./ln-if-absent ../tools/taxblast.c .
./ln-if-absent /*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/misc/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/misc/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ssparse/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ssparse/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libparsn/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libparsn/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/smart/smartnet/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/smart/smartnet/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/www/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/www/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/query/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/query/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/ctlib/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/ctlib/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/oslib/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/oslib/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/idloadlib/*.c .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/idloadlib/*.h ../include
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/nsclilib/*.h ../include
./ln-if-absent ../network/nsclilib/*.c .
./ln-if-absent ../network/vibnet/*.c .
./ln-if-absent ../network/vibnet/*.h ../include
./ln-if-absent ../cdromlib/*.h ../include
./ln-if-absent ../network/wwwblast/Src/*.c .
./ln-if-absent ../cdromlib/accentr.c .
./ln-if-absent ../cdromlib/accutils.c .
./ln-if-absent ../sequin/*.* .
./ln-if-absent ../demo/entrez.c .
./ln-if-absent ../demo/seqget.c .
./ln-if-absent ../demo/entrcmd.c .
./ln-if-absent ../demo/batch.c .
./ln-if-absent ../demo/qbatch.c .
./ln-if-absent ../demo/elecpcr.c .
./ln-if-absent ../demo/asn2fast.c .
./ln-if-absent ../demo/asn2asn.c .
./ln-if-absent ../demo/cleanasn.c .
./ln-if-absent ../demo/cspeedtest.c .
./ln-if-absent ../demo/sqn2agp.c .
./ln-if-absent ../demo/sugint.c .
./ln-if-absent ../demo/fetchent.c .
./ln-if-absent ../demo/udvmain.c .
./ln-if-absent ../demo/rtestval.c .
./ln-if-absent ../demo/aceread_tst.c .
./ln-if-absent ../demo/asn2ff.c .
./ln-if-absent ../demo/asn2gb.c .
./ln-if-absent ../demo/asn2fsa.c .
./ln-if-absent ../demo/asn2all.c .
./ln-if-absent ../demo/gene2xml.c .
./ln-if-absent ../demo/asnval.c .
./ln-if-absent ../demo/asndisc.c .
./ln-if-absent ../demo/asnbarval.c .
./ln-if-absent ../demo/aceread_tst.c .
./ln-if-absent ../demo/asnmacro.c .
./ln-if-absent ../demo/asnstrip.c .
./ln-if-absent ../demo/tbl2asn.c .
./ln-if-absent ../demo/raw2delt.c .
./ln-if-absent ../demo/flint.c .
./ln-if-absent ../demo/xlint.c .
./ln-if-absent ../demo/diffshift.c .
./ln-if-absent ../demo/gbseqget.c .
./ln-if-absent ../demo/insdseqget.c .
./ln-if-absent ../demo/nps2gps.c .
./ln-if-absent ../demo/testent2.c .
./ln-if-absent ../demo/trna2sap.c .
./ln-if-absent ../demo/trna2tbl.c .
./ln-if-absent ../demo/entrez2.c .
./ln-if-absent ../demo/condense.c .
./ln-if-absent ../demo/spideymain.c .
./ln-if-absent ../demo/dotmain.c .
./ln-if-absent ../demo/ingenmain.c .
./ln-if-absent ../demo/bl2seq.c .
./ln-if-absent ../demo/blastall.c .
./ln-if-absent ../demo/blast_driver.c .
./ln-if-absent ../demo/src_chk.c .
./ln-if-absent ../demo/tbl_chk.c .
./ln-if-absent ../demo/srchnt.c ../demo/srchaa.c ../demo/mts.c ../demo/sigme.c ../demo/dst.c ../demo/ccp.c ../demo/epi.c ../demo/twop.c ../demo/cnsrt.c ../demo/cnsgn.c ../demo/ccpv.c ../demo/dustv.c ../demo/epiv.c ../demo/sigmev.c ../demo/twopv.c ../demo/cnsrtv.c ../demo/cnsgnv.c ../demo/searchv.c .
./ln-if-absent ../network/entrez/server/*.* .
set: No match.
makenet.unx:468: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/suggest/server/*.* .
chmod -R ug+rw,o+r .
echo Waiting...go
Waiting...go
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_lib_.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ni_types.h:84,
from ../include/ncbinet.h:84,
from ni_lib_.c:76:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_debug.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ni_debug.c:55:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_service.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ni_service.c:122:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ni_service.c: In function 's_GenericGetService':
ni_service.c:199:19: warning: unused variable 'c' [-Wunused-variable]
CONNECTOR c;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_error.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ni_types.h:84,
from ../include/ncbinet.h:84,
from ../include/ni_error.h:76,
from ni_error.c:72:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rm -f libnetcli.a
ar cru libnetcli.a ni_lib_.o ni_debug.o ni_service.o ni_error.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libnetcli.a ../lib
ranlib ../lib/libnetcli.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from netentr.c:161:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netentr.c: In function 's_NetEntTLEvalCount':
netentr.c:798:5: warning: "/*" within comment [-Wcomment]
/*MsgSetReadTimeout(Entrez_ni, 60);*/
netentr.c: In function 's_NetDocSumListGet':
netentr.c:856:18: warning: variable 'amp' set but not used [-Wunused-but-set-variable]
AsnModulePtr amp;
^~~
netentr.c: In function 's_NetTermListByTerm':
netentr.c:1212:9: warning: variable 'terms_to_read' set but not used [-Wunused-but-set-variable]
int terms_to_read;
^~~~~~~~~~~~~
netentr.c:1200:14: warning: unused variable 'asnout' [-Wunused-variable]
AsnIoPtr asnout = Entrez_asnout;
^~~~~~
netentr.c: In function 's_NetTermListByPage':
netentr.c:1343:14: warning: unused variable 'asnout' [-Wunused-variable]
AsnIoPtr asnout = Entrez_asnout;
^~~~~~
netentr.c: In function 'NetEntTLEval':
netentr.c:675:12: warning: 'lsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return lsp;
^~~
netentr.c: In function 'NetEntTLEvalCount':
netentr.c:800:8: warning: 'atp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (atp == ENTREZ_BACK_eval_count)
^
netentr.c:782:16: note: 'atp' was declared here
AsnTypePtr atp;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netlib.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from netlib.c:82:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netlib.c: In function 'BoolExprAsnWrite':
netlib.c:307:16: warning: unused variable 'n' [-Wunused-variable]
static int n = 0;
^
At top level:
netlib.c:307:16: warning: 'n' defined but not used [-Wunused-variable]
netlib.c:96:16: warning: 'loaded' defined but not used [-Wunused-variable]
static Boolean loaded = FALSE;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objneten.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asnneten.h:9,
from objneten.c:86:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objneten.c: In function 'NetEntAsnLoad':
objneten.c:106:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (loaded)
^~
objneten.c:108:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
loaded = TRUE;
^~~~~~
objneten.c: In function 'EntrezNeighborTextAsnRead':
objneten.c:2938:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c: In function 'ChildLinkAsnRead':
objneten.c:3148:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c: In function 'EntrezHierarchyAsnRead':
objneten.c:3442:15: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c: In function 'EntrezBlastreqAsnRead':
objneten.c:3705:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:3704:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objneten.c: In function 'EntrezExtraInfoAsnRead':
objneten.c:3911:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:3910:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objneten.c: In function 'ClusterArticlesAsnRead':
objneten.c:4262:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:4261:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objneten.c: In function 'ClusterRespAsnRead':
objneten.c:4455:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c: In function 'DateConstraintsAsnRead':
objneten.c:4622:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c: In function 'DateVectorAsnRead':
objneten.c:4785:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:4784:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objneten.c: In function 'GetByFidAsnRead':
objneten.c:4963:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:4962:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objneten.c: In function 'GetFeatIdsAsnRead':
objneten.c:5133:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objneten.c:5132:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
rm -f libnetentr.a
ar cru libnetentr.a netentr.o netlib.o objneten.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libnetentr.a ../lib
ranlib ../lib/libnetentr.a
./ln-if-absent accentr.c Naccentr.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -D_NETENT_ Naccentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from Naccentr.c:297:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
Naccentr.c:357:93: warning: missing braces around initializer [-Wmissing-braces]
Uint1 AdaptiveDocSumMatrix[MAX_CHUNK_IN_ADAPTIVE_MATRIX+1][MAX_SECS_IN_ADAPTIVE_MATRIX+1] = {
^
Naccentr.c:357:93: note: (near initialization for 'AdaptiveDocSumMatrix')
Naccentr.c: In function 'EntrezDocSumListGet':
Naccentr.c:1409:14: warning: variable 'actual' set but not used [-Wunused-but-set-variable]
Int2 actual;
^~~~~~
Naccentr.c: In function 'EntrezGIForSeqIdFunc':
Naccentr.c:3283:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! gi) return OM_MSG_RET_OK;
^~
Naccentr.c:3285:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sip2 = ValNodeNew(NULL);
^~~~
rm -f libncbiNacc.a
ar cru libncbiNacc.a Naccentr.o accutils.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbiNacc.a ../lib
ranlib ../lib/libncbiNacc.a
./ln-if-absent accentr.c Caccentr.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -D_NET_AND_CD_ Caccentr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from Caccentr.c:297:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
Caccentr.c:357:93: warning: missing braces around initializer [-Wmissing-braces]
Uint1 AdaptiveDocSumMatrix[MAX_CHUNK_IN_ADAPTIVE_MATRIX+1][MAX_SECS_IN_ADAPTIVE_MATRIX+1] = {
^
Caccentr.c:357:93: note: (near initialization for 'AdaptiveDocSumMatrix')
Caccentr.c: In function 'EntrezDocSumListGet':
Caccentr.c:1409:14: warning: variable 'actual' set but not used [-Wunused-but-set-variable]
Int2 actual;
^~~~~~
Caccentr.c: In function 'EntrezGIForSeqIdFunc':
Caccentr.c:3283:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! gi) return OM_MSG_RET_OK;
^~
Caccentr.c:3285:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
sip2 = ValNodeNew(NULL);
^~~~
rm -f libncbiCacc.a
ar cru libncbiCacc.a Caccentr.o accutils.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbiCacc.a ../lib
ranlib ../lib/libncbiCacc.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netcnfg.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from netcnfg.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" trmlst.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from trmlst.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
trmlst.c: In function 'FetchFromTermList':
trmlst.c:1048:16: warning: variable 'numRead' set but not used [-Wunused-but-set-variable]
Int2 numRead;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" docsum.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from docsum.c:252:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
docsum.c: In function 'ImportDocSumForm':
docsum.c:2298:21: warning: unused variable 'sephead' [-Wunused-variable]
SeqEntryPtr sephead = NULL;
^~~~~~~
docsum.c:2296:21: warning: unused variable 'is_na' [-Wunused-variable]
Boolean is_na = TRUE;
^~~~~
docsum.c:2290:21: warning: unused variable 'choice' [-Wunused-variable]
Uint1 choice = 0;
^~~~~~
docsum.c: In function 'SaveDocsumProject':
docsum.c:3042:16: warning: variable 'sfp' set but not used [-Wunused-but-set-variable]
SummFormPtr sfp;
^~~
docsum.c: In function 'LaunchStructureViewer':
docsum.c:4192:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
docsum.c:439:15: warning: 'checkmark' defined but not used [-Wunused-variable]
static Uint1 checkmark [] = {
^~~~~~~~~
docsum.c: In function 'FetchLocalBioseq':
docsum.c:1223:6: warning: 'str' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (str == NULL) return failed;
^
rm -f libvibnet.a
ar cru libvibnet.a netcnfg.o trmlst.o docsum.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libvibnet.a ../lib
ranlib ../lib/libvibnet.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objtax1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objtax1.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objtax1.c: In function 'Taxon1ReqFree':
objtax1.c:49:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtax1.c: In function 'Taxon1ReqAsnRead':
objtax1.c:96:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1InfoAsnRead':
objtax1.c:467:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:466:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1ErrorAsnRead':
objtax1.c:1067:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1066:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1NameAsnRead':
objtax1.c:1232:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1231:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1DataAsnRead':
objtax1.c:1418:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1417:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon2DataAsnRead':
objtax1.c:1606:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c: In function 'Taxon1ReqAsnRead':
objtax1.c:265:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax1.c: In function 'Taxon1RespAsnRead':
objtax1.c:868:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/utilpub.h:4,
from taxutil.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
taxutil.c: In function 'taxname_match':
taxutil.c:66:24: warning: unused variable 'taxstr' [-Wunused-variable]
CharPtr taxstr = NULL;
^~~~~~
taxutil.c: In function 'get_lineage':
taxutil.c:140:28: warning: 'onp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return Nlm_StringSave(onp->lineage);
~~~^~~~~~~~~
taxutil.c: In function 'get_gcode':
taxutil.c:160:23: warning: 'onp' may be used uninitialized in this function [-Wmaybe-uninitialized]
gclp->genomic = onp->gcode;
~~~^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -c -o tc2dproc.o -DTAXSERVICE tc2proc.c
tc2proc.c: In function 'getIdByOrgRef':
tc2proc.c:407:17: warning: unused variable 'om_flag' [-Wunused-variable]
Boolean om_flag= FALSE;
^~~~~~~
tc2proc.c: In function 'bldLineage':
tc2proc.c:1095:10: warning: unused variable 'rank' [-Wunused-variable]
Int2 rank= 0;
^~~~
tc2proc.c: In function 'storedTaxId':
tc2proc.c:2114:17: warning: unused variable 'object_id' [-Wunused-variable]
ObjectIdPtr object_id;
^~~~~~~~~
tc2proc.c: In function 'tax1e_needUpdate':
tc2proc.c:2181:13: warning: unused variable 'hit_name' [-Wunused-variable]
CharPtr hit_name;
^~~~~~~~
tc2proc.c:2180:13: warning: unused variable 'need_search_name' [-Wunused-variable]
Boolean need_search_name= TRUE;
^~~~~~~~~~~~~~~~
tc2proc.c:2179:9: warning: unused variable 'is_species' [-Wunused-variable]
int is_species;
^~~~~~~~~~
tc2proc.c:2176:19: warning: unused variable 'res' [-Wunused-variable]
Taxon1DataPtr res;
^~~
At top level:
tc2proc.c:403:13: warning: 'getIdByOrgRef' defined but not used [-Wunused-function]
static Int4 getIdByOrgRef(CharPtr sname, OrgNamePtr orNm)
^~~~~~~~~~~~~
tc2proc.c: In function 'mergeOrgMod':
tc2proc.c:1619:22: warning: 'lst' may be used uninitialized in this function [-Wmaybe-uninitialized]
lst->next= src;
~~~~~~~~~^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -c -o txcdproc.o -DTAXSERVICE txcdproc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ni_types.h:84,
from ../include/ncbinet.h:84,
from txcdproc.c:116:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" parttree.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/txclient.h:70,
from parttree.c:79:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
parttree.c: In function 'tax_ptree_addSubtree':
parttree.c:392:13: warning: unused variable 'need_remove' [-Wunused-variable]
Boolean need_remove= FALSE;
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxcs.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxblast.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from taxblast.c:158:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
taxblast.c: In function 'TXBHtmlReportInternal':
taxblast.c:1294:37: warning: variable 'linlines' set but not used [-Wunused-but-set-variable]
Int2 numtaxa, numorgs, numhits, linlines, longname;
^~~~~~~~
taxblast.c: In function 'RDTaxLookupReset':
taxblast.c:1985:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
At top level:
taxblast.c:1902:13: warning: 'getTotalTaxIdCount' defined but not used [-Wunused-function]
static Int4 getTotalTaxIdCount(TreeCursorPtr cursor)
^~~~~~~~~~~~~~~~~~
taxblast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: taxblast.c,v 6.30 2008/07/18 19:26:35 madden Exp $";
^~~~~
taxblast.c: In function 'TXBGetTargetGi.isra.2':
taxblast.c:501:12: warning: 'gi' may be used uninitialized in this function [-Wmaybe-uninitialized]
return gi;
^~
rm -f libncbitxc2.a
ar cru libncbitxc2.a objtax1.o taxutil.o tc2dproc.o txcdproc.o parttree.o taxcs.o taxblast.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbitxc2.a ../lib
ranlib ../lib/libncbitxc2.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" id1gen.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from id1gen.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
id1gen.c: In function 'ID1serverRequestFree':
id1gen.c:49:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
id1gen.c: In function 'ID1serverRequestAsnRead':
id1gen.c:90:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
id1gen.c: In function 'ID1serverMaxcomplexAsnRead':
id1gen.c:348:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
id1gen.c:347:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
id1gen.c: In function 'ID1SeqHistAsnRead':
id1gen.c:530:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
id1gen.c:529:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
id1gen.c: In function 'ID1SeqEntryInfoAsnRead':
id1gen.c:979:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
id1gen.c:978:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
id1gen.c: In function 'ID1blobInfoAsnRead':
id1gen.c:1147:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
id1gen.c:1146:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
id1gen.c: In function 'ID1serverDebugAsnRead':
id1gen.c:1368:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
id1gen.c: In function 'ID1serverBackAsnRead':
id1gen.c:811:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
id1gen.c: In function 'ID1serverRequestAsnRead':
id1gen.c:186:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" id1arch.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from id1arch.c:31:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
id1arch.c: In function 'ID1ArchSeqEntryGet':
id1arch.c:173:7: warning: unused variable 'retval' [-Wunused-variable]
Int4 retval = 0;
^~~~~~
id1arch.c: In function 'ID1ArchGIGet':
id1arch.c:486:10: warning: unused variable 'retval' [-Wunused-variable]
Int4 retval = 0;
^~~~~~
id1arch.c: In function 'SeqHistPrintTable':
id1arch.c:553:59: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=]
sprintf(repl_date,"%0.2d/%0.2d/%0.4d",
^~~~~~~~~~~~~~~~~~~
id1arch.c:553:59: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=]
id1arch.c:553:59: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=]
id1arch.c:563:47: warning: spurious trailing '%' in format [-Wformat=]
fprintf(fp,"%-20d%-20s%",old_gi,repl_date);
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" accid1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objmgr.h:51,
from ../include/seqmgr.h:48,
from accid1.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
accid1.c: In function 's_ID1BioseqFetchFunc':
accid1.c:262:9: warning: unused variable 'retcode' [-Wunused-variable]
Int2 retcode=0;
^~~~~~~
rm -f libncbiid1.a
ar cru libncbiid1.a id1gen.o id1arch.o accid1.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbiid1.a ../lib
ranlib ../lib/libncbiid1.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objblst3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objblst3.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objblst3.c: In function 'BlastSearchAsnRead':
objblst3.c:91:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:90:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastRequestFree':
objblst3.c:287:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objblst3.c: In function 'BlastRequestAsnRead':
objblst3.c:337:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'Cutoff2_cutoff2Free':
objblst3.c:999:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objblst3.c: In function 'BlastParametersAsnRead':
objblst3.c:1027:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'Cutoff2_cutoff2AsnRead':
objblst3.c:1422:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'Cutoff_cutoffAsnRead':
objblst3.c:1788:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'Cutoff_cutoffFree':
objblst3.c:1871:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objblst3.c: In function 'BlastMatrixAsnRead':
objblst3.c:1936:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'BlastDbinfoAsnRead':
objblst3.c:2153:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:2152:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastMaskAsnRead':
objblst3.c:2357:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'BlastKABlkAsnRead':
objblst3.c:2517:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:2516:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastErrorAsnRead':
objblst3.c:2697:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:2696:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastPhialignAsnRead':
objblst3.c:2861:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'BlastDbinfoGetAsnRead':
objblst3.c:3022:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3021:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastSeqIdAsnRead':
objblst3.c:3187:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3186:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastSequenceAsnRead':
objblst3.c:3364:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3363:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastPartsAsnRead':
objblst3.c:3532:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'BlastQueuedAsnRead':
objblst3.c:3694:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3693:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastProgressAsnRead':
objblst3.c:3846:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3845:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastDeflineAsnRead':
objblst3.c:4000:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:3999:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'BlastVersionAsnRead':
objblst3.c:4168:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:4167:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'MegaBlastHitAsnRead':
objblst3.c:4335:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c:4334:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objblst3.c: In function 'MegaBlastResultsAsnRead':
objblst3.c:4546:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objblst3.c: In function 'BlastRequestAsnRead':
objblst3.c:430:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objblst3.c: In function 'BlastResponseAsnRead':
objblst3.c:791:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objblst3.c: In function 'BlastParametersAsnRead':
objblst3.c:1474:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objblst3.c:1421:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objblst3.c:1840:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objblst3.c:1787:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netblap3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ni_types.h:84,
from ../include/ncbinet.h:84,
from netblap3.c:359:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netblap3.c: In function 'BlastNetBioseqFetchFunc':
netblap3.c:1835:16: warning: variable 'omdp' set but not used [-Wunused-but-set-variable]
OMUserDataPtr omdp;
^~~~
netblap3.c: In function 'MegaBlastSeqLocNetCore':
netblap3.c:2049:8: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID = 0;
^~~~~~~~
In file included from ../include/netblap3.h:135:0,
from netblap3.c:364:
netblap3.c: At top level:
../include/objblst3.h:180:35: warning: 'Cutoff2_cutoff2Free' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr ));
^~~~~~~~~~~~~~~~~~~
../include/objblst3.h:181:35: warning: 'Cutoff2_cutoff2AsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:182:24: warning: 'Cutoff2_cutoff2AsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:199:33: warning: 'Cutoff_cutoffFree' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr ));
^~~~~~~~~~~~~~~~~
../include/objblst3.h:200:33: warning: 'Cutoff_cutoffAsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:201:24: warning: 'Cutoff_cutoffAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
netblap3.c:452:1: warning: 'BlastResetOldHook' defined but not used [-Wunused-function]
BlastResetOldHook(void)
^~~~~~~~~~~~~~~~~
netblap3.c:445:1: warning: 'BlastGetErrorStatus' defined but not used [-Wunused-function]
BlastGetErrorStatus(void)
^~~~~~~~~~~~~~~~~~~
netblap3.c:438:1: warning: 'BlastSetErrorStatus' defined but not used [-Wunused-function]
BlastSetErrorStatus(Boolean status)
^~~~~~~~~~~~~~~~~~~
netblap3.c:430:1: warning: 'BlastSetErrorHook' defined but not used [-Wunused-function]
BlastSetErrorHook(void)
^~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:134:0,
from netblap3.c:364:
../include/blstspc.h:229:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/blstspc.h:228:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/blstspc.h:227:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/blstspc.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "blstspc.h23";
^~~~~~~~~~~
netblap3.c: In function 'BlastNetMatrixToBlastMatrix':
netblap3.c:1212:35: warning: 'index2' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (index1 != blast_matrix->rows || index2 != blast_matrix->columns)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
netblap3.c: In function 'TraditionalBlastReportEngine':
netblap3.c:2570:11: warning: 'next_seqalign' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (seqalign) {
^
rm -f libnetblast.a
ar cru libnetblast.a objblst3.o netblap3.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libnetblast.a ../lib
ranlib ../lib/libnetblast.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -DNLM_OBJ_INCL=\"mapmla.h\" objmla.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from objmla.c:1:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
objmla.c: In function 'MlaRequestFree':
objmla.c:49:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmla.c: In function 'MlaRequestAsnRead':
objmla.c:96:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmla.c: In function 'TitleMsgAsnRead':
objmla.c:447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmla.c:446:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmla.c: In function 'TitleMsgListAsnRead':
objmla.c:612:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmla.c: In function 'MlaRequestAsnRead':
objmla.c:249:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmla.c: In function 'MlaBackAsnRead':
objmla.c:902:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" medarch.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/ni_types.h:84,
from ../include/ncbinet.h:84,
from medarch.c:122:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
medarch.c:758:8: warning: 's_MedArchPubSetEntryGetUid' defined but not used [-Wunused-function]
/*FCN*/s_MedArchPubSetEntryGetUid (
^~~~~~~~~~~~~~~~~~~~~~~~~~
medarch.c:710:8: warning: 's_MedArchPubSetEntryGetPmId' defined but not used [-Wunused-function]
/*FCN*/s_MedArchPubSetEntryGetPmId (
^~~~~~~~~~~~~~~~~~~~~~~~~~~
medarch.c: In function 'MedArchPubSetCreate':
medarch.c:1693:9: warning: 'pubSetEAtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
MedlineEntryAsnWrite (lastmep, aip, pubSetEAtp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/ni_types.h:85:0,
from ../include/ncbinet.h:84,
from medarch.c:122:
../include/asn.h:465:27: warning: 'pubSetAtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AsnEndStruct(x,y) AsnCloseStruct(x, y, NULL)
^~~~~~~~~~~~~~
medarch.c:1625:16: note: 'pubSetAtp' was declared here
AsnTypePtr pubSetAtp;
^~~~~~~~~
medarch.c:1655:5: warning: 'startAtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
AsnWrite (aip, startAtp, NULL);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" medutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/medutil.h:79,
from medutil.c:58:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
rm -f libncbimla.a
ar cru libncbimla.a objmla.o medarch.o medutil.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libncbimla.a ../lib
ranlib ../lib/libncbimla.a
gcc -o Psequin -I. -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF -UINTERNAL_NCBI_SEQUIN sequin1.c sequin2.c sequin3.c sequin4.c sequin5.c sequin6.c sequin7.c sequin8.c sequin9.c sequin10.c sequinx.c \
-lvibnet -lncbidesk -lblastapi -lnetblast -lncbitool -lncbimla \
-lvibrant -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin1.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequin1.c: In function 'SQACT_GuessWhatIAm':
sequin1.c:4930:76: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if ((Int4)(*cp) < 0 || (Int4)(*cp) >= 256 || ! isprint ((Int4)(*cp)) && ! isspace ((Int4)(*cp)))
^
sequin1.c: In function 'FinishAlignmentRead':
sequin1.c:5242:16: warning: variable 'rsult' set but not used [-Wunused-but-set-variable]
Boolean rsult;
^~~~~
sequin1.c: In function 'DeleteSelectedFeatureOrDescriptor':
sequin1.c:8907:19: warning: variable 'itemtype' set but not used [-Wunused-but-set-variable]
Uint2 itemtype;
^~~~~~~~
sequin1.c:8906:19: warning: variable 'itemID' set but not used [-Wunused-but-set-variable]
Uint4 itemID;
^~~~~~
sequin1.c:8904:19: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sequin1.c: In function 'WizardTrackerFree':
sequin1.c:15645:20: warning: variable 'sep_next' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep, sep_next;
^~~~~~~~
sequin1.c: In function 'AddCodingRegionFromWizard':
sequin1.c:15714:33: warning: variable 'nsep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr old, psep, nsep;
^~~~
sequin1.c: In function 'SetWizardTrackerBaseSrcQuals':
sequin1.c:15993:7: warning: enumeration value 'eVirusClass_Unknown' not handled in switch [-Wswitch]
switch (wiz->virus_class) {
^~~~~~
sequin1.c:16040:7: warning: enumeration value 'eCulturedKingdom_Unknown' not handled in switch [-Wswitch]
switch (wiz->cultured_kingdom) {
^~~~~~
sequin1.c: In function 'SetWizardTrackerExtraSrcQuals':
sequin1.c:16139:7: warning: enumeration value 'eVirusClass_Unknown' not handled in switch [-Wswitch]
switch (wiz->virus_class) {
^~~~~~
sequin1.c:16164:7: warning: enumeration value 'eCulturedKingdom_Unknown' not handled in switch [-Wswitch]
switch (wiz->cultured_kingdom) {
^~~~~~
sequin1.c: In function 'AddWizardFeatureCallback':
sequin1.c:16491:3: warning: enumeration value 'eVirusFeat_None' not handled in switch [-Wswitch]
switch (wiz->virus_feat) {
^~~~~~
sequin1.c:16491:3: warning: enumeration value 'eVirusFeat_CDS' not handled in switch [-Wswitch]
sequin1.c: In function 'HaveUniqueCombinationOfQuals':
sequin1.c:17144:15: warning: variable 'num_quals' set but not used [-Wunused-but-set-variable]
Int4 num_quals;
^~~~~~~~~
sequin1.c: In function 'VirusQualsOk':
sequin1.c:20712:5: warning: enumeration value 'eVirusClass_Unknown' not handled in switch [-Wswitch]
switch (wiz->virus_class) {
^~~~~~
sequin1.c: In function 'CulturedSamplesOk':
sequin1.c:20817:5: warning: enumeration value 'eCulturedKingdom_Unknown' not handled in switch [-Wswitch]
switch (wiz->cultured_kingdom) {
^~~~~~
sequin1.c: In function 'CheckFeatureQualsUniqueness':
sequin1.c:22418:8: warning: variable 'num_rows' set but not used [-Wunused-but-set-variable]
Int4 num_rows, row_num;
^~~~~~~~
sequin1.c: In function 'WizardFeatureQualsOk':
sequin1.c:22509:11: warning: variable 'num_features' set but not used [-Wunused-but-set-variable]
Int4 num_features;
^~~~~~~~~~~~
sequin1.c: In function 'TabTableToMultiModTabTable':
sequin1.c:22877:16: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp = NULL;
^~~
sequin1.c: In function 'MultiModTableToTabTable':
sequin1.c:22956:21: warning: variable 'fq' set but not used [-Wunused-but-set-variable]
WizardFeatQualPtr fq;
^~
sequin1.c: In function 'ShowAllFeatureQualSequences':
sequin1.c:23513:15: warning: variable 'show_all' set but not used [-Wunused-but-set-variable]
Boolean show_all = TRUE;
^~~~~~~~
sequin1.c: In function 'TabTableLineFromFeature':
sequin1.c:24459:14: warning: unused variable 'vals' [-Wunused-variable]
ValNodePtr vals = NULL, q_vnp;
^~~~
sequin1.c: In function 'PregenerateFeatures':
sequin1.c:24509:22: warning: unused variable 'problems' [-Wunused-variable]
CharPtr PNTR problems = NULL;
^~~~~~~~
sequin1.c: In function 'CollectWizardSetType':
sequin1.c:25700:3: warning: enumeration value 'eWizardType_TSA' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:25700:3: warning: enumeration value 'eWizardType_Microsatellite' not handled in switch [-Wswitch]
sequin1.c: In function 'SequencingMethodToDialog':
sequin1.c:26182:27: warning: variable 'info' set but not used [-Wunused-but-set-variable]
SequencingMethodInfoPtr info;
^~~~
sequin1.c: In function 'CollectWizardSourceType':
sequin1.c:26625:5: warning: enumeration value 'eWizardType_TSA' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:26625:5: warning: enumeration value 'eWizardType_Microsatellite' not handled in switch [-Wswitch]
sequin1.c:26625:5: warning: enumeration value 'eWizardType_DLoop' not handled in switch [-Wswitch]
sequin1.c: In function 'HaveWizardSourceType':
sequin1.c:26658:3: warning: enumeration value 'eWizardType_UnculturedSamples' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:26658:3: warning: enumeration value 'eWizardType_TSA' not handled in switch [-Wswitch]
sequin1.c:26658:3: warning: enumeration value 'eWizardType_Microsatellite' not handled in switch [-Wswitch]
sequin1.c:26658:3: warning: enumeration value 'eWizardType_DLoop' not handled in switch [-Wswitch]
sequin1.c: In function 'WizardSourceTypeForm':
sequin1.c:26720:3: warning: enumeration value 'eWizardType_UnculturedSamples' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:26720:3: warning: enumeration value 'eWizardType_TSA' not handled in switch [-Wswitch]
sequin1.c:26720:3: warning: enumeration value 'eWizardType_Microsatellite' not handled in switch [-Wswitch]
sequin1.c:26720:3: warning: enumeration value 'eWizardType_DLoop' not handled in switch [-Wswitch]
sequin1.c: In function 'PopulateAAPopup':
sequin1.c:27748:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
sequin1.c: In function 'CountAmbiProc':
sequin1.c:29129:11: warning: unused variable 'normal' [-Wunused-variable]
Int4 normal = 0;
^~~~~~
sequin1.c: In function 'SetFastaText':
sequin1.c:29949:15: warning: unused variable 'intro' [-Wunused-variable]
CharPtr intro = NULL;
^~~~~
sequin1.c: In function 'WizardFASTAFwd':
sequin1.c:30290:3: warning: enumeration value 'eWizardType_UnculturedSamples' not handled in switch [-Wswitch]
switch (frm->wiz->wizard_type) {
^~~~~~
sequin1.c:30290:3: warning: enumeration value 'eWizardType_Viruses' not handled in switch [-Wswitch]
sequin1.c:30290:3: warning: enumeration value 'eWizardType_CulturedSamples' not handled in switch [-Wswitch]
sequin1.c:30290:3: warning: enumeration value 'eWizardType_IGS' not handled in switch [-Wswitch]
sequin1.c:30290:3: warning: enumeration value 'eWizardType_Microsatellite' not handled in switch [-Wswitch]
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/accutils.h:119,
from sequin1.c:81:
sequin1.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/accutils.h:119,
from sequin1.c:81:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/accutils.h:119,
from sequin1.c:81:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/accutils.h:119,
from sequin1.c:81:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from sequin1.c:87:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:135:0,
from ../include/ingenwin.h:62,
from sequin1.c:92:
../include/objblst3.h:180:35: warning: 'Cutoff2_cutoff2Free' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr ));
^~~~~~~~~~~~~~~~~~~
../include/objblst3.h:181:35: warning: 'Cutoff2_cutoff2AsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:182:24: warning: 'Cutoff2_cutoff2AsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:199:33: warning: 'Cutoff_cutoffFree' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr ));
^~~~~~~~~~~~~~~~~
../include/objblst3.h:200:33: warning: 'Cutoff_cutoffAsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:201:24: warning: 'Cutoff_cutoffAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/tax3api.h:51:0,
from sequin1.c:95:
../include/objtax3.h:183:31: warning: 'Value_valueFree' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr ));
^~~~~~~~~~~~~~~
../include/objtax3.h:184:31: warning: 'Value_valueAsnRead' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~
../include/objtax3.h:185:24: warning: 'Value_valueAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~
In file included from sequin1.c:119:0:
../include/objmime.h:145:29: warning: 'Data_dataFree' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr ));
^~~~~~~~~~~~~
../include/objmime.h:146:29: warning: 'Data_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~
../include/objmime.h:147:24: warning: 'Data_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~
../include/objmime.h:285:47: warning: 'SeqAlignData_seq_align_dataFree' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:286:47: warning: 'SeqAlignData_seq_align_dataAsnRead' declared 'static' but never defined [-Wunused-function]
static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmime.h:287:24: warning: 'SeqAlignData_seq_align_dataAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin1.c: In function 'LaunchedGoogleEarth':
sequin1.c:1525:11: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
sequin1.c: In function 'Entrez2QueryProc':
sequin1.c:9728:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system ("entrez2 &");
^~~~~~~~~~~~~~~~~~~~
At top level:
sequin1.c:26805:16: warning: 'WizardCommentForm' defined but not used [-Wunused-function]
static Boolean WizardCommentForm (WizardTrackerPtr wiz)
^~~~~~~~~~~~~~~~~
sequin1.c:25867:16: warning: 'WizardStructuredCommentForm' defined but not used [-Wunused-function]
static Boolean WizardStructuredCommentForm
^~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin1.c:25269:13: warning: 'SaveVirusFeatureTableChoice' defined but not used [-Wunused-function]
static void SaveVirusFeatureTableChoice (Pointer data, WizardTrackerPtr wiz)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin1.c:24732:16: warning: 'IsAllATGC' defined but not used [-Wunused-function]
static Boolean IsAllATGC (CharPtr val)
^~~~~~~~~
sequin1.c:24625:13: warning: 'ApplyLocStop' defined but not used [-Wunused-function]
static void ApplyLocStop (SeqFeatPtr sfp, CharPtr val)
^~~~~~~~~~~~
sequin1.c:24609:13: warning: 'ApplyLocStart' defined but not used [-Wunused-function]
static void ApplyLocStart (SeqFeatPtr sfp, CharPtr val)
^~~~~~~~~~~~~
sequin1.c:24596:16: warning: 'GetLocStop' defined but not used [-Wunused-function]
static CharPtr GetLocStop (SeqFeatPtr sfp)
^~~~~~~~~~
sequin1.c:24583:16: warning: 'GetLocStart' defined but not used [-Wunused-function]
static CharPtr GetLocStart (SeqFeatPtr sfp)
^~~~~~~~~~~
sequin1.c:23481:16: warning: 'EqualIgnoreWhiteSpacePunctAndCaps' defined but not used [-Wunused-function]
static Boolean EqualIgnoreWhiteSpacePunctAndCaps (CharPtr a, CharPtr b)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin1.c:18855:16: warning: 'RNAAnnotationWindow' defined but not used [-Wunused-function]
static Boolean RNAAnnotationWindow(WizardTrackerPtr wiz)
^~~~~~~~~~~~~~~~~~~
sequin1.c:18662:16: warning: 'MultOrganelleFeat' defined but not used [-Wunused-function]
static Boolean MultOrganelleFeat (WizardTrackerPtr wiz)
^~~~~~~~~~~~~~~~~
sequin1.c:18188:13: warning: 'GroupChoiceFromName' defined but not used [-Wunused-function]
static Int2 GroupChoiceFromName (CharPtr rna_name, CharPtr PNTR standard_names)
^~~~~~~~~~~~~~~~~~~
sequin1.c:18087:16: warning: 'JumpToMainSubmission' defined but not used [-Wunused-function]
static Boolean JumpToMainSubmission (WizardTrackerPtr wiz)
^~~~~~~~~~~~~~~~~~~~
sequin1.c:17327:13: warning: 'ClearModifierValues' defined but not used [-Wunused-function]
static void ClearModifierValues (SeqEntryPtr sep, DialoG d, CharPtr mod_name)
^~~~~~~~~~~~~~~~~~~
sequin1.c:17295:13: warning: 'ModTableToSeqEntryList' defined but not used [-Wunused-function]
static void ModTableToSeqEntryList (SeqEntryPtr sep, DialoG d, CharPtr mod_name)
^~~~~~~~~~~~~~~~~~~~~~
sequin1.c:17260:13: warning: 'SeqEntryToModTabTable' defined but not used [-Wunused-function]
static void SeqEntryToModTabTable (SeqEntryPtr sep, DialoG d, CharPtr mod_name)
^~~~~~~~~~~~~~~~~~~~~
sequin1.c:17190:16: warning: 'DoAllSequencesHaveAnExtraQual' defined but not used [-Wunused-function]
static Boolean DoAllSequencesHaveAnExtraQual (SeqEntryPtr sep, ValNodePtr extra_src_quals)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin1.c:10827:13: warning: 'ObjMgrReport' defined but not used [-Wunused-function]
static void ObjMgrReport (IteM i)
^~~~~~~~~~~~
sequin1.c:9074:13: warning: 'DocumentSummaryFormMessage' defined but not used [-Wunused-function]
static void DocumentSummaryFormMessage (ForM f, Int2 mssg)
^~~~~~~~~~~~~~~~~~~~~~~~~~
sequin1.c:9054:13: warning: 'TermSelectionFormMessage' defined but not used [-Wunused-function]
static void TermSelectionFormMessage (ForM f, Int2 mssg)
^~~~~~~~~~~~~~~~~~~~~~~~
sequin1.c:7910:13: warning: 'PreferencesProc' defined but not used [-Wunused-function]
static void PreferencesProc (IteM i)
^~~~~~~~~~~~~~~
sequin1.c:7897:13: warning: 'DefaultMessageProc' defined but not used [-Wunused-function]
static void DefaultMessageProc (ForM f, Int2 mssg)
^~~~~~~~~~~~~~~~~~
sequin1.c:7671:13: warning: 'FindAlu' defined but not used [-Wunused-function]
static void FindAlu (IteM i)
^~~~~~~
sequin1.c:7087:16: warning: 'LookupJournalFuncNew' defined but not used [-Wunused-function]
static Boolean LookupJournalFuncNew (CharPtr title, size_t maxsize, Int1Ptr jtaType, ValNodePtr PNTR all_titlesP)
^~~~~~~~~~~~~~~~~~~~
sequin1.c:2291:13: warning: 'StyleManagerProc' defined but not used [-Wunused-function]
static void StyleManagerProc (IteM i)
^~~~~~~~~~~~~~~~
sequin1.c:633:13: warning: 'ReplaceString' defined but not used [-Wunused-function]
static void ReplaceString (CharPtr PNTR target, CharPtr newstr)
^~~~~~~~~~~~~
sequin1.c:384:13: warning: 'SetSequinAppParamTF' defined but not used [-Wunused-function]
static void SetSequinAppParamTF (CharPtr section, CharPtr type, Boolean value)
^~~~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:134:0,
from ../include/ingenwin.h:62,
from sequin1.c:92:
../include/blstspc.h:229:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/blstspc.h:228:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/blstspc.h:227:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/blstspc.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "blstspc.h23";
^~~~~~~~~~~
sequin1.c: In function 'SubtoolDoneFuncEx':
sequin1.c:2021:5: warning: 'bfp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqMgrClearFeatureIndexes (bfp->input_entityID, NULL);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/vibrant.h:133:0,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin1.c:56:
sequin1.c: In function 'BioseqViewFormMenus':
../include/vibforms.h:522:25: warning: 'mssgupd_idx' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SetFormMenuItem Nlm_SetFormMenuItem
^~~~~~~~~~~~~~~~~~~
sequin1.c:8349:27: note: 'mssgupd_idx' was declared here
Int2 mssgupd, mssgupd_idx;
^~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin2.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequin2.c: In function 'ValidateModifierTableSequenceIDs':
sequin2.c:2845:16: warning: variable 'deleted_rows' set but not used [-Wunused-but-set-variable]
Int4 deleted_rows;
^~~~~~~~~~~~
sequin2.c: In function 'ImportFastaDialog':
sequin2.c:4568:17: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep, new_sep_list, new_sep, test_sep;
^~~
sequin2.c: In function 'ExportOneRawSequence':
sequin2.c:4830:15: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
Char buffer [EXPORT_PAGE_WIDTH + 1];
^~~~~~
sequin2.c: In function 'ExportOneDeltaBioseq':
sequin2.c:4929:15: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
Char buffer [EXPORT_PAGE_WIDTH + 1];
^~~~~~
sequin2.c: In function 'FindBioseqWithValue':
sequin2.c:7883:17: warning: variable 'bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr bsp = NULL;
^~~
sequin2.c: In function 'CollectNucleotideProteinAssociations':
sequin2.c:9250:73: warning: variable 'p_msg' set but not used [-Wunused-but-set-variable]
GrouP h, title_grp, all_gene_grp, all_prot_grp, k, c, p_msg;
^~~~~
sequin2.c: In function 'GetModNameStartFromEqLoc':
sequin2.c:11839:11: warning: variable 'match_quote' set but not used [-Wunused-but-set-variable]
Char match_quote;
^~~~~~~~~~~
sequin2.c: In function 'GetValueFromTitle':
sequin2.c:12403:15: warning: variable 'is_nontext' set but not used [-Wunused-but-set-variable]
Boolean is_nontext;
^~~~~~~~~~
sequin2.c: In function 'PrepareSourceAssistantTableData':
sequin2.c:13654:36: warning: variable 'num_columns' set but not used [-Wunused-but-set-variable]
Int4 column_width, num_columns = 0;
^~~~~~~~~~~
sequin2.c: In function 'SetOrganismText':
sequin2.c:13856:30: warning: variable 'changed_val' set but not used [-Wunused-but-set-variable]
Boolean changed_val = FALSE;
^~~~~~~~~~~
sequin2.c: In function 'ApplyRowListToIDAndTitleEdit':
sequin2.c:15507:32: warning: variable 'next_org' set but not used [-Wunused-but-set-variable]
CharPtr org_loc, org_end, next_org;
^~~~~~~~
sequin2.c: In function 'EditOrgModColumn':
sequin2.c:16418:26: warning: variable 'row_list' set but not used [-Wunused-but-set-variable]
ValNodePtr row_list = NULL;
^~~~~~~~
sequin2.c: In function 'ApplyOrgModColumn':
sequin2.c:17267:11: warning: variable 'is_nontext' set but not used [-Wunused-but-set-variable]
Boolean is_nontext;
^~~~~~~~~~
sequin2.c: In function 'PrepareSequenceAssistantTableData':
sequin2.c:18241:36: warning: variable 'num_columns' set but not used [-Wunused-but-set-variable]
Int4 column_width, num_columns = 0;
^~~~~~~~~~~
sequin2.c: In function 'UpdateIdAndTitleEditDialog':
sequin2.c:19658:50: warning: variable 'has_space' set but not used [-Wunused-but-set-variable]
Boolean has_dups, has_missing, has_bracket, has_space, has_unrec_mods = FALSE;
^~~~~~~~~
sequin2.c: In function 'SetIDAndTitleEditDialogErrorColumn':
sequin2.c:19808:74: warning: variable 'has_space' set but not used [-Wunused-but-set-variable]
Boolean has_dups, has_missing, has_bracket, has_unrec_mods = FALSE, has_space;
^~~~~~~~~
sequin2.c: In function 'GetDiffDlgCoord':
sequin2.c:20978:19: warning: variable 'start_col' set but not used [-Wunused-but-set-variable]
Int4 start_row, start_col;
^~~~~~~~~
sequin2.c:20978:8: warning: variable 'start_row' set but not used [-Wunused-but-set-variable]
Int4 start_row, start_col;
^~~~~~~~~
sequin2.c: In function 'DownloadAndDisplay':
sequin2.c:26788:17: warning: variable 'dbname' set but not used [-Wunused-but-set-variable]
CharPtr dbname;
^~~~~~
sequin2.c: In function 'DownloadProc':
sequin2.c:26956:17: warning: variable 'dbname' set but not used [-Wunused-but-set-variable]
CharPtr dbname;
^~~~~~
sequin2.c: In function 'LoadSecondaryAccessionNumbersPlusHistFromFile':
sequin2.c:28210:17: warning: variable 'need_seqid' set but not used [-Wunused-but-set-variable]
Boolean need_seqid;
^~~~~~~~~~
sequin2.c: In function 'RemoveEmptyGenomeProjectIDCallback':
sequin2.c:28350:13: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (oip != NULL
~~~~~~~~~~~
&& StringCmp (oip->str, "ProjectID") == 0 || StringCmp (oip->str, "ParentID") == 0) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/aliparse.h:15,
from sequin2.c:66:
sequin2.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
sequin2.c:26384:13: warning: 'GetRawBsps' defined but not used [-Wunused-function]
static void GetRawBsps (BioseqPtr bsp, Pointer userdata)
^~~~~~~~~~
sequin2.c:24973:1: warning: 'SequenceAssistantValidateSegments' defined but not used [-Wunused-function]
SequenceAssistantValidateSegments
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin2.c:10754:17: warning: 'GetSeqIdFromSeqEntryPtr' defined but not used [-Wunused-function]
static SeqIdPtr GetSeqIdFromSeqEntryPtr (SeqEntryPtr sep)
^~~~~~~~~~~~~~~~~~~~~~~
sequin2.c:8182:20: warning: 'FindSeqEntryWithTranscriptID' defined but not used [-Wunused-function]
static SeqEntryPtr FindSeqEntryWithTranscriptID (SeqEntryPtr sep, CharPtr transcript_id)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin2.c:3920:1: warning: 'ReadOneSegSet' defined but not used [-Wunused-function]
ReadOneSegSet
^~~~~~~~~~~~~
sequin2.c: In function 'InsertMostUsedFeatureValNodes':
sequin2.c:28480:22: warning: 'new_item' may be used uninitialized in this function [-Wmaybe-uninitialized]
new_item->next = old_list->next;
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin3.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequin3.c: In function 'FarToNearProc':
sequin3.c:941:12: warning: variable 'olddelta' set but not used [-Wunused-but-set-variable]
Pointer olddelta;
^~~~~~~~
sequin3.c: In function 'FixLocus':
sequin3.c:1404:15: warning: variable 'embl_code' set but not used [-Wunused-but-set-variable]
CharPtr ptr, embl_code;
^~~~~~~~~
sequin3.c: In function 'RemoveGeneXrefsOnBioseqs':
sequin3.c:2667:22: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sequin3.c: In function 'MakeCDS':
sequin3.c:6938:27: warning: variable 'nsep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr psep, nsep, old, topsep;
^~~~
sequin3.c: In function 'ConvertOneCDSToMiscFeat':
sequin3.c:9351:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| must_have_stops && !HasInternalStops (sfp))
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
sequin3.c: In function 'SuppressGenesOnFeatures':
sequin3.c:11193:20: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
sequin3.c: In function 'CheckForExistingMolInfo':
sequin3.c:12866:17: warning: variable 'bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr bsp;
^~~
sequin3.c: In function 'UniqueAndCountValNodeCS':
sequin3.c:13830:17: warning: variable 'curr' set but not used [-Wunused-but-set-variable]
ValNodePtr curr;
^~~~
sequin3.c: In function 'RemoveNthCDS':
sequin3.c:21998:17: warning: variable 'segCount' set but not used [-Wunused-but-set-variable]
Int4 segCount;
^~~~~~~~
sequin3.c: In function 'InstantiateGapFeatCallback':
sequin3.c:23218:15: warning: variable 'fuzz' set but not used [-Wunused-but-set-variable]
IntFuzzPtr fuzz;
^~~~
In file included from ../include/tax3api.h:51:0,
from sequin3.c:71:
sequin3.c: At top level:
../include/objtax3.h:183:31: warning: 'Value_valueFree' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr ));
^~~~~~~~~~~~~~~
../include/objtax3.h:184:31: warning: 'Value_valueAsnRead' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~
../include/objtax3.h:185:24: warning: 'Value_valueAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from sequin3.c:73:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
sequin3.c:24720:13: warning: 'TestSegregateByList' defined but not used [-Wunused-function]
static void TestSegregateByList (IteM i)
^~~~~~~~~~~~~~~~~~~
sequin3.c:24389:13: warning: 'WriteAccessionsCallback' defined but not used [-Wunused-function]
static void WriteAccessionsCallback (BioseqPtr bsp, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:23962:13: warning: 'ModernizeGenes' defined but not used [-Wunused-function]
static void ModernizeGenes (IteM i)
^~~~~~~~~~~~~~
sequin3.c:23935:13: warning: 'ModernizeRNAs' defined but not used [-Wunused-function]
static void ModernizeRNAs (IteM i)
^~~~~~~~~~~~~
sequin3.c:23908:13: warning: 'ModernizePCRs' defined but not used [-Wunused-function]
static void ModernizePCRs (IteM i)
^~~~~~~~~~~~~
sequin3.c:23549:13: warning: 'TestTax3B' defined but not used [-Wunused-function]
static void TestTax3B (IteM i)
^~~~~~~~~
sequin3.c:23543:13: warning: 'TestTax3A' defined but not used [-Wunused-function]
static void TestTax3A (IteM i)
^~~~~~~~~
sequin3.c:23410:13: warning: 'NewAligmentViewer' defined but not used [-Wunused-function]
static void NewAligmentViewer (IteM i)
^~~~~~~~~~~~~~~~~
sequin3.c:23365:13: warning: 'AddAllDbxrefsMenuItem' defined but not used [-Wunused-function]
static void AddAllDbxrefsMenuItem (IteM i)
^~~~~~~~~~~~~~~~~~~~~
sequin3.c:18047:1: warning: 'TruncProtsAtStopsExEx' defined but not used [-Wunused-function]
TruncProtsAtStopsExEx
^~~~~~~~~~~~~~~~~~~~~
sequin3.c:17573:13: warning: 'DoGeneReset' defined but not used [-Wunused-function]
static void DoGeneReset (IteM i)
^~~~~~~~~~~
sequin3.c:14618:13: warning: 'PrepareTaxListProc' defined but not used [-Wunused-function]
static void PrepareTaxListProc (IteM i)
^~~~~~~~~~~~~~~~~~
sequin3.c:12650:13: warning: 'RibosomalRNAToGenomicDNAMenuItem' defined but not used [-Wunused-function]
static void RibosomalRNAToGenomicDNAMenuItem (IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:12594:13: warning: 'NewMolInfoFieldsApply' defined but not used [-Wunused-function]
static void NewMolInfoFieldsApply (IteM i)
^~~~~~~~~~~~~~~~~~~~~
sequin3.c:8121:13: warning: 'MultiTransformProc' defined but not used [-Wunused-function]
static void MultiTransformProc (IteM i, Uint1 targettype)
^~~~~~~~~~~~~~~~~~
sequin3.c:6014:13: warning: 'EnableFeatureToGeneControlsText' defined but not used [-Wunused-function]
static void EnableFeatureToGeneControlsText (TexT t)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:6006:13: warning: 'EnableFeatureToGeneControlsPopup' defined but not used [-Wunused-function]
static void EnableFeatureToGeneControlsPopup (PopuP p)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:4412:13: warning: 'RawSeqToDeltaSeqUnknown100LengthGaps' defined but not used [-Wunused-function]
static void RawSeqToDeltaSeqUnknown100LengthGaps (IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:4395:13: warning: 'RawSeqToDeltaSeqUnknownLengthGaps' defined but not used [-Wunused-function]
static void RawSeqToDeltaSeqUnknownLengthGaps (IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:4381:13: warning: 'RawSeqToDeltaSeq' defined but not used [-Wunused-function]
static void RawSeqToDeltaSeq (IteM i)
^~~~~~~~~~~~~~~~
sequin3.c:4349:13: warning: 'CorrectAlignmentsAfterNToGapConversion' defined but not used [-Wunused-function]
static void CorrectAlignmentsAfterNToGapConversion (SeqEntryPtr sep, Uint2 entityID)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:2548:13: warning: 'NewRemoveDuplicateFeatsGenes' defined but not used [-Wunused-function]
static void NewRemoveDuplicateFeatsGenes (IteM i)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:2382:13: warning: 'JustTaxonFixup' defined but not used [-Wunused-function]
static void JustTaxonFixup (IteM i)
^~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin4.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequin4.c: In function 'SplitSegmentedFeatsOnOneSet':
sequin4.c:1692:20: warning: variable 'set_sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep, set_sep;
^~~~~~~
sequin4.c: In function 'RemoveOneSegSet':
sequin4.c:2363:30: warning: variable 'seg_bssp' set but not used [-Wunused-but-set-variable]
BioseqSetPtr seg_nuc_prot, seg_bssp;
^~~~~~~~
sequin4.c: In function 'NewUpdateSeqAlign':
sequin4.c:3418:20: warning: variable 'bssp' set but not used [-Wunused-but-set-variable]
BioseqSetPtr bssp;
^~~~
sequin4.c: In function 'ImportAlignmentForSeqHistInterval':
sequin4.c:3613:21: warning: unused variable 'bssp' [-Wunused-variable]
BioseqSetPtr bssp = NULL;
^~~~
sequin4.c:3600:21: warning: unused variable 'salp' [-Wunused-variable]
SeqAlignPtr salp=NULL,
^~~~
sequin4.c: In function 'GenerateSeqAlignFromSeqEntryMasterOption':
sequin4.c:5300:21: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp = NULL;
^~~
sequin4.c: In function 'LaunchOrfViewer':
sequin4.c:7681:9: warning: variable 'qu' set but not used [-Wunused-but-set-variable]
ButtoN qu, b1;
^~
sequin4.c: In function 'MRnaFromCdsCallback':
sequin4.c:8579:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sequin4.c: In function 'FindNonACGT':
sequin4.c:10240:21: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
sequin4.c: In function 'ConsolidateOrganismNotesProc':
sequin4.c:11481:21: warning: variable 'note_mod' set but not used [-Wunused-but-set-variable]
OrgModPtr mod, note_mod;
^~~~~~~~
sequin4.c:11480:21: warning: variable 'note_ssp' set but not used [-Wunused-but-set-variable]
SubSourcePtr ssp, note_ssp;
^~~~~~~~
sequin4.c: In function 'GetPubStatus':
sequin4.c:13310:14: warning: variable 'csp' set but not used [-Wunused-but-set-variable]
CitSubPtr csp;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from sequin4.c:72:
sequin4.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
sequin4.c:16818:13: warning: 'CleanupTruncateByProtAlignForm' defined but not used [-Wunused-function]
static void CleanupTruncateByProtAlignForm (GraphiC g, VoidPtr data)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin4.c:16360:25: warning: 'FeatToDeltaSeq' defined but not used [-Wunused-function]
static Int2 LIBCALLBACK FeatToDeltaSeq (Pointer data)
^~~~~~~~~~~~~~
sequin4.c:12398:13: warning: 'PubConstraintClearText' defined but not used [-Wunused-function]
static void PubConstraintClearText (PubConstraintPtr pcp)
^~~~~~~~~~~~~~~~~~~~~~
sequin4.c:7172:13: warning: 'AddOrfListToDoc' defined but not used [-Wunused-function]
static void AddOrfListToDoc(DoC doc, ValNodePtr list)
^~~~~~~~~~~~~~~
sequin4.c:3513:18: warning: 'FindBioseqForSeqHist' defined but not used [-Wunused-function]
static BioseqPtr FindBioseqForSeqHist (SeqAlignPtr salp)
^~~~~~~~~~~~~~~~~~~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:374,
from sequin4.c:55:
../include/asnprt.h:61:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnprt.h:60:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnprt.h:59:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = NULL;
^~~
../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnprt.h60";
^~~~~~~~~~~
sequin4.c: In function 'SplitSegmentedFeats.isra.80':
sequin4.c:1700:27: warning: 'new_frame' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 len_modulo, new_frame;
^~~~~~~~~
sequin4.c: In function 'ExplodeGroup.isra.88':
sequin4.c:5933:9: warning: 'nucbsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SetExplodedProtein (orig_prot, nucprot_bssp, nucbsp, sfp, prot_id_str_prefix, cum_offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin5.c:47:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequin5.c: In function 'GeneExtendFunc':
sequin5.c:262:18: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
sequin5.c: In function 'RemoveGBIDsProc':
sequin5.c:1562:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
sequin5.c: In function 'RemoveGBProtIDsProc':
sequin5.c:1612:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
sequin5.c: In function 'RemoveGIProc':
sequin5.c:1663:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
sequin5.c: In function 'SetmRNAFieldString':
sequin5.c:6823:17: warning: variable 'field_choice' set but not used [-Wunused-but-set-variable]
Int4 field_choice;
^~~~~~~~~~~~
sequin5.c: In function 'GetCDSGeneProtField':
sequin5.c:7508:11: warning: variable 'field_choice' set but not used [-Wunused-but-set-variable]
Int4 field_choice;
^~~~~~~~~~~~
sequin5.c: In function 'GetRNAFieldString':
sequin5.c:7903:21: warning: variable 'field_choice' set but not used [-Wunused-but-set-variable]
Int4 field_choice;
^~~~~~~~~~~~
sequin5.c:7897:14: warning: variable 'rrp' set but not used [-Wunused-but-set-variable]
RnaRefPtr rrp;
^~~
sequin5.c: In function 'SetRNAFieldString':
sequin5.c:8138:17: warning: variable 'rrp' set but not used [-Wunused-but-set-variable]
RnaRefPtr rrp;
^~~
sequin5.c: In function 'BioseqConstrainedFeaturesCallback':
sequin5.c:11568:21: warning: variable 'cop' set but not used [-Wunused-but-set-variable]
ConstraintOpPtr cop;
^~~
sequin5.c: In function 'SampleDialogCopy':
sequin5.c:13820:53: warning: variable 'last_col' set but not used [-Wunused-but-set-variable]
Int2 start_col = 0, end_col = 0, first_col, last_col;
^~~~~~~~
sequin5.c:13820:42: warning: variable 'first_col' set but not used [-Wunused-but-set-variable]
Int2 start_col = 0, end_col = 0, first_col, last_col;
^~~~~~~~~
sequin5.c: In function 'TestFeatureFieldChoice':
sequin5.c:14341:31: warning: variable 'dlg' set but not used [-Wunused-but-set-variable]
FeatureFieldChoiceDialogPtr dlg;
^~~
sequin5.c: In function 'CreateClickableListForSourceFeats':
sequin5.c:15126:27: warning: variable 'insertion_seq_txt' set but not used [-Wunused-but-set-variable]
CharPtr transposon_txt, insertion_seq_txt, note_txt;
^~~~~~~~~~~~~~~~~
sequin5.c:15126:11: warning: variable 'transposon_txt' set but not used [-Wunused-but-set-variable]
CharPtr transposon_txt, insertion_seq_txt, note_txt;
^~~~~~~~~~~~~~
sequin5.c: In function 'CDSToMiscFeatConvertFunc':
sequin5.c:15286:24: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE;
^~~~
sequin5.c: In function 'GetRegionOpts':
sequin5.c:15424:25: warning: unused variable 'rval' [-Wunused-variable]
Boolean rval = FALSE;
^~~~
sequin5.c: In function 'NewConvertFeaturesByList':
sequin5.c:15594:14: warning: unused variable 'only_pseudo' [-Wunused-variable]
Boolean only_pseudo = FALSE;
^~~~~~~~~~~
sequin5.c: In function 'FeatureRemoveOrConvertAction':
sequin5.c:15860:25: warning: variable 'sfp' set but not used [-Wunused-but-set-variable]
SeqFeatPtr sfp;
^~~
sequin5.c: In function 'CDSGeneProtAECRDialog':
sequin5.c:18829:25: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin5.c: In function 'CDSGeneProtConvert':
sequin5.c:19196:18: warning: unused variable 'str_dst' [-Wunused-variable]
CharPtr str_dst = NULL;
^~~~~~~
sequin5.c: In function 'CDSGeneProtParse':
sequin5.c:19406:18: warning: variable 'avd' set but not used [-Wunused-but-set-variable]
ApplyValueData avd;
^~~
sequin5.c: In function 'RNAQualListDialog':
sequin5.c:21868:22: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin5.c: In function 'GetRNAFeatureList':
sequin5.c:22057:14: warning: variable 'matches' set but not used [-Wunused-but-set-variable]
Boolean matches;
^~~~~~~
sequin5.c: In function 'RNAQualConvertSwapParseList':
sequin5.c:22189:26: warning: variable 'avd' set but not used [-Wunused-but-set-variable]
ApplyValueData avd;
^~~
sequin5.c: In function 'RNAQualEditRemoveList':
sequin5.c:22285:20: warning: unused variable 'rval' [-Wunused-variable]
Boolean rval = TRUE;
^~~~
sequin5.c: In function 'GetGBQualSampleName':
sequin5.c:22998:14: warning: variable 'num_feature_choices' set but not used [-Wunused-but-set-variable]
Int4 num_feature_choices;
^~~~~~~~~~~~~~~~~~~
sequin5.c: In function 'ConvertGeneLocusTagToOldLocusTagCallback':
sequin5.c:23233:28: warning: variable 'mp' set but not used [-Wunused-but-set-variable]
LocusTagToOldLocusTagPtr mp;
^~
sequin5.c: In function 'GetCombinedCDSLocationCallback':
sequin5.c:23550:21: warning: unused variable 'fcontext' [-Wunused-variable]
SeqMgrFeatContext fcontext;
^~~~~~~~
sequin5.c: In function 'NewSegregateBioseqSet':
sequin5.c:26583:22: warning: variable 'p' set but not used [-Wunused-but-set-variable]
PrompT p, p2;
^
sequin5.c: In function 'CompareBulkRows':
sequin5.c:28054:8: warning: variable 'col' set but not used [-Wunused-but-set-variable]
Int4 col;
^~~
sequin5.c: In function 'ResortBulkEditorRows':
sequin5.c:28321:20: warning: unused variable 'matches' [-Wunused-variable]
ValNodePtr matches = NULL, vnp;
^~~~~~~
sequin5.c:28318:26: warning: unused variable 'last_inserted' [-Wunused-variable]
Int4 row_num, sub_num, last_inserted = 0, comp, col;
^~~~~~~~~~~~~
sequin5.c: In function 'UpdateBulkEdDisplay':
sequin5.c:29402:17: warning: unused variable 'text_len' [-Wunused-variable]
Int4 i, text_len = 0, sub_num;
^~~~~~~~
sequin5.c: In function 'AddColumnToRowList':
sequin5.c:30137:11: warning: unused variable 'm' [-Wunused-variable]
Int4 i, m = 0, f = 0, num_columns = 1;
^
sequin5.c: In function 'ApplyBulkEditCommon':
sequin5.c:30562:23: warning: unused variable 'need_redraw' [-Wunused-variable]
Boolean need_redraw = FALSE;
^~~~~~~~~~~
sequin5.c: In function 'CopyAllFieldsFromList':
sequin5.c:30917:8: warning: unused variable 'num_full' [-Wunused-variable]
Int4 num_full = 0;
^~~~~~~~
sequin5.c: In function 'BulkEditorObjectList':
sequin5.c:32879:22: warning: unused variable 'subtype' [-Wunused-variable]
Uint1 subtype = 0;
^~~~~~~
sequin5.c: In function 'BulkEditor':
sequin5.c:32937:22: warning: variable 'field_list' set but not used [-Wunused-but-set-variable]
BulkEdFieldPtr field_list = NULL;
^~~~~~~~~~
sequin5.c: In function 'GetSpecificHostCorrectionCategory':
sequin5.c:33691:22: warning: unused variable 'fmt' [-Wunused-variable]
CharPtr fmt = "Unable to suggest correction for '%s'";
^~~
In file included from ../include/tax3api.h:51:0,
from sequin5.c:78:
sequin5.c: At top level:
../include/objtax3.h:183:31: warning: 'Value_valueFree' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr ));
^~~~~~~~~~~~~~~
../include/objtax3.h:184:31: warning: 'Value_valueAsnRead' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~
../include/objtax3.h:185:24: warning: 'Value_valueAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~
sequin5.c:32200:13: warning: 'BulkSrcSetOrgModDescTF' defined but not used [-Wunused-function]
static void BulkSrcSetOrgModDescTF (Pointer target, Pointer data, Uint2 mod_type)
^~~~~~~~~~~~~~~~~~~~~~
sequin5.c:32179:16: warning: 'BulkSrcGetOrgModDescTF' defined but not used [-Wunused-function]
static Pointer BulkSrcGetOrgModDescTF (Uint1 data_choice, Pointer data, Uint2 mod_type)
^~~~~~~~~~~~~~~~~~~~~~
sequin5.c:31877:23: warning: 'GetBulkEditorFieldListForFeature' defined but not used [-Wunused-function]
static BulkEdFieldPtr GetBulkEditorFieldListForFeature (SeqFeatPtr sfp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin5.c:31412:16: warning: 'BulkGetPseudo' defined but not used [-Wunused-function]
static Pointer BulkGetPseudo (Pointer data)
^~~~~~~~~~~~~
sequin5.c:31401:13: warning: 'BulkSetPseudo' defined but not used [-Wunused-function]
static void BulkSetPseudo (Pointer target, Pointer val)
^~~~~~~~~~~~~
sequin5.c:31390:16: warning: 'BulkReleaseTrueFalse' defined but not used [-Wunused-function]
static Pointer BulkReleaseTrueFalse (Pointer p)
^~~~~~~~~~~~~~~~~~~~
sequin5.c:31224:15: warning: 'BulkNucLocationDialog' defined but not used [-Wunused-function]
static DialoG BulkNucLocationDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
^~~~~~~~~~~~~~~~~~~~~
sequin5.c:29002:28: warning: 'TwoFieldBulkEditNew' defined but not used [-Wunused-function]
static TwoFieldBulkEditPtr TwoFieldBulkEditNew (void)
^~~~~~~~~~~~~~~~~~~
sequin5.c:28749:28: warning: 'OneFieldBulkEditNew' defined but not used [-Wunused-function]
static OneFieldBulkEditPtr OneFieldBulkEditNew (void)
^~~~~~~~~~~~~~~~~~~
sequin5.c:28245:13: warning: 'FlatCopyRows' defined but not used [-Wunused-function]
static Int4 FlatCopyRows (BulkEditorRowPtr new_rows, BulkEditorRowPtr orig_rows, BulkEdFieldPtr field_list)
^~~~~~~~~~~~
sequin5.c:27713:13: warning: 'FreeBulkEditorValuesList' defined but not used [-Wunused-function]
static void FreeBulkEditorValuesList (ValNodePtr PNTR values_list, Int4 num_rows, BulkEdFieldPtr field_list)
^~~~~~~~~~~~~~~~~~~~~~~~
sequin5.c:21552:23: warning: 'AECRRNAQualFree' defined but not used [-Wunused-function]
static AECRRNAQualPtr AECRRNAQualFree (AECRRNAQualPtr ap)
^~~~~~~~~~~~~~~
sequin5.c:13071:25: warning: 'ParseFieldSrcFree' defined but not used [-Wunused-function]
static ParseFieldSrcPtr ParseFieldSrcFree (ParseFieldSrcPtr pfsp)
^~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:134:0,
from sequin5.c:53:
../include/blstspc.h:229:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/blstspc.h:228:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/blstspc.h:227:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/blstspc.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "blstspc.h23";
^~~~~~~~~~~
sequin5.c: In function 'ResortBulkEditorRows':
sequin5.c:28381:6: warning: 'smallest_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (smallest_pos < row_num - 1) {
^
sequin5.c: In function 'ConvertDescriptorFieldCallback':
sequin5.c:6059:18: warning: 'dst_text' may be used uninitialized in this function [-Wmaybe-uninitialized]
avd.new_text = dst_text;
~~~~~~~~~~~~~^~~~~~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin5.c:47:
sequin5.c: In function 'ApplyEditConvertRemoveCombo.constprop':
../include/vibdefns.h:505:22: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AlignObjects Nlm_AlignObjects
^~~~~~~~~~~~~~~~
sequin5.c:17828:42: note: 'm' was declared here
GrouP h, g1, k, n, m;
^
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin6.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequin6.c: In function 'CleanupDeleteByTextConvertForm':
sequin6.c:1489:19: warning: variable 'cfp' set but not used [-Wunused-but-set-variable]
ConvertFormPtr cfp;
^~~
sequin6.c: In function 'RemoveOrgModText':
sequin6.c:3680:35: warning: variable 'next_mod' set but not used [-Wunused-but-set-variable]
OrgModPtr mod, prev_mod = NULL, next_mod;
^~~~~~~~
sequin6.c: In function 'GapLocationsFromNs':
sequin6.c:5229:15: warning: variable 'seq_ext' set but not used [-Wunused-but-set-variable]
ValNodePtr seq_ext;
^~~~~~~
sequin6.c:5228:15: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
sequin6.c: In function 'RemoveTerminalNsFromLocation':
sequin6.c:5772:21: warning: unused variable 'seq_offset' [-Wunused-variable]
Int4 seq_offset = 0, start, stop;
^~~~~~~~~~
sequin6.c: In function 'ApplyBioFeatToList':
sequin6.c:6890:23: warning: variable 'oldscope' set but not used [-Wunused-but-set-variable]
SeqEntryPtr nsep, oldscope;
^~~~~~~~
sequin6.c: In function 'CopyContactToAuthors':
sequin6.c:8820:16: warning: unused variable 'list' [-Wunused-variable]
ValNodePtr list = NULL;
^~~~
sequin6.c: In function 'AddCommentsToList':
sequin6.c:14010:22: warning: unused variable 'comment_len' [-Wunused-variable]
Int4 comment_len = 0, num_segments = 0;
^~~~~~~~~~~
sequin6.c: In function 'RNAWordsFromString':
sequin6.c:14124:32: warning: variable 'last_pos' set but not used [-Wunused-but-set-variable]
CharPtr last_hit = NULL, last_pos = NULL;
^~~~~~~~
sequin6.c:14124:15: warning: variable 'last_hit' set but not used [-Wunused-but-set-variable]
CharPtr last_hit = NULL, last_pos = NULL;
^~~~~~~~
sequin6.c: In function 'FeatureEditorActionGroup':
sequin6.c:15192:15: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin6.c: In function 'DoPartialFeatureProc':
sequin6.c:15455:16: warning: variable 'dash_at_end' set but not used [-Wunused-but-set-variable]
Boolean dash_at_end = FALSE;
^~~~~~~~~~~
sequin6.c: In function 'FeatureEditorDoOneAction':
sequin6.c:16047:19: warning: unused variable 'act' [-Wunused-variable]
AECRActionPtr act = NULL;
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from sequin6.c:60:
sequin6.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
sequin6.c:15251:13: warning: 'DoPseudoFeatureProc' defined but not used [-Wunused-function]
static void DoPseudoFeatureProc (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
^~~~~~~~~~~~~~~~~~~
sequin6.c:7713:13: warning: 'SetContactNameFromString' defined but not used [-Wunused-function]
static void SetContactNameFromString (SubmitFormPtr sbfp, CharPtr txt)
^~~~~~~~~~~~~~~~~~~~~~~~
sequin6.c:650:16: warning: 'TrimOffEndQuotes' defined but not used [-Wunused-function]
static Boolean TrimOffEndQuotes (CharPtr trimString,
^~~~~~~~~~~~~~~~
sequin6.c:225:13: warning: 'PopulateParseQualPopup' defined but not used [-Wunused-function]
static void PopulateParseQualPopup (PopuP p)
^~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/vibrant.h:133:0,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin6.c:45:
sequin6.c:154:19: warning: 'rnax_short_field_alist' defined but not used [-Wunused-variable]
static ENUM_ALIST(rnax_short_field_alist)
^
../include/vibforms.h:61:45: note: in definition of macro 'ENUM_ALIST'
#define ENUM_ALIST(name) Nlm_EnumFieldAssoc name[] = {
^~~~
sequin6.c:123:19: warning: 'cds_short_field_alist' defined but not used [-Wunused-variable]
static ENUM_ALIST(cds_short_field_alist)
^
../include/vibforms.h:61:45: note: in definition of macro 'ENUM_ALIST'
#define ENUM_ALIST(name) Nlm_EnumFieldAssoc name[] = {
^~~~
sequin6.c:85:20: warning: 'publication_field_alist' defined but not used [-Wunused-variable]
static ENUM_ALIST (publication_field_alist)
^
../include/vibforms.h:61:45: note: in definition of macro 'ENUM_ALIST'
#define ENUM_ALIST(name) Nlm_EnumFieldAssoc name[] = {
^~~~
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin6.c:45:
sequin6.c: In function 'CreateFieldSubfieldDlg.constprop':
../include/vibdefns.h:505:22: warning: 'g2' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AlignObjects Nlm_AlignObjects
^~~~~~~~~~~~~~~~
sequin6.c:496:29: note: 'g2' was declared here
GrouP p, g, g2;
^~
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin7.c:56:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequin7.c: In function 'GeneExtendFunc':
sequin7.c:962:18: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
sequin7.c: In function 'FinishConvertingToCDS':
sequin7.c:2770:17: warning: variable 'nsep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr nsep;
^~~~
sequin7.c: In function 'SetBestFrame':
sequin7.c:5532:26: warning: variable 'seq_str2' set but not used [-Wunused-but-set-variable]
CharPtr seq_str1, seq_str2;
^~~~~~~~
sequin7.c:5532:16: warning: variable 'seq_str1' set but not used [-Wunused-but-set-variable]
CharPtr seq_str1, seq_str2;
^~~~~~~~
sequin7.c: In function 'FixFeatureIntervalSeqLoc':
sequin7.c:7057:17: warning: variable 'tmpsip' set but not used [-Wunused-but-set-variable]
SeqIdPtr tmpsip;
^~~~~~
sequin7.c: In function 'RNABlastOptionNew':
sequin7.c:7595:17: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Int2 rval;
^~~~
sequin7.c: In function 'GetSubListForRNAStrandCorrection':
sequin7.c:7875:27: warning: variable 'found_id' set but not used [-Wunused-but-set-variable]
Boolean found_id;
^~~~~~~~
sequin7.c: In function 'ShowClickableItemListEx':
sequin7.c:10120:28: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin7.c: In function 'ChooseFeaturesForConversion':
sequin7.c:10261:28: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin7.c: In function 'GetTableOptions':
sequin7.c:14440:30: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin7.c: In function 'RemoveCDSandmRNAForGene':
sequin7.c:14723:27: warning: variable 'prev_xref' set but not used [-Wunused-but-set-variable]
SeqFeatXrefPtr xref, prev_xref, next_xref;
^~~~~~~~~
sequin7.c: In function 'CombineToCreatePseudoGene':
sequin7.c:14806:48: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| best_left == fcontext.left && best_right < fcontext.right) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin7.c: In function 'TrimTaxFix':
sequin7.c:16291:46: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| word_break - t->suggested_fix == 10 && StringNICmp (t->suggested_fix, "uncultured ", 11) == 0) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin7.c: In function 'FindBestNTrimSites':
sequin7.c:17134:21: warning: unused variable 'trim_list' [-Wunused-variable]
ValNodePtr trim_list = NULL;
^~~~~~~~~
sequin7.c: In function 'BarcodeBlastOptionNew':
sequin7.c:17377:17: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Int2 rval;
^~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from sequin7.c:77:
sequin7.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/tax3api.h:51:0,
from sequin7.c:80:
../include/objtax3.h:183:31: warning: 'Value_valueFree' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr ));
^~~~~~~~~~~~~~~
../include/objtax3.h:184:31: warning: 'Value_valueAsnRead' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~
../include/objtax3.h:185:24: warning: 'Value_valueAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~
sequin7.c: In function 'GetSubListForRNAStrandCorrection':
sequin7.c:7940:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
sequin7.c:16484:25: warning: 'NTrimIntervalFree' defined but not used [-Wunused-function]
static NTrimIntervalPtr NTrimIntervalFree (NTrimIntervalPtr n)
^~~~~~~~~~~~~~~~~
sequin7.c:14969:13: warning: 'FindBadLatLonSourceFeat' defined but not used [-Wunused-function]
static void FindBadLatLonSourceFeat (SeqFeatPtr sfp, Pointer userdata)
^~~~~~~~~~~~~~~~~~~~~~~
sequin7.c:12855:13: warning: 'RemoveBarcodeKeywordsFromLowTrace' defined but not used [-Wunused-function]
static void RemoveBarcodeKeywordsFromLowTrace (ButtoN b)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin7.c:7179:16: warning: 'DoesBioseqMatchStringConstraint' defined but not used [-Wunused-function]
static Boolean DoesBioseqMatchStringConstraint (BioseqPtr bsp, StringConstraintXPtr scp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin7.c:5095:13: warning: 'RemoveMultipleTitles' defined but not used [-Wunused-function]
static void RemoveMultipleTitles (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent)
^~~~~~~~~~~~~~~~~~~~
sequin7.c:47:14: warning: 'time_of_compilation' defined but not used [-Wunused-variable]
static char *time_of_compilation = BUILD_TIME;
^~~~~~~~~~~~~~~~~~~
sequin7.c: In function 'CombineToCreatePseudoGene':
sequin7.c:14920:27: warning: 'int_strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
first_sfp->location = SeqLocIntNew (int_left, int_right, int_strand, sip);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin7.c:14806:48: warning: 'best_right' may be used uninitialized in this function [-Wmaybe-uninitialized]
|| best_left == fcontext.left && best_right < fcontext.right) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin7.c:14806:18: warning: 'best_left' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (feat_list == NULL
~~~~~~~~~~~~~~~~~
|| best_left > fcontext.left
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|| best_left == fcontext.left && best_right < fcontext.right) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin8.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequin8.c: In function 'PopulateAAPopup':
sequin8.c:1531:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
sequin8.c: In function 'UserObjectPtrToUnverifiedDialog':
sequin8.c:4313:28: warning: unused variable 'status' [-Wunused-variable]
Int2 status = 0;
^~~~~~
sequin8.c: In function 'SelectBestRepeatsFromList':
sequin8.c:8316:18: warning: variable 'best_len' set but not used [-Wunused-but-set-variable]
Int4 best_len;
^~~~~~~~
sequin8.c:8311:18: warning: variable 'strand2' set but not used [-Wunused-but-set-variable]
Uint1 strand1, strand2;
^~~~~~~
sequin8.c:8311:9: warning: variable 'strand1' set but not used [-Wunused-but-set-variable]
Uint1 strand1, strand2;
^~~~~~~
sequin8.c: In function 'ExamineAln':
sequin8.c:8832:8: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len, num_aln = 0;
^~~
sequin8.c: In function 'FindIntervalConflict':
sequin8.c:10738:39: warning: self-comparison always evaluates to true [-Wtautological-compare]
} else if (left2 <= left1 && right2 >= right2) {
^~
sequin8.c: In function 'BuildConflictLists':
sequin8.c:11080:69: warning: self-comparison always evaluates to false [-Wtautological-compare]
if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) {
^~
sequin8.c:11086:69: warning: self-comparison always evaluates to false [-Wtautological-compare]
if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) {
^~
sequin8.c: In function 'GetWindowForReportType':
sequin8.c:15341:3: warning: enumeration value 'eReportTypeTSA' not handled in switch [-Wswitch]
switch (report_type) {
^~~~~~
sequin8.c: In function 'SetWindowForReportType':
sequin8.c:15372:3: warning: enumeration value 'eReportTypeTSA' not handled in switch [-Wswitch]
switch (report_type) {
^~~~~~
sequin8.c: In function 'GetReportConfigName':
sequin8.c:15390:3: warning: enumeration value 'eReportTypeTSA' not handled in switch [-Wswitch]
switch (report_type) {
^~~~~~
sequin8.c: In function 'ScrollToDiscrepancyItem':
sequin8.c:16161:17: warning: variable 'special_flag' set but not used [-Wunused-but-set-variable]
Boolean special_flag = FALSE;
^~~~~~~~~~~~
sequin8.c: In function 'GetReportEditButtonProc':
sequin8.c:16944:3: warning: enumeration value 'eReportTypeTSA' not handled in switch [-Wswitch]
switch (report_type) {
^~~~~~
sequin8.c: In function 'GetReportName':
sequin8.c:16968:3: warning: enumeration value 'eReportTypeTSA' not handled in switch [-Wswitch]
switch (report_type) {
^~~~~~
sequin8.c: In function 'SortVnpByLinkStatus':
sequin8.c:18983:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (fcontext2.itemID < fcontext2.itemID) {
^
sequin8.c: In function 'SortVnpBymRNAPos':
sequin8.c:19000:22: warning: variable 'mrna2' set but not used [-Wunused-but-set-variable]
SeqFeatPtr mrna1, mrna2;
^~~~~
sequin8.c:19000:15: warning: variable 'mrna1' set but not used [-Wunused-but-set-variable]
SeqFeatPtr mrna1, mrna2;
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from sequin8.c:57:
sequin8.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/tax3api.h:51:0,
from sequin8.c:63:
../include/objtax3.h:183:31: warning: 'Value_valueFree' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr ));
^~~~~~~~~~~~~~~
../include/objtax3.h:184:31: warning: 'Value_valueAsnRead' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~
../include/objtax3.h:185:24: warning: 'Value_valueAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~
sequin8.c:20204:19: warning: 'DivideClickableItemListByEntityID' defined but not used [-Wunused-function]
static ValNodePtr DivideClickableItemListByEntityID (ValNodePtr clickable_list)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:19897:13: warning: 'TrimCDSFortRNAOverlap' defined but not used [-Wunused-function]
static void TrimCDSFortRNAOverlap (ValNodePtr item_list)
^~~~~~~~~~~~~~~~~~~~~
sequin8.c:15651:13: warning: 'VisitFeaturesInViewedBioseqs' defined but not used [-Wunused-function]
static void VisitFeaturesInViewedBioseqs (Pointer userdata, VisitFeaturesFunc callback)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:13113:13: warning: 'ShowAssemblyAlignment' defined but not used [-Wunused-function]
static void ShowAssemblyAlignment (SeqAlignPtr salp)
^~~~~~~~~~~~~~~~~~~~~
sequin8.c:8830:13: warning: 'ExamineAln' defined but not used [-Wunused-function]
static void ExamineAln (SeqAlignPtr sap)
^~~~~~~~~~
sequin8.c:8768:20: warning: 'GetOldBlastTPAHistAlignPiece' defined but not used [-Wunused-function]
static SeqAlignPtr GetOldBlastTPAHistAlignPiece (BioseqPtr bsp1, BioseqPtr bsp2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:8745:20: warning: 'GetNewBlastTPAHistAlignPiece' defined but not used [-Wunused-function]
static SeqAlignPtr GetNewBlastTPAHistAlignPiece (BioseqPtr bsp1, BioseqPtr bsp2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:7711:16: warning: 'DoesFirstRepeatContainAllOtherRepeats' defined but not used [-Wunused-function]
static Boolean DoesFirstRepeatContainAllOtherRepeats (ValNodePtr start, ValNodePtr stop)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:7259:16: warning: 'DoesRowContainPoint' defined but not used [-Wunused-function]
static Boolean DoesRowContainPoint (SeqAlignRowPtr row, Int4 point)
^~~~~~~~~~~~~~~~~~~
sequin8.c:6931:13: warning: 'CKA_ShowAln' defined but not used [-Wunused-function]
static void CKA_ShowAln(SeqAlignPtr sap, CKA_AccPtr acc_head)
^~~~~~~~~~~
sequin8.c:6725:16: warning: 'CKA_ValidateSeqAlign' defined but not used [-Wunused-function]
static Boolean CKA_ValidateSeqAlign(SeqAlignPtr sap, CKA_AccPtr acc_head, Int4 bioseqlen, ValNodePtr PNTR errors)
^~~~~~~~~~~~~~~~~~~~
sequin8.c:1890:18: warning: 'SqnGetBioseqGivenSeqLoc' defined but not used [-Wunused-function]
static BioseqPtr SqnGetBioseqGivenSeqLoc (SeqLocPtr slp, Uint2 entityID)
^~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:664:13: warning: 'FixReadingFrame' defined but not used [-Wunused-function]
static void FixReadingFrame (
^~~~~~~~~~~~~~~
sequin8.c:452:13: warning: 'ExtendOnePartialFeatureToEndOrGap' defined but not used [-Wunused-function]
static void ExtendOnePartialFeatureToEndOrGap (SeqFeatPtr sfp, Pointer userdata)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/objsub.h:76,
from ../include/subutil.h:50,
from sequin9.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequin9.c: In function 'DoVecScreens':
sequin9.c:633:19: warning: variable 'hits' set but not used [-Wunused-but-set-variable]
Int2 hits;
^~~~
sequin9.c: In function 'AcceptArgumentFormProc':
sequin9.c:1468:18: warning: variable 'choice' set but not used [-Wunused-but-set-variable]
Int2 choice;
^~~~~~
sequin9.c: In function 'ExtendBothEnds':
sequin9.c:4777:17: warning: variable 'oldbsp' set but not used [-Wunused-but-set-variable]
BioseqPtr oldbsp;
^~~~~~
sequin9.c: In function 'Extend5Prime':
sequin9.c:4845:17: warning: variable 'oldbsp' set but not used [-Wunused-but-set-variable]
BioseqPtr oldbsp;
^~~~~~
sequin9.c: In function 'Extend3Prime':
sequin9.c:4905:17: warning: variable 'oldbsp' set but not used [-Wunused-but-set-variable]
BioseqPtr oldbsp;
^~~~~~
sequin9.c: In function 'FixProteinString':
sequin9.c:5116:16: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start, stop, new_stop, prot_len;
^~~~~
sequin9.c: In function 'ShiftStopForLengthChange':
sequin9.c:5193:13: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start, stop, new_stop;
^~~~~
sequin9.c: In function 'ExtendProtein5':
sequin9.c:5386:23: warning: variable 'new_stop' set but not used [-Wunused-but-set-variable]
Int4 stop, new_stop;
^~~~~~~~
sequin9.c: In function 'PrepareUpdateAlignmentForProtein':
sequin9.c:5914:17: warning: variable 'changed_frame' set but not used [-Wunused-but-set-variable]
Boolean changed_frame;
^~~~~~~~~~~~~
sequin9.c: In function 'DrawAlignDiffs':
sequin9.c:7508:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, i;
^~~~
sequin9.c:7508:14: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, i;
^~~~
sequin9.c: In function 'MakeAlignDetails':
sequin9.c:7643:12: warning: variable 'aln_length' set but not used [-Wunused-but-set-variable]
Int4 aln_length;
^~~~~~~~~~
sequin9.c: In function 'MakeAlignSequence':
sequin9.c:7692:56: warning: variable 'to' set but not used [-Wunused-but-set-variable]
Int4 aln_length, len, lens, start, stop, from, to, i, j;
^~
sequin9.c:7692:50: warning: variable 'from' set but not used [-Wunused-but-set-variable]
Int4 aln_length, len, lens, start, stop, from, to, i, j;
^~~~
sequin9.c: In function 'DrawUpdateAlignmentDiffs':
sequin9.c:13384:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, i;
^~~~
sequin9.c:13384:14: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, i;
^~~~
sequin9.c: In function 'MakeAlignmentDetailsPicture':
sequin9.c:13469:12: warning: variable 'aln_length' set but not used [-Wunused-but-set-variable]
Int4 aln_length;
^~~~~~~~~~
sequin9.c: In function 'MakeUpdateAlignmentSequenceString':
sequin9.c:13551:44: warning: variable 'to' set but not used [-Wunused-but-set-variable]
Int4 len, lens, start, stop, from, to, i, j;
^~
sequin9.c:13551:38: warning: variable 'from' set but not used [-Wunused-but-set-variable]
Int4 len, lens, start, stop, from, to, i, j;
^~~~
sequin9.c: In function 'SetPreviewSequenceSelectionByPosition':
sequin9.c:15725:46: warning: variable 'curr_scroll' set but not used [-Wunused-but-set-variable]
Int4 prevrow, curr_scroll, max_scroll;
^~~~~~~~~~~
sequin9.c: In function 'DoTestUpdateOneSequence':
sequin9.c:16781:30: warning: variable 'update_bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr update_bsp = NULL;
^~~~~~~~~~
sequin9.c:16780:30: warning: variable 'update_entityID' set but not used [-Wunused-but-set-variable]
Uint2 update_entityID = 0;
^~~~~~~~~~~~~~~
sequin9.c: In function 'UpdateAllSequences':
sequin9.c:17071:30: warning: unused variable 'update_entityID' [-Wunused-variable]
Uint2 update_entityID = 0;
^~~~~~~~~~~~~~~
sequin9.c:17070:30: warning: unused variable 'update_bsp' [-Wunused-variable]
BioseqPtr update_bsp = NULL;
^~~~~~~~~~
sequin9.c: In function 'CleanupUpdateMultiSequence':
sequin9.c:17390:30: warning: unused variable 'entityIDList' [-Wunused-variable]
ValNodePtr entityIDList = NULL;
^~~~~~~~~~~~
sequin9.c: In function 'UpdateSequenceViaDownload':
sequin9.c:18717:15: warning: variable 'is_na' set but not used [-Wunused-but-set-variable]
Boolean is_na;
^~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from sequin9.c:47:
sequin9.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from sequin9.c:50:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from sequin9.c:50:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from sequin9.c:50:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from sequin9.c:50:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from ../include/alignmgr2.h:111,
from ../include/actutils.h:105,
from sequin9.c:56:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
sequin9.c:215:13: warning: 'TruncateCDS' declared 'static' but never defined [-Wunused-function]
static void TruncateCDS (SeqFeatPtr sfp, Uint1 frame, BioseqPtr pbsp);
^~~~~~~~~~~
sequin9.c:17033:29: warning: 'FeatureUpdateNew' defined but not used [-Wunused-function]
static FeatureUpdateInfoPtr FeatureUpdateNew (BioseqPtr orig_bsp, BioseqPtr update_bsp)
^~~~~~~~~~~~~~~~
sequin9.c:1405:16: warning: 'StrSaveNoNullEncodeSpaces' defined but not used [-Wunused-function]
static CharPtr StrSaveNoNullEncodeSpaces (CharPtr from)
^~~~~~~~~~~~~~~~~~~~~~~~~
sequin9.c: In function 'TruncateSeqGraphValues':
sequin9.c:3131:14: warning: 'fmax' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (((FloatHiPtr)new_values)[newpos] > fmax) {
^
sequin9.c:3134:14: warning: 'fmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (((FloatHiPtr)new_values)[newpos] < fmin) {
^
sequin9.c: In function 'PrepareUpdateAlignmentForProtein':
sequin9.c:5855:56: warning: 'gene_sfp' may be used uninitialized in this function [-Wmaybe-uninitialized]
new_slp = SeqLocMerge (bsp, sfp->location, gene_sfp->location, TRUE, FALSE, FALSE);
~~~~~~~~^~~~~~~~~~
sequin9.c:5920:17: note: 'gene_sfp' was declared here
SeqFeatPtr gene_sfp;
^~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin10.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sequin10.c: In function 'ApplyTableQuals':
sequin10.c:4530:26: warning: variable 'fqtd' set but not used [-Wunused-but-set-variable]
FeatureQualTableData fqtd;
^~~~
sequin10.c: In function 'EraseAllFieldsWhenBlank':
sequin10.c:5591:19: warning: unused variable 'columns' [-Wunused-variable]
ValNodePtr columns = NULL;
^~~~~~~
sequin10.c: In function 'ExternalSourceQualifierTableReader':
sequin10.c:6515:22: warning: variable 'any_valid' set but not used [-Wunused-but-set-variable]
Boolean any_valid = FALSE;
^~~~~~~~~
sequin10.c: In function 'LoadFeatureFieldTable':
sequin10.c:8816:24: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin10.c: In function 'OrgModListsMatch':
sequin10.c:10557:14: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
sequin10.c: In function 'SubtypeListsMatch':
sequin10.c:10750:14: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
sequin10.c: In function 'RetranscribemRNA':
sequin10.c:12121:21: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin10.c: In function 'TrimSequencesByAlignment':
sequin10.c:12516:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
sequin10.c: In function 'AddOneFeatureBetween':
sequin10.c:12907:14: warning: variable 'seqfeattype' set but not used [-Wunused-but-set-variable]
Int4 seqfeattype;
^~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from sequin10.c:63:
sequin10.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/tax3api.h:51:0,
from sequin10.c:68:
../include/objtax3.h:183:31: warning: 'Value_valueFree' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr ));
^~~~~~~~~~~~~~~
../include/objtax3.h:184:31: warning: 'Value_valueAsnRead' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~
../include/objtax3.h:185:24: warning: 'Value_valueAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~
sequin10.c:8902:16: warning: 'GetRevSectionInterval' defined but not used [-Wunused-function]
static Pointer GetRevSectionInterval (Uint1 data_choice, Pointer data, Pointer metadata)
^~~~~~~~~~~~~~~~~~~~~
sequin10.c:8884:16: warning: 'GetRevSectionSequence' defined but not used [-Wunused-function]
static Pointer GetRevSectionSequence (Uint1 data_choice, Pointer data, Pointer metadata)
^~~~~~~~~~~~~~~~~~~~~
sequin10.c:3013:19: warning: 'FreeTableData' defined but not used [-Wunused-function]
static ValNodePtr FreeTableData (ValNodePtr lines)
^~~~~~~~~~~~~
sequin10.c:1452:19: warning: 'OrgModTableColumnListFree' defined but not used [-Wunused-function]
static ValNodePtr OrgModTableColumnListFree (ValNodePtr vnp)
^~~~~~~~~~~~~~~~~~~~~~~~~
sequin10.c: In function 'CreateOneProteinId':
sequin10.c:15363:5: warning: 'sip_local' may be used uninitialized in this function [-Wmaybe-uninitialized]
ReplaceSeqIdWithSeqId (sip_local, sip, sep);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequin10.c:45:
sequin10.c: In function 'AutoDefBaseFormCommon':
../include/vibdefns.h:297:18: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define CheckBox Nlm_CheckBox
^~~~~~~~~~~~
sequin10.c:716:24: note: 'k' was declared here
GrouP p, g1, s1, s2, k, k2;
^
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sequinx.c:46:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
: Psequin
gcc -o sbtedit -I. -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF -UINTERNAL_NCBI_SEQUIN sbtedit.c \
-lncbidesk -lncbitool -lvibrant -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from ../include/dlogutil.h:48,
from sequin.h:85,
from sbtedit.c:58:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sbtedit.c: In function 'LookupTaxonomyFunc':
sbtedit.c:607:15: warning: variable 'rsult' set but not used [-Wunused-but-set-variable]
Int4 rsult;
^~~~~
At top level:
sbtedit.c:49:14: warning: 'time_of_compilation' defined but not used [-Wunused-variable]
static char *time_of_compilation = BUILD_TIME;
^~~~~~~~~~~~~~~~~~~
sbtedit.c:48:14: warning: 'date_of_compilation' defined but not used [-Wunused-variable]
static char *date_of_compilation = BUILD_DATE;
^~~~~~~~~~~~~~~~~~~
: sbtedit
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" udvmain.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/explore.h:49,
from ../include/udviewer.h:209,
from udvmain.c:80:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
udvmain.c: In function 'Nlm_Main':
udvmain.c:232:8: warning: unused variable 'rcL' [-Wunused-variable]
RecT rcL;
^~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from udvmain.c:81:
udvmain.c: At top level:
../include/objmmdb1.h:206:57: warning: 'VersionOfDatabase_version_of_databaseFree' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:72:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from udvmain.c:81:
../include/objmmdb1.h:207:57: warning: 'VersionOfDatabase_version_of_databaseAsnRead' declared 'static' but never defined [-Wunused-function]
static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb1.h:208:24: warning: 'VersionOfDatabase_version_of_databaseAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from udvmain.c:81:
../include/objmmdb2.h:151:43: warning: 'Coordinates_coordinatesFree' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr ));
^~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:152:43: warning: 'Coordinates_coordinatesAsnRead' declared 'static' but never defined [-Wunused-function]
static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:153:24: warning: 'Coordinates_coordinatesAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:247:35: warning: 'Surface_surfaceFree' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr ));
^~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:248:35: warning: 'Surface_surfaceAsnRead' declared 'static' but never defined [-Wunused-function]
static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb2.h:249:24: warning: 'Surface_surfaceAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/strimprt.h:74:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from udvmain.c:81:
../include/objmmdb3.h:287:37: warning: 'Location_locationFree' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:288:37: warning: 'Location_locationAsnRead' declared 'static' but never defined [-Wunused-function]
static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:289:24: warning: 'Location_locationAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:310:37: warning: 'Property_propertyFree' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr ));
^~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:311:37: warning: 'Property_propertyAsnRead' declared 'static' but never defined [-Wunused-function]
static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:312:24: warning: 'Property_propertyAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:419:33: warning: 'Region_regionFree' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr ));
^~~~~~~~~~~~~~~~~
../include/objmmdb3.h:420:33: warning: 'Region_regionAsnRead' declared 'static' but never defined [-Wunused-function]
static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objmmdb3.h:421:24: warning: 'Region_regionAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
gcc -o udv -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF udvmain.o -lvibnet -lncbidesk \
-lncbiNacc -lnetentr -lvibrant -lncbiobj -lncbi
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ddvmain.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ddvmain.c:138:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ddvmain.c:147:13: warning: 'DDV_myargs' initialized and declared 'extern'
extern Args DDV_myargs[NUMARGS] = {
^~~~~~~~~~
ddvmain.c:267:16: warning: 'DDV_UseNetwork' defined but not used [-Wunused-function]
static Boolean DDV_UseNetwork(void)
^~~~~~~~~~~~~~
ddvmain.c: In function 'Nlm_Main':
ddvmain.c:441:5: warning: 'UseNetwork' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (UseNetwork && EntrezIsInited()) EntrezBioseqFetchDisable();
^
gcc -o ddv -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF ddvmain.o -lvibnet -lncbidesk -lddvlib \
-lncbiNacc -lnetentr -lvibrant -lncbiobj -lncbi
gcc -g -o blastcl3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF -DBLAST_CS_API blastall.c \
-lblastapi -lblast -lnetblast -lncbitool -lncbiobj -lncbi
blastall.c: In function 'Main_old':
blastall.c:1812:26: warning: variable 'nuc_concat' set but not used [-Wunused-but-set-variable]
Boolean concat_done, nuc_concat;
^~~~~~~~~~
blastall.c:1800:23: warning: variable 'handle_results' set but not used [-Wunused-but-set-variable]
int (LIBCALLBACK *handle_results)(VoidPtr srch);
^~~~~~~~~~~~~~
blastall.c:1795:20: warning: unused variable 'index' [-Wunused-variable]
Int4 num_bsps, index;
^~~~~
blastall.c:1794:42: warning: unused variable 'seqalignp' [-Wunused-variable]
SeqAlignPtr sap, next_seqalign, PNTR seqalignp;
^~~~~~~~~
blastall.c: In function 'Nlm_Main':
blastall.c:2963:13: warning: unused variable 'use_new_engine' [-Wunused-variable]
Boolean use_new_engine=FALSE;
^~~~~~~~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from blastall.c:727:
blastall.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
In file included from blastall.c:733:0:
../include/objblst3.h:180:35: warning: 'Cutoff2_cutoff2Free' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr ));
^~~~~~~~~~~~~~~~~~~
../include/objblst3.h:181:35: warning: 'Cutoff2_cutoff2AsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:182:24: warning: 'Cutoff2_cutoff2AsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:199:33: warning: 'Cutoff_cutoffFree' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr ));
^~~~~~~~~~~~~~~~~
../include/objblst3.h:200:33: warning: 'Cutoff_cutoffAsnRead' declared 'static' but never defined [-Wunused-function]
static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objblst3.h:201:24: warning: 'Cutoff_cutoffAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
blastall.c:2931:1: warning: 'readdb_use_new_blast' defined but not used [-Wunused-function]
readdb_use_new_blast(char* dbname)
^~~~~~~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:134:0,
from blastall.c:734:
../include/blstspc.h:229:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/blstspc.h:228:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/blstspc.h:227:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/blstspc.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "blstspc.h23";
^~~~~~~~~~~
blastall.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastall.c,v 6.206 2011/12/19 18:40:17 gouriano Exp $";
^~~~~
blastall.c: In function 'Main_old':
blastall.c:2410:74: warning: 'fake_bsp_arr' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr_bsp = (num_queries>0) ? *(fake_bsp_arr + bsp_iter) : query_bsp;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
blastall.c:2743:88: warning: 'seq_annot_arr' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr_seqannot = (num_queries > 0) ? *(seq_annot_arr + sap_iter) : seqannot;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
blastall.c:2742:84: warning: 'sap_array' may be used uninitialized in this function [-Wmaybe-uninitialized]
curr_seqalign = (num_queries > 0) ? *(sap_array + sap_iter) : seqalign;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
blastall.c:2618:18: warning: 'next_seqalign' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (seqalign) {
^
blastall.c:2895:12: warning: 'err_ticket' may be used uninitialized in this function [-Wmaybe-uninitialized]
BlastDeleteUserErrorString(err_ticket);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blastall.c:2812:18: warning: 'xml_aip' may be used uninitialized in this function [-Wmaybe-uninitialized]
BXMLPrintOutput(xml_aip, NULL, options, blast_program,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast_database, fake_bsp, other_returns, 0,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
message, mask_loc);
~~~~~~~~~~~~~~~~~~
gcc -g -o taxblast -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF taxblast_main.c \
-lblastapi -lblast -lnetblast -lncbiid1 -lncbitxc2 -lncbitool \
-lncbiobj -lncbi -lm
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from taxblast_main.c:35:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
taxblast_main.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: taxblast_main.c,v";
^~~~~
gcc -g -o idfetch -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF idfetch.c -lncbiid1 -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from idfetch.c:30:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
idfetch.c: In function 'Nlm_Main':
idfetch.c:354:46: warning: variable 'any_type' set but not used [-Wunused-but-set-variable]
found_colon = FALSE, dna_type = FALSE, any_type = FALSE;
^~~~~~~~
idfetch.c:354:28: warning: variable 'dna_type' set but not used [-Wunused-but-set-variable]
found_colon = FALSE, dna_type = FALSE, any_type = FALSE;
^~~~~~~~
idfetch.c: In function 'IdFetch_func':
idfetch.c:828:13: warning: missing braces around initializer [-Wmissing-braces]
SeqId si={SEQID_GI,0,0};
^
idfetch.c:828:13: note: (near initialization for 'si')
idfetch.c:835:10: warning: variable 'group_segs' set but not used [-Wunused-but-set-variable]
Uint1 group_segs;
^~~~~~~~~~
idfetch.c: In function 'BEGetUidsFromQuery':
idfetch.c:1089:14: warning: unused variable 'e2rp' [-Wunused-variable]
E2ReplyPtr e2rp;
^~~~
idfetch.c: In function 'IdFetch_func':
idfetch.c:937:5: warning: 'gi_state' may be used uninitialized in this function [-Wmaybe-uninitialized]
id_print_gi_state(gi_state,buf,sizeof(buf));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
idfetch.c: In function 'Nlm_Main':
idfetch.c:497:13: warning: 'type_int' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 tgi = TryGetGi( type_int, tacc, NULL, 0);
^~~
idfetch.c:500:4: warning: 'sip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqIdPrint(sip, tbuf, PRINTID_FASTA_SHORT);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -o bl2seq -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF bl2seq.c -lblastapi -lblast -lncbitool \
-lncbiid1 -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from bl2seq.c:296:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bl2seq.c: In function 'BioseqFromAccession':
bl2seq.c:331:10: warning: unused variable 'dummy_ptr' [-Wunused-variable]
char* dummy_ptr = NULL;
^~~~~~~~~
bl2seq.c:330:10: warning: unused variable 'defline' [-Wunused-variable]
char* defline = NULL;
^~~~~~~
bl2seq.c:329:10: warning: unused variable 'buf' [-Wunused-variable]
Uint1 buf[512];
^~~
bl2seq.c:328:17: warning: unused variable 'buf_length' [-Wunused-variable]
Int2 retval, buf_length=512;
^~~~~~~~~~
bl2seq.c:328:9: warning: unused variable 'retval' [-Wunused-variable]
Int2 retval, buf_length=512;
^~~~~~
bl2seq.c:327:15: warning: unused variable 'spp' [-Wunused-variable]
SeqPortPtr spp;
^~~
bl2seq.c:322:24: warning: unused variable 'number' [-Wunused-variable]
Int4 version=0, gi, number;
^~~~~~
bl2seq.c: In function 'Main_new':
bl2seq.c:803:21: warning: unused variable 'seqalign' [-Wunused-variable]
SeqAlignPtr seqalign=NULL;
^~~~~~~~
In file included from ../include/sqnutils.h:51:0,
from bl2seq.c:305:
bl2seq.c: At top level:
../include/objentgene.h:176:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
bl2seq.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bl2seq.c,v 6.89 2009/05/27 19:29:17 camacho Exp $";
^~~~~
gcc -g -o asn2gb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF asn2gb.c -lncbitool -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2gb.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2gb.c: In function 'HandleMultipleRecords':
asn2gb.c:1739:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c: In function 'CompareFlatFiles':
asn2gb.c:1184:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1191:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1216:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1242:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1245:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1250:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1253:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c: In function 'ReportDiffs':
asn2gb.c:1071:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1074:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1077:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1080:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1083:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1096:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
asn2gb.c:1290:13: warning: 'CheckOrder' defined but not used [-Wunused-function]
static void CheckOrder (
^~~~~~~~~~
asn2gb.c:967:13: warning: 'FreeUnpubAffil' defined but not used [-Wunused-function]
static void FreeUnpubAffil (
^~~~~~~~~~~~~~
asn2gb.c: In function 'Nlm_Main':
asn2gb.c:1824:9: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
sfp = SeqMgrGetDesiredFeature (entityID, 0, itemID, 0, NULL, NULL);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gb.c:1774:15: note: 'entityID' was declared here
Uint2 entityID;
^~~~~~~~
gcc -o tbl2asn -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF tbl2asn.c -lncbitool -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from tbl2asn.c:51:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
tbl2asn.c: In function 'ProcessOneAnnot':
tbl2asn.c:2533:15: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
tbl2asn.c: In function 'MakeOneRnaTitle':
tbl2asn.c:5127:22: warning: variable 'cds' set but not used [-Wunused-but-set-variable]
SeqFeatPtr cds;
^~~
tbl2asn.c: In function 'FindSingleNucleotideOrNucProtSetInBioseqInSet':
tbl2asn.c:6936:30: warning: variable 'single_result' set but not used [-Wunused-but-set-variable]
SeqEntryPtr single = NULL, single_result;
^~~~~~~~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr.h:266,
from ../include/aliparse.h:15,
from tbl2asn.c:69:
tbl2asn.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
In file included from ../include/tax3api.h:51:0,
from tbl2asn.c:72:
../include/objtax3.h:183:31: warning: 'Value_valueFree' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr ));
^~~~~~~~~~~~~~~
../include/objtax3.h:184:31: warning: 'Value_valueAsnRead' declared 'static' but never defined [-Wunused-function]
static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~
../include/objtax3.h:185:24: warning: 'Value_valueAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~
tbl2asn.c:2621:16: warning: 'ExceptionExplainsMismatch' defined but not used [-Wunused-function]
static Boolean ExceptionExplainsMismatch (CharPtr except_text)
^~~~~~~~~~~~~~~~~~~~~~~~~
tbl2asn.c: In function 'DBLinkFieldsConflict':
tbl2asn.c:2143:40: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (CompareBioProjects (cpp2[i], field1->data.ptrvalue) == 0) {
^
tbl2asn.c:2096:18: note: 'i' was declared here
Int4 i;
^
gcc -g -o gene2xml -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF gene2xml.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from gene2xml.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gene2xml.c: In function 'ProcessOneRecord':
gene2xml.c:364:9: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
gcc -g -o entrez2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF entrez2.c -lncbidesk \
-lncbiobj -lvibrant -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from entrez2.c:49:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
entrez2.c: In function 'Nlm_Main':
entrez2.c:866:12: warning: variable 'server' set but not used [-Wunused-but-set-variable]
CharPtr server = "www.ncbi.nlm.nih.gov";
^~~~~~
entrez2.c:864:12: warning: variable 'port' set but not used [-Wunused-but-set-variable]
Uint2 port = 2441;
^~~~
entrez2.c:863:12: warning: variable 'path' set but not used [-Wunused-but-set-variable]
CharPtr path = "/entrez/utils/entrez2server.fcgi";
^~~~
At top level:
entrez2.c:724:13: warning: 'AboutProc' defined but not used [-Wunused-function]
static void AboutProc (IteM i)
^~~~~~~~~
: entrez2
gcc -g -o gbseqget -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF gbseqget.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from gbseqget.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -g -o asn2all -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF asn2all.c ncbithr.o -lncbiobj -lncbi \
-lpthread
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2all.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2all.c: In function 'DoLockFarComponents':
asn2all.c:67:27: warning: variable 'stop_time' set but not used [-Wunused-but-set-variable]
time_t start_time, stop_time;
^~~~~~~~~
asn2all.c:67:15: warning: variable 'start_time' set but not used [-Wunused-but-set-variable]
time_t start_time, stop_time;
^~~~~~~~~~
gcc -o asn2asn -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF asn2asn.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from asn2asn.c:17:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -g -o asn2fsa -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF asn2fsa.c ncbithr.o \
-lncbitool -lncbiobj -lncbi -lpthread
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asn2fsa.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asn2fsa.c: In function 'AddBspToList':
asn2fsa.c:216:15: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
asn2fsa.c: In function 'DoLockFarComponents':
asn2fsa.c:406:27: warning: variable 'stop_time' set but not used [-Wunused-but-set-variable]
time_t start_time, stop_time;
^~~~~~~~~
asn2fsa.c:406:15: warning: variable 'start_time' set but not used [-Wunused-but-set-variable]
time_t start_time, stop_time;
^~~~~~~~~~
gcc -g -o asndisc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF asndisc.c ncbithr.o -lncbiid1 \
-lncbitool -lncbiobj -lncbi -lpthread
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asndisc.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asndisc.c: In function 'ProcessMultipleRecord':
asndisc.c:728:19: warning: variable 'memory_usage' set but not used [-Wunused-but-set-variable]
Boolean memory_usage = FALSE;
^~~~~~~~~~~~
asndisc.c:726:19: warning: variable 'detailed_report' set but not used [-Wunused-but-set-variable]
Boolean detailed_report = FALSE;
^~~~~~~~~~~~~~~
asndisc.c:722:19: warning: variable 'subcit' set but not used [-Wunused-but-set-variable]
SeqDescrPtr subcit = NULL;
^~~~~~
gcc -o asnmacro -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF asnmacro.c -lblastapi -lblast -lncbitool \
-lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asnmacro.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from asnmacro.c:54:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
asnmacro.c:147:20: warning: 'GlobalAlign2Seq' defined but not used [-Wunused-function]
static SeqAlignPtr GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp)
^~~~~~~~~~~~~~~
In file included from asnmacro.c:57:0:
../include/asnmacro.h:1327:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnmacro.h:1326:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnmacro.h:1325:23: warning: 'avn' defined but not used [-Wunused-variable]
static AsnValxNodePtr avn = avnx;
^~~
../include/asnmacro.h:12:15: warning: 'asnfilename' defined but not used [-Wunused-variable]
static char * asnfilename = "asnmacro.h11";
^~~~~~~~~~~
asnmacro.c: In function 'AsnIoFromOutputStream':
asnmacro.c:233:14: warning: 'aip' may be used uninitialized in this function [-Wmaybe-uninitialized]
AsnIoPtr aip;
^~~
gcc -g -o asnval -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF asnval.c ncbithr.o -lncbiobj -lncbi \
-lpthread
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from asnval.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
asnval.c: In function 'DoLockFarComponents':
asnval.c:556:27: warning: variable 'stop_time' set but not used [-Wunused-but-set-variable]
time_t start_time, stop_time;
^~~~~~~~~
asnval.c:556:15: warning: variable 'start_time' set but not used [-Wunused-but-set-variable]
time_t start_time, stop_time;
^~~~~~~~~~
asnval.c: In function 'ReportBadTaxID':
asnval.c:1049:20: warning: zero-length gnu_printf format string [-Wformat-zero-length]
sprintf (buf1, "");
^~
asnval.c:1058:20: warning: zero-length gnu_printf format string [-Wformat-zero-length]
sprintf (buf2, "");
^~
gcc -o cleanasn -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF cleanasn.c -lncbitool -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cleanasn.c:45:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cleanasn.c: In function 'JournalIsPresent':
cleanasn.c:8001:14: warning: variable 'is_issn' set but not used [-Wunused-but-set-variable]
Boolean is_issn = FALSE;
^~~~~~~
cleanasn.c: In function 'RemoveGIProc':
cleanasn.c:8305:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
cleanasn.c: In function 'ReportAsnDiffs':
cleanasn.c:2914:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c: In function 'DoGBFFReport':
cleanasn.c:5978:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:5981:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:6007:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:6036:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:6094:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:6097:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c: In function 'DoValidatorReport':
cleanasn.c:6153:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:6156:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:6184:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c: In function 'CppBasicCleanup':
cleanasn.c:8686:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8690:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8716:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8718:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8720:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8722:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8724:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8734:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
cleanasn.c:9952:13: warning: 'AccessionToGi' defined but not used [-Wunused-function]
static Int4 AccessionToGi (CharPtr string)
^~~~~~~~~~~~~
cleanasn.c:9911:16: warning: 'PvtStrToLong' defined but not used [-Wunused-function]
static Boolean PvtStrToLong (CharPtr str, Int4Ptr longval)
^~~~~~~~~~~~
cleanasn.c:7647:13: warning: 'DoUnpublishedReport' defined but not used [-Wunused-function]
static void DoUnpublishedReport (
^~~~~~~~~~~~~~~~~~~
cleanasn.c:6613:19: warning: 'DuplicateStringList' defined but not used [-Wunused-function]
static ValNodePtr DuplicateStringList (
^~~~~~~~~~~~~~~~~~~
cleanasn.c:4116:13: warning: 'FindOneCds' defined but not used [-Wunused-function]
static void FindOneCds (
^~~~~~~~~~
cleanasn.c:4096:13: warning: 'PrintSegSeqTitleAfter' defined but not used [-Wunused-function]
static void PrintSegSeqTitleAfter (
^~~~~~~~~~~~~~~~~~~~~
cleanasn.c:4076:13: warning: 'PrintSegSeqTitleBefore' defined but not used [-Wunused-function]
static void PrintSegSeqTitleBefore (
^~~~~~~~~~~~~~~~~~~~~~
cleanasn.c:4063:13: warning: 'PrintPartsTitle' defined but not used [-Wunused-function]
static void PrintPartsTitle (
^~~~~~~~~~~~~~~
cleanasn.c:3905:13: warning: 'CountParts' defined but not used [-Wunused-function]
static void CountParts (
^~~~~~~~~~
cleanasn.c:3854:13: warning: 'NormalizeSegSetTitle' defined but not used [-Wunused-function]
static void NormalizeSegSetTitle (
^~~~~~~~~~~~~~~~~~~~
cleanasn.c: In function 'RemoveFeatEvInf':
cleanasn.c:585:9: warning: 'nextqual' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (gbq != NULL) {
^
gcc -g -o insdseqget -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF insdseqget.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from insdseqget.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -g -o nps2gps -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF nps2gps.c -lncbitool -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from nps2gps.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
nps2gps.c: In function 'LclMakeOneRnaTitle':
nps2gps.c:417:22: warning: variable 'cds' set but not used [-Wunused-but-set-variable]
SeqFeatPtr cds;
^~~
nps2gps.c: In function 'LoopThroughCDSs':
nps2gps.c:910:22: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
At top level:
nps2gps.c:584:17: warning: 'MakeIdFromLocusTag' defined but not used [-Wunused-function]
static SeqIdPtr MakeIdFromLocusTag (
^~~~~~~~~~~~~~~~~~
gcc -o spidey -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF spideymain.c -lncbiid1 -lncbitool \
-lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from spideymain.c:79:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/spidey.h:103,
from spideymain.c:80:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
gcc -g -o trna2sap -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF trna2sap.c -lncbiobj -lncbi
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from trna2sap.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
trna2sap.c: In function 'ProcessOneRecord':
trna2sap.c:290:28: warning: unused variable 'entityID' [-Wunused-variable]
Uint2 datatype, entityID = 0;
^~~~~~~~
trna2sap.c: In function 'Nlm_Main':
trna2sap.c:460:12: warning: variable 'tsp' set but not used [-Wunused-but-set-variable]
T2SPtr tsp;
^~~
gcc -g -o trna2tbl -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF trna2tbl.c
trna2tbl.c: In function 'RunTrnaScan':
trna2tbl.c:142:13: warning: unused variable 'str' [-Wunused-variable]
Char str [80];
^~~
trna2tbl.c:139:13: warning: unused variable 'speed' [-Wunused-variable]
CharPtr speed;
^~~~~
trna2tbl.c:127:13: warning: unused variable 'cmmd' [-Wunused-variable]
Char cmmd [256];
^~~~
trna2tbl.c: At top level:
trna2tbl.c:232:1: warning: return type defaults to 'int' [-Wimplicit-int]
main (int argc, char *argv[])
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" cn3dmain.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from cn3dmain.c:210:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
cn3dmain.c: In function 'OpenMimeFile':
cn3dmain.c:237:5: warning: "/*" within comment [-Wcomment]
/* the Web browsers on other platforms get upset if you delete the file, */
cn3dmain.c: In function 'NetConfigureProc':
cn3dmain.c:267:13: warning: unused variable 'netCurrentlyOn' [-Wunused-variable]
Boolean netCurrentlyOn = FALSE;
^~~~~~~~~~~~~~
cn3dmain.c: In function 'Cn3D_PrintImage':
cn3dmain.c:288:10: warning: variable 'pmldVec' set but not used [-Wunused-but-set-variable]
PMLD pmldVec = NULL;
^~~~~~~
cn3dmain.c:284:11: warning: unused variable 'pdnmlFirst' [-Wunused-variable]
PDNML pdnmlFirst = NULL;
^~~~~~~~~~
cn3dmain.c: In function 'Nlm_Main':
cn3dmain.c:334:13: warning: unused variable 'netCurrentlyOn' [-Wunused-variable]
Boolean netCurrentlyOn = FALSE;
^~~~~~~~~~~~~~
At top level:
cn3dmain.c:246:25: warning: 'seqedprocs' defined but not used [-Wunused-variable]
static SeqEditViewProcs seqedprocs;
^~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF netentcf.c -o netentcf
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from ../include/vibrant.h:124,
from netentcf.c:41:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gcc -o Cn3D -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_DATE='"Aug 20 2016"' -DBUILD_TIME='"07:20:38"' -fPIE -pie -Wl,-z,relro -Wl,-z,now -I../include -L../shlib -DWIN_MOTIF cn3dmain.o -lvibnet -lncbicn3dOGL -lncbidesk \
-lddvlib -lncbimmdb -lncbiNacc -lnetentr \
-lvibrantOGL -lncbiobj -lncbi
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
install -d debian/tmp/usr/lib/arm-linux-gnueabihf
install -m 644 lib/* shlib/*.so.6.1.20120620 debian/tmp/usr/lib/arm-linux-gnueabihf
for x in ncbiacc ncbiCacc netentr; do \
rm -f debian/tmp/usr/lib/arm-linux-gnueabihf/lib$x.so.6.1.20120620 && \
ln -s libncbiNacc.so.6 \
debian/tmp/usr/lib/arm-linux-gnueabihf/lib$x.so.6 && \
ln -s libncbiNacc.so debian/tmp/usr/lib/arm-linux-gnueabihf/lib$x.so; \
done
for x in ncbicn3d vibrant; do \
rm -f debian/tmp/usr/lib/arm-linux-gnueabihf/lib$x.so.6.1.20120620 && \
ln -s lib${x}OGL.so.6 \
debian/tmp/usr/lib/arm-linux-gnueabihf/lib$x.so.6 && \
ln -s lib${x}OGL.so debian/tmp/usr/lib/arm-linux-gnueabihf/lib$x.so; \
done
rm -f debian/tmp/usr/lib/arm-linux-gnueabihf/libregexp.*
cd debian/tmp/usr/lib/arm-linux-gnueabihf && \
for f in *.so.6.1.20120620; do \
base=`basename $f .so.6.1.20120620` && \
ln -s $f $base.so.6 && \
ln -s $f $base.so; \
done
install -d debian/tmp/usr/include/ncbi
cp -LRp include/* debian/tmp/usr/include/ncbi
cd debian/tmp/usr/include/ncbi && \
rm -f FSpCompat.h FullPath.h More*.h Optimization*.h pcre*.h
find debian/tmp/usr/include -type f | xargs chmod 644
install -d debian/tmp/usr/bin
install `find build -type f -perm /111 -print` debian/tmp/usr/bin
rm -f debian/tmp/usr/bin/*test*
rm -f debian/tmp/usr/bin/*demo*
rm -f debian/tmp/usr/bin/dosimple
rm -f debian/tmp/usr/bin/ncbisort
rm -f debian/tmp/usr/bin/cdscan
rm -f debian/tmp/usr/bin/entrcmd
rm -f debian/tmp/usr/bin/blast.REAL
mv debian/tmp/usr/bin/Cn3D debian/tmp/usr/bin/Cn3D-3.0
mv debian/tmp/usr/bin/blast debian/tmp/usr/bin/blast2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
debian/rules override_dh_installdocs-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installdocs
install -m 644 config/README \
debian/libncbi6/usr/share/doc/libncbi6/README.config
install -m 644 network/nsclilib/readme \
debian/libncbi6/usr/share/doc/libncbi6/README.net-cfg
install -m 644 doc/fa2htgs/README \
debian/ncbi-tools-bin/usr/share/doc/ncbi-tools-bin/README.fa2htgs
install -m 644 sequin/README \
debian/ncbi-tools-x11/usr/share/doc/ncbi-tools-x11/README.sequin
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs -k README
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installexamples -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_link # otherwise runs too late to influence debian/installman
chmod +x debian/installman
debian/installman blast2
debian/installman blast2 blast
debian/installman ncbi-tools-bin
debian/installman ncbi-tools-x11
dh_installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_installmenu-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
chmod +x debian/makemenu
debian/makemenu debian/ncbi-tools-x11.install
debian/makemenu -v debian/ncbi-tools-bin.install
debian/makemenu -v debian/blast2.install
dh_installmenu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installmime -a
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
debian/rules override_dh_strip-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_strip -plibncbi6 --dbg-package=libncbi6-dbg
dh_strip -plibvibrant6b --dbg-package=libvibrant6b-dbg
dh_strip -Nlibncbi6 -Nlibvibrant6b
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
debian/rules override_dh_gencontrol-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_gencontrol -pblast2 -- -v1:2.2.26.20120620-12
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_gencontrol -Nblast2
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_md5sums -a
debian/rules override_dh_builddeb
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_builddeb -pncbi-rrna-data -- -Zxz -z7 -Sextreme
dh_builddeb: No packages to build.
dh_builddeb -Nncbi-rrna-data
dpkg-deb: building package 'libncbi6-dev' in '../libncbi6-dev_6.1.20120620-12_armhf.deb'.
dpkg-deb: building package 'libncbi6' in '../libncbi6_6.1.20120620-12_armhf.deb'.
dpkg-deb: building package 'libncbi6-dbg' in '../libncbi6-dbg_6.1.20120620-12_armhf.deb'.
dpkg-deb: building package 'ncbi-tools-bin-dbgsym' in '../ncbi-tools-bin-dbgsym_6.1.20120620-12_armhf.deb'.
dpkg-deb: building package 'ncbi-tools-bin' in '../ncbi-tools-bin_6.1.20120620-12_armhf.deb'.
dpkg-deb: building package 'ncbi-tools-x11-dbgsym' in '../ncbi-tools-x11-dbgsym_6.1.20120620-12_armhf.deb'.
dpkg-deb: building package 'ncbi-tools-x11' in '../ncbi-tools-x11_6.1.20120620-12_armhf.deb'.
dpkg-deb: building package 'blast2-dbgsym' in '../blast2-dbgsym_2.2.26.20120620-12_armhf.deb'.
dpkg-deb: building package 'libvibrant6b' in '../libvibrant6b_6.1.20120620-12_armhf.deb'.
dpkg-deb: building package 'blast2' in '../blast2_2.2.26.20120620-12_armhf.deb'.
dpkg-deb: building package 'libvibrant6-dev' in '../libvibrant6-dev_6.1.20120620-12_armhf.deb'.
dpkg-deb: building package 'libvibrant6b-dbg' in '../libvibrant6b-dbg_6.1.20120620-12_armhf.deb'.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../ncbi-tools6_6.1.20120620-12_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build ncbi-tools6-6.1.20120620
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160828-1642
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
ncbi-tools6_6.1.20120620-12_armhf.changes:
------------------------------------------
Format: 1.8
Date: Sat, 20 Aug 2016 10:20:38 +0300
Source: ncbi-tools6
Binary: libncbi6 libncbi6-dev libncbi6-dbg ncbi-data ncbi-rrna-data ncbi-tools-bin ncbi-tools-x11 blast2 libvibrant6b libvibrant6-dev libvibrant6b-dbg
Architecture: armhf
Version: 6.1.20120620-12
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Canberk Koç <canberkkoc@gmail.com>
Description:
blast2 - Basic Local Alignment Search Tool
libncbi6 - NCBI libraries for biology applications
libncbi6-dbg - NCBI libraries for biology applications (debugging symbols)
libncbi6-dev - NCBI libraries for biology applications (development files)
libvibrant6-dev - NCBI libraries for graphic biology applications (development file
libvibrant6b - NCBI libraries for graphic biology applications
libvibrant6b-dbg - NCBI libraries for graphic biology applications (debugging symbol
ncbi-data - Platform-independent data for the NCBI toolkit
ncbi-rrna-data - large rRNA BLAST databases distributed with the NCBI toolkit
ncbi-tools-bin - NCBI libraries for biology applications (text-based utilities)
ncbi-tools-x11 - NCBI libraries for biology applications (X-based utilities)
Changes:
ncbi-tools6 (6.1.20120620-12) unstable; urgency=medium
.
* Team upload.
* Autopkgtest added.
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
blast2-dbgsym_2.2.26.20120620-12_armhf.deb
------------------------------------------
new debian package, version 2.0.
size 571380 bytes: control archive=1384 bytes.
1109 bytes, 13 lines control
1802 bytes, 17 lines md5sums
Package: blast2-dbgsym
Source: ncbi-tools6 (6.1.20120620-12)
Version: 1:2.2.26.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 734
Depends: blast2 (= 1:2.2.26.20120620-12)
Section: debug
Priority: extra
Homepage: http://www.ncbi.nih.gov/BLAST/
Description: Debug symbols for blast2
Auto-Built-Package: debug-symbols
Build-Ids: 07ece8b2e406bf86f5a844466255654e27e99e6d 1a586da5e462c3bd5461bc9d03a9e6ff88533fba 3acf33ed895e5e8fa94d5dddb900f9e9cf280de5 4e905788e886a03847aa678d39df6e0763446308 622737ffee2a556e1cd1a1a44da0d569d9d1bb0f 683152999ab1e8ecf8d6a2332cedda107666dd3b 83ad87237b911ae5fdaa9b6af6bd1726043659d4 8a7d362564669856e9b6db815cbdf0ae6f3a4020 942edd8cd81ad9079701c272cf040a2337790951 9672d34edc291001d835b2e7609dc144310a92a4 982c1a9650ffa95ff1c2831d2c2f4b68a8c7cd0b 9a46256f087af3f5f04b9ce37679b97ba89f03cd bc1d68a998dbc65b4ca55206ad3d8733c251c3c9 bcfe536d0644dd23e375c222f9116c0dbc95296a e27aea0df044170d111dc95730460cb4cc74b5c5 e481fa2e45154c9b64c5f0f56a87a0a375b22a1f e7b3eed8f0ab84ccdc9f8fdd59538af5e6a30ddf
drwxr-xr-x root/root 0 2016-08-20 07:20 ./
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/07/
-rw-r--r-- root/root 11080 2016-08-20 07:20 ./usr/lib/debug/.build-id/07/ece8b2e406bf86f5a844466255654e27e99e6d.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/1a/
-rw-r--r-- root/root 32996 2016-08-20 07:20 ./usr/lib/debug/.build-id/1a/586da5e462c3bd5461bc9d03a9e6ff88533fba.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/3a/
-rw-r--r-- root/root 46944 2016-08-20 07:20 ./usr/lib/debug/.build-id/3a/cf33ed895e5e8fa94d5dddb900f9e9cf280de5.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/4e/
-rw-r--r-- root/root 19732 2016-08-20 07:20 ./usr/lib/debug/.build-id/4e/905788e886a03847aa678d39df6e0763446308.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/62/
-rw-r--r-- root/root 48808 2016-08-20 07:20 ./usr/lib/debug/.build-id/62/2737ffee2a556e1cd1a1a44da0d569d9d1bb0f.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/68/
-rw-r--r-- root/root 35880 2016-08-20 07:20 ./usr/lib/debug/.build-id/68/3152999ab1e8ecf8d6a2332cedda107666dd3b.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/83/
-rw-r--r-- root/root 53216 2016-08-20 07:20 ./usr/lib/debug/.build-id/83/ad87237b911ae5fdaa9b6af6bd1726043659d4.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/8a/
-rw-r--r-- root/root 9384 2016-08-20 07:20 ./usr/lib/debug/.build-id/8a/7d362564669856e9b6db815cbdf0ae6f3a4020.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/94/
-rw-r--r-- root/root 28376 2016-08-20 07:20 ./usr/lib/debug/.build-id/94/2edd8cd81ad9079701c272cf040a2337790951.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/96/
-rw-r--r-- root/root 75040 2016-08-20 07:20 ./usr/lib/debug/.build-id/96/72d34edc291001d835b2e7609dc144310a92a4.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/98/
-rw-r--r-- root/root 50292 2016-08-20 07:20 ./usr/lib/debug/.build-id/98/2c1a9650ffa95ff1c2831d2c2f4b68a8c7cd0b.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/9a/
-rw-r--r-- root/root 38952 2016-08-20 07:20 ./usr/lib/debug/.build-id/9a/46256f087af3f5f04b9ce37679b97ba89f03cd.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/bc/
-rw-r--r-- root/root 70720 2016-08-20 07:20 ./usr/lib/debug/.build-id/bc/1d68a998dbc65b4ca55206ad3d8733c251c3c9.debug
-rw-r--r-- root/root 56240 2016-08-20 07:20 ./usr/lib/debug/.build-id/bc/fe536d0644dd23e375c222f9116c0dbc95296a.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/e2/
-rw-r--r-- root/root 62804 2016-08-20 07:20 ./usr/lib/debug/.build-id/e2/7aea0df044170d111dc95730460cb4cc74b5c5.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/e4/
-rw-r--r-- root/root 49480 2016-08-20 07:20 ./usr/lib/debug/.build-id/e4/81fa2e45154c9b64c5f0f56a87a0a375b22a1f.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/debug/.build-id/e7/
-rw-r--r-- root/root 26208 2016-08-20 07:20 ./usr/lib/debug/.build-id/e7/b3eed8f0ab84ccdc9f8fdd59538af5e6a30ddf.debug
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/doc/blast2-dbgsym -> blast2
blast2_2.2.26.20120620-12_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 538772 bytes: control archive=2315 bytes.
870 bytes, 21 lines control
3180 bytes, 51 lines md5sums
185 bytes, 7 lines * postinst #!/bin/sh
160 bytes, 5 lines * postrm #!/bin/sh
Package: blast2
Source: ncbi-tools6 (6.1.20120620-12)
Version: 1:2.2.26.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1148
Depends: libncbi6 (<< 6.1.20120620.1), libncbi6 (>= 6.1.20120620), libc6 (>= 2.7)
Suggests: libvibrant6b, ncbi-rrna-data, ncbi-tools-bin, ncbi-tools-x11
Conflicts: ncbi-blast
Section: science
Priority: optional
Multi-Arch: foreign
Homepage: http://www.ncbi.nih.gov/BLAST/
Description: Basic Local Alignment Search Tool
The famous sequence alignment program. This is "official" NCBI version,
#2. The blastall executable allows you to give a nucleotide or protein
sequence to the program. It is compared against databases and a summary of
matches is returned to the user.
.
Note that databases are not included in Debian; they must be retrieved
manually.
drwxr-xr-x root/root 0 2016-08-20 07:20 ./
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/bin/
-rwxr-xr-x root/root 23044 2016-08-20 07:20 ./usr/bin/bl2seq
-rwxr-xr-x root/root 31996 2016-08-20 07:20 ./usr/bin/blast2
-rwxr-xr-x root/root 52396 2016-08-20 07:20 ./usr/bin/blastall
-rwxr-xr-x root/root 40068 2016-08-20 07:20 ./usr/bin/blastall_old
-rwxr-xr-x root/root 40028 2016-08-20 07:20 ./usr/bin/blastcl3
-rwxr-xr-x root/root 30796 2016-08-20 07:20 ./usr/bin/blastclust
-rwxr-xr-x root/root 40148 2016-08-20 07:20 ./usr/bin/blastpgp
-rwxr-xr-x root/root 13972 2016-08-20 07:20 ./usr/bin/copymat
-rwxr-xr-x root/root 10276 2016-08-20 07:20 ./usr/bin/fastacmd
-rwxr-xr-x root/root 22604 2016-08-20 07:20 ./usr/bin/formatdb
-rwxr-xr-x root/root 22444 2016-08-20 07:20 ./usr/bin/formatrpsdb
-rwxr-xr-x root/root 26940 2016-08-20 07:20 ./usr/bin/impala
-rwxr-xr-x root/root 14092 2016-08-20 07:20 ./usr/bin/makemat
-rwxr-xr-x root/root 44124 2016-08-20 07:20 ./usr/bin/megablast
-rwxr-xr-x root/root 22924 2016-08-20 07:20 ./usr/bin/rpsblast
-rwxr-xr-x root/root 26900 2016-08-20 07:20 ./usr/bin/seedtop
-rwxr-xr-x root/root 9836 2016-08-20 07:20 ./usr/bin/taxblast
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc-base/
-rw-r--r-- root/root 616 2016-08-20 07:20 ./usr/share/doc-base/blast2
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/blast2/
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/doc/blast2/README.gz -> changelog.gz
-rw-r--r-- root/root 1829 2004-05-17 15:07 ./usr/share/doc/blast2/bl2seq.html
-rw-r--r-- root/root 12158 2010-03-26 14:52 ./usr/share/doc/blast2/blast.html
-rw-r--r-- root/root 4898 2009-08-11 14:43 ./usr/share/doc/blast2/blastall.html
-rw-r--r-- root/root 8338 2005-08-24 15:20 ./usr/share/doc/blast2/blastclust.html
-rw-r--r-- root/root 16243 2008-10-02 16:01 ./usr/share/doc/blast2/blastdb.html
-rw-r--r-- root/root 25538 2006-03-02 15:40 ./usr/share/doc/blast2/blastftp.html
-rw-r--r-- root/root 23272 2004-07-19 17:20 ./usr/share/doc/blast2/blastpgp.html
-rw-r--r-- root/root 15367 2016-08-20 07:20 ./usr/share/doc/blast2/changelog.Debian.gz
-rw-r--r-- root/root 18160 2008-06-16 15:51 ./usr/share/doc/blast2/changelog.gz
-rw-r--r-- root/root 1623 2016-08-20 07:20 ./usr/share/doc/blast2/copyright
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/blast2/examples/
-rw-r--r-- root/root 1885 2009-01-12 18:48 ./usr/share/doc/blast2/examples/web_blast.pl.gz
-rw-r--r-- root/root 5664 2007-01-04 17:27 ./usr/share/doc/blast2/fastacmd.html
-rw-r--r-- root/root 2379 2004-05-17 15:07 ./usr/share/doc/blast2/filter.html
-rw-r--r-- root/root 30660 2006-08-14 14:39 ./usr/share/doc/blast2/formatdb.html
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-rw-r--r-- root/root 11256 2004-07-02 14:41 ./usr/share/doc/blast2/megablast.html
-rw-r--r-- root/root 53064 2006-03-02 15:40 ./usr/share/doc/blast2/netblast.html
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-rw-r--r-- root/root 309857 2006-04-07 13:58 ./usr/share/doc/blast2/scoring.pdf.gz
-rw-r--r-- root/root 28065 2006-03-02 15:40 ./usr/share/doc/blast2/seedtop.html
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/lintian/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 57 2016-08-20 07:20 ./usr/share/lintian/overrides/blast2
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/man/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/man/man1/bl2seq.1.gz -> blast.1.gz
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/man/man1/blast2.1.gz -> blast.1.gz
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/man/man1/blastall.1.gz -> blast.1.gz
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/man/man1/blastall_old.1.gz -> blast.1.gz
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/man/man1/blastcl3.1.gz -> blast.1.gz
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/man/man1/blastpgp.1.gz -> blast.1.gz
-rw-r--r-- root/root 549 2016-08-20 07:20 ./usr/share/man/man1/copymat.1.gz
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/man/man1/rpsblast.1.gz -> blast.1.gz
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drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/menu/
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libncbi6-dbg_6.1.20120620-12_armhf.deb
--------------------------------------
new debian package, version 2.0.
size 8106656 bytes: control archive=1600 bytes.
1402 bytes, 21 lines control
1816 bytes, 18 lines md5sums
Package: libncbi6-dbg
Source: ncbi-tools6
Version: 6.1.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8739
Depends: libncbi6 (= 6.1.20120620-12)
Recommends: gdb
Section: debug
Priority: extra
Multi-Arch: same
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
Description: NCBI libraries for biology applications (debugging symbols)
This package is useful to provide a backtrace with symbol names in a
debugger; this facilitates interpretation of core dumps, and aids in finding
logic errors in programs using the libraries in this package (or the
libraries themselves).
.
Non-programmers will likely have little use for this package. See the
libncbi6 package for more information.
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drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/libncbi6-dbg/
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/doc/libncbi6-dbg/README.gz -> changelog.gz
-rw-r--r-- root/root 15367 2016-08-20 07:20 ./usr/share/doc/libncbi6-dbg/changelog.Debian.gz
-rw-r--r-- root/root 18160 2008-06-16 15:51 ./usr/share/doc/libncbi6-dbg/changelog.gz
-rw-r--r-- root/root 1623 2016-08-20 07:20 ./usr/share/doc/libncbi6-dbg/copyright
libncbi6-dev_6.1.20120620-12_armhf.deb
--------------------------------------
new debian package, version 2.0.
size 4562084 bytes: control archive=13992 bytes.
587 bytes, 16 lines control
33875 bytes, 503 lines md5sums
Package: libncbi6-dev
Source: ncbi-tools6
Version: 6.1.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 18169
Depends: libncbi6 (= 6.1.20120620-12)
Recommends: ncbi-tools-bin
Provides: ncbi-tools-dev
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
Description: NCBI libraries for biology applications (development files)
This package supplies development versions of NCBI's non-graphical C
libraries, along with the corresponding header files.
drwxr-xr-x root/root 0 2016-08-20 07:20 ./
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drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/include/ncbi/algo/blast/core/
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libncbi6_6.1.20120620-12_armhf.deb
----------------------------------
new debian package, version 2.0.
size 3123906 bytes: control archive=72790 bytes.
627 bytes, 15 lines control
2203 bytes, 27 lines md5sums
334 bytes, 15 lines shlibs
424797 bytes, 11219 lines symbols
60 bytes, 2 lines triggers
Package: libncbi6
Source: ncbi-tools6
Version: 6.1.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9816
Depends: ncbi-data (= 6.1.20120620-12), libc6 (>= 2.15)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
Description: NCBI libraries for biology applications
The NCBI Software Development Toolkit was developed for the production and
distribution of GenBank, Entrez, BLAST, and related services by NCBI. It
allows you to read and write NCBI ASN.1 files, builds Blast or Entrez, etc.
drwxr-xr-x root/root 0 2016-08-20 07:20 ./
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libblast.so.6 -> libblast.so.6.1.20120620
-rw-r--r-- root/root 552680 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libblast.so.6.1.20120620
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libblastapi.so.6 -> libblastapi.so.6.1.20120620
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libblastcompadj.so.6 -> libblastcompadj.so.6.1.20120620
-rw-r--r-- root/root 71108 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libblastcompadj.so.6.1.20120620
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbi.so.6 -> libncbi.so.6.1.20120620
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbiCacc.so.6 -> libncbiNacc.so.6
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbiNacc.so.6 -> libncbiNacc.so.6.1.20120620
-rw-r--r-- root/root 135256 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbiNacc.so.6.1.20120620
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbiacc.so.6 -> libncbiNacc.so.6
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbicdr.so.6 -> libncbicdr.so.6.1.20120620
-rw-r--r-- root/root 105648 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbicdr.so.6.1.20120620
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbiid1.so.6 -> libncbiid1.so.6.1.20120620
-rw-r--r-- root/root 33080 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbiid1.so.6.1.20120620
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbimla.so.6 -> libncbimla.so.6.1.20120620
-rw-r--r-- root/root 49944 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbimla.so.6.1.20120620
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbimmdb.so.6 -> libncbimmdb.so.6.1.20120620
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbiobj.so.6 -> libncbiobj.so.6.1.20120620
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbitool.so.6 -> libncbitool.so.6.1.20120620
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbitxc2.so.6 -> libncbitxc2.so.6.1.20120620
-rw-r--r-- root/root 91788 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbitxc2.so.6.1.20120620
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libnetcli.so.6 -> libnetcli.so.6.1.20120620
-rw-r--r-- root/root 18184 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libnetcli.so.6.1.20120620
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libnetentr.so.6 -> libncbiNacc.so.6
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibgif.so.6 -> libvibgif.so.6.1.20120620
-rw-r--r-- root/root 124960 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibgif.so.6.1.20120620
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc-base/
-rw-r--r-- root/root 580 2016-08-20 07:20 ./usr/share/doc-base/ncbi-tools-dispatcher
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/libncbi6/
-rw-r--r-- root/root 4354 2009-10-26 15:01 ./usr/share/doc/libncbi6/FAQ.txt.gz
-rw-r--r-- root/root 5135 2016-08-20 07:20 ./usr/share/doc/libncbi6/README.config.gz
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/doc/libncbi6/README.gz -> changelog.gz
-rw-r--r-- root/root 59597 2008-06-16 15:51 ./usr/share/doc/libncbi6/README.htm
-rw-r--r-- root/root 392 2016-08-20 07:20 ./usr/share/doc/libncbi6/README.net-cfg
-rw-r--r-- root/root 94 2016-08-20 07:20 ./usr/share/doc/libncbi6/TODO.Debian
-rw-r--r-- root/root 15367 2016-08-20 07:20 ./usr/share/doc/libncbi6/changelog.Debian.gz
-rw-r--r-- root/root 18160 2008-06-16 15:51 ./usr/share/doc/libncbi6/changelog.gz
-rw-r--r-- root/root 1623 2016-08-20 07:20 ./usr/share/doc/libncbi6/copyright
-rw-r--r-- root/root 22838 2011-09-06 22:30 ./usr/share/doc/libncbi6/dispatcher.html
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/libncbi6/examples/
-rwxr-xr-x root/root 3782 2016-08-20 07:20 ./usr/share/doc/libncbi6/examples/fwd_check.sh
-rw-r--r-- root/root 5529 2001-12-12 20:36 ./usr/share/doc/libncbi6/ncbixml.txt.gz
libvibrant6-dev_6.1.20120620-12_armhf.deb
-----------------------------------------
new debian package, version 2.0.
size 1384888 bytes: control archive=4112 bytes.
617 bytes, 14 lines control
7633 bytes, 122 lines md5sums
337 bytes, 13 lines * postinst #!/bin/sh
Package: libvibrant6-dev
Source: ncbi-tools6
Version: 6.1.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5956
Depends: libglu1-mesa-dev | libglu-dev, libmotif-dev, libncbi6-dev (= 6.1.20120620-12), libvibrant6b (= 6.1.20120620-12), libxmu-dev
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
Description: NCBI libraries for graphic biology applications (development files)
Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic
biological applications.
drwxr-xr-x root/root 0 2016-08-20 07:20 ./
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/include/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/include/ncbi/
-rw-r--r-- root/root 491 1997-08-25 18:21 ./usr/include/ncbi/aacomp.h
-rw-r--r-- root/root 15032 2000-04-25 00:22 ./usr/include/ncbi/algorend.h
-rw-r--r-- root/root 4028 1997-08-25 18:21 ./usr/include/ncbi/apparam.h
-rw-r--r-- root/root 5146 2008-09-30 20:24 ./usr/include/ncbi/biosrc.h
-rw-r--r-- root/root 15659 2011-04-08 16:03 ./usr/include/ncbi/bspview.h
-rw-r--r-- root/root 6284 2010-09-21 12:54 ./usr/include/ncbi/cdrgn.h
-rw-r--r-- root/root 16040 2012-06-20 13:46 ./usr/include/ncbi/cn3d.h
-rw-r--r-- root/root 2819 1999-10-29 14:15 ./usr/include/ncbi/cn3dentr.h
-rw-r--r-- root/root 7553 2000-03-08 21:46 ./usr/include/ncbi/cn3dmain.h
-rw-r--r-- root/root 2391 1999-10-29 14:15 ./usr/include/ncbi/cn3dmesh.h
-rw-r--r-- root/root 4737 2000-04-08 00:37 ./usr/include/ncbi/cn3dmodl.h
-rw-r--r-- root/root 2408 1999-10-29 14:15 ./usr/include/ncbi/cn3dmsel.h
-rw-r--r-- root/root 8082 2000-03-18 00:06 ./usr/include/ncbi/cn3dmsg.h
-rw-r--r-- root/root 6076 2000-07-08 20:43 ./usr/include/ncbi/cn3dopen.h
-rw-r--r-- root/root 2526 2000-03-22 23:17 ./usr/include/ncbi/cn3dsave.h
-rw-r--r-- root/root 9343 2000-07-08 20:43 ./usr/include/ncbi/cn3dshim.h
-rw-r--r-- root/root 2534 2000-03-17 22:48 ./usr/include/ncbi/cn3dstyl.h
-rw-r--r-- root/root 2313 1999-10-29 14:15 ./usr/include/ncbi/cn3dxprt.h
-rw-r--r-- root/root 5320 2000-07-12 15:38 ./usr/include/ncbi/ddvclick.h
-rw-r--r-- root/root 11193 2001-01-29 20:35 ./usr/include/ncbi/ddvcreate.h
-rw-r--r-- root/root 5600 2000-07-24 22:00 ./usr/include/ncbi/ddvgraph.h
-rw-r--r-- root/root 13081 2000-07-17 13:32 ./usr/include/ncbi/ddvmain.h
-rw-r--r-- root/root 11963 2000-07-17 17:46 ./usr/include/ncbi/ddvopen.h
-rw-r--r-- root/root 9546 2000-07-12 22:22 ./usr/include/ncbi/ddvpanel.h
-rw-r--r-- root/root 2954 1997-08-25 18:55 ./usr/include/ncbi/diagnost.h
-rw-r--r-- root/root 32105 2012-05-14 19:57 ./usr/include/ncbi/dlogutil.h
-rw-r--r-- root/root 13885 2008-04-29 13:53 ./usr/include/ncbi/document.h
-rw-r--r-- root/root 3586 1999-03-17 17:05 ./usr/include/ncbi/dotmatrx.h
-rw-r--r-- root/root 10039 2001-08-08 22:47 ./usr/include/ncbi/dotviewer.h
-rw-r--r-- root/root 4672 2002-03-20 22:10 ./usr/include/ncbi/drawingp.h
-rw-r--r-- root/root 14693 2006-07-13 17:13 ./usr/include/ncbi/drawseq.h
-rw-r--r-- root/root 7216 2000-07-08 20:44 ./usr/include/ncbi/entrez.h
-rw-r--r-- root/root 5627 2002-01-23 21:24 ./usr/include/ncbi/entrez2.h
-rw-r--r-- root/root 5367 1997-09-16 21:20 ./usr/include/ncbi/fea2seg.h
-rw-r--r-- root/root 10913 1998-12-01 16:47 ./usr/include/ncbi/fstyle.h
-rw-r--r-- root/root 4593 1997-08-25 18:22 ./usr/include/ncbi/fstylep.h
-rw-r--r-- root/root 5830 1998-12-01 16:59 ./usr/include/ncbi/glbpic.h
-rw-r--r-- root/root 3123 1998-10-13 17:13 ./usr/include/ncbi/gphdraw.h
-rw-r--r-- root/root 2315 1998-09-16 19:00 ./usr/include/ncbi/gtrdraw.h
-rw-r--r-- root/root 2684 1998-09-16 19:00 ./usr/include/ncbi/gxydraw.h
-rw-r--r-- root/root 6237 1997-08-25 18:55 ./usr/include/ncbi/image.h
-rw-r--r-- root/root 3713 1998-03-31 21:22 ./usr/include/ncbi/imagelst.h
-rw-r--r-- root/root 6700 2011-08-03 19:30 ./usr/include/ncbi/import.h
-rw-r--r-- root/root 4460 2001-10-16 13:13 ./usr/include/ncbi/ingenext.h
-rw-r--r-- root/root 11155 2006-07-13 17:13 ./usr/include/ncbi/ingengraph.h
-rw-r--r-- root/root 9422 2002-01-17 19:05 ./usr/include/ncbi/ingenwin.h
-rw-r--r-- root/root 2710 1998-07-22 18:59 ./usr/include/ncbi/layout.h
-rw-r--r-- root/root 295 1997-08-25 18:22 ./usr/include/ncbi/legend.h
-rw-r--r-- root/root 7615 2012-05-18 14:27 ./usr/include/ncbi/macrodlg.h
-rw-r--r-- root/root 3359 1997-09-16 20:11 ./usr/include/ncbi/mapgene.h
-rw-r--r-- root/root 5101 1999-10-04 17:16 ./usr/include/ncbi/mappingp.h
-rw-r--r-- root/root 3887 2000-07-27 21:14 ./usr/include/ncbi/medview.h
-rw-r--r-- root/root 2781 2001-08-08 23:18 ./usr/include/ncbi/motif.h
-rw-r--r-- root/root 14796 2008-02-29 19:36 ./usr/include/ncbi/ncbidraw.h
-rw-r--r-- root/root 3304 1999-10-20 23:13 ./usr/include/ncbi/ncbigif.h
-rw-r--r-- root/root 4913 2008-02-29 19:36 ./usr/include/ncbi/ncbiport.h
-rw-r--r-- root/root 6328 1998-01-21 21:22 ./usr/include/ncbi/netscape.h
-rw-r--r-- root/root 3925 1999-06-07 15:41 ./usr/include/ncbi/odlbox.h
-rw-r--r-- root/root 4069 1997-08-25 18:56 ./usr/include/ncbi/panels.h
-rw-r--r-- root/root 9730 1997-08-25 18:56 ./usr/include/ncbi/pictur3d.h
-rw-r--r-- root/root 19940 2004-02-17 19:22 ./usr/include/ncbi/picture.h
-rw-r--r-- root/root 4750 2002-08-07 18:13 ./usr/include/ncbi/picturep.h
-rw-r--r-- root/root 5445 1998-08-12 23:04 ./usr/include/ncbi/ppict3d.h
-rw-r--r-- root/root 1086 1997-10-08 20:17 ./usr/include/ncbi/prtgene.h
-rw-r--r-- root/root 4679 2010-07-20 17:01 ./usr/include/ncbi/pubdesc.h
-rw-r--r-- root/root 2539 1998-04-01 18:17 ./usr/include/ncbi/saldist.h
-rw-r--r-- root/root 3176 2006-07-13 17:13 ./usr/include/ncbi/saled.h
-rw-r--r-- root/root 11560 2012-05-21 16:16 ./usr/include/ncbi/saledit.h
-rw-r--r-- root/root 3944 2000-07-26 17:26 ./usr/include/ncbi/salfiles.h
-rw-r--r-- root/root 3650 2003-11-20 18:36 ./usr/include/ncbi/salogif.h
-rw-r--r-- root/root 6121 2007-09-10 18:35 ./usr/include/ncbi/salpanel.h
-rw-r--r-- root/root 5066 2006-07-13 17:13 ./usr/include/ncbi/salparam.h
-rw-r--r-- root/root 2826 1997-08-25 18:24 ./usr/include/ncbi/sdisplay.h
-rw-r--r-- root/root 1240 2006-07-13 17:13 ./usr/include/ncbi/seqanal.h
-rw-r--r-- root/root 5649 2000-04-27 13:36 ./usr/include/ncbi/seqcons.h
-rw-r--r-- root/root 675 1997-08-25 18:24 ./usr/include/ncbi/seqfltr.h
-rw-r--r-- root/root 1340 2006-07-13 17:13 ./usr/include/ncbi/seqgraph.h
-rw-r--r-- root/root 1978 2006-07-13 17:13 ./usr/include/ncbi/seqgrphx.h
-rw-r--r-- root/root 1501 1997-08-25 18:24 ./usr/include/ncbi/seqmtrx.h
-rw-r--r-- root/root 2903 2010-12-06 17:16 ./usr/include/ncbi/seqpanel.h
-rw-r--r-- root/root 337 1997-08-25 18:24 ./usr/include/ncbi/seqpcc.h
-rw-r--r-- root/root 951 1998-07-06 21:20 ./usr/include/ncbi/seqscrl.h
-rw-r--r-- root/root 3740 2005-05-24 13:28 ./usr/include/ncbi/seqsub.h
-rw-r--r-- root/root 15278 2000-07-28 21:05 ./usr/include/ncbi/shim3d.h
-rw-r--r-- root/root 10669 2001-03-28 16:06 ./usr/include/ncbi/treeview.h
-rw-r--r-- root/root 4375 1999-08-12 18:31 ./usr/include/ncbi/treevint.h
-rw-r--r-- root/root 7897 2000-07-08 20:43 ./usr/include/ncbi/udvdef.h
-rw-r--r-- root/root 27253 2006-07-13 17:13 ./usr/include/ncbi/udviewer.h
-rw-r--r-- root/root 11321 2006-07-13 17:06 ./usr/include/ncbi/udvseq.h
-rw-r--r-- root/root 5896 1998-09-16 17:46 ./usr/include/ncbi/urkgraph.h
-rw-r--r-- root/root 2020 2009-04-10 15:46 ./usr/include/ncbi/valdlg.h
-rw-r--r-- root/root 23354 2011-09-20 18:38 ./usr/include/ncbi/vibdefns.h
-rw-r--r-- root/root 317 1997-10-09 21:02 ./usr/include/ncbi/vibfltr.h
-rw-r--r-- root/root 23853 2011-09-20 18:41 ./usr/include/ncbi/vibforms.h
-rw-r--r-- root/root 1616 1997-12-15 21:19 ./usr/include/ncbi/vibgraph.h
-rw-r--r-- root/root 20306 2008-02-29 19:36 ./usr/include/ncbi/vibincld.h
-rw-r--r-- root/root 2505 2006-12-13 17:26 ./usr/include/ncbi/vibmain.h
-rw-r--r-- root/root 8697 2004-04-01 13:43 ./usr/include/ncbi/vibmouse.h
-rw-r--r-- root/root 264 1997-10-01 13:30 ./usr/include/ncbi/vibpcc.h
-rw-r--r-- root/root 49398 2011-09-20 18:38 ./usr/include/ncbi/vibprocs.h
-rw-r--r-- root/root 5489 1999-05-06 21:23 ./usr/include/ncbi/vibrant.h
-rw-r--r-- root/root 25957 2008-04-29 13:43 ./usr/include/ncbi/vibrgb.h
-rw-r--r-- root/root 241 1997-09-29 17:36 ./usr/include/ncbi/vibtree.h
-rw-r--r-- root/root 12888 1998-03-22 03:01 ./usr/include/ncbi/vibtypes.h
-rw-r--r-- root/root 7758 2002-03-20 22:10 ./usr/include/ncbi/viewer.h
-rw-r--r-- root/root 15567 2000-01-11 01:16 ./usr/include/ncbi/viewer3d.h
-rw-r--r-- root/root 3373 1997-11-19 17:38 ./usr/include/ncbi/viewerp.h
-rw-r--r-- root/root 4721 2007-10-18 15:18 ./usr/include/ncbi/vsm.h
-rw-r--r-- root/root 3664 2010-01-22 16:26 ./usr/include/ncbi/vsmfile.h
-rw-r--r-- root/root 4127 2006-07-13 17:13 ./usr/include/ncbi/vsmpriv.h
-rw-r--r-- root/root 6743 2011-10-05 14:46 ./usr/include/ncbi/vsmutil.h
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 110016 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libddvlib.a
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libddvlib.so -> libddvlib.so.6.1.20120620
-rw-r--r-- root/root 209642 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbicn3d.a
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbicn3d.so -> libncbicn3dOGL.so
-rw-r--r-- root/root 217074 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbicn3dOGL.a
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbicn3dOGL.so -> libncbicn3dOGL.so.6.1.20120620
-rw-r--r-- root/root 2764788 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbidesk.a
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbidesk.so -> libncbidesk.so.6.1.20120620
-rw-r--r-- root/root 150308 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibgif.a
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibgif.so -> libvibgif.so.6.1.20120620
-rw-r--r-- root/root 124702 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibnet.a
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibnet.so -> libvibnet.so.6.1.20120620
-rw-r--r-- root/root 773442 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibrant.a
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibrant.so -> libvibrantOGL.so
-rw-r--r-- root/root 818978 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibrantOGL.a
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibrantOGL.so -> libvibrantOGL.so.6.1.20120620
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/doc/libvibrant6-dev/
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/doc/libvibrant6-dev/README.gz -> changelog.gz
-rw-r--r-- root/root 15367 2016-08-20 07:20 ./usr/share/doc/libvibrant6-dev/changelog.Debian.gz
-rw-r--r-- root/root 18160 2008-06-16 15:51 ./usr/share/doc/libvibrant6-dev/changelog.gz
-rw-r--r-- root/root 1623 2016-08-20 07:20 ./usr/share/doc/libvibrant6-dev/copyright
libvibrant6b-dbg_6.1.20120620-12_armhf.deb
------------------------------------------
new debian package, version 2.0.
size 3374012 bytes: control archive=1091 bytes.
1055 bytes, 22 lines control
768 bytes, 8 lines md5sums
Package: libvibrant6b-dbg
Source: ncbi-tools6
Version: 6.1.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3694
Depends: libvibrant6b (= 6.1.20120620-12)
Recommends: gdb
Suggests: libncbi6-dbg (= 6.1.20120620-12)
Section: debug
Priority: extra
Multi-Arch: same
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
Description: NCBI libraries for graphic biology applications (debugging symbols)
This package is useful to provide a backtrace with symbol names in a
debugger; this facilitates interpretation of core dumps, and aids in finding
logic errors in programs using the libraries in this package (or the
libraries themselves).
.
Non-programmers will likely have little use for this package. See the
libvibrant6b package for more information.
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/doc/libvibrant6b-dbg/README.gz -> changelog.gz
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-rw-r--r-- root/root 18160 2008-06-16 15:51 ./usr/share/doc/libvibrant6b-dbg/changelog.gz
-rw-r--r-- root/root 1623 2016-08-20 07:20 ./usr/share/doc/libvibrant6b-dbg/copyright
libvibrant6b_6.1.20120620-12_armhf.deb
--------------------------------------
new debian package, version 2.0.
size 1054450 bytes: control archive=17350 bytes.
821 bytes, 17 lines control
752 bytes, 9 lines md5sums
136 bytes, 5 lines shlibs
90901 bytes, 2449 lines symbols
60 bytes, 2 lines triggers
Package: libvibrant6b
Source: ncbi-tools6
Version: 6.1.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2811
Depends: libncbi6 (<< 6.1.20120620.1), libncbi6 (>= 6.1.20120620), libc6 (>= 2.11), libgl1-mesa-glx | libgl1, libglu1-mesa | libglu1, libpng16-16 (>= 1.6.2-1), libx11-6, libxm4 (>= 2.3.4), libxmu6, libxt6
Conflicts: libvibrant6, libvibrant6a
Replaces: libvibrant6, libvibrant6a
Section: libs
Priority: optional
Multi-Arch: same
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
Description: NCBI libraries for graphic biology applications
This is the library for those who just want to run Vibrant applications.
It also includes a wrapper (vibrate) that allows many NCBI applications to
provide a GUI for selecting options.
drwxr-xr-x root/root 0 2016-08-20 07:20 ./
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libddvlib.so.6 -> libddvlib.so.6.1.20120620
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbicn3d.so.6 -> libncbicn3dOGL.so.6
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libncbicn3dOGL.so.6 -> libncbicn3dOGL.so.6.1.20120620
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibnet.so.6 -> libvibnet.so.6.1.20120620
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibrant.so.6 -> libvibrantOGL.so.6
lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/lib/arm-linux-gnueabihf/libvibrantOGL.so.6 -> libvibrantOGL.so.6.1.20120620
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/doc/libvibrant6b/README.gz -> changelog.gz
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ncbi-tools-bin-dbgsym_6.1.20120620-12_armhf.deb
-----------------------------------------------
new debian package, version 2.0.
size 1074700 bytes: control archive=2320 bytes.
1854 bytes, 13 lines control
3710 bytes, 35 lines md5sums
Package: ncbi-tools-bin-dbgsym
Source: ncbi-tools6
Version: 6.1.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1377
Depends: ncbi-tools-bin (= 6.1.20120620-12)
Section: debug
Priority: extra
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
Description: Debug symbols for ncbi-tools-bin
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/doc/ncbi-tools-bin-dbgsym -> ncbi-tools-bin
ncbi-tools-bin_6.1.20120620-12_armhf.deb
----------------------------------------
new debian package, version 2.0.
size 415044 bytes: control archive=3291 bytes.
926 bytes, 20 lines control
5285 bytes, 85 lines md5sums
185 bytes, 7 lines * postinst #!/bin/sh
160 bytes, 5 lines * postrm #!/bin/sh
Package: ncbi-tools-bin
Source: ncbi-tools6
Version: 6.1.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1512
Depends: libncbi6 (<< 6.1.20120620.1), libncbi6 (>= 6.1.20120620), libc6 (>= 2.7)
Suggests: blast2, libvibrant6b, ncbi-tools-x11
Breaks: libncbi6-dev (<< 6.1.20110713-3~)
Replaces: libncbi6-dev (<< 6.1.20110713-3~)
Section: science
Priority: optional
Multi-Arch: foreign
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
Description: NCBI libraries for biology applications (text-based utilities)
This package includes various utilities distributed with the NCBI C SDK,
including the development tools asntool and errhdr (formerly of
libncbi6-dev). None of the programs in this package require X; you can
find the X-based utilities in the ncbi-tools-x11 package. BLAST and
related tools are in a separate package (blast2).
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ncbi-tools-x11-dbgsym_6.1.20120620-12_armhf.deb
-----------------------------------------------
new debian package, version 2.0.
size 2204360 bytes: control archive=791 bytes.
665 bytes, 13 lines control
636 bytes, 6 lines md5sums
Package: ncbi-tools-x11-dbgsym
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Version: 6.1.20120620-12
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Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2457
Depends: ncbi-tools-x11 (= 6.1.20120620-12)
Section: debug
Priority: extra
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
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ncbi-tools-x11_6.1.20120620-12_armhf.deb
----------------------------------------
new debian package, version 2.0.
size 986862 bytes: control archive=2369 bytes.
789 bytes, 17 lines control
4069 bytes, 55 lines md5sums
194 bytes, 8 lines * postinst #!/bin/sh
68 bytes, 5 lines * prerm #!/bin/sh
Package: ncbi-tools-x11
Source: ncbi-tools6
Version: 6.1.20120620-12
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2391
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Suggests: blast2, ncbi-tools-bin
Section: science
Priority: optional
Multi-Arch: foreign
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
Description: NCBI libraries for biology applications (X-based utilities)
This package includes some X-based utilities distributed with the
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drwxr-xr-x root/root 0 2016-08-20 07:20 ./
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lrwxrwxrwx root/root 0 2016-08-20 07:20 ./usr/share/doc/ncbi-tools-x11/README.gz -> changelog.gz
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drwxr-xr-x root/root 0 2016-08-20 07:20 ./usr/share/man/
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Build Architecture: armhf
Build-Space: 689028
Build-Time: 9026
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 518
Job: ncbi-tools6_6.1.20120620-12
Machine Architecture: armhf
Package: ncbi-tools6
Package-Time: 9621
Source-Version: 6.1.20120620-12
Space: 689028
Status: successful
Version: 6.1.20120620-12
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Finished at 20160828-1642
Build needed 02:40:21, 689028k disc space