ncbi-tools6 →
6.1.20170106-4 →
armhf → 2018-06-28 06:48:26
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| ncbi-tools6 6.1.20170106-4 (armhf) Thu, 28 Jun 2018 05:59:57 +0000 |
+==============================================================================+
Package: ncbi-tools6
Version: 6.1.20170106-4
Source Version: 6.1.20170106-4
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-cdbb983e-e947-4c11-9fb3-f139978a0608' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.8 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.6 MB]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
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:
https://salsa.debian.org/med-team/ncbi-tools6.git
Please use:
git clone https://salsa.debian.org/med-team/ncbi-tools6.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 157 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main ncbi-tools6 6.1.20170106-4 (dsc) [2784 B]
Get:2 http://172.17.0.1/private buster-staging/main ncbi-tools6 6.1.20170106-4 (tar) [156 MB]
Get:3 http://172.17.0.1/private buster-staging/main ncbi-tools6 6.1.20170106-4 (diff) [1509 kB]
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I: NOTICE: Log filtering will replace 'build/ncbi-tools6-DtPwQL/ncbi-tools6-6.1.20170106' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ncbi-tools6-DtPwQL' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-F56az9/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-F56az9/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-F56az9/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-F56az9/apt_archive ./ InRelease
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Get:3 copy:/<<BUILDDIR>>/resolver-F56az9/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-F56az9/apt_archive ./ Sources [349 B]
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Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 19 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-F56az9/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 15728 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), csh | c-shell, libglu1-mesa-dev | libglu-dev, libgnutls28-dev | gnutls-dev, libmotif-dev, libpcre3-dev, libpng-dev, libxmu-dev
Filtered Build-Depends: debhelper (>= 11~), csh, libglu1-mesa-dev, libgnutls28-dev, libmotif-dev, libpcre3-dev, libpng-dev, libxmu-dev
dpkg-deb: building package 'sbuild-build-depends-ncbi-tools6-dummy' in '/<<BUILDDIR>>/resolver-F56az9/apt_archive/sbuild-build-depends-ncbi-tools6-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-ncbi-tools6-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-F56az9/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-F56az9/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-F56az9/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-F56az9/apt_archive ./ Sources [559 B]
Get:5 copy:/<<BUILDDIR>>/resolver-F56az9/apt_archive ./ Packages [618 B]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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 packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libnss-systemd
libpam-systemd libsasl2-modules libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils csh debhelper
dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config
fonts-dejavu-core gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libbsd0 libcroco3 libdrm-amdgpu1 libdrm-dev
libdrm-etnaviv1 libdrm-exynos1 libdrm-freedreno1 libdrm-nouveau2
libdrm-omap1 libdrm-radeon1 libdrm-tegra0 libedit2 libegl-mesa0 libegl1
libelf1 libevent-2.1-6 libexpat1-dev libfile-stripnondeterminism-perl
libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev libgbm1
libgl1 libgl1-mesa-dev libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa
libgles2 libglib2.0-0 libglu1-mesa libglu1-mesa-dev libglvnd-core-dev
libglvnd-dev libglvnd0 libglx-mesa0 libglx0 libgmp-dev libgmpxx4ldbl
libgnutls-dane0 libgnutls-openssl27 libgnutls28-dev libgnutlsxx28
libgraphite2-3 libharfbuzz0b libice-dev libice6 libicu-le-hb0 libicu60
libidn2-0-dev libidn2-dev libjpeg62-turbo libllvm6.0 libmagic-mgc libmagic1
libmotif-common libmotif-dev libmrm4 libopengl0 libp11-kit-dev libpcre16-3
libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpng-dev
libpthread-stubs0-dev libsensors4 libsigsegv2 libsm-dev libsm6
libtasn1-6-dev libtimedate-perl libtool libuil4 libunbound2
libwayland-client0 libwayland-server0 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 nettle-dev pkg-config po-debconf ucf uil uuid-dev
x11-common x11proto-core-dev x11proto-damage-dev x11proto-dev
x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-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 gmp-doc
libgmp10-doc libmpfr-dev dns-root-data gnutls-doc gnutls-bin libice-doc
lm-sensors libsm-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
libxcb-doc libxext-doc libxt-doc m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libpng-tools libtasn1-doc libltdl-dev libx11-doc
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils csh debhelper
dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config
fonts-dejavu-core gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libbsd0 libcroco3 libdrm-amdgpu1 libdrm-dev
libdrm-etnaviv1 libdrm-exynos1 libdrm-freedreno1 libdrm-nouveau2
libdrm-omap1 libdrm-radeon1 libdrm-tegra0 libedit2 libegl-mesa0 libegl1
libelf1 libevent-2.1-6 libexpat1-dev libfile-stripnondeterminism-perl
libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev libgbm1
libgl1 libgl1-mesa-dev libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa
libgles2 libglib2.0-0 libglu1-mesa libglu1-mesa-dev libglvnd-core-dev
libglvnd-dev libglvnd0 libglx-mesa0 libglx0 libgmp-dev libgmpxx4ldbl
libgnutls-dane0 libgnutls-openssl27 libgnutls28-dev libgnutlsxx28
libgraphite2-3 libharfbuzz0b libice-dev libice6 libicu-le-hb0 libicu60
libidn2-0-dev libidn2-dev libjpeg62-turbo libllvm6.0 libmagic-mgc libmagic1
libmotif-common libmotif-dev libmrm4 libopengl0 libp11-kit-dev libpcre16-3
libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpng-dev
libpthread-stubs0-dev libsensors4 libsigsegv2 libsm-dev libsm6
libtasn1-6-dev libtimedate-perl libtool libuil4 libunbound2
libwayland-client0 libwayland-server0 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 nettle-dev pkg-config po-debconf
sbuild-build-depends-ncbi-tools6-dummy ucf uil uuid-dev x11-common
x11proto-core-dev x11proto-damage-dev x11proto-dev x11proto-dri2-dev
x11proto-fixes-dev x11proto-gl-dev x11proto-xext-dev
x11proto-xf86vidmode-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
0 upgraded, 168 newly installed, 0 to remove and 19 not upgraded.
Need to get 45.1 MB/61.0 MB of archives.
After this operation, 338 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-F56az9/apt_archive ./ sbuild-build-depends-ncbi-tools6-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmotif-common all 2.3.8-2 [40.3 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.5-1 [292 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.5-1 [683 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.0-5 [280 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.0-5 [325 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libxm4 armhf 2.3.8-2 [820 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libmrm4 armhf 2.3.8-2 [81.5 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libuil4 armhf 2.3.8-2 [137 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-3 [234 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-3 [106 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-3 [64.7 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libedit2 armhf 3.1-20180525-1 [70.6 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libgnutls-openssl27 armhf 3.5.18-1 [202 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf csh armhf 20110502-3 [223 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.4 [160 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.4 [980 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libdrm-amdgpu1 armhf 2.4.92-1+rpi1 [27.0 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libdrm-radeon1 armhf 2.4.92-1+rpi1 [28.8 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libdrm-nouveau2 armhf 2.4.92-1+rpi1 [24.4 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libdrm-omap1 armhf 2.4.92-1+rpi1 [16.0 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libdrm-freedreno1 armhf 2.4.92-1+rpi1 [25.2 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libdrm-exynos1 armhf 2.4.92-1+rpi1 [19.0 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libdrm-tegra0 armhf 2.4.92-1+rpi1 [15.4 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libdrm-etnaviv1 armhf 2.4.92-1+rpi1 [20.0 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libdrm-dev armhf 2.4.92-1+rpi1 [212 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libwayland-server0 armhf 1.15.0-2 [25.8 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libgbm1 armhf 18.1.2-1 [60.0 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libglapi-mesa armhf 18.1.2-1 [69.9 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libwayland-client0 armhf 1.15.0-2 [21.0 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libx11-xcb1 armhf 2:1.6.5-1 [185 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libxshmfence1 armhf 1.3-1 [8636 B]
Get:58 http://172.17.0.1/private buster-staging/main armhf libegl-mesa0 armhf 18.1.2-1 [109 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libglvnd0 armhf 1.0.0+git20180308-3 [53.1 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libegl1 armhf 1.0.0+git20180308-3 [27.6 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libfreetype6-dev armhf 2.8.1-2 [2594 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf uuid-dev armhf 2.32-0.1 [91.3 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libfontconfig1-dev armhf 2.13.0-5 [922 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libllvm6.0 armhf 1:6.0-3+rpi1 [12.5 MB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libsensors4 armhf 1:3.4.0-4+b1 [50.4 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libgl1-mesa-dri armhf 18.1.2-1 [4515 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libglx-mesa0 armhf 18.1.2-1 [158 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libglx0 armhf 1.0.0+git20180308-3 [24.6 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libgl1 armhf 1.0.0+git20180308-3 [104 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf x11proto-dev all 2018.4-4 [251 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf x11proto-core-dev all 2018.4-4 [3128 B]
Get:74 http://172.17.0.1/private buster-staging/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.4 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:78 http://172.17.0.1/private buster-staging/main armhf libxcb1-dev armhf 1.13-1 [168 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libx11-dev armhf 2:1.6.5-1 [754 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf mesa-common-dev armhf 18.1.2-1 [579 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libglvnd-core-dev armhf 1.0.0+git20180308-3 [13.1 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libgles2 armhf 1.0.0+git20180308-3 [20.8 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libopengl0 armhf 1.0.0+git20180308-3 [38.9 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libglvnd-dev armhf 1.0.0+git20180308-3 [5008 B]
Get:85 http://172.17.0.1/private buster-staging/main armhf libx11-xcb-dev armhf 2:1.6.5-1 [187 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libxcb-dri3-dev armhf 1.13-1 [100 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libxcb-randr0 armhf 1.13-1 [108 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libxcb-render0-dev armhf 1.13-1 [110 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libxcb-randr0-dev armhf 1.13-1 [112 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libxcb-shape0 armhf 1.13-1 [98.5 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libxcb-shape0-dev armhf 1.13-1 [99.8 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libxcb-xfixes0-dev armhf 1.13-1 [104 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libxcb-sync-dev armhf 1.13-1 [103 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libxcb-present-dev armhf 1.13-1 [99.7 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libxshmfence-dev armhf 1.3-1 [8224 B]
Get:96 http://172.17.0.1/private buster-staging/main armhf libxcb-dri2-0-dev armhf 1.13-1 [101 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libxcb-glx0-dev armhf 1.13-1 [119 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf x11proto-fixes-dev all 1:2018.4-4 [3140 B]
Get:99 http://172.17.0.1/private buster-staging/main armhf libxfixes-dev armhf 1:5.0.3-1 [22.7 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf x11proto-damage-dev all 1:2018.4-4 [3140 B]
Get:101 http://172.17.0.1/private buster-staging/main armhf libxdamage-dev armhf 1:1.1.4-3 [13.9 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf x11proto-xext-dev all 2018.4-4 [3128 B]
Get:103 http://172.17.0.1/private buster-staging/main armhf libxext-dev armhf 2:1.3.3-1+b2 [102 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf x11proto-xf86vidmode-dev all 2018.4-4 [3140 B]
Get:105 http://172.17.0.1/private buster-staging/main armhf libxxf86vm-dev armhf 1:1.1.4-1+b2 [24.9 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf x11proto-dri2-dev all 2018.4-4 [3132 B]
Get:107 http://172.17.0.1/private buster-staging/main armhf x11proto-gl-dev all 2018.4-4 [3124 B]
Get:108 http://172.17.0.1/private buster-staging/main armhf libgl1-mesa-dev armhf 18.1.2-1 [44.1 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libgl1-mesa-glx armhf 18.1.2-1 [43.4 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libglu1-mesa-dev armhf 9.0.0-2.1 [169 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libgmpxx4ldbl armhf 2:6.1.2+dfsg-3 [21.8 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libgmp-dev armhf 2:6.1.2+dfsg-3 [562 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libunbound2 armhf 1.7.3-1 [381 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libgnutls-dane0 armhf 3.5.18-1 [202 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libgnutlsxx28 armhf 3.5.18-1 [11.9 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf nettle-dev armhf 3.4-1 [1077 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libtasn1-6-dev armhf 4.13-3 [96.8 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libp11-kit-dev armhf 0.23.12-2 [186 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf libidn2-dev armhf 2.0.4-1.1 [73.6 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf libidn2-0-dev armhf 2.0.4-1.1 [17.8 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf libgnutls28-dev armhf 3.5.18-1 [767 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf libice-dev armhf 2:1.0.9-2 [58.8 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf libxrender-dev armhf 1:0.9.10-1 [37.7 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libxft-dev armhf 2.3.2-2 [60.3 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf libsm-dev armhf 2:1.2.2-1+b3 [33.4 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libxt-dev armhf 1:1.1.5-1 [390 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf uil armhf 2.3.8-2 [38.4 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf libmotif-dev armhf 2.3.8-2 [2238 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-9 [234 kB]
Get:130 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-9 [226 kB]
Get:131 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-9 [150 kB]
Get:132 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-9 [561 kB]
Get:133 http://172.17.0.1/private buster-staging/main armhf libxmu-headers all 2:1.1.2-2 [51.9 kB]
Get:134 http://172.17.0.1/private buster-staging/main armhf libxmu-dev armhf 2:1.1.2-2 [56.2 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libbsd0:armhf.
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Unpacking libbsd0:armhf (0.9.1-1) ...
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Unpacking bsdmainutils (11.1.2) ...
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Unpacking groff-base (1.22.3-10) ...
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Setting up x11-common (1:7.7+19) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of restart.
Selecting previously unselected package libmotif-common.
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Unpacking libmotif-common (2.3.8-2) ...
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Unpacking libxcb1:armhf (1.13-1) ...
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Selecting previously unselected package libx11-6:armhf.
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Unpacking libx11-6:armhf (2:1.6.5-1) ...
Selecting previously unselected package libfreetype6:armhf.
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Unpacking libfreetype6:armhf (2.8.1-2) ...
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Moving old data out of the way
Unpacking ucf (3.0038) ...
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Unpacking fonts-dejavu-core (2.37-1) ...
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Unpacking fontconfig-config (2.13.0-5) ...
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Unpacking libfontconfig1:armhf (2.13.0-5) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
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Unpacking libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Selecting previously unselected package libxext6:armhf.
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Unpacking libxext6:armhf (2:1.3.3-1+b2) ...
Selecting previously unselected package libxrender1:armhf.
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Unpacking libxrender1:armhf (1:0.9.10-1) ...
Selecting previously unselected package libxft2:armhf.
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Unpacking libxft2:armhf (2.3.2-2) ...
Selecting previously unselected package libice6:armhf.
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Unpacking libice6:armhf (2:1.0.9-2) ...
Selecting previously unselected package libsm6:armhf.
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Unpacking libsm6:armhf (2:1.2.2-1+b3) ...
Selecting previously unselected package libxt6:armhf.
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Selecting previously unselected package libxm4:armhf.
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Unpacking libmagic-mgc (1:5.33-3) ...
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Unpacking gettext-base (0.19.8.1-6) ...
Selecting previously unselected package libedit2:armhf.
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Selecting previously unselected package libevent-2.1-6:armhf.
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Selecting previously unselected package libgnutls-openssl27:armhf.
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Selecting previously unselected package libelf1:armhf.
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Selecting previously unselected package libglib2.0-0:armhf.
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Unpacking libglib2.0-0:armhf (2.56.1-2) ...
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Unpacking gettext (0.19.8.1-6) ...
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Selecting previously unselected package libdrm-etnaviv1:armhf.
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Selecting previously unselected package libwayland-server0:armhf.
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Unpacking libgbm1:armhf (18.1.2-1) ...
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Setting up libpcre32-3:armhf (2:8.39-9) ...
Setting up libdrm-radeon1:armhf (2.4.92-1+rpi1) ...
Setting up libpcre16-3:armhf (2:8.39-9) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libdrm-nouveau2:armhf (2.4.92-1+rpi1) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up csh (20110502-3) ...
update-alternatives: using /bin/bsd-csh to provide /bin/csh (csh) in auto mode
Setting up libgmpxx4ldbl:armhf (2:6.1.2+dfsg-3) ...
Setting up libidn2-dev:armhf (2.0.4-1.1) ...
Setting up libglvnd-core-dev:armhf (1.0.0+git20180308-3) ...
Setting up libidn2-0-dev (2.0.4-1.1) ...
Setting up libx11-data (2:1.6.5-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up autopoint (0.19.8.1-6) ...
Setting up libwayland-server0:armhf (1.15.0-2) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.042-1) ...
Setting up libedit2:armhf (3.1-20180525-1) ...
Setting up libgmp-dev:armhf (2:6.1.2+dfsg-3) ...
Setting up x11proto-dri2-dev (2018.4-4) ...
Setting up libsm6:armhf (2:1.2.2-1+b3) ...
Setting up libunbound2:armhf (1.7.3-1) ...
Setting up libpcre3-dev:armhf (2:8.39-9) ...
Setting up fontconfig-config (2.13.0-5) ...
Installing new version of config file /etc/fonts/fonts.conf ...
Setting up x11proto-core-dev (2018.4-4) ...
Setting up libxshmfence-dev:armhf (1.3-1) ...
Setting up libdrm-dev:armhf (2.4.92-1+rpi1) ...
Setting up x11proto-fixes-dev (1:2018.4-4) ...
Setting up libgbm1:armhf (18.1.2-1) ...
Setting up libharfbuzz0b:armhf (1.7.6-1+b1) ...
Setting up x11proto-xf86vidmode-dev (2018.4-4) ...
Setting up libxau-dev:armhf (1:1.0.8-1+b2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.33-3) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up libice-dev:armhf (2:1.0.9-2) ...
Setting up libgnutls-dane0:armhf (3.5.18-1) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up nettle-dev:armhf (3.4-1) ...
Setting up libpng-dev:armhf (1.6.34-1) ...
Setting up libxcb1:armhf (1.13-1) ...
Setting up libtool (2.4.6-2.1) ...
Setting up libxcb-present0:armhf (1.13-1) ...
Setting up libfontconfig1:armhf (2.13.0-5) ...
Setting up libxcb-dri2-0:armhf (1.13-1) ...
Setting up libxcb-dri3-0:armhf (1.13-1) ...
Setting up libsm-dev:armhf (2:1.2.2-1+b3) ...
Setting up libxcb-glx0:armhf (1.13-1) ...
Setting up libxcb-randr0:armhf (1.13-1) ...
Setting up libxcb-xfixes0:armhf (1.13-1) ...
Setting up libxcb-render0:armhf (1.13-1) ...
Setting up libx11-6:armhf (2:1.6.5-1) ...
Setting up libgnutls28-dev:armhf (3.5.18-1) ...
Setting up libxcb-sync1:armhf (1.13-1) ...
Setting up libfreetype6-dev:armhf (2.8.1-2) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxcb-shape0:armhf (1.13-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libxcb1-dev:armhf (1.13-1) ...
Setting up libxcb-glx0-dev:armhf (1.13-1) ...
Setting up libegl-mesa0:armhf (18.1.2-1) ...
Setting up libx11-dev:armhf (2:1.6.5-1) ...
Setting up libxft2:armhf (2.3.2-2) ...
Setting up libxcb-sync-dev:armhf (1.13-1) ...
Setting up libfontconfig1-dev:armhf (2.13.0-5) ...
Setting up libx11-xcb-dev:armhf (2:1.6.5-1) ...
Setting up libxt-dev:armhf (1:1.1.5-1) ...
Setting up mesa-common-dev:armhf (18.1.2-1) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libxfixes3:armhf (1:5.0.3-1) ...
Setting up libxmu-headers (2:1.1.2-2) ...
Setting up libxrender-dev:armhf (1:0.9.10-1) ...
Setting up libxmu6:armhf (2:1.1.2-2) ...
Setting up libxcb-dri2-0-dev:armhf (1.13-1) ...
Setting up libxcb-render0-dev:armhf (1.13-1) ...
Setting up libegl1:armhf (1.0.0+git20180308-3) ...
Setting up libxft-dev:armhf (2.3.2-2) ...
Setting up libxcb-dri3-dev:armhf (1.13-1) ...
Setting up libxext-dev:armhf (2:1.3.3-1+b2) ...
Setting up libxm4:armhf (2.3.8-2) ...
Setting up libxcb-shape0-dev:armhf (1.13-1) ...
Setting up libxxf86vm1:armhf (1:1.1.4-1+b2) ...
Setting up libxxf86vm-dev:armhf (1:1.1.4-1+b2) ...
Setting up libxfixes-dev:armhf (1:5.0.3-1) ...
Setting up libxcb-randr0-dev:armhf (1.13-1) ...
Setting up libxdamage1:armhf (1:1.1.4-3) ...
Setting up libxmu-dev:armhf (2:1.1.2-2) ...
Setting up libxcb-xfixes0-dev:armhf (1.13-1) ...
Setting up libmrm4:armhf (2.3.8-2) ...
Setting up libxdamage-dev:armhf (1:1.1.4-3) ...
Setting up libuil4:armhf (2.3.8-2) ...
Setting up libxcb-present-dev:armhf (1.13-1) ...
Setting up uil (2.3.8-2) ...
Setting up libmotif-dev:armhf (2.3.8-2) ...
Setting up dh-autoreconf (19) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libllvm6.0:armhf (1:6.0-3+rpi1) ...
Setting up gettext (0.19.8.1-6) ...
Setting up libgl1-mesa-dri:armhf (18.1.2-1) ...
Installing new version of config file /etc/drirc ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libglx-mesa0:armhf (18.1.2-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libglx0:armhf (1.0.0+git20180308-3) ...
Setting up debhelper (11.3.4) ...
Setting up dh-strip-nondeterminism (0.042-1) ...
Setting up libgl1:armhf (1.0.0+git20180308-3) ...
Setting up libglu1-mesa:armhf (9.0.0-2.1) ...
Setting up libglvnd-dev:armhf (1.0.0+git20180308-3) ...
Setting up libgl1-mesa-dev:armhf (18.1.2-1) ...
Setting up libgl1-mesa-glx:armhf (18.1.2-1) ...
Setting up libglu1-mesa-dev:armhf (9.0.0-2.1) ...
Setting up sbuild-build-depends-ncbi-tools6-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.30-21+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 linux-libc-dev_4.16.12-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3 binutils_2.30-21+rpi1 binutils-arm-linux-gnueabihf_2.30-21+rpi1 binutils-common_2.30-21+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.3.0-3+rpi1 cpp-7_7.3.0-19 csh_20110502-3 dash_0.5.8-2.10 dbus_1.12.8-3 dbus-user-session_1.12.8-3 debconf_1.5.67 debhelper_11.3.4 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.8-1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 e2fsprogs-l10n_1.44.2-1 fakeroot_1.22-2 fdisk_2.32-0.1 file_1:5.33-3 findutils_4.6.0+git+20171230-2 fontconfig-config_2.13.0-5 fonts-dejavu-core_2.37-1 g++_4:7.3.0-3+rpi1 g++-7_7.3.0-19 gcc_4:7.3.0-3+rpi1 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_4.9.4-2+rpi1+b7 gcc-5-base_5.5.0-8 gcc-7_7.3.0-19 gcc-7-base_7.3.0-19 gcc-8-base_8.1.0-8+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.8-1 gnupg-agent_2.2.8-1 gnupg-l10n_2.2.8-1 gnupg-utils_2.2.8-1 gpg_2.2.8-1 gpg-agent_2.2.8-1 gpg-wks-client_2.2.8-1 gpg-wks-server_2.2.8-1 gpgconf_2.2.8-1 gpgsm_2.2.8-1 gpgv_2.2.8-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-19 libassuan0_2.5.1-2 libatomic1_8.1.0-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-21+rpi1 libblkid1_2.32-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-8+rpi1 libcilkrts5_7.3.0-19 libcom-err2_1.44.2-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.8-3 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-amdgpu1_2.4.92-1+rpi1 libdrm-common_2.4.92-1+rpi1 libdrm-dev_2.4.92-1+rpi1 libdrm-etnaviv1_2.4.92-1+rpi1 libdrm-exynos1_2.4.92-1+rpi1 libdrm-freedreno1_2.4.92-1+rpi1 libdrm-nouveau2_2.4.92-1+rpi1 libdrm-omap1_2.4.92-1+rpi1 libdrm-radeon1_2.4.92-1+rpi1 libdrm-tegra0_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libedit2_3.1-20180525-1 libegl-mesa0_18.1.2-1 libegl1_1.0.0+git20180308-3 libelf1_0.170-0.4 libevent-2.1-6_2.1.8-stable-4 libexpat1_2.2.5-3 libexpat1-dev_2.2.5-3 libext2fs2_1.44.2-1 libfakeroot_1.22-2 libfdisk1_2.32-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfontconfig1_2.13.0-5 libfontconfig1-dev_2.13.0-5 libfreetype6_2.8.1-2 libfreetype6-dev_2.8.1-2 libgbm1_18.1.2-1 libgcc-7-dev_7.3.0-19 libgcc1_1:8.1.0-8+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgl1_1.0.0+git20180308-3 libgl1-mesa-dev_18.1.2-1 libgl1-mesa-dri_18.1.2-1 libgl1-mesa-glx_18.1.2-1 libglapi-mesa_18.1.2-1 libgles2_1.0.0+git20180308-3 libglib2.0-0_2.56.1-2 libglu1-mesa_9.0.0-2.1 libglu1-mesa-dev_9.0.0-2.1 libglvnd-core-dev_1.0.0+git20180308-3 libglvnd-dev_1.0.0+git20180308-3 libglvnd0_1.0.0+git20180308-3 libglx-mesa0_18.1.2-1 libglx0_1.0.0+git20180308-3 libgmp-dev_2:6.1.2+dfsg-3 libgmp10_2:6.1.2+dfsg-3 libgmpxx4ldbl_2:6.1.2+dfsg-3 libgnutls-dane0_3.5.18-1 libgnutls-openssl27_3.5.18-1 libgnutls28-dev_3.5.18-1 libgnutls30_3.5.18-1 libgnutlsxx28_3.5.18-1 libgomp1_8.1.0-8+rpi1 libgpg-error0_1.31-1 libgraphite2-3_1.3.11-2 libharfbuzz0b_1.7.6-1+b1 libhogweed4_3.4-1 libice-dev_2:1.0.9-2 libice6_2:1.0.9-2 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libidn2-0-dev_2.0.4-1.1 libidn2-dev_2.0.4-1.1 libip4tc0_1.6.2-1 libisl19_0.19-1 libjpeg62-turbo_1:1.5.2-2+b1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 libllvm6.0_1:6.0-3+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmotif-common_2.3.8-2 libmotif-dev_2.3.8-2 libmount1_2.32-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libmrm4_2.3.8-2 libncurses5_6.1+20180210-4 libncurses6_6.1+20180210-4 libncursesw5_6.1+20180210-4 libncursesw6_6.1+20180210-4 libnettle6_3.4-1 libnpth0_1.5-4 libnss-systemd_238-4 libopengl0_1.0.0+git20180308-3 libp11-kit-dev_0.23.12-2 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpcre16-3_2:8.39-9 libpcre3_2:8.39-9 libpcre3-dev_2:8.39-9 libpcre32-3_2:8.39-9 libpcrecpp0v5_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-6 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng-dev_1.6.34-1 libpng16-16_1.6.34-1 libprocps7_2:3.3.15-2 libpthread-stubs0-dev_0.3-4 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-2 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsensors4_1:3.4.0-4+b1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsm-dev_2:1.2.2-1+b3 libsm6_2:1.2.2-1+b3 libsmartcols1_2.32-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.2-1 libssl1.1_1.1.0h-4 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 libsystemd0_238-4 libtasn1-6_4.13-3 libtasn1-6-dev_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4 libtinfo6_6.1+20180210-4 libtool_2.4.6-2.1 libubsan0_7.3.0-19 libudev1_238-4 libuil4_2.3.8-2 libunbound2_1.7.3-1 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32-0.1 libwayland-client0_1.15.0-2 libwayland-server0_1.15.0-2 libx11-6_2:1.6.5-1 libx11-data_2:1.6.5-1 libx11-dev_2:1.6.5-1 libx11-xcb-dev_2:1.6.5-1 libx11-xcb1_2:1.6.5-1 libxau-dev_1:1.0.8-1+b2 libxau6_1:1.0.8-1+b2 libxcb-dri2-0_1.13-1 libxcb-dri2-0-dev_1.13-1 libxcb-dri3-0_1.13-1 libxcb-dri3-dev_1.13-1 libxcb-glx0_1.13-1 libxcb-glx0-dev_1.13-1 libxcb-present-dev_1.13-1 libxcb-present0_1.13-1 libxcb-randr0_1.13-1 libxcb-randr0-dev_1.13-1 libxcb-render0_1.13-1 libxcb-render0-dev_1.13-1 libxcb-shape0_1.13-1 libxcb-shape0-dev_1.13-1 libxcb-sync-dev_1.13-1 libxcb-sync1_1.13-1 libxcb-xfixes0_1.13-1 libxcb-xfixes0-dev_1.13-1 libxcb1_1.13-1 libxcb1-dev_1.13-1 libxdamage-dev_1:1.1.4-3 libxdamage1_1:1.1.4-3 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.3-1+b2 libxext6_2:1.3.3-1+b2 libxfixes-dev_1:5.0.3-1 libxfixes3_1:5.0.3-1 libxft-dev_2.3.2-2 libxft2_2.3.2-2 libxm4_2.3.8-2 libxml2_2.9.4+dfsg1-7 libxmu-dev_2:1.1.2-2 libxmu-headers_2:1.1.2-2 libxmu6_2:1.1.2-2 libxrender-dev_1:0.9.10-1 libxrender1_1:0.9.10-1 libxshmfence-dev_1.3-1 libxshmfence1_1.3-1 libxt-dev_1:1.1.5-1 libxt6_1:1.1.5-1 libxxf86vm-dev_1:1.1.4-1+b2 libxxf86vm1_1:1.1.4-1+b2 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.12-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mesa-common-dev_18.1.2-1 mount_2.32-0.1 multiarch-support_2.27-3+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180210-4 ncurses-bin_6.1+20180210-4 netbase_5.4 nettle-dev_3.4-1 openssl_1.1.0h-4 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-6 perl-base_5.26.2-6 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-6 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ncbi-tools6-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 ucf_3.0038 udev_238-4 uil_2.3.8-2 util-linux_2.32-0.1 uuid-dev_2.32-0.1 x11-common_1:7.7+19 x11proto-core-dev_2018.4-4 x11proto-damage-dev_1:2018.4-4 x11proto-dev_2018.4-4 x11proto-dri2-dev_2018.4-4 x11proto-fixes-dev_1:2018.4-4 x11proto-gl-dev_2018.4-4 x11proto-xext-dev_2018.4-4 x11proto-xf86vidmode-dev_2018.4-4 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Jun 26 01:48:13 2018 UTC
gpgv: using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./ncbi-tools6_6.1.20170106-4.dsc
dpkg-source: info: extracting ncbi-tools6 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking ncbi-tools6_6.1.20170106.orig.tar.gz
dpkg-source: info: unpacking ncbi-tools6_6.1.20170106-4.debian.tar.xz
dpkg-source: info: applying debian-changes
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-cdbb983e-e947-4c11-9fb3-f139978a0608
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package ncbi-tools6
dpkg-buildpackage: info: source version 6.1.20170106-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build ncbi-tools6-6.1.20170106
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from ncbi-tools6-6.1.20170106/debian/source/options: --single-debian-patch
debian/rules clean
dh clean
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 binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" GNUTLS_INCLUDE=-DHAVE_LIBGNUTLS 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 -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_lbos.h .
./ln-if-absent ../connect/ncbi_lbosp.h .
./ln-if-absent ../connect/parson.h .
./ln-if-absent ../connect/ncbi_lbsm.h .
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../connect/ncbi_lbsm_ipc.h .
makefile:686: 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:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/compr/*.h ../include
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libindx/*.c .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libindx/*.h ../include
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libpars/*.c .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libpars/*.h ../include
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/*.c .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/*.dat .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideochr*.h ../include
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideoorgs.h .
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.c .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.dat .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.h ../include
set: No match.
makefile:686: 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 -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:61,
from ncbithr.c:289:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:310:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbimath.c: In function 'general_lngamma':
ncbimath.c:230:5: warning: 'y[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
++y[0];
~^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:46:
/usr/include/features.h:184:3: 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 -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:184:3: 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:2966:58: 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 -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:184:3: 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 -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:184:3: 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 -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:83:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:565:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
asndebin.c:568:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
if (atp == NULL)
^~
asndebin.c:634:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* empty sequence written */
^~~~
asndebin.c:636:7: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:45:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:54:
/usr/include/features.h:184:3: 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:698:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* use alternative write function */
^~~~
asnio.c:701:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:52:
/usr/include/features.h:184:3: 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:198:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((token == END_STRUCT) && ((isa == SEQ_TYPE) || (isa == SET_TYPE)))
^~
asnlex.c:201:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (token != IDENT)
^~
asnlex.c: In function 'AsnTxtReadVal':
asnlex.c:345:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* empty sequence written */
^~~~
asnlex.c:347:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
while (atp2 != NULL)
^~~~~
At top level:
asnlex.c:1290:13: 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 -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:184:3: 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 -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:184:3: 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 were 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 were 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 were 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 were 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 -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:184:3: 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:1774:7: warning: variable 'isa' set but not used [-Wunused-but-set-variable]
Int2 isa;
^~~
asnprint.c: In function 'AsnPrintModuleXMLInc':
asnprint.c:2095:10: 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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:61,
from ncbithrs.c:289:
/usr/include/features.h:184:3: 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 -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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:75:
/usr/include/features.h:184:3: 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:440:50: 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:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:116:12: 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:2572:73: 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:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:208:12: 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 's_CreateOnTop':
ncbi_socket.c:4435:35: 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:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:130:12: 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:4471:43: 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:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:116:12: 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_CreateListening':
ncbi_socket.c:4865:48: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
error = getsockname(x_lsock, &addr.sa, &addrlen) != 0
^
In file included from ncbi_socketp.h:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:116:12: 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:5105:49: 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:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:232:12: 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_RecvMsg':
ncbi_socket.c:5409:52: 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:269:0,
from ncbi_socketp.h:54,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/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,
^~~~~~~~
ncbi_socket.c: In function 'TRIGGER_Create':
ncbi_socket.c:5661:18: warning: unused variable 'x_id' [-Wunused-variable]
unsigned int x_id = ++s_ID_Counter;
^~~~
ncbi_socket.c: In function 'DSOCK_Bind':
ncbi_socket.c:7390:51: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
error = getsockname(sock->sock, &addr.sa, &addrlen) != 0
^
In file included from ncbi_socketp.h:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:116:12: 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,
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_buffer.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_buffer.c:33:
/usr/include/features.h:184:3: 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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:61,
from ncbi_priv.c:33:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:61,
from ncbi_connection.c:34:
/usr/include/features.h:184:3: 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 -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:61,
from ncbi_connector.c:34:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:61,
from ncbi_heapmgr.c:115:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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 -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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:49:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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 -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 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_lbos.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_lbos.c:36:
/usr/include/features.h:184:3: 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_lbos.c: In function 's_LBOS_ReadLbosresolver':
ncbi_lbos.c:756:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (s_LBOS_Lbosresolver == NULL)
^~
ncbi_lbos.c:759:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
s_LBOS_Lbosresolver = strdup(str + 7);
^~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF parson.c
parson.c: In function 'remove_comments':
parson.c:281:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for (i = 0; i < (ptr - string) + end_token_len; i++)
^~~
parson.c:283:12: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
string = ptr + end_token_len - 1;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_ipv6.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_ipv6.c:33:
/usr/include/features.h:184:3: 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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 ncbi_lbos.o parson.o ncbi_ipv6.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 -fPIC -D_PNG -I../include -DWIN_MOTIF -DHAVE_LIBGNUTLS ncbi_gnutls.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_gnutls.c:33:
/usr/include/features.h:184:3: 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_gnutls.c: In function 's_GnuTlsCreate':
ncbi_gnutls.c:293:5: warning: 'gnutls_connection_end_t' is deprecated [-Wdeprecated-declarations]
gnutls_connection_end_t end = (side == eSOCK_Client
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ncbi_gnutls.c:35:0:
ncbi_gnutls.c: In function 's_GnuTlsInit':
ncbi_priv.h:217:33: warning: 'version' may be used uninitialized in this function [-Wmaybe-uninitialized]
_mess.message = NcbiMessagePlusError(&_mess.dynamic, \
^~~~~~~~~~~~~~~~~~~~
ncbi_gnutls.c:582:17: note: 'version' was declared here
const char* version;
^~~~~~~
rm -f libconnssl.a
ar cru libconnssl.a ncbi_gnutls.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libconnssl.a ../lib
ranlib ../lib/libconnssl.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:65:
/usr/include/features.h:184:3: 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:140:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:143:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (lsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objacces.c: In function 'LinkSetAsnRead':
objacces.c:216:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:219:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
lsp = LinkSetNew();
^~~
objacces.c:220:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (lsp == NULL)
^~
objacces.c:223:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objacces.c:226:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:228:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:184:3: 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:597:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:600:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
sap = SeqAlignNew();
^~~
objalign.c:601:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sap == NULL)
^~
objalign.c:604:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'DenseDiagAsnWrite':
objalign.c:1020:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1023:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ddp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c: In function 'DenseDiagAsnRead':
objalign.c:1112:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1115:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ddp = DenseDiagNew();
^~~
objalign.c:1116:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ddp == NULL)
^~
objalign.c:1119:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'DenseSegAsnWrite':
objalign.c:1268:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1271:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (dsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c: In function 'DenseSegAsnRead':
objalign.c:1374:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1377:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
dsp = DenseSegNew();
^~~
objalign.c:1378:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dsp == NULL)
^~
objalign.c:1381:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'StdSegAsnWrite':
objalign.c:1559:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1562:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c:1581:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! SeqLocSetAsnWrite(ssp->loc, aip, STD_SEG_loc, STD_SEG_loc_E))
^~
objalign.c:1584:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ssp->scores != NULL)
^~
objalign.c: In function 'StdSegAsnRead':
objalign.c:1626:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1629:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ssp = StdSegNew();
^~~
objalign.c:1630:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ssp == NULL)
^~
objalign.c:1633:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'SeqAlignSetAsnWrite':
objalign.c:1704:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1708:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
oldsap = sap;
^~~~~~
objalign.c: In function 'PackSegAsnWrite':
objalign.c:1892:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1895:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (psp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c:1926:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnCloseStruct(aip, PACKED_SEG_starts, (Pointer)psp->starts))
^~
objalign.c:1929:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
av.ptrvalue = psp->present;
^~
objalign.c: In function 'PackSegAsnRead':
objalign.c:1999:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:2002:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
psp = PackSegNew();
^~~
objalign.c:2003:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (psp == NULL)
^~
objalign.c:2006:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'SplicedSegAsnRead':
objalign.c:2179:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseSegAsnRead':
objalign.c:2422:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedExonAsnRead':
objalign.c:2614:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedSegModifierFree':
objalign.c:2875:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'ProductPosFree':
objalign.c:3050:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'SplicedExonChunkFree':
objalign.c:3225:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'SpliceSiteAsnRead':
objalign.c:3469:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'ProtPosAsnRead':
objalign.c:3626:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseAlignAsnRead':
objalign.c:3798:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseSegExtAsnRead':
objalign.c:4020:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedSegModifierAsnRead':
objalign.c:2955:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objalign.c: In function 'SplicedExonChunkAsnRead':
objalign.c:3326:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objalign.c: In function 'ProductPosAsnRead':
objalign.c:3130:16: 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 -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:184:3: 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 -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:113:
/usr/include/features.h:184:3: 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:208:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:211:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
afp = AffilNew();
^~~
objbibli.c: In function 'AffilAsnWrite':
objbibli.c:296:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:299:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (afp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'AuthListFree':
objbibli.c:458:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (alp->affil != NULL)
^~
objbibli.c:460:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return (AuthListPtr)MemFree(alp);
^~~~~~
objbibli.c: In function 'AuthListAsnRead':
objbibli.c:489:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:492:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
alp = AuthListNew();
^~~
objbibli.c: In function 'AuthListAsnWrite':
objbibli.c:583:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:586:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (alp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:590:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)alp)) /* open AuthList SEQUENCE */
^~
objbibli.c:593:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
av.ptrvalue = alp->names;
^~
objbibli.c: In function 'AuthorFree':
objbibli.c:677:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ap->affil != NULL)
^~
objbibli.c:679:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return (AuthorPtr)MemFree(ap);
^~~~~~
objbibli.c: In function 'AuthorAsnRead':
objbibli.c:707:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:710:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ap = AuthorNew();
^~
objbibli.c: In function 'AuthorAsnWrite':
objbibli.c:779:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:782:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ap == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitArtAsnRead':
objbibli.c:925:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:928:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cap = CitArtNew();
^~~
objbibli.c: In function 'CitArtAsnWrite':
objbibli.c:1027:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1030:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cap == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1034:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)cap)) /* open the SEQUENCE */
^~
objbibli.c:1037:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cap->title != NULL)
^~
objbibli.c: In function 'ImprintAsnRead':
objbibli.c:1152:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1155:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ip = ImprintNew();
^~
objbibli.c: In function 'ImprintAsnWrite':
objbibli.c:1251:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1254:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitRetractAsnRead':
objbibli.c:1391:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1394:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
crp = CitRetractNew();
^~~
objbibli.c: In function 'CitRetractAsnWrite':
objbibli.c:1445:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1448:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (crp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitJourAsnRead':
objbibli.c:1524:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1527:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cjp = CitJourNew();
^~~
objbibli.c: In function 'CitJourAsnWrite':
objbibli.c:1576:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1579:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cjp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1585:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! ImprintAsnWrite(cjp->imp, aip, CIT_JOUR_imp))
^~
objbibli.c:1587:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cjp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitBookAsnRead':
objbibli.c:1676:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1679:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cbp = CitBookNew();
^~~
objbibli.c: In function 'CitBookAsnWrite':
objbibli.c:1744:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1747:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1760:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! ImprintAsnWrite(cbp->imp, aip, CIT_BOOK_imp))
^~
objbibli.c:1762:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cbp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitProcAsnWrite':
objbibli.c:1879:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1882:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1901:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnCloseStruct(aip, CIT_PROC_meet, (Pointer)cpp->otherdata))
^~
objbibli.c:1903:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cpp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitLetAsnWrite':
objbibli.c:1995:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1998:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (clp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitPatAsnRead':
objbibli.c:2091:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2094:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cpp = CitPatNew();
^~~
objbibli.c: In function 'CitPatAsnWrite':
objbibli.c:2213:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2216:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'IdPatAsnRead':
objbibli.c:2346:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2349:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
idp = IdPatNew();
^~~
objbibli.c: In function 'IdPatAsnWrite':
objbibli.c:2412:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2415:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (idp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitGenAsnRead':
objbibli.c:2546:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2549:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cgp = CitGenNew();
^~~
objbibli.c: In function 'CitGenAsnWrite':
objbibli.c:2627:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2630:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cgp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'TitleAsnWrite':
objbibli.c:2825:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2828:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (tp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitSubFree':
objbibli.c:2909:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (csp == NULL)
^~
objbibli.c:2912:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
AuthListFree(csp->authors);
^~~~~~~~~~~~
objbibli.c: In function 'CitSubAsnRead':
objbibli.c:2943:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2946:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
csp = CitSubNew();
^~~
objbibli.c:2958:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2961:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (atp == CIT_SUB_imp)
^~
objbibli.c: In function 'CitSubAsnWrite':
objbibli.c:3029:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3032:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (csp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:3038:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AuthListAsnWrite(csp->authors, aip, CIT_SUB_authors))
^~
objbibli.c:3041:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (csp->imp != NULL)
^~
objbibli.c: In function 'PatPrioritySetAsnRead':
objbibli.c:3694:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ppp == NULL)
^~
objbibli.c:3697:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (head == NULL)
^~
objbibli.c:3715:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3717:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ppp->date = DateAsnRead(aip, atp);
^~~
objbibli.c: In function 'PatPrioritySetAsnWrite':
objbibli.c:3755:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, set, (Pointer)ppp)) /* open the SEQUENCE OF */
^~
objbibli.c:3758:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
for (tmp = ppp; tmp != NULL; tmp = tmp->next)
^~~
objbibli.c: In function 'ArticleIdAsnRead':
objbibli.c:3849:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3852:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
aidp = ArticleIdNew();
^~~~
objbibli.c: In function 'ArticleIdAsnWrite':
objbibli.c:3925:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3928:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (aidp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'PubStatusDateAsnRead':
objbibli.c:4039:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:4042:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
psdp = PubStatusDateNew();
^~~~
objbibli.c: In function 'PubStatusDateAsnWrite':
objbibli.c:4091:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:4094:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:184:3: 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:1500:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ExperimentSupportAsnRead':
objfeat.c:1748:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ProgramIdAsnRead':
objfeat.c:1933:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'EvidenceBasisAsnRead':
objfeat.c:2103:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'InferenceSupportAsnRead':
objfeat.c:2267:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ModelEvidenceItemAsnRead':
objfeat.c:2483:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SeqFeatSupportAsnRead':
objfeat.c:2688:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAQualAsnRead':
objfeat.c:4244:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAQualSetAsnRead':
objfeat.c:4396:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAGenAsnRead':
objfeat.c:4524:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'GeneNomenclatureAsnRead':
objfeat.c:4707:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'OrgNameMatch':
objfeat.c:5957:28: warning: self-comparison always evaluates to false [-Wtautological-compare]
|| onp2->mgcode != onp2->mgcode
^~
objfeat.c: In function 'TaxElementAsnWrite':
objfeat.c:7399:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)tep))
^~
objfeat.c:7402:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
av.intvalue = (Int4)(tep->fixed_level);
^~
objfeat.c: In function 'PCRPrimerAsnRead':
objfeat.c:8276:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRPrimerSetAsnRead':
objfeat.c:8421:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRReactionAsnRead':
objfeat.c:8542:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRReactionSetAsnRead':
objfeat.c:8685:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneRefAsnRead':
objfeat.c:8812:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneSeqSetAsnRead':
objfeat.c:9005:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneSeqAsnRead':
objfeat.c:9135:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SomaticOriginAsnRead':
objfeat.c:9487:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SomaticOriginConditionAsnRead':
objfeat.c:9566:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'VariationRefAsnRead':
objfeat.c:9645:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_loss_of_heterozygosityAsnRead':
objfeat.c:10687:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_frameshiftAsnRead':
objfeat.c:10765:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'VarRefDataFree':
objfeat.c:10865:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'VarRefDataSetAsnRead':
objfeat.c:10918:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_elementFree':
objfeat.c:11112:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'VariationInstAsnRead':
objfeat.c:11241:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: At top level:
objfeat.c:11393:1: warning: "/*" within comment [-Wcomment]
/**************************************************
objfeat.c: In function 'VariantPropertiesAsnRead':
objfeat.c:11422:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PhenotypeAsnRead':
objfeat.c:11746:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PopulationDataAsnRead':
objfeat.c:11945:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ExtLocAsnRead':
objfeat.c:12161:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Seq_seqFree':
objfeat.c:12327:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'DeltaItemAsnRead':
objfeat.c:12360:16: 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 -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:184:3: 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 were 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 were guarded by the 'if'
if (dp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'DateAsnRead':
objgen.c:494:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:497:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
dp = DateNew();
^~
objgen.c:498:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dp == NULL)
^~
objgen.c:501:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */
^~
objgen.c: In function 'DbtagFree':
objgen.c:752:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt == NULL)
^~
objgen.c:755:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
dbt->tag = ObjectIdFree(dbt->tag);
^~~
objgen.c: In function 'DbtagAsnRead':
objgen.c:784:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:787:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
dbt = DbtagNew();
^~~
objgen.c:788:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt == NULL)
^~
objgen.c:791:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */
^~
objgen.c:799:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt->tag == NULL)
^~
objgen.c:802:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
atp = AsnReadId(aip, amp, atp); if (atp == NULL) goto erret; /* END_STRUCT */
^~~
objgen.c: In function 'DbtagAsnWrite':
objgen.c:833:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:836:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (dbt == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'ObjectIdAsnRead':
objgen.c:980:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:983:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */
^~
objgen.c:989:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oid == NULL)
^~
objgen.c:991:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (atp == OBJECT_ID_id)
^~
objgen.c: In function 'ObjectIdAsnWrite':
objgen.c:1024:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1027:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (oid == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'NameStdFree':
objgen.c:1174:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (nsp == NULL)
^~
objgen.c:1177:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
for (i = 0; i < 7; i++)
^~~
objgen.c: In function 'NameStdAsnRead':
objgen.c:1208:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1211:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
nsp = NameStdNew();
^~~
objgen.c:1212:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (nsp == NULL)
^~
objgen.c:1215:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */
^~
objgen.c: In function 'NameStdAsnWrite':
objgen.c:1271:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1274:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (nsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'PersonIdFree':
objgen.c:1368:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pid == NULL)
^~
objgen.c:1371:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (pid->choice == 1) /* Dbtag */
^~
objgen.c: In function 'PersonIdAsnWrite':
objgen.c:1464:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1467:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (pid == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'IntFuzzAsnRead':
objgen.c:1682:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1685:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ifp = IntFuzzNew();
^~~
objgen.c:1686:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ifp == NULL)
^~
objgen.c:1689:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE (nothing) */
^~
objgen.c: In function 'UserFieldAsnRead':
objgen.c:1944:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1947:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ufp = UserFieldNew();
^~~
objgen.c: In function 'UserObjectAsnRead':
objgen.c:2434:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:2437:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
uop = UserObjectNew();
^~~
objgen.c:2438:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (uop == NULL)
^~
objgen.c:2441:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:88,
from objloc.c:43:
/usr/include/features.h:184:3: 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 were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqIdAsnRead':
objloc.c:443:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:446:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
anp = ValNodeNew(NULL);
^~~
objloc.c: In function 'SeqIdDup':
objloc.c:587:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oldid == NULL)
^~
objloc.c:590:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
newid = ValNodeNew(NULL);
^~~~~
objloc.c: In function 'SeqIdSetAsnRead':
objloc.c:752:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, atp, &av) <= 0) /* end struct */
^~
objloc.c:754:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (first == NULL)
^~
objloc.c: In function 'SeqIdSetAsnWrite':
objloc.c:786:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp2 == NULL)
^~
objloc.c:789:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, settype); goto erret; }
^~
objloc.c: In function 'TextSeqIdAsnWrite':
objloc.c:864:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:867:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (tsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'TextSeqIdAsnRead':
objloc.c:934:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:937:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
tsip = TextSeqIdNew();
^~~~
objloc.c:938:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (tsip == NULL)
^~
objloc.c:941:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PatentSeqIdAsnWrite':
objloc.c:1018:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1021:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (psip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PatentSeqIdAsnRead':
objloc.c:1068:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1071:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
psip = PatentSeqIdNew();
^~~~
objloc.c:1072:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (psip == NULL)
^~
objloc.c:1075:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'GiimAsnWrite':
objloc.c:1151:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1154:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (gip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'GiimAsnRead':
objloc.c:1216:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (gip == NULL)
^~
objloc.c:1219:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PDBSeqIdAsnWrite':
objloc.c:1305:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1308:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (pdbsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PDBSeqIdAsnRead':
objloc.c:1374:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1377:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
pdbsip = PDBSeqIdNew();
^~~~~~
objloc.c:1378:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pdbsip == NULL)
^~
objloc.c:1381:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'SeqLocAsnWrite':
objloc.c:1528:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1531:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocAsnRead':
objloc.c:1624:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1627:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
anp = ValNodeNew(NULL);
^~~
objloc.c:1628:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (anp == NULL)
^~
objloc.c:1631:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the CHOICE value (nothing) */
^~
objloc.c: In function 'SeqLocMixAsnWrite':
objloc.c:1738:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1741:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocEquivAsnWrite':
objloc.c:1805:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1808:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocSetAsnWrite':
objloc.c:1873:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp2 == NULL)
^~
objloc.c:1876:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, set); goto erret; }
^~
objloc.c: In function 'SeqLocSetAsnRead':
objloc.c:1940:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, atp, &av) <= 0) /* read END_STRUCT */
^~
objloc.c:1942:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (first == NULL)
^~
objloc.c: In function 'SeqIntAsnWrite':
objloc.c:2022:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2025:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (sip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqIntAsnRead':
objloc.c:2095:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2098:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
sip = SeqIntNew();
^~~
objloc.c:2099:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sip == NULL)
^~
objloc.c:2102:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PackSeqIntAsnWrite':
objloc.c:2179:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2181:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
oldsip = sip;
^~~~~~
objloc.c:2185:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)oldsip))
^~
objloc.c:2187:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
for ( ;sip != NULL; sip = sip->next)
^~~
objloc.c: In function 'SeqPntAsnWrite':
objloc.c:2309:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2312:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (spp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqPntAsnRead':
objloc.c:2374:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2377:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
spp = SeqPntNew();
^~~
objloc.c:2378:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (spp == NULL)
^~
objloc.c:2381:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PackSeqPntAsnWrite':
objloc.c:2479:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2482:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (pspp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PackSeqPntAsnRead':
objloc.c:2553:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2556:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
pspp = PackSeqPntNew();
^~~~
objloc.c:2557:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pspp == NULL)
^~
objloc.c:2560:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'SeqBondAsnWrite':
objloc.c:2724:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2727:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqBondAsnRead':
objloc.c:2776:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2779:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
sbp = SeqBondNew();
^~~
objloc.c:2780:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sbp == NULL)
^~
objloc.c:2783:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:104:
/usr/include/features.h:184:3: 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:248:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objmedli.c:251:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
mmp = MedlineMeshNew();
^~~
objmedli.c: In function 'DocRefFree':
objmedli.c:1190:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (drp == NULL)
^~
objmedli.c:1193:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:125:
/usr/include/features.h:184:3: 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:831:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, settype, &av) <= 0) /* read START_STRUCT */
^~
objpub.c:834:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (settype == PUB_SET_pub)
^~
objpub.c:901:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, settype, &av) <= 0) /* read END_STRUCT for SET OF */
^~
objpub.c:903:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL)
^~
objpub.c: In function 'PubLabelUnique':
objpub.c:1360:17: warning: unused variable 'pmid' [-Wunused-variable]
Int4 muid = 0, pmid = 0;
^~~~
objpub.c:1360:7: warning: unused variable 'muid' [-Wunused-variable]
Int4 muid = 0, pmid = 0;
^~~~
objpub.c: In function 'PubSetAsnRead':
objpub.c:876:13: warning: 'func' may be used uninitialized in this function [-Wmaybe-uninitialized]
pnt = (* func)(aip, atp);
~~~~^~~~~~~~~~~~~~~~~~~~
objpub.c:887:25: 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 -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:84:
/usr/include/features.h:184:3: 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 -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:184:3: 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:339:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmFinalDataAsnRead':
objscoremat.c:548:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmParametersAsnRead':
objscoremat.c:766:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmWithParametersAsnRead':
objscoremat.c:946:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'BlockPropertyAsnRead':
objscoremat.c:1113:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'CoreBlockAsnRead':
objscoremat.c:1289:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'LoopConstraintAsnRead':
objscoremat.c:1480:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'CoreDefAsnRead':
objscoremat.c:1646:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'FormatRpsDbParametersAsnRead':
objscoremat.c:1817:16: 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 -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:184:3: 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:1609:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objseq.c: In function 'SeqGapAsnRead':
objseq.c:1764:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objseq.c: In function 'SeqDescrAsnWriteExtra':
objseq.c:2035:48: 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:4841:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:4843:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
break;
^~~~~
objseq.c:4849:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:4851:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
break;
^~~~~
objseq.c: In function 'AnnotDescAsnWrite':
objseq.c:5226:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:5228:12: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:74:
/usr/include/features.h:184:3: 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:900:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ebp == NULL)
^~
objblock.c:903:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -fPIC -D_PNG -I../include -DWIN_MOTIF objcode.c
objcode.c:48:51: 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:105:
/usr/include/features.h:184:3: 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 -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:184:3: 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 were guarded by the 'if'
if (bsp->idx.parentptr == NULL || bsp->idx.parenttype == OBJ_SEQSUB) {
^~
objsset.c: In function 'SeqEntryFree':
objsset.c:878:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (sep->choice == 2)
^~
objsset.c:881:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return (SeqEntryPtr)MemFree(sep);
^~~~~~
objsset.c: In function 'SeqEntryFreeComponents':
objsset.c:898:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (sep->choice == 2)
^~
objsset.c:901:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return sep;
^~~~~~
objsset.c: In function 'SeqEntryAsnGet':
objsset.c:1075:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (retcode == 1) /* just after a Bioseq */
^~
objsset.c:1077:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:84:
/usr/include/features.h:184:3: 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:341:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (loaded)
^~
objsub.c:344:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! SeqSetAsnLoad ())
^~
objsub.c:347:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnLoad())
^~
objsub.c:350:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ObjMgrTypeLoad(OBJ_SEQSUB, "Seq-submit", seqsubtypename, "Sequence Data Submission",
^~~~~~~~~~~~~~
objsub.c: In function 'SeqSubmitAsnWrite':
objsub.c:455:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:458:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:462:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)ssp))
^~
objsub.c:465:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! SubmitBlockAsnWrite(ssp->sub, aip, SEQ_SUBMIT_sub)) goto erret;
^~
objsub.c: In function 'SeqSubmitAsnRead':
objsub.c:539:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:542:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ssp = SeqSubmitNew();
^~~
objsub.c:543:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ssp == NULL)
^~
objsub.c:546:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objsub.c: In function 'SubmitBlockAsnWrite':
objsub.c:682:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:685:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:689:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)sbp))
^~
objsub.c:692:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! ContactInfoAsnWrite(sbp->contact, aip, SUBMIT_BLOCK_contact))
^~
objsub.c: In function 'SubmitBlockAsnRead':
objsub.c:770:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:773:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
oldatp = atp;
^~~~~~
objsub.c:775:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sbp == NULL)
^~
objsub.c:778:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objsub.c: In function 'ContactInfoAsnWrite':
objsub.c:942:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:945:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:949:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)cip))
^~
objsub.c:952:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cip->name != NULL)
^~
objsub.c: In function 'ContactInfoAsnRead':
objsub.c:1068:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:1070:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
oldatp = atp;
^~~~~~
objsub.c:1073:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (cip == NULL)
^~
objsub.c:1076:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:81:
/usr/include/features.h:184:3: 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:892:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormBooleanFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormEnumAsnRead':
objprt.c:1010:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormEnumFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormTextAsnRead':
objprt.c:1119:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormTextFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormAsnRead':
objprt.c:600:6: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp = PrintFormFree(vnp);
~~~~^~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormatAsnRead':
objprt.c:435:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormatFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintTemplateAsnRead':
objprt.c:250:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintTemplateFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormBlockAsnRead':
objprt.c:767:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintFormBlockFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'UserFormatAsnRead':
objprt.c:1231:5: 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 -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:184:3: 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 -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:184:3: 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:527:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalignloc.c: In function 'AlignIdAsnRead':
objalignloc.c:559:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignBoxAsnRead':
objalignloc.c:750:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:749:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignRowsAsnRead':
objalignloc.c:932:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:931:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignColumnsAsnRead':
objalignloc.c:1096:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:1095:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignIdAsnRead':
objalignloc.c:615:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objalignloc.c: In function 'AlignLocAsnRead':
objalignloc.c:370:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objalignloc.c:312:10: 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 -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:184:3: 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:269:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c:268:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtable.c: In function 'SeqTableAsnRead':
objtable.c:474:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'CommonStringTableAsnRead':
objtable.c:657:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'CommonBytesTableAsnRead':
objtable.c:819:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'SeqTableSingleDataFree':
objtable.c:1225:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtable.c: In function 'SeqTableSingleDataAsnRead':
objtable.c:1269:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtable.c: In function 'SeqTableMultiDataAsnRead':
objtable.c:1111:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtable.c: In function 'SeqTableSingleDataAsnRead':
objtable.c:1354:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtable.c: In function 'SeqTableSparseIndexAsnRead':
objtable.c:1559:16: 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 -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:184:3: 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:288:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objpubme.c:287:12: 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 -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:184:3: 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:259:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmdrs.c:258:12: 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 -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:184:3: 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:720:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objproj.c: In function 'ProjdescFree':
objproj.c:857:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objproj.c: In function 'ProjdescAsnRead':
objproj.c:898:12: 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:958:16: 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 -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:184:3: 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:69:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:66:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objgbseq.c: In function 'GBSeqAsnRead':
objgbseq.c:235:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBReferenceAsnRead':
objgbseq.c:742:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBCommentAsnRead':
objgbseq.c:983:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBStrucCommentAsnRead':
objgbseq.c:1150:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBFeatureAsnRead':
objgbseq.c:1321:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBFeatureSetAsnRead':
objgbseq.c:1548:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBAltSeqDataAsnRead':
objgbseq.c:1715:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBXrefAsnRead':
objgbseq.c:1882:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:1881:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objgbseq.c: In function 'GBStrucCommentItemAsnRead':
objgbseq.c:2053:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:2052:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objgbseq.c: In function 'GBIntervalAsnRead':
objgbseq.c:2233:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:2232:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objgbseq.c: In function 'GBQualifierAsnRead':
objgbseq.c:2447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:2446:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objgbseq.c: In function 'GBAltSeqItemAsnRead':
objgbseq.c:2622:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:2621:12: 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 -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:184:3: 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:325:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtseq.c: In function 'BioseqToTSeq':
objtseq.c:452:8: warning: variable 'seqcode' set but not used [-Wunused-but-set-variable]
Uint1 seqcode;
^~~~~~~
objtseq.c: In function 'BioseqToMiniTSeq':
objtseq.c:564:8: 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 -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:184:3: 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:69:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:66:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objinsdseq.c: In function 'INSDSeqAsnRead':
objinsdseq.c:235:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDReferenceAsnRead':
objinsdseq.c:742:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDCommentAsnRead':
objinsdseq.c:983:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDStrucCommentAsnRead':
objinsdseq.c:1150:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDFeatureAsnRead':
objinsdseq.c:1321:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDFeatureSetAsnRead':
objinsdseq.c:1548:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDAltSeqDataAsnRead':
objinsdseq.c:1715:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDXrefAsnRead':
objinsdseq.c:1882:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:1881:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objinsdseq.c: In function 'INSDStrucCommentItemAsnRead':
objinsdseq.c:2053:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:2052:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objinsdseq.c: In function 'INSDIntervalAsnRead':
objinsdseq.c:2233:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:2232:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objinsdseq.c: In function 'INSDQualifierAsnRead':
objinsdseq.c:2447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:2446:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objinsdseq.c: In function 'INSDAltSeqItemAsnRead':
objinsdseq.c:2622:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:2621:12: 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 -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:184:3: 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:272:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:271:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MacroActionListAsnRead':
objmacro.c:478:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:475:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SuspectRuleSetAsnRead':
objmacro.c:595:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:592:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'WordSubstitutionAsnRead':
objmacro.c:731:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c: In function 'WordSubstitutionSetAsnRead':
objmacro.c:899:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:896:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'StringConstraintAsnRead':
objmacro.c:1045:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1044:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StringConstraintSetAsnRead':
objmacro.c:1307:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1304:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'LocationPosConstraintFree':
objmacro.c:1403:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationPosConstraintAsnRead':
objmacro.c:1432:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationConstraintAsnRead':
objmacro.c:1633:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1632:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalValAsnRead':
objmacro.c:1849:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1848:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalValChoiceFree':
objmacro.c:1979:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FeatQualLegalValChoiceAsnRead':
objmacro.c:2011:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalSetAsnRead':
objmacro.c:2165:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2162:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'FeatQualChoiceFree':
objmacro.c:2261:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FeatQualChoiceAsnRead':
objmacro.c:2293:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldAsnRead':
objmacro.c:2474:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2473:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldLegalAsnRead':
objmacro.c:2641:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2640:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldPairAsnRead':
objmacro.c:2807:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2806:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaFeatTypeFree':
objmacro.c:2950:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'RnaFeatTypeAsnRead':
objmacro.c:2982:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaQualAsnRead':
objmacro.c:3232:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3231:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaQualPairAsnRead':
objmacro.c:3400:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3399:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualPairAsnRead':
objmacro.c:3576:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3575:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualChoiceFree':
objmacro.c:3704:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SourceQualChoiceAsnRead':
objmacro.c:3733:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualTextValAsnRead':
objmacro.c:3950:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3949:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualValChoiceFree':
objmacro.c:4080:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SourceQualValChoiceAsnRead':
objmacro.c:4112:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualValSetAsnRead':
objmacro.c:4310:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4307:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'CDSGeneProtFieldPairAsnRead':
objmacro.c:4442:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4441:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldFree':
objmacro.c:4570:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MolinfoFieldAsnRead':
objmacro.c:4599:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoMoleculePairAsnRead':
objmacro.c:4826:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4825:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoTechniquePairAsnRead':
objmacro.c:4990:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4989:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoCompletednessPairAsnRead':
objmacro.c:5154:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5153:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoMolClassPairAsnRead':
objmacro.c:5318:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5317:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoTopologyPairAsnRead':
objmacro.c:5482:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5481:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoStrandPairAsnRead':
objmacro.c:5646:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5645:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldPairFree':
objmacro.c:5774:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MolinfoFieldPairAsnRead':
objmacro.c:5821:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldListAsnRead':
objmacro.c:6015:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6012:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MolinfoFieldConstraintAsnRead':
objmacro.c:6149:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6148:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StructuredCommentFieldFree':
objmacro.c:6280:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'StructuredCommentFieldAsnRead':
objmacro.c:6312:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StructuredCommentFieldPairAsnRead':
objmacro.c:6508:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6507:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'DBLinkFieldPairAsnRead':
objmacro.c:6678:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6677:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldConstraintAsnRead':
objmacro.c:6843:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6842:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeFree':
objmacro.c:6974:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeAsnRead':
objmacro.c:7003:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintAsnRead':
objmacro.c:7220:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7219:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PublicationConstraintAsnRead':
objmacro.c:7389:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7388:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceConstraintAsnRead':
objmacro.c:7571:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7570:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtPseudoConstraintAsnRead':
objmacro.c:7763:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7762:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtConstraintFieldFree':
objmacro.c:7891:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'CDSGeneProtConstraintFieldAsnRead':
objmacro.c:7920:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtQualConstraintAsnRead':
objmacro.c:8095:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:8094:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldConstraintAsnRead':
objmacro.c:8279:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:8278:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldTypeFree':
objmacro.c:8413:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FieldTypeAsnRead':
objmacro.c:8457:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintFree':
objmacro.c:8666:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintAsnRead':
objmacro.c:8695:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'QuantityConstraintFree':
objmacro.c:8875:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'QuantityConstraintAsnRead':
objmacro.c:8904:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceConstraintAsnRead':
objmacro.c:9104:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9103:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TranslationConstraintAsnRead':
objmacro.c:9332:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9331:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConstraintChoiceFree':
objmacro.c:9487:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConstraintChoiceAsnRead':
objmacro.c:9549:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConstraintChoiceSetAsnRead':
objmacro.c:9783:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9780:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'TextMarkerFree':
objmacro.c:9879:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TextMarkerAsnRead':
objmacro.c:9911:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TextPortionAsnRead':
objmacro.c:10109:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10108:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldEditAsnRead':
objmacro.c:10328:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10327:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldPairTypeFree':
objmacro.c:10478:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FieldPairTypeAsnRead':
objmacro.c:10528:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyActionAsnRead':
objmacro.c:10747:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10746:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditActionAsnRead':
objmacro.c:10927:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10926:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TextTransformFree':
objmacro.c:11061:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TextTransformAsnRead':
objmacro.c:11096:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TextTransformSetAsnRead':
objmacro.c:11269:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11266:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'ConvertActionAsnRead':
objmacro.c:11405:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11404:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CopyActionAsnRead':
objmacro.c:11600:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11599:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SwapActionAsnRead':
objmacro.c:11768:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11767:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AECRParseActionAsnRead':
objmacro.c:11932:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11931:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveActionAsnRead':
objmacro.c:12151:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:12150:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveOutsideActionAsnRead':
objmacro.c:12312:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:12311:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ActionChoiceFree':
objmacro.c:12455:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ActionChoiceAsnRead':
objmacro.c:12508:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcOrgChoiceFree':
objmacro.c:12697:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcOrgChoiceAsnRead':
objmacro.c:12726:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcOrgAsnRead':
objmacro.c:12911:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:12910:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcGeneralIdFree':
objmacro.c:13042:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcGeneralIdAsnRead':
objmacro.c:13074:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcFree':
objmacro.c:13232:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcAsnRead':
objmacro.c:13270:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseDstOrgAsnRead':
objmacro.c:13526:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:13525:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseDestFree':
objmacro.c:13657:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseDestAsnRead':
objmacro.c:13695:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationIntervalAsnRead':
objmacro.c:13905:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:13904:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationChoiceFree':
objmacro.c:14033:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationChoiceAsnRead':
objmacro.c:14065:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceListAsnRead':
objmacro.c:14241:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14238:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SequenceListChoiceFree':
objmacro.c:14337:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SequenceListChoiceAsnRead':
objmacro.c:14369:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyFeatureActionAsnRead':
objmacro.c:14560:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14559:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveFeatureActionAsnRead':
objmacro.c:14827:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14826:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFromCDSOptionsAsnRead':
objmacro.c:14994:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14993:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureSrcOptionsFree':
objmacro.c:15131:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConvertFeatureSrcOptionsAsnRead':
objmacro.c:15163:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RegionTypeAsnRead':
objmacro.c:15332:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15331:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureDstOptionsFree':
objmacro.c:15451:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConvertFeatureDstOptionsAsnRead':
objmacro.c:15486:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureActionAsnRead':
objmacro.c:15702:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15701:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditLocationStrandAsnRead':
objmacro.c:15911:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15910:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'Partial5SetActionAsnRead':
objmacro.c:16075:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16074:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'Partial3SetActionAsnRead':
objmacro.c:16239:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16238:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PartialBothSetActionAsnRead':
objmacro.c:16403:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16402:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ExtendToFeatureAsnRead':
objmacro.c:16568:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16567:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationEditTypeFree':
objmacro.c:16708:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationEditTypeAsnRead':
objmacro.c:16755:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditFeatureLocationActionAsnRead':
objmacro.c:17032:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17031:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoBlockAsnRead':
objmacro.c:17232:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17231:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveDescriptorActionAsnRead':
objmacro.c:17415:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17414:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AutodefActionAsnRead':
objmacro.c:17584:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c: In function 'FixPubCapsActionAsnRead':
objmacro.c:17758:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17757:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SortFieldsActionAsnRead':
objmacro.c:17963:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17962:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixAuthorCapsAsnRead':
objmacro.c:18142:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18141:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixCapsActionFree':
objmacro.c:18261:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixCapsActionAsnRead':
objmacro.c:18296:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixFormatActionFree':
objmacro.c:18470:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixFormatActionAsnRead':
objmacro.c:18499:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveDuplicateFeatureActionAsnRead':
objmacro.c:18705:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18704:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'GeneXrefTypeAsnRead':
objmacro.c:18899:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18898:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'XrefTypeFree':
objmacro.c:19036:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'XrefTypeAsnRead':
objmacro.c:19068:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveXrefsActionAsnRead':
objmacro.c:19239:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19238:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MakeGeneXrefActionAsnRead':
objmacro.c:19410:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19409:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AuthorFixActionAsnRead':
objmacro.c:19578:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19577:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'UpdateSequencesActionAsnRead':
objmacro.c:19747:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19746:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CreateTSAIdsSrcFree':
objmacro.c:19877:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'CreateTSAIdsSrcAsnRead':
objmacro.c:19909:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CreateTSAIdsActionAsnRead':
objmacro.c:20092:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:20091:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AutofixActionAsnRead':
objmacro.c:20274:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:20273:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixSetsActionFree':
objmacro.c:20395:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixSetsActionAsnRead':
objmacro.c:20424:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TableMatchTypeFree':
objmacro.c:20582:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TableMatchTypeAsnRead':
objmacro.c:20614:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TableMatchAsnRead':
objmacro.c:20873:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:20872:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyTableExtraDataFree':
objmacro.c:21004:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ApplyTableExtraDataAsnRead':
objmacro.c:21033:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyTableActionAsnRead':
objmacro.c:21210:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21209:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AddFileActionAsnRead':
objmacro.c:21411:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21410:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AddDescriptorListActionAsnRead':
objmacro.c:21582:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21581:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveSequencesActionAsnRead':
objmacro.c:21753:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21752:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'UpdateReplacedEcNumbersActionAsnRead':
objmacro.c:21911:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21910:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RetranslateCdsActionAsnRead':
objmacro.c:22084:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:22083:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AdjustFeaturesForGapsActionAsnRead':
objmacro.c:22239:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:22238:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MacroActionChoiceFree':
objmacro.c:22412:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MacroActionChoiceAsnRead':
objmacro.c:22522:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SearchFuncFree':
objmacro.c:23116:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SearchFuncAsnRead':
objmacro.c:23154:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SimpleReplaceAsnRead':
objmacro.c:23425:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:23424:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ReplaceFuncFree':
objmacro.c:23564:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ReplaceFuncAsnRead':
objmacro.c:23599:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ReplaceRuleAsnRead':
objmacro.c:23781:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:23780:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SuspectRuleAsnRead':
objmacro.c:23955:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:23954:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualChoiceAsnRead':
objmacro.c:3806:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SourceQualValChoiceAsnRead':
objmacro.c:4182:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MolinfoFieldAsnRead':
objmacro.c:4679:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MolinfoFieldPairAsnRead':
objmacro.c:5883:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'StructuredCommentFieldAsnRead':
objmacro.c:6371:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FieldTypeAsnRead':
objmacro.c:8543:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ConstraintChoiceAsnRead':
objmacro.c:9631:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'TextTransformAsnRead':
objmacro.c:11149:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcGeneralIdAsnRead':
objmacro.c:13133:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixCapsActionAsnRead':
objmacro.c:18363:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixFormatActionAsnRead':
objmacro.c:18565:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixSetsActionAsnRead':
objmacro.c:20483:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MacroActionChoiceAsnRead':
objmacro.c:22829:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationPosConstraintAsnRead':
objmacro.c:1491:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FeatQualChoiceAsnRead':
objmacro.c:2342:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'RnaFeatTypeAsnRead':
objmacro.c:3076:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeAsnRead':
objmacro.c:7076:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintAsnRead':
objmacro.c:8768:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'QuantityConstraintAsnRead':
objmacro.c:8963:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'TextMarkerAsnRead':
objmacro.c:9970:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FieldPairTypeAsnRead':
objmacro.c:10594:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ActionChoiceAsnRead':
objmacro.c:12578:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcOrgChoiceAsnRead':
objmacro.c:12778:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcAsnRead':
objmacro.c:13365:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseDestAsnRead':
objmacro.c:13762:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationChoiceAsnRead':
objmacro.c:14121:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SequenceListChoiceAsnRead':
objmacro.c:14418:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ConvertFeatureDstOptionsAsnRead':
objmacro.c:15556:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationEditTypeAsnRead':
objmacro.c:16859:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'CreateTSAIdsSrcAsnRead':
objmacro.c:19958:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'TableMatchTypeAsnRead':
objmacro.c:20712:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SearchFuncAsnRead':
objmacro.c:23259:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ReplaceFuncAsnRead':
objmacro.c:23648:16: 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 -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:184:3: 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:277:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2BooleanElementFree':
objent2.c:416:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'Entrez2BooleanElementAsnRead':
objent2.c:457:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LimitsAsnRead':
objent2.c:666:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:665:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2BooleanTermAsnRead':
objent2.c:844:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:843:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2RequestAsnRead':
objent2.c:1041:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1040:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'E2RequestFree':
objent2.c:1203:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'E2RequestAsnRead':
objent2.c:1256:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2EvalBooleanAsnRead':
objent2.c:1493:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1492:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermQueryAsnRead':
objent2.c:1670:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1669:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermPosAsnRead':
objent2.c:1849:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1848:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2HierQueryAsnRead':
objent2.c:2036:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2035:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2GetLinksAsnRead':
objent2.c:2224:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2223:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2IdAsnRead':
objent2.c:2419:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2418:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DtFilterAsnRead':
objent2.c:2584:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2583:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2ReplyAsnRead':
objent2.c:2762:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2761:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'E2ReplyFree':
objent2.c:2935:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'E2ReplyAsnRead':
objent2.c:2991:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2InfoAsnRead':
objent2.c:3237:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2BooleanReplyAsnRead':
objent2.c:3409:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:3408:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumListAsnRead':
objent2.c:3587:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2TermListAsnRead':
objent2.c:3749:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2HierNodeAsnRead':
objent2.c:3922:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2LinkSetAsnRead':
objent2.c:4122:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4121:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkCountListAsnRead':
objent2.c:4299:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2DbInfoAsnRead':
objent2.c:4466:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2FieldInfoAsnRead':
objent2.c:4706:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4705:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkInfoAsnRead':
objent2.c:4950:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4949:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumFieldInfoAsnRead':
objent2.c:5149:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5148:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumAsnRead':
objent2.c:5325:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2DocsumDataAsnRead':
objent2.c:5488:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5487:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermAsnRead':
objent2.c:5655:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5654:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkCountAsnRead':
objent2.c:5838:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5837:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2BooleanElementAsnRead':
objent2.c:524:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objent2.c: In function 'E2RequestAsnRead':
objent2.c:1333:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objent2.c: In function 'E2ReplyAsnRead':
objent2.c:3075:16: 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 -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:184:3: 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 -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:184:3: 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:2813:24: warning: 'SortByInt4' defined but not used [-Wunused-function]
static int LIBCALLBACK SortByInt4 (VoidPtr vp1, VoidPtr vp2)
^~~~~~~~~~
pmfapi.c: In function 'ConfirmAccStrInSep':
pmfapi.c:1314:3: warning: 'tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqIdFree (tmp);
^~~~~~~~~~~~~~~
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:1479:58: 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:1663:58: 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:1744:58: 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:1817:61: 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:1869:60: 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:1920:63: 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:1971:62: 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:2021:60: 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 -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:184:3: 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:1072:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'Value_valueFree':
objtax3.c:1253:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtax3.c: In function 'T3StatusFlagsAsnRead':
objtax3.c:1283:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'T3RefreshFlagsAsnRead':
objtax3.c:1608:16: 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:1421:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax3.c:1362:10: 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 -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:184:3: 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:189:27: warning: variable 't3' set but not used [-Wunused-but-set-variable]
time_t t1, t2, t3;
^~
tax3api.c: In function 'CheckSuggestedFixes':
tax3api.c:1030:20: warning: variable 'tep' set but not used [-Wunused-but-set-variable]
T3ErrorPtr tep;
^~~
tax3api.c: In function 'TryNewSuggestedFixes':
tax3api.c:1142:20: warning: variable 'tep' set but not used [-Wunused-but-set-variable]
T3ErrorPtr tep;
^~~
tax3api.c: In function 'RemoveSpeciesSpecific':
tax3api.c:1398:13: warning: unused variable 'cp' [-Wunused-variable]
CharPtr cp;
^~
At top level:
tax3api.c:3399:13: warning: 'AddBioSourcesToChecklist' defined but not used [-Wunused-function]
static void AddBioSourcesToChecklist (ValNodePtr biop_list, ValNodePtr check_list)
^~~~~~~~~~~~~~~~~~~~~~~~
tax3api.c:2699:16: warning: 'MatchesGenBankSynonym' defined but not used [-Wunused-function]
static Boolean MatchesGenBankSynonym (CharPtr txt, OrgRefPtr response_org)
^~~~~~~~~~~~~~~~~~~~~
tax3api.c:2682:16: warning: 'MatchesSynonym' defined but not used [-Wunused-function]
static Boolean MatchesSynonym (CharPtr txt, OrgRefPtr response_org)
^~~~~~~~~~~~~~
tax3api.c:2273:16: warning: 'EndsWithSp' defined but not used [-Wunused-function]
static Boolean EndsWithSp (CharPtr str)
^~~~~~~~~~
tax3api.c:990:19: warning: 'MakeTaxFixRequestList' defined but not used [-Wunused-function]
static ValNodePtr MakeTaxFixRequestList (ValNodePtr biop_list)
^~~~~~~~~~~~~~~~~~~~~
tax3api.c:362:16: warning: 'HasMisspellingFlag' defined but not used [-Wunused-function]
static Boolean HasMisspellingFlag (T3DataPtr t)
^~~~~~~~~~~~~~~~~~
tax3api.c:298:13: 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 -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:184:3: 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 -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:184:3: 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:412:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:409:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objentgene.c: In function 'GeneTrackAsnRead':
objentgene.c:547:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c: In function 'GeneCommentaryAsnRead':
objentgene.c:768:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c: In function 'Method_methodFree':
objentgene.c:1073:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objentgene.c: In function 'MapsAsnRead':
objentgene.c:1104:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1103:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'Method_methodAsnRead':
objentgene.c:1184:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'GeneSourceAsnRead':
objentgene.c:1426:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1425:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'XtraTermsAsnRead':
objentgene.c:1641:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1640:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'OtherSourceAsnRead':
objentgene.c:1812:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1811:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'MapsAsnRead':
objentgene.c:1236:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objentgene.c:1183:10: 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 -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:184:3: 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:613:16: 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:904:16: 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 -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:184:3: 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 -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:123:
/usr/include/features.h:184:3: 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:262:15: warning: variable 'waiting' set but not used [-Wunused-but-set-variable]
Boolean waiting = FALSE;
^~~~~~~
qblastapi.c: In function 'BLASTGetSeqAnnotByRIDEx':
qblastapi.c:826:18: warning: variable 'status' set but not used [-Wunused-but-set-variable]
EIO_Status status;
^~~~~~
qblastapi.c: In function 'BLASTGetQueryBioseqByRIDEx':
qblastapi.c:871:18: warning: variable 'status' set but not used [-Wunused-but-set-variable]
EIO_Status status;
^~~~~~
qblastapi.c: In function 'QBlastCheckQueue':
qblastapi.c:688:36: warning: '&FORMAT_OBJECT=Alignment&FORMAT_TYPE=ASN.1
' directive writing 43 bytes into a region of size between 5 and 68 [-Wformat-overflow=]
sprintf (str, "CMD=Get&RID=%s&FORMAT_OBJECT=Alignment&FORMAT_TYPE=ASN.1\n", curr->rid);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from qblastapi.c:123:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 56 and 119 bytes into a destination of size 80
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:448:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimCitAsnRead':
objmim.c:909:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:908:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimTextAsnRead':
objmim.c:1096:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:1095:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimEditItemAsnRead':
objmim.c:1276:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:1275:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimAllelicVariantAsnRead':
objmim.c:1448:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimIndexTermAsnRead':
objmim.c:1640:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimReferenceAsnRead':
objmim.c:1819:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimLinkAsnRead':
objmim.c:2195:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2194:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimAuthorAsnRead':
objmim.c:2369:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2368:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimPageAsnRead':
objmim.c:2535:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2534:12: 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 -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:184:3: 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:259:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:256:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'DependentFieldRuleAsnRead':
objvalid.c:396:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:395:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objvalid.c: In function 'DependentFieldSetAsnRead':
objvalid.c:582:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:579:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'CommentRuleAsnRead':
objvalid.c:721:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:720:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objvalid.c: In function 'CommentSetAsnRead':
objvalid.c:926:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:923:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'PhraseListAsnRead':
objvalid.c:1043:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:1040:12: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:4260:13: warning: variable 'is_cdregion' set but not used [-Wunused-but-set-variable]
Boolean is_cdregion = FALSE;
^~~~~~~~~~~
seqport.c: In function 'NaLocFromNaInterval':
seqport.c:4590:8: 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:4706:18: warning: variable 'cds_right' set but not used [-Wunused-but-set-variable]
Int4 cds_left, cds_right;
^~~~~~~~~
seqport.c:4706:8: warning: variable 'cds_left' set but not used [-Wunused-but-set-variable]
Int4 cds_left, cds_right;
^~~~~~~~
seqport.c: In function 'DeltaRevComp':
seqport.c:5388:21: warning: variable 'dspnext' set but not used [-Wunused-but-set-variable]
DeltaSeqPtr dsp, dspnext;
^~~~~~~
seqport.c: In function 'SeqSearchEnterNucWord':
seqport.c:6943:18: warning: variable 'patLen' set but not used [-Wunused-but-set-variable]
Int2 next, patLen, state;
^~~~~~
seqport.c: In function 'ProtSearchEnterProtWord':
seqport.c:7817:18: 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 -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:184:3: 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:7994:11: warning: variable 'first_strand' set but not used [-Wunused-but-set-variable]
Uint1 first_strand, last_strand;
^~~~~~~~~~~~
sequtil.c: In function 'SeqPointWriteEx':
sequtil.c:8532:15: warning: variable 'fuzzlen' set but not used [-Wunused-but-set-variable]
Int4 fuzzlen, id_len;
^~~~~~~
sequtil.c: In function 'TaxNameFromCommon':
sequtil.c:8687:42: warning: missing braces around initializer [-Wmissing-braces]
static Nlm_TaxCommon taxcommon[40] = {
^
"Chinese hamsters", "Cricetulus sp."
{
,"Syrian golden hamsters", "Mesocricetus auratus"
}{
,"Syrian hamsters", "Mesocricetus sp."
}{
,"barley", "Hordeum sp."
}{
,"carrots", "Daucus sp."
}{
,"cats", "Felis sp."
}{
,"cattles", "Bos sp."
}{
,"chickens", "Gallus sp."
}{
,"chimpanzees", "Pan sp."
}{
,"chimpanzes", "Pan sp."
}{
,"corn", "Zea sp."
}{
,"cucumber", "Cucumis sativus"
}{
,"dogs", "Canis sp."
}{
,"goats", "Capra sp."
}{
,"gorillas", "Gorilla sp."
}{
,"guinea pigs", "Cavia sp."
}{
,"hamsters", "Cricetidae gen. sp."
}{
,"horses", "Equus sp."
}{
,"humans", "Homo sapiens"
}{
,"maize", "Zea sp."
}{
,"mice", "Mus sp."
}{
,"mouse", "Mus sp."
}{
,"peas", "Pisum sp."
}{
,"potatoes", "Solanum sp."
}{
,"potato", "Solanum sp."
}{
,"quails", "Phasianidae gen. sp."
}{
,"rabbits", "Oryctolagus sp."
}{
,"rats", "Rattus sp."
}{
,"rices", "Oryza sp."
}{
,"sheeps", "Ovis sp."
}{
,"sorghums", "Sorghum sp."
}{
,"soybeans", "Glycine sp."
}{
,"spinach", "Spinacia sp."
}{
,"swine", "Sus sp."
}{
,"tobacco", "Nicotiania sp."
}{
,"tomatoes", "Lycopersicon sp."
}{
,"tomato", "Lycopersicon sp."
}{
,"turkeys", "Meleagris sp."
}{
,"wheat", "Triticum sp."
}{
,"zebrafish", "Brachydanio sp."
}{
};
}
sequtil.c: In function 'GetBestScoreAndEvalueFromScorePtr':
sequtil.c:9510:48: 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:10110:38: warning: variable 'sip2' set but not used [-Wunused-but-set-variable]
SeqIdPtr sip2;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:7293:0: warning: "RNA_QUAL" redefined
#define RNA_QUAL &at[2254]
../include/all.h:5823:0: note: this is the location of the previous definition
#define RNA_QUAL &at[1025]
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:1461:22: warning: variable 'gene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr gene = NULL;
^~~~
tofasta.c: In function 'FastaIdEx':
tofasta.c:3100:15: warning: variable 'sip' set but not used [-Wunused-but-set-variable]
SeqIdPtr sip;
^~~
tofasta.c: In function 'CreateDefLineExEx':
tofasta.c:4991:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (vnp != NULL)
^~
tofasta.c:4993:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (title != NULL) {
^~
tofasta.c: In function 'x_SetSuffix':
tofasta.c:8313:24: warning: variable 'buf2' set but not used [-Wunused-but-set-variable]
Char buf1 [512], buf2 [256];
^~~~
tofasta.c: In function 'FastaToSeqEntryInternalExEx':
tofasta.c:2838:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(buffer+1, BuffSize, fd);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tofasta.c:2863:13: 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:8058:17: warning: 'x_StringInList' defined but not used [-Wunused-function]
static Boolean x_StringInList (
^~~~~~~~~~~~~~
tofasta.c:3661:19: warning: 'GatherGenesForCDS' defined but not used [-Wunused-function]
static ValNodePtr GatherGenesForCDS(SeqLocPtr slp)
^~~~~~~~~~~~~~~~~
tofasta.c:3627:19: warning: 'GatherSeqFeatProt' defined but not used [-Wunused-function]
static SeqFeatPtr GatherSeqFeatProt(BioseqPtr bsp)
^~~~~~~~~~~~~~~~~
tofasta.c:3541:19: warning: 'GetCDSProtUnindexed' defined but not used [-Wunused-function]
static SeqFeatPtr GetCDSProtUnindexed (
^~~~~~~~~~~~~~~~~~~
tofasta.c:3378:19: warning: 'IndexedGatherDescrOnBioseq' defined but not used [-Wunused-function]
static ValNodePtr IndexedGatherDescrOnBioseq (ItemInfoPtr iip, BioseqPtr bsp, Uint1 choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~
tofasta.c:3283:16: warning: 'get_descr' defined but not used [-Wunused-function]
static Boolean get_descr (GatherContextPtr gcp)
^~~~~~~~~
tofasta.c:3254:16: 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:2713:27: warning: 'mask_to' may be used uninitialized in this function [-Wmaybe-uninitialized]
mask_sint->to = mask_to;
~~~~~~~~~~~~~~^~~~~~~~~
tofasta.c: In function 'FastaToSeqEntryInternalExEx':
tofasta.c:2774:25: 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 -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:184:3: 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 -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:153:
/usr/include/features.h:184:3: 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 -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:184:3: 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 'GetUserFieldValueString':
valid.c:2212:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", ufp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
valid.c: In function 'ValidateSeqIdCase':
valid.c:3574:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'ValidateGenProdSet':
valid.c:6046:19: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'CountAdjacentProc':
valid.c:6730:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'CheckBioseqEndsForNAndGap':
valid.c:7040:44: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (str [0] == 'n' || str [0] == 'N' && begin_n != NULL) {
^
valid.c:7061:56: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (str [len - 1] == 'n' || str [len - 1] == 'N' && end_n != NULL) {
^
valid.c: In function 'ValidateBioseqInst':
valid.c:7341:19: warning: variable 'tech' set but not used [-Wunused-but-set-variable]
Uint1 tech;
^~~~
valid.c:7278:19: warning: variable 'prot' set but not used [-Wunused-but-set-variable]
SeqFeatPtr prot;
^~~~
valid.c: In function 'FixOrgModVoucher':
valid.c:13882:22: warning: unused variable 'allowed_type' [-Wunused-variable]
Uint1 type = 0, allowed_type = 0;
^~~~~~~~~~~~
valid.c: In function 'ValidateBioSource':
valid.c:15514:19: warning: variable 'isMicrosporidia' set but not used [-Wunused-but-set-variable]
Boolean isMicrosporidia = FALSE;
^~~~~~~~~~~~~~~
valid.c:15512:19: warning: variable 'isEukaryote' set but not used [-Wunused-but-set-variable]
Boolean isEukaryote = FALSE;
^~~~~~~~~~~
valid.c:15503:19: warning: variable 'id' set but not used [-Wunused-but-set-variable]
Int4 id;
^~
valid.c: In function 'ValidateDblink':
valid.c:16786:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'ValidateSeqDescrCommon':
valid.c:16883:19: warning: variable 'pdp' set but not used [-Wunused-but-set-variable]
PubdescPtr pdp;
^~~
valid.c: In function 'GetFeatsInGaps':
valid.c:18858:21: warning: variable 'realBases' set but not used [-Wunused-but-set-variable]
Int4 realBases;
^~~~~~~~~
valid.c:18857:21: warning: variable 'plusses' set but not used [-Wunused-but-set-variable]
Int4 plusses;
^~~~~~~
valid.c:18854:21: warning: variable 'Ns' set but not used [-Wunused-but-set-variable]
Int4 Ns;
^~
valid.c:18851:21: warning: variable 'dashes' set but not used [-Wunused-but-set-variable]
Int4 dashes;
^~~~~~
valid.c: In function 'ValidateBioseqContextIndexed':
valid.c:20267:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (bvsp->is_mrna || cdscount == 1 && genecount < 2) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
valid.c:19476:65: warning: variable 'cdsmgene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr utr5pgene, cdspgene, utr3pgene, utr5mgene, cdsmgene, utr3mgene;
^~~~~~~~
valid.c:19476:33: warning: variable 'cdspgene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr utr5pgene, cdspgene, utr3pgene, utr5mgene, cdsmgene, utr3mgene;
^~~~~~~~
valid.c:19475:51: warning: variable 'utr5minus' set but not used [-Wunused-but-set-variable]
SeqFeatPtr utr5plus, cdsplus, utr3plus, utr5minus, cdsminus, utr3minus;
^~~~~~~~~
valid.c:19475:41: warning: variable 'utr3plus' set but not used [-Wunused-but-set-variable]
SeqFeatPtr utr5plus, cdsplus, utr3plus, utr5minus, cdsminus, utr3minus;
^~~~~~~~
valid.c:19442:41: warning: variable 'utr3gene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr cdsgene, utr5gene, utr3gene;
^~~~~~~~
valid.c: In function 'ReportBadWGSGap':
valid.c:21153:18: warning: unused variable 'is_wgs' [-Wunused-variable]
Boolean is_wgs = FALSE;
^~~~~~
valid.c: In function 'ValidateBarcodeIndexNumber':
valid.c:21432:21: warning: variable 'bin_len' set but not used [-Wunused-but-set-variable]
Int4 bin_len;
^~~~~~~
valid.c: In function 'ValidateRptUnit':
valid.c:23411:32: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean badchars, found, just_nuc_letters, multi_rpt_unit, in_range;
^~~~~
valid.c: In function 'CheckForCommonCDSProduct':
valid.c:25628:19: warning: variable 'is_nw' set but not used [-Wunused-but-set-variable]
Boolean is_nw = FALSE;
^~~~~
valid.c:25625:19: warning: variable 'is_nc' set but not used [-Wunused-but-set-variable]
Boolean is_nc = FALSE;
^~~~~
valid.c: In function 'CheckForIllegalDbxref':
valid.c:26017:16: warning: variable 'id' set but not used [-Wunused-but-set-variable]
Int4 id;
^~
valid.c: In function 'ValidateAnticodon':
valid.c:26781:53: warning: variable 'circular' set but not used [-Wunused-but-set-variable]
ordered = TRUE, adjacent = FALSE, circular = FALSE, exception = FALSE;
^~~~~~~~
valid.c:26780:19: 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:28000:17: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
valid.c: In function 'ValidateSeqFeat':
valid.c:28328:19: warning: unused variable 'is_nc' [-Wunused-variable]
Boolean is_nc = FALSE;
^~~~~
valid.c:28308:19: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
valid.c:28286:19: warning: variable 'pdp' set but not used [-Wunused-but-set-variable]
PubdescPtr pdp;
^~~
valid.c: In function 'CdTransCheck':
valid.c:30490:19: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'SpliceCheckEx':
valid.c:31313:19: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
valid.c: In function 'CdsProductIdCheck':
valid.c:31689:15: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'ValidateSeqLoc':
valid.c:31754:19: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = TRUE, tmpval, mixed_strand = FALSE, unmarked_strand = FALSE,
^~~~~~
valid.c:31753:24: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
SeqLocPtr tmp, prev;
^~~~
valid.c: In function 'SortSeqGraphProc':
valid.c:32156:26: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (gip2->right < gip2->right) {
^
At top level:
valid.c:30138:13: warning: 'ValidateTranslExcept' defined but not used [-Wunused-function]
static void ValidateTranslExcept (
^~~~~~~~~~~~~~~~~~~~
valid.c:27650:16: warning: 'CouldExtendPartial' defined but not used [-Wunused-function]
static Boolean CouldExtendPartial (SeqLocPtr slp, Boolean partial5)
^~~~~~~~~~~~~~~~~~
valid.c:20878:28: warning: 'MultiGeneOverlapFree' defined but not used [-Wunused-function]
static MultiGeneOverlapPtr MultiGeneOverlapFree (MultiGeneOverlapPtr m)
^~~~~~~~~~~~~~~~~~~~
valid.c:20828:19: warning: 'ListFeaturesContainedInLocation' defined but not used [-Wunused-function]
static ValNodePtr ListFeaturesContainedInLocation (BioseqPtr bsp, SeqLocPtr slp, Uint1 seqfeatChoice, Uint1 featdefChoice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
valid.c:17541:16: warning: 'IsEMBLAccn' defined but not used [-Wunused-function]
static Boolean IsEMBLAccn (SeqEntryPtr sep, SeqLocPtr location)
^~~~~~~~~~
valid.c:14642:16: warning: 'CountryIsClosestToLatLon' defined but not used [-Wunused-function]
static Boolean CountryIsClosestToLatLon (
^~~~~~~~~~~~~~~~~~~~~~~~
valid.c:14545:16: warning: 'LatLonInRange' defined but not used [-Wunused-function]
static Boolean LatLonInRange (
^~~~~~~~~~~~~
valid.c:13478:16: warning: 'LatLonIsValid' defined but not used [-Wunused-function]
static Boolean LatLonIsValid (CharPtr name)
^~~~~~~~~~~~~
valid.c:10462:16: warning: 'ConsistentWithC' defined but not used [-Wunused-function]
static Boolean ConsistentWithC (Char ch)
^~~~~~~~~~~~~~~
valid.c:6952:13: warning: 'ReportLongSeqId' defined but not used [-Wunused-function]
static void ReportLongSeqId (SeqIdPtr sip, ValidStructPtr vsp, Int4 max_len)
^~~~~~~~~~~~~~~
valid.c:5932:13: warning: 'CheckMutSetSources' defined but not used [-Wunused-function]
static void CheckMutSetSources (BioSourcePtr biop, Pointer userdata)
^~~~~~~~~~~~~~~~~~
valid.c:4360:13: warning: 'FindLongIdsThatCollideWhenTruncated' defined but not used [-Wunused-function]
static void FindLongIdsThatCollideWhenTruncated (SeqEntryPtr sep, ValidStructPtr vsp, Int4 trunc_len)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
valid.c:1511:16: 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 -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:184:3: 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:263:15: warning: variable 'errstr' set but not used [-Wunused-but-set-variable]
const char *errstr;
^~~~~~
valapi.c: In function 'DoesFieldValueMatchExpression':
valapi.c:292:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", ufp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:748:3: warning: 'cLineType' may be used uninitialized in this function [-Wmaybe-uninitialized]
fprintf(stderr,"%04d: 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 -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:184:3: 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 -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:184:3: 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:1267:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if(stptrtemp[j+i*aligndim]+lenptrtemp[i]>bslen)
^
alignval.c: In function 'PercentStringMatch':
alignval.c:1579:32: 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:2004:12: warning: variable 'aln_len' set but not used [-Wunused-but-set-variable]
Int4 aln_len, start, stop;
^~~~~~~
alignval.c: In function 'ValidateSeqAlign':
alignval.c:2125:16: warning: variable 'ans' set but not used [-Wunused-but-set-variable]
MsgAnswer ans;
^~~
alignval.c: In function 'GetAlignmentColumnPercentIdentities':
alignval.c:2511:14: 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:2002:13: warning: 'CheckAlnSeqLens' defined but not used [-Wunused-function]
static void CheckAlnSeqLens (SeqAlignPtr salp)
^~~~~~~~~~~~~~~
alignval.c:1560:16: warning: 'IsSipContainedInStdseg' defined but not used [-Wunused-function]
static Boolean IsSipContainedInStdseg(SeqIdPtr sip, StdSegPtr ssp)
^~~~~~~~~~~~~~~~~~~~~~
alignval.c:602:13: 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 -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:184:3: 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:2012:18: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
sqnutil1.c: In function 'ParseAnticodon':
sqnutil1.c:3494:14: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil1.c: In function 'ParseCodeBreak':
sqnutil1.c:3617:17: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil1.c: In function 'CleanUpPubdescAuthors':
sqnutil1.c:9093:20: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
ValNodePtr PNTR prev;
^~~~
sqnutil1.c: In function 'FixWrongFuzzOnPlusStrand':
sqnutil1.c:11948:15: warning: unused variable 'spp' [-Wunused-variable]
SeqPntPtr spp;
^~~
sqnutil1.c: In function 'FixWrongFuzzOnMinusStrand':
sqnutil1.c:12007:15: warning: unused variable 'spp' [-Wunused-variable]
SeqPntPtr spp;
^~~
sqnutil1.c: In function 'ConsolidateBioSourceNotes':
sqnutil1.c:13250:21: warning: variable 'note_mod' set but not used [-Wunused-but-set-variable]
OrgModPtr mod, note_mod;
^~~~~~~~
sqnutil1.c:13249:21: warning: variable 'note_ssp' set but not used [-Wunused-but-set-variable]
SubSourcePtr ssp, note_ssp;
^~~~~~~~
sqnutil1.c: In function 'RemoveUnnecessaryGeneXrefs':
sqnutil1.c:15059:24: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil1.c: In function 'LinkTwoFeatures':
sqnutil1.c:17930:25: warning: variable 'prev_xref' set but not used [-Wunused-but-set-variable]
SeqFeatXrefPtr xref, prev_xref, next_xref;
^~~~~~~~~
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:10386:16: warning: 'CleanUpSgml' defined but not used [-Wunused-function]
static CharPtr CleanUpSgml (
^~~~~~~~~~~
sqnutil1.c:10272:13: warning: 'SortGoTermsSfp' defined but not used [-Wunused-function]
static void SortGoTermsSfp (
^~~~~~~~~~~~~~
sqnutil1.c:7405:16: warning: 'IsStringSingleToken' defined but not used [-Wunused-function]
static Boolean IsStringSingleToken (CharPtr str)
^~~~~~~~~~~~~~~~~~~
sqnutil1.c:4942:13: warning: 'CleanupConsSplice' defined but not used [-Wunused-function]
static void CleanupConsSplice (GBQualPtr gbq)
^~~~~~~~~~~~~~~~~
sqnutil1.c:2007:16: 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 -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:184:3: 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:5223:11: warning: variable 'last' set but not used [-Wunused-but-set-variable]
Uint1 last;
^~~~
sqnutil2.c: In function 'ReadFeatureTableEx':
sqnutil2.c:7254:18: warning: variable 'isnote' set but not used [-Wunused-but-set-variable]
Boolean isnote;
^~~~~~
sqnutil2.c:7246:18: warning: variable 'endsinspace' set but not used [-Wunused-but-set-variable]
Boolean endsinspace;
^~~~~~~~~~~
sqnutil2.c: In function 'SeqEntryCopyReplace':
sqnutil2.c:9270:8: warning: variable 'type' set but not used [-Wunused-but-set-variable]
Uint1 type = 0;
^~~~
sqnutil2.c: In function 'StreamingReadBioseq':
sqnutil2.c:10095:10: warning: variable 'level' set but not used [-Wunused-but-set-variable]
Int2 level;
^~~~~
sqnutil2.c: In function 'StreamAsnForDescriptors':
sqnutil2.c:10328:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (rval = StreamingReadSeqEntry (aip, sp, &sr)) {
^~~~
sqnutil2.c: In function 'WriteAsnWithReplacedDescriptors':
sqnutil2.c:10749:12: 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:11700:18: warning: variable 'begin' set but not used [-Wunused-but-set-variable]
Int4 begin;
^~~~~
sqnutil2.c: In function 'ReadFastaOnly':
sqnutil2.c:11894:18: warning: variable 'seqid' set but not used [-Wunused-but-set-variable]
Char seqid [2048];
^~~~~
sqnutil2.c: In function 'ReadDeltaFastaWithEmptyDefline':
sqnutil2.c:12446:29: warning: variable 'seqid' set but not used [-Wunused-but-set-variable]
Char line [4096], seqid [2048];
^~~~~
sqnutil2.c: In function 'SortSeqGraphProc':
sqnutil2.c:13002:26: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (gip2->right < gip2->right) {
^
sqnutil2.c: In function 'PrintQualityScoresToBuffer':
sqnutil2.c:13052:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil2.c: In function 'GetScoresbySeqId':
sqnutil2.c:13461:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil2.c: In function 'RemoveGapsFromDeltaLocation':
sqnutil2.c:15480:15: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil2.c: In function 'IsStringInSpanInList':
sqnutil2.c:16693:11: warning: variable 'str_val' set but not used [-Wunused-but-set-variable]
Int4 str_val;
^~~~~~~
sqnutil2.c:16691:27: 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:18415:35: 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:18779:14: warning: variable 'target_strand' set but not used [-Wunused-but-set-variable]
Uint1 target_strand;
^~~~~~~~~~~~~
sqnutil2.c:18778:14: warning: variable 'seq_len' set but not used [-Wunused-but-set-variable]
Int4 seq_len;
^~~~~~~
sqnutil2.c: In function 'AdjustForConsensusSpliceCallback':
sqnutil2.c:20313:33: 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:20926:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
sqnutil2.c: In function 'RemoveBadCodonRecognizedCallback':
sqnutil2.c:22812:13: warning: variable 'rcodon' set but not used [-Wunused-but-set-variable]
Uint1 rcodon [4];
^~~~~~
sqnutil2.c: In function 'CompareStructuredComment':
sqnutil2.c:25151:23: warning: variable 'ovp2' set but not used [-Wunused-but-set-variable]
ObjValNodePtr ovp1, ovp2;
^~~~
sqnutil2.c:25151:17: warning: variable 'ovp1' set but not used [-Wunused-but-set-variable]
ObjValNodePtr ovp1, ovp2;
^~~~
sqnutil2.c: In function 'UniqueAndCountValNodeCS':
sqnutil2.c:25546:17: warning: variable 'curr' set but not used [-Wunused-but-set-variable]
ValNodePtr curr;
^~~~
sqnutil2.c: In function 'PerformArticleQuery':
sqnutil2.c:25810:20: warning: variable 'debug_mode' set but not used [-Wunused-but-set-variable]
Boolean debug_mode = FALSE;
^~~~~~~~~~
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:18065:19: warning: 'AuthAffilListFree' defined but not used [-Wunused-function]
static ValNodePtr AuthAffilListFree (ValNodePtr list)
^~~~~~~~~~~~~~~~~
sqnutil2.c:18044:21: warning: 'AuthAffilNew' defined but not used [-Wunused-function]
static AuthAffilPtr AuthAffilNew (CharPtr affil)
^~~~~~~~~~~~
sqnutil2.c:16282:19: warning: 'MakeTranscriptomeIDTokensFromLine' defined but not used [-Wunused-function]
static ValNodePtr MakeTranscriptomeIDTokensFromLine (CharPtr line)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil2.c:16188:13: warning: 'RevCompFeatsOnBioseq' defined but not used [-Wunused-function]
static void RevCompFeatsOnBioseq (BioseqPtr bsp)
^~~~~~~~~~~~~~~~~~~~
sqnutil2.c:8333:16: warning: 'DoesSeqEntryAccessionMatchList' defined but not used [-Wunused-function]
static Boolean DoesSeqEntryAccessionMatchList (SeqEntryPtr sep, ValNodePtr accn_list)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil2.c:4684:16: 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 -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:184:3: 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:528:22: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil3.c: In function 'CautiousSeqEntryCleanup':
sqnutil3.c:2178:16: warning: variable 'taxserver' set but not used [-Wunused-but-set-variable]
Boolean taxserver;
^~~~~~~~~
sqnutil3.c: In function 'AddGapSeqLit':
sqnutil3.c:3127:19: warning: unused variable 'gap_chars' [-Wunused-variable]
CharPtr gap_chars = "NNNNNNNNNN"
^~~~~~~~~
sqnutil3.c: In function 'ConvertSegSetsToDeltaSequencesInt':
sqnutil3.c:3382:26: 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:4797:32: warning: variable 'num_sets' set but not used [-Wunused-but-set-variable]
Int4 index, curr_seg, num_sets;
^~~~~~~~
sqnutil3.c:4791:26: warning: variable 'salp_last' set but not used [-Wunused-but-set-variable]
SeqAlignPtr salp_list, salp_last;
^~~~~~~~~
sqnutil3.c:4791:15: warning: variable 'salp_list' set but not used [-Wunused-but-set-variable]
SeqAlignPtr salp_list, salp_last;
^~~~~~~~~
sqnutil3.c: In function 'ConvertContainedCDSToMiscFeat':
sqnutil3.c:12824:14: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil3.c: In function 'OrgNameMatchExceptOldName':
sqnutil3.c:13713:28: warning: self-comparison always evaluates to false [-Wtautological-compare]
|| onp2->mgcode != onp2->mgcode
^~
sqnutil3.c: In function 'FindMismatchedCitSubAffiliations':
sqnutil3.c:19281:14: warning: variable 'has_seq_submit' set but not used [-Wunused-but-set-variable]
Boolean has_seq_submit = TRUE;
^~~~~~~~~~~~~~
sqnutil3.c: In function 'GetCDSformRNA':
sqnutil3.c:20267:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil3.c: In function 'FindTextInFlatfileOncaller':
sqnutil3.c:22140:19: warning: variable 'okay' set but not used [-Wunused-but-set-variable]
Boolean okay;
^~~~
sqnutil3.c: In function 'CheckForTitleAuthorConflicts':
sqnutil3.c:23168:14: warning: variable 'author_conflict' set but not used [-Wunused-but-set-variable]
Boolean author_conflict = FALSE;
^~~~~~~~~~~~~~~
sqnutil3.c: In function 'SortVnpByBspProjectId':
sqnutil3.c:26956:31: 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:31033:21: warning: variable 'special_flag' set but not used [-Wunused-but-set-variable]
Boolean special_flag = FALSE;
^~~~~~~~~~~~
sqnutil3.c: In function 'CollectionDateIsInTheFuture':
sqnutil3.c:34586:20: warning: variable 'time' set but not used [-Wunused-but-set-variable]
CharPtr str, time;
^~~~
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:35189:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
sqnutil3.c:36777:13: warning: 'TestLatLonFormatting' defined but not used [-Wunused-function]
static void TestLatLonFormatting (FILE *fp)
^~~~~~~~~~~~~~~~~~~~
sqnutil3.c:34406:22: warning: 'BetterDateFree' defined but not used [-Wunused-function]
static BetterDatePtr BetterDateFree (BetterDatePtr dp)
^~~~~~~~~~~~~~
sqnutil3.c:33998:16: warning: 'GetColon' defined but not used [-Wunused-function]
static CharPtr GetColon (CharPtr str)
^~~~~~~~
sqnutil3.c:17224:24: warning: 'IntervalPairFree' defined but not used [-Wunused-function]
static IntervalPairPtr IntervalPairFree (IntervalPairPtr i)
^~~~~~~~~~~~~~~~
sqnutil3.c:10883:16: warning: 'IsMitochondrionBioseq' defined but not used [-Wunused-function]
static Boolean IsMitochondrionBioseq(BioseqPtr bsp)
^~~~~~~~~~~~~~~~~~~~~
sqnutil3.c: In function 'LinkCDSmRNAbyLabelAndLocationCallback':
sqnutil3.c:876:23: warning: 'best_diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (diff < best_diff) {
^
sqnutil3.c: In function 'tRNASameStrandBioseqCallback':
sqnutil3.c:16769:8: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (strand == Seq_strand_minus) {
^
sqnutil3.c: In function 'CheckForDivConflicts':
sqnutil3.c:8132:15: warning: 'sfp' may be used uninitialized in this function [-Wmaybe-uninitialized]
else ValNodeAddPointer(&(grp_sdp_sfp[num_grp]), OBJ_SEQFEAT, sfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:8131:13: warning: 'sdp' may be used uninitialized in this function [-Wmaybe-uninitialized]
ValNodeAddPointer(&(grp_sdp_sfp[num_grp]), OBJ_SEQDESC, sdp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c: In function 'FindMismatchedComments':
sqnutil3.c:26612:47: warning: 'sdp' may be used uninitialized in this function [-Wmaybe-uninitialized]
sprintf (fmt, sub_fmt, (CharPtr) sdp->data.ptrvalue);
~~~~~~~~~^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:8566:43: warning: variable 'twobefore' set but not used [-Wunused-but-set-variable]
FeatureClausePtr thisclause, onebefore, twobefore, oneafter, twoafter;
^~~~~~~~~
sqnutil4.c: In function 'SmashOneTallClause':
sqnutil4.c:9900:20: warning: variable 'subclause_featlist' set but not used [-Wunused-but-set-variable]
ValNodePtr subclause_featlist;
^~~~~~~~~~~~~~~~~~
sqnutil4.c: In function 'GetFeatureClauseForSeg':
sqnutil4.c:10787:21: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start, stop;
^~~~~
sqnutil4.c: In function 'RemoveAutodefObjectsForDesc':
sqnutil4.c:13618:18: warning: unused variable 'bssp' [-Wunused-variable]
BioseqSetPtr bssp;
^~~~
sqnutil4.c:13617:15: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp;
^~~
sqnutil4.c: In function 'ConvertProtToImpFunc':
sqnutil4.c:15072:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil4.c: In function 'ExtraCDSCreationActions':
sqnutil4.c:15989:28: warning: variable 'nsep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr psep, nsep;
^~~~
sqnutil4.c: In function 'TESTDisplayQualCombo':
sqnutil4.c:17099:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Int4 val;
^~~
sqnutil4.c: In function 'ConvertCDSToMatPeptideForOverlappingCDS':
sqnutil4.c:18589:15: warning: variable 'crp' set but not used [-Wunused-but-set-variable]
CdRegionPtr crp;
^~~
sqnutil4.c: In function 'AddNewUniqueAnnotations':
sqnutil4.c:18780:39: 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:19443:27: warning: variable 'vnp_last' set but not used [-Wunused-but-set-variable]
ValNodePtr list, vnp, vnp_last = NULL;
^~~~~~~~
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:64:
../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:17248:13: warning: 'TESTDisplayList' defined but not used [-Wunused-function]
static void TESTDisplayList (ValNodePtr new_list)
^~~~~~~~~~~~~~~
sqnutil4.c:17219:19: warning: 'ExpandOneComboListUsingAllPresentQuals' defined but not used [-Wunused-function]
static ValNodePtr ExpandOneComboListUsingAllPresentQuals (QualComboPtr q)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil4.c:16930:16: warning: 'RemoveFieldFromUniqBioSrcGrpList' defined but not used [-Wunused-function]
static Boolean RemoveFieldFromUniqBioSrcGrpList (ValNodePtr list, FieldTypePtr field)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil4.c:10029:19: warning: 'RemoveAllButLastCDS' defined but not used [-Wunused-function]
static ValNodePtr RemoveAllButLastCDS (
^~~~~~~~~~~~~~~~~~~
sqnutil4.c:9998:13: warning: 'SmashTallClauses' defined but not used [-Wunused-function]
static void SmashTallClauses (
^~~~~~~~~~~~~~~~
sqnutil4.c:9834:13: warning: 'RemoveFeats' defined but not used [-Wunused-function]
static void RemoveFeats (
^~~~~~~~~~~
sqnutil4.c:5211:13: warning: 'CountFeatures' defined but not used [-Wunused-function]
static Int4 CountFeatures (
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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;
^~~
subutil.c: In function 'MakeRNAFeature':
subutil.c:3639:29: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (AA_for_tRNA != '\0')
^~
subutil.c:3639:17: note: did you mean to dereference the pointer?
if (AA_for_tRNA != '\0')
^
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 -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:184:3: 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 -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:184:3: 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:50,
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 'print_taxinfo':
asn2ff1.c:4356:19: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(tmp, "%d", gcode);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 4 bytes into a destination of size 3
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:169,
from asn2ff2.c:216:
/usr/include/features.h:184:3: 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:50,
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 -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:48,
from asn2ff3.c:39:
/usr/include/features.h:184:3: 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:1073:26: warning: unused variable 'qual_temp' [-Wunused-variable]
GBQualPtr gbqual, qual, qual_temp=NULL, qual_gene=NULL;
^~~~~~~~~
asn2ff3.c:1072:10: warning: unused variable 'still_looking' [-Wunused-variable]
Boolean still_looking=TRUE;
^~~~~~~~~~~~~
asn2ff3.c: In function 'mRNAEvidenceComment':
asn2ff3.c:1157:9: warning: unused variable 'Locus_id' [-Wunused-variable]
Int4 Locus_id = 0;
^~~~~~~~
asn2ff3.c: In function 'Add_gene_id':
asn2ff3.c:2717:24: 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);
~^ ~~~~~~~~~~~~~~~~~~
%p
asn2ff3.c: In function 'Add_trid':
asn2ff3.c:3142:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf(buf, "%ld", sip->data.intvalue);
~~^ ~~~~~~~~~~~~~~~~~~
%lld
asn2ff3.c:3123:9: warning: unused variable 'gi' [-Wunused-variable]
BIG_ID gi = -1;
^~
asn2ff3.c: In function 'AddPID':
asn2ff3.c:3185:21: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf(buf, "%ld", sip->data.intvalue);
~~^ ~~~~~~~~~~~~~~~~~~
%lld
At top level:
asn2ff3.c:2702:13: 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:50,
from asn2ff3.c:39:
../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:48,
from asn2ff3.c:39:
asn2ff3.c: In function 'Add_dbxref.isra.1':
../include/ncbimem.h:232:23: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
asn2ff3.c:216:10: note: 'val' was declared here
CharPtr val;
^~~
asn2ff3.c: In function 'GettRNAaa':
asn2ff3.c:1619:9: warning: 'seq_code' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr = Get3LetterSymbol(seq_code, table, trna->aa, error_msgs);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2ff3.c: In function 'ConvertToNAImpFeat':
asn2ff3.c:2254:23: warning: '%ld' directive writing between 1 and 3 bytes into a region of size 2 [-Wformat-overflow=]
sprintf(buf_ptr, "%ld", (long) (cdr->frame));
^~~
asn2ff3.c:2254:22: note: directive argument in the range [1, 255]
sprintf(buf_ptr, "%ld", (long) (cdr->frame));
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:48,
from asn2ff3.c:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 4 bytes into a destination of size 2
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:48,
from asn2ff4.c:273:
/usr/include/features.h:184:3: 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' [-Wdangling-else]
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 were 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 were guarded by the 'if'
gsc.seglevels = 1;
^~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:50,
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)) {
^~~~~~~~~~~~~~
asn2ff4.c: In function 'CreateImpFeatFromProt':
asn2ff4.c:1723:18: warning: '%d' directive writing between 1 and 3 bytes into a region of size 2 [-Wformat-overflow=]
sprintf(buf, "%d", cdr->frame);
^~
asn2ff4.c:1723:17: note: directive argument in the range [1, 255]
sprintf(buf, "%d", cdr->frame);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:48,
from asn2ff4.c:273:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 4 bytes into a destination of size 2
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:48,
from asn2ff5.c:177:
/usr/include/features.h:184:3: 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' [-Wdangling-else]
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:50,
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 -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:184:3: 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 were 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 -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:184:3: 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:2202:19: warning: variable 'right' set but not used [-Wunused-but-set-variable]
Boolean left, right;
^~~~~
asn2gnb1.c: In function 's_LocusGetBaseName':
asn2gnb1.c:2350:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
asn2gnb1.c:2352:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
newLength = segNameLen - deleteChars;
^~~~~~~~~
asn2gnb1.c: In function 'DoOneSection':
asn2gnb1.c:2522:24: warning: variable 'iasp' set but not used [-Wunused-but-set-variable]
IntAsn2gbSectPtr iasp;
^~~~
asn2gnb1.c:2514:24: warning: variable 'bkmask' set but not used [-Wunused-but-set-variable]
BlockMask bkmask;
^~~~~~
asn2gnb1.c: In function 'Count2Seg':
asn2gnb1.c:3438:18: warning: variable 'to' set but not used [-Wunused-but-set-variable]
Int4 to;
^~
asn2gnb1.c:3436:18: warning: variable 'parent' set but not used [-Wunused-but-set-variable]
BioseqPtr parent;
^~~~~~
asn2gnb1.c: At top level:
asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces]
static ModeFlags flagTable [] = {
^
asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces]
asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces]
asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces]
asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces]
asn2gnb1.c: In function 'SeqIdWriteForTable':
asn2gnb1.c:5808:13: warning: variable 'pdb' set but not used [-Wunused-but-set-variable]
pdb = NULL, general = NULL, gi = NULL;
^~~
asn2gnb1.c:5807:40: 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:255:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb1.c:6951:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb1.c:6930:20: 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:255:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb1.c:7072:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb1.c: In function 'asn2gnbk_cleanup':
asn2gnb1.c:7118:21: warning: variable 'iasp' set but not used [-Wunused-but-set-variable]
IntAsn2gbSectPtr iasp;
^~~~
asn2gnb1.c: In function 'SeqEntryToGnbk':
asn2gnb1.c:7304:22: warning: variable 'userdata' set but not used [-Wunused-but-set-variable]
Pointer userdata = NULL;
^~~~~~~~
asn2gnb1.c:7299:22: 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 -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:184:3: 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:217:11: warning: variable 'ch' set but not used [-Wunused-but-set-variable]
Char ch;
^~
asn2gnb2.c: In function 'AddLocusBlock':
asn2gnb2.c:1361:66: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
} else if ((moltype >= 2 && moltype <= 8) || moltype >= 10 && moltype <= 11) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
asn2gnb2.c: In function 'IsSuccessor':
asn2gnb2.c:1742:15: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (accp != '\0' && prevp != '\0') {
^~
asn2gnb2.c:1742:10: note: did you mean to dereference the pointer?
while (accp != '\0' && prevp != '\0') {
^
asn2gnb2.c:1742:34: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (accp != '\0' && prevp != '\0') {
^~
asn2gnb2.c:1742:28: note: did you mean to dereference the pointer?
while (accp != '\0' && prevp != '\0') {
^
asn2gnb2.c: In function 'IsProjectAccn':
asn2gnb2.c:1767:38: warning: comparison between pointer and zero character constant [-Wpointer-compare]
for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr); ++ptr, ++letters) continue;
^~
asn2gnb2.c:1767:34: note: did you mean to dereference the pointer?
for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr); ++ptr, ++letters) continue;
^
asn2gnb2.c: In function 'AddDblinkBlock':
asn2gnb2.c:2892:22: warning: variable 'parentID' set but not used [-Wunused-but-set-variable]
Int4 parentID;
^~~~~~~~
asn2gnb2.c: In function 'AddSPBlock':
asn2gnb2.c:3409:14: warning: implicit declaration of function 'PrintDate'; did you mean 'truncate'? [-Wimplicit-function-declaration]
string = PrintDate (spb->created);
^~~~~~~~~
truncate
asn2gnb2.c:3409:12: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
string = PrintDate (spb->created);
^
asn2gnb2.c:3417:12: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
string = PrintDate (spb->sequpd);
^
asn2gnb2.c:3424:12: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
string = PrintDate (spb->annotupd);
^
asn2gnb2.c: In function 'AddSourceOrganismBlock':
asn2gnb2.c:5056:22: warning: variable 'common' set but not used [-Wunused-but-set-variable]
CharPtr common;
^~~~~~
asn2gnb2.c: In function 'GetRefsOnBioseq':
asn2gnb2.c:5893:22: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
asn2gnb2.c:5890:22: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb2.c:5884:22: warning: variable 'right' set but not used [-Wunused-but-set-variable]
Int4 right;
^~~~~
asn2gnb2.c:5878:22: warning: variable 'left' set but not used [-Wunused-but-set-variable]
Int4 left;
^~~~
asn2gnb2.c: In function 'AddLocusBlock':
asn2gnb2.c:244:25: warning: '%0*d' directive writing between 1 and 32768 bytes into a region of size 4 [-Wformat-overflow=]
sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg);
^~~~
asn2gnb2.c:244:23: note: directive argument in the range [0, 65535]
sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg);
^~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 3 and 32770 bytes into a destination of size 5
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:246:24: warning: '%0*d' directive writing between 1 and 32768 bytes into a region of size 5 [-Wformat-overflow=]
sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg);
^~~~
asn2gnb2.c:246:23: note: directive argument in the range [0, 65535]
sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg);
^~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 32769 bytes into a destination of size 5
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:1514:48: warning: '" title="Jump to the comment section of this record">Comment</a></li>' directive writing 69 bytes into a region of size between 66 and 106 [-Wformat-overflow=]
sprintf (sect, "<li><a href=\"#comment_%s\" title=\"Jump to the comment section of this record\">Comment</a></li>",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 92 and 132 bytes into a destination of size 128
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:1518:46: warning: '" title="Jump to the feature table of this record">Features</a></li>' directive writing 68 bytes into a region of size between 66 and 106 [-Wformat-overflow=]
sprintf (sect, "<li><a href=\"#feature_%s\" title=\"Jump to the feature table of this record\">Features</a></li>",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 91 and 131 bytes into a destination of size 128
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:1527:117: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (sect, "<li><a href=\"#genome_%s\" title=\"Jump to the genome section of this record\">Genome</a></li>",
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 89 and 129 bytes into a destination of size 128
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:1532:117: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (sect, "<li><a href=\"#contig_%s\" title=\"Jump to the contig section of this record\">Contig</a></li>",
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 89 and 129 bytes into a destination of size 128
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:796:22: warning: variable 'urf' set but not used [-Wunused-but-set-variable]
UserFieldPtr ufp, urf = NULL;
^~~
asn2gnb3.c: In function 'AddCommentBlock':
asn2gnb3.c:2656:22: warning: variable 'is_wgs' set but not used [-Wunused-but-set-variable]
Boolean is_wgs = FALSE;
^~~~~~
asn2gnb3.c: In function 'GetSourcesOnBioseq':
asn2gnb3.c:5472:22: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
asn2gnb3.c:5470:22: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start;
^~~~~
asn2gnb3.c:5468:22: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb3.c: In function 'AddSourceFeatBlock':
asn2gnb3.c:5989:22: warning: unused variable 'sip' [-Wunused-variable]
SeqIdPtr sip;
^~~
asn2gnb3.c: In function 'GetFeatsOnCdsProduct':
asn2gnb3.c:6446:22: warning: variable 'isRefSeq' set but not used [-Wunused-but-set-variable]
Boolean isRefSeq;
^~~~~~~~
asn2gnb3.c: In function 'GetRemoteFeatsOnCdsProduct':
asn2gnb3.c:6595:20: warning: variable 'lastsfp' set but not used [-Wunused-but-set-variable]
SeqFeatPtr lastsfp;
^~~~~~~
asn2gnb3.c:6594:20: warning: variable 'lastsap' set but not used [-Wunused-but-set-variable]
SeqAnnotPtr lastsap;
^~~~~~~
asn2gnb3.c:6593:20: warning: variable 'lastright' set but not used [-Wunused-but-set-variable]
Int4 lastright;
^~~~~~~~~
asn2gnb3.c:6592:20: warning: variable 'lastleft' set but not used [-Wunused-but-set-variable]
Int4 lastleft;
^~~~~~~~
asn2gnb3.c:6591:20: warning: variable 'isRefSeq' set but not used [-Wunused-but-set-variable]
Boolean isRefSeq;
^~~~~~~~
asn2gnb3.c: In function 'GetFeatsOnBioseq':
asn2gnb3.c:6895:22: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start;
^~~~~
asn2gnb3.c:6866:22: 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));
^~~~~~~~~~~~~~~
asn2gnb3.c:1582:16: warning: 'nsWGSGapsString' defined but not used [-Wunused-variable]
static CharPtr nsWGSGapsString = "The strings of n's in this record represent gaps between contigs or uncallable bases.";
^~~~~~~~~~~~~~~
asn2gnb3.c:1581:16: warning: 'nsAreGapsString' defined but not used [-Wunused-variable]
static CharPtr nsAreGapsString = "The strings of n's in this record represent gaps between contigs, and the length of each string corresponds to the length of the gap.";
^~~~~~~~~~~~~~~
asn2gnb3.c: In function 'AddCommentBlock':
asn2gnb3.c:3429:29: warning: 'nm' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (IS_protdb_accession (nm)) {
^~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:3723:50: warning: "/*" within comment [-Wcomment]
StringChr (str + 1, '(') == NULL /* && StringChr (str, ',') != NULL */) {
asn2gnb4.c:3101:24: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb4.c:3042:24: warning: variable 'at_end' set but not used [-Wunused-but-set-variable]
Boolean at_end = FALSE;
^~~~~~
asn2gnb4.c: In function 'FF_asn2gb_www_featkey_Ex':
asn2gnb4.c:5325:16: warning: variable 'prefix' set but not used [-Wunused-but-set-variable]
CharPtr prefix = "?";
^~~~~~
asn2gnb4.c: In function 'FormatFeatureBlockEx':
asn2gnb4.c:6572:22: 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:255:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb4.c:8796:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb4.c: In function 'FormatFeatureQuals':
../include/ncbistd.h:255:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb4.c:8869:19: 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:7695:24: 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 -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:184:3: 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:2108:16: 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 -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:184:3: 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:2546:27: 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:5701:20: warning: variable 'dspnext' set but not used [-Wunused-but-set-variable]
DeltaSeqPtr dspnext;
^~~~~~~
asn2gnb6.c: In function 'ProcessGapSpecialFormat':
asn2gnb6.c:6041:13: warning: unused variable 'sip' [-Wunused-variable]
SeqIdPtr sip;
^~~
asn2gnb6.c: In function 'FormatSequenceBlock':
asn2gnb6.c:6168:21: 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));
^~~~~~~~~~~~~~~
asn2gnb6.c:76:16: warning: 'link_lat_lon' defined but not used [-Wunused-variable]
static CharPtr link_lat_lon = "https://www.ncbi.nlm.nih.gov/projects/Sequin/latlonview.html?";
^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -fPIC -D_PNG -I../include -DWIN_MOTIF gbfeat.c
gbfeat.c: In function 'CkLabelType':
gbfeat.c:1465:33: 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 -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 -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:102:
/usr/include/features.h:184:3: 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:2134:24: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (*current_col != '\0')
^
gbparint.c: In function 'Nlm_gbparselex_ver':
gbparint.c:2520:24: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
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 -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] = {
^
"Ala", 'A',
{ }
"Asx", 'B',
{ }
"Cys", 'C',
{ }
"Asp", 'D',
{ }
"Glu", 'E',
{ }
"Phe", 'F',
{ }
"Gly", 'G',
{ }
"His", 'H',
{ }
"Ile", 'I',
{ }
"Xle", 'J', /* was - notice no 'J', breaks naive meaning of index -Karl */
{ }
"Lys", 'K',
{ }
"Leu", 'L',
{ }
"Met", 'M',
{ }
"Asn", 'N',
{ }
"Pyl", 'O', /* was - no 'O' */
{ }
"Pro", 'P',
{ }
"Gln", 'Q',
{ }
"Arg", 'R',
{ }
"Ser", 'S',
{ }
"Thr", 'T',
{ }
"Val", 'V',
{ }
"Trp", 'W',
{ }
"Sec", 'U', /* was - not in iupacaa */
{ }
"Xxx", 'X',
{ }
"Tyr", 'Y',
{ }
"Glx", 'Z',
{ }
"TERM", '*', /* not in iupacaa */ /*changed by Tatiana 06.07.95?`*/
{ }
"OTHER", 'X'};
{ }
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:48,
from ffprint.c:127:
/usr/include/features.h:184:3: 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:50,
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 -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:184:3: 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:50,
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";
^~~~~~~~~~~
wprint.c: In function 'PrintDate':
wprint.c:188:20: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(day, "%d", (int) (date -> data[3] ));
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from wprint.c:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 4 bytes into a destination of size 3
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
wprint.c: In function 'www_db_xref':
wprint.c:969:20: warning: '%d' directive writing between 1 and 6 bytes into a region of size between 4 and 9 [-Wformat-overflow=]
sprintf(id, "%d%d", id1, id2);
^~
wprint.c:969:17: note: directive argument in the range [-32768, 32767]
sprintf(id, "%d%d", id1, id2);
^~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from wprint.c:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 3 and 13 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:184:3: 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 -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:53:
/usr/include/features.h:184:3: 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:311:13: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
seqmgr.c: In function 'ClearBioseqFindCache':
seqmgr.c:897:14: 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 were 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:5657:14: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
SeqLocPtr prev, tmp;
^~~~
seqmgr.c: In function 'SeqEntryAsnOut':
seqmgr.c:11799:41: warning: variable 'aopp_desc' set but not used [-Wunused-but-set-variable]
AsnOptionPtr aopp_feat = NULL, aopp_desc = NULL;
^~~~~~~~~
seqmgr.c:11799:23: 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:63:
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));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 were 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 were 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 -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:169,
from gather.c:44:
/usr/include/features.h:184:3: 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:4827:30: 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)));
^
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:169,
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:2280:11: 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:2280:12: 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:2470:58: 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:2218:10: warning: 'mag_val' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 mag_val; /*the magnification value */
^~~~~~~
gather.c: In function 'GatherBioseqFunc':
gather.c:3307:53: warning: 'tlen' may be used uninitialized in this function [-Wmaybe-uninitialized]
rdp->right = offset + tlen - 1;
~~~~~~~^~~~~~
gather.c:3280:39: warning: 'trunc_r' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (trunc_r)
^
gather.c:3285:40: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 'coll_align_data':
jzcoll.c:2631:20: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf(buf, "%d", gilist->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~~~~
%lld
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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:4463:23: 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:6981:27: warning: variable 'does_match' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE, does_match, do_remove;
^~~~~~~~~~
macroapi.c: In function 'ParseCodonsRecognizedFromCommaDelimitedList':
macroapi.c:7726:41: warning: pointer targets in passing argument 1 of 'ExpandWobbleCodon' differ in signedness [-Wpointer-sign]
wobble_list = ExpandWobbleCodon(codon);
^~~~~
macroapi.c:7636:19: note: expected 'Nlm_CharPtr {aka char *}' but argument is of type 'Nlm_Uint1 * {aka unsigned char *}'
static ValNodePtr ExpandWobbleCodon (CharPtr codon)
^~~~~~~~~~~~~~~~~
macroapi.c: In function 'GetQualFromFeatureAnyType':
macroapi.c:8537:8: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (str == NULL
~~~~~~~~~~~
&& (field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_pseudo)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:8681:23: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", vnp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'SetNameInPrimerList':
macroapi.c:10682:21: warning: variable 'prev_pp' set but not used [-Wunused-but-set-variable]
PCRPrimerPtr pp, prev_pp = NULL;
^~~~~~~
macroapi.c: In function 'SetSeqInPrimerList':
macroapi.c:10703:21: warning: variable 'prev_pp' set but not used [-Wunused-but-set-variable]
PCRPrimerPtr pp, prev_pp = NULL;
^~~~~~~
macroapi.c: In function 'GetGenomeProjectIdFromBioseq':
macroapi.c:12881:27: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", ufp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'RemoveGenomeProjectIdFromBioseq':
macroapi.c:12916:27: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", ufp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'SetGenomeProjectIdOnBioseq':
macroapi.c:12957:27: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", ufp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'GetPubFieldFromPub':
macroapi.c:15043:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (str, "%d", the_pub->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'GetCitListsForSeqEntry':
macroapi.c:15825:19: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
macroapi.c:15823:19: warning: variable 'okay' set but not used [-Wunused-but-set-variable]
Boolean okay;
^~~~
macroapi.c: In function 'GetPubclassQualFromPub':
macroapi.c:18324:11: warning: unused variable 'str' [-Wunused-variable]
CharPtr str = NULL;
^~~
macroapi.c: In function 'GetPubMLStatus':
macroapi.c:18681:14: warning: variable 'csp' set but not used [-Wunused-but-set-variable]
CitSubPtr csp;
^~~
macroapi.c: In function 'CollectDBLinkObjectsForApply':
macroapi.c:20029:72: warning: unused variable 'tmp_tail' [-Wunused-variable]
ValNodePtr target_list = NULL, bsp_list = NULL, tmp_list = NULL, tmp_tail = NULL, vnp;
^~~~~~~~
macroapi.c:20029:55: warning: unused variable 'tmp_list' [-Wunused-variable]
ValNodePtr target_list = NULL, bsp_list = NULL, tmp_list = NULL, tmp_tail = NULL, vnp;
^~~~~~~~
macroapi.c: In function 'DoConvertActionToObjectListEx':
macroapi.c:20844:20: warning: unused variable 'already_added' [-Wunused-variable]
Boolean already_added, field_change;
^~~~~~~~~~~~~
macroapi.c: In function 'ApplyPartial5SetActionToSeqFeat':
macroapi.c:25749:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'ApplyPartial3SetActionToSeqFeat':
macroapi.c:25872:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'ApplyPartialBothSetActionToSeqFeat':
macroapi.c:25939:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'FindPosBeforeFeat':
macroapi.c:26236:15: warning: variable 'regulator' set but not used [-Wunused-but-set-variable]
SeqFeatPtr regulator = NULL, candidate;
^~~~~~~~~
macroapi.c: In function 'PerformAutofixInSeqEntry':
macroapi.c:29471:8: warning: unused variable 'num_created' [-Wunused-variable]
Int4 num_created = 0;
^~~~~~~~~~~
macroapi.c: In function 'AddFileDescriptors':
macroapi.c:29871:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (sdp = SeqDescAsnRead (aip, NULL)) {
^~~
macroapi.c: In function 'ApplyMacroToSeqEntryExEx':
macroapi.c:31907:28: warning: too many arguments for format [-Wformat-extra-args]
fprintf (log_fp, "Instantiated protein titles\n", num);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'PreprocessAddDescriptorListMacro':
macroapi.c:32020:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (sdp = SeqDescAsnRead (aip, NULL)) {
^~~
macroapi.c: In function 'FieldTypeFromString':
macroapi.c:32370:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (ft == NULL && StringsAreEquivalent(str, "location") || StringsAreEquivalent(str, "genome")) {
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'SummarizeRemoveOutsideAction':
macroapi.c:32939:11: warning: unused variable 'case_insensitive' [-Wunused-variable]
CharPtr case_insensitive = " (case insensitive)";
^~~~~~~~~~~~~~~~
macroapi.c: In function 'GetObjectTableForTabTable':
macroapi.c:37508:63: 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 'FormatMultipleDestinationErrorMessage':
macroapi.c:37987:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", vnp->data.intvalue + 1);
~^ ~~~~~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'CheckObjTableForExistingText':
macroapi.c:38084:14: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
macroapi.c: In function 'FixSuspectProductNamesInEntrezGene':
macroapi.c:40352:18: warning: variable 'prefix' set but not used [-Wunused-but-set-variable]
CharPtr prefix = NULL;
^~~~~~
In file included from ../include/tax3api.h:51:0,
from macroapi.c:67:
macroapi.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));
^~~~~~~~~~~~~~~~~~~
macroapi.c:37233:16: warning: 'IsFieldTypeProteinDesc' defined but not used [-Wunused-function]
static Boolean IsFieldTypeProteinDesc (FieldTypePtr ft)
^~~~~~~~~~~~~~~~~~~~~~
macroapi.c:27097:13: warning: 'GetDescriptorTypeFromDescriptorChoice' defined but not used [-Wunused-function]
static Int4 GetDescriptorTypeFromDescriptorChoice (Uint1 descriptor_choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:21298:13: warning: 'GetFieldsFromAECR' defined but not used [-Wunused-function]
static void GetFieldsFromAECR (AECRActionPtr act, FieldTypePtr PNTR pField, ValNodePtr PNTR pFieldPair)
^~~~~~~~~~~~~~~~~
macroapi.c:20787:16: warning: 'NoFieldChange' defined but not used [-Wunused-function]
static Boolean NoFieldChange (CharPtr new_val, ValNodePtr vnp, FieldTypePtr field_from, StringConstraintPtr scp, BatchExtraPtr batch_extra)
^~~~~~~~~~~~~
macroapi.c:16014:13: warning: 'InitBatchExtraForAECRActionAndObjectList' defined but not used [-Wunused-function]
static void InitBatchExtraForAECRActionAndObjectList (BatchExtraPtr batch_extra, AECRActionPtr action, ValNodePtr object_list)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:10389:16: warning: 'HasMultiplePrimerSets' defined but not used [-Wunused-function]
static Boolean HasMultiplePrimerSets (CharPtr value)
^~~~~~~~~~~~~~~~~~~~~
macroapi.c:5482:16: warning: 'DoesLocationMatchConstraint' defined but not used [-Wunused-function]
static Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:4590:13: warning: 'TestAdvancedStringMatch' defined but not used [-Wunused-function]
static void TestAdvancedStringMatch (void)
^~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:2806:13: warning: 'OriginFromOriginName' defined but not used [-Wunused-function]
static Int4 OriginFromOriginName (CharPtr origin_name)
^~~~~~~~~~~~~~~~~~~~
macroapi.c:1200:16: warning: 'IsObjectAppropriateForFieldPair' defined but not used [-Wunused-function]
static Boolean IsObjectAppropriateForFieldPair (Uint1 choice, Pointer data, FieldPairTypePtr fieldpair)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'ReadNameListFromString':
macroapi.c:14037:14: warning: 'ch_r1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*p_repl1 = ch_r1;
~~~~~~~~~^~~~~~~
macroapi.c:13946:11: note: 'ch_r1' was declared here
Char ch_r1, ch_r2, ch_r3;
^~~~~
macroapi.c: In function 'SetAuthorListFromString':
macroapi.c:14298:17: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
name_list = FreeNameList (1, vnp);
^~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'AlsoChangeMrnaForObject':
macroapi.c:20637:10: warning: 'mrna' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (mrna != NULL) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:363:33: warning: 'spp_1' may be used uninitialized in this function [-Wmaybe-uninitialized]
res_1 = SeqPortGetResidue(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 -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:184:3: 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 -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:184:3: 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 were 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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:1662:29: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j=0; j < numseg*dim && strandp!=NULL; j++, strandp++)
~~~~~~^~~~
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 -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:184:3: 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 'prot_to_rputprot':
salstruc.c:734:18: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (strptmp == '\0') break;
^~
salstruc.c:734:10: note: did you mean to dereference the pointer?
if (strptmp == '\0') break;
^
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 'data_collect_arrange':
salstruc.c:920:20: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
bspssp = new_seledstruct (entityID, itemID, OBJ_(tdp->feattype), 0,itemID,
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
from + adp->bufferstart, to + adp->bufferstart,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bspsip, Seq_strand_plus, TRUE, NULL, (Pointer) tdp, 0, 1);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:184:3: 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' [-Wdangling-else]
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:753:19: warning: 'PosFeat' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 BeginLines=0,PosFeat,StartLetter,StopLetter;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -fPIC -D_PNG -I../include -DWIN_MOTIF pgppop.c
pgppop.c:58:2: warning: missing braces around initializer [-Wmissing-braces]
{
^
pgppop.c:60:4:
255, 255, 255, /* default 0 0xffffff - */
{ }
255, 00, 153, /* hotpink 1 0xff1493 0xff0099 */
{ }
255, 0, 255, /* magenta 2 0xff00ff - */
{ }
153, 51, 255, /* purple 3 0x9b30ff 0x9933ff */
{ }
0, 0, 255, /* blue 4 0x0000ff - */
{ }
00, 153, 255, /* sky 5 0x1e90ff 0x0099ff */
{ }
0, 255, 255, /* cyan 6 0x00ffff - */
{ }
0, 255, 153, /* sea 7 0x00ff8f 0x00ff99 */
{ }
0, 255, 0, /* green 8 0x00ff00 - */
{ }
255, 255, 0, /* yellow 9 0xffff00 - */
{ }
255, 204, 0, /* gold 10 0xffa500 0xffcc00 */
{ }
255, 102, 0, /* orange 11 0xff4500 0xff6600 */
{ }
255, 0, 0, /* red 12 0xff0000 - */
{ }
255, 153, 153, /* pink 13 0xff7256 0xff9999 */
{ }
255, 204, 204, /* pinktint 14 0xffaeb9 0xffcccc */
{ }
255, 255, 255, /* white 15 0xffffff -*/
{ }
0, 0, 0, /* black 16 0x000000 - */
{ }
204, 204, 255, /* bluetint 17 0xb0e2ff - 0xccccff*/
{ }
153, 255, 153, /* greentint 18 0x9aff9a - 0x99ff99 */
{ }
255, 255, 153, /* yellowtint 19 0xffec8b - 0xffff99 */
{ }
102, 102, 102, /* gray 20 0x7d7d7d 0x666666 */
{ }
153, 102, 51, /* brown 21 0x8b5742 01x996633 */
{ }
255, 0, 0, /* perm colors 22: red 0xff0000 - */
{ }
0, 255, 0, /* perm colors 23: green 0x00ff00 - */
{ }
255, 0, 255, /* perm colors 24: magenta 0xff00ff - */
{ }
00, 153, 255, /* perm colors 25: sky 0x1e90ff 0x0099ff */
{ }
153, 51, 255, /* perm colors 26: purple 0x9b30ff 0x9933ff */
{ }
0, 255, 0, /* SS colors 27: helix, green 0x00ff00 - */
{ }
255, 204, 0, /* SS colors 28: strand, gold 0xffa500 0xffcc00 */
{ }
255, 102, 0, /* SS colors 29: turn, orange 0xff4500 0xff6600 */
{ }
0, 255, 255, /* SS colors 30: coil, cyan ox00ffff - */
{ }
255, 255, 0, /* highlight colors 31: yellow 0xffff00 - */
{ }
0, 0, 0 /* background colors 32: black 0x000000 - */
{
};
}
pgppop.c: In function 'DDV_WWW_get_CDS_minus':
pgppop.c:329:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
pgppop.c:327:5: warning: variable 'numivals2' set but not used [-Wunused-but-set-variable]
numivals2=0;
^~~~~~~~~
pgppop.c: In function 'DDV_WWW_get_CDS_plus':
pgppop.c:451:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
pgppop.c: In function 'DDV_DisplayTopScale':
pgppop.c:1300:7: warning: unused variable 'szBlank' [-Wunused-variable]
Char szBlank[TABLE_LEFT_MARGIN+5]={""};
^~~~~~~
pgppop.c: In function 'DDV_GetBLASTCompLine_1':
pgppop.c:1736:31: warning: array subscript has type 'char' [-Wchar-subscripts]
if (matrix[s][q]>0){
^
pgppop.c:1736:34: warning: array subscript has type 'char' [-Wchar-subscripts]
if (matrix[s][q]>0){
^
pgppop.c: In function 'DDV_DisplayDefaultAlign':
pgppop.c:3169:13: warning: unused variable 'sabp' [-Wunused-variable]
SABlockPtr sabp=NULL;/*indexed SeqAlign*/
^~~~
pgppop.c: In function 'DDV_ShowSeqAlign':
pgppop.c:3512:10: warning: unused variable 'szPopSetAuth' [-Wunused-variable]
Char szPopSetAuth[INFO_SIZE+1]={""};
^~~~~~~~~~~~
pgppop.c:3510:10: 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:3683:9: 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:49:
pgppop.c: At top level:
../include/objentgene.h:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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: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));
^~~~~~~~~~~~~~~
pgppop.c:2664:13: warning: 'DDV_PrintFastaGappedSequence' defined but not used [-Wunused-function]
static void DDV_PrintFastaGappedSequence(CharPtr szSequence,FILE *fp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pgppop.c:2617:13: warning: 'DDV_GetGappedSequence' defined but not used [-Wunused-function]
static void DDV_GetGappedSequence(SegmentPtr segp,CharPtr szSequence,
^~~~~~~~~~~~~~~~~~~~~
pgppop.c:1841:13: warning: 'DDV_HideMaskedLetters' defined but not used [-Wunused-function]
static void DDV_HideMaskedLetters(CharPtr szSeqMaster,ParaGPtr pgp,ValNodePtr mask)
^~~~~~~~~~~~~~~~~~~~~
pgppop.c:314:13: 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: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";
^~~~~~~~~~~
pgppop.c: In function 'DDV_GetPubValues':
pgppop.c:2873:20: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(szBuf,"%d",year);
^
In file included from /usr/include/stdio.h:862:0,
from pgppop.c:41:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 7 bytes into a destination of size 6
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pgppop.c: In function 'DDV_PopDisplay2':
pgppop.c:997:23: warning: 'pgp2' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (pgp2 && ((pgp2->StopLetter-pgp2->StartLetter+1)>=AbsLengthAli)) {
~~~~^~~~~~~~~~~~
pgppop.c:1004:14: 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 -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:61,
from ../include/samutil.h:230,
from samutil.c:42:
/usr/include/features.h:184:3: 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:796:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((a == NULL) || (b == NULL))
^~
samutil.c:799:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
choice = a->choice;
^~~~~~
samutil.c: In function 'SAM_AlignIdDup':
samutil.c:852:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oldid == NULL)
^~
samutil.c:855:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
newid = ValNodeNew(NULL);
^~~~~
samutil.c: In function 'DDE_FreeStack':
samutil.c:1556:11: warning: operation on 'Index' may be undefined [-Wsequence-point]
Index = ++Index % DDE_STACK_SIZE;
samutil.c: In function 'DDE_Add':
samutil.c:1611:22: warning: operation on 'pStack->StackMin' may be undefined [-Wsequence-point]
pStack->StackMin = ++pStack->StackMin % DDE_STACK_SIZE;
samutil.c:1622:22: 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:1686:22: 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:1717:22: 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:1984:26: 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:3106:41: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr ptxtList, last_vnp, vnp;
^~~
samutil.c: In function 'DDE_RightAddNode':
samutil.c:3707:33: 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:3757:24: warning: variable 'RetVal2' set but not used [-Wunused-but-set-variable]
Boolean RetVal1, RetVal2, IsLeftAlignedGap, NodeDeleted;
^~~~~~~
samutil.c: In function 'DDE_RightMergeAndAddNodeList':
samutil.c:3813:38: 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:4592:41: 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:5028:22: 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:3143:9: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return(last_vnp);
^
samutil.c: In function 'DDE_GetNumResidues':
samutil.c:3166:13: 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:292:4:
255, 255, 255, /* default 0 0xffffff - */
{ }
255, 0, 153, /* hotpink 1 0xff1493 0xff0099 */
{ }
255, 0, 255, /* magenta 2 0xff00ff - */
{ }
153, 51, 255, /* purple 3 0x9b30ff 0x9933ff */
{ }
0, 0, 255, /* blue 4 0x0000ff - */
{ }
00, 153, 255, /* sky 5 0x1e90ff 0x0099ff */
{ }
0, 255, 255, /* cyan 6 0x00ffff - */
{ }
0, 255, 153, /* sea 7 0x00ff8f 0x00ff99 */
{ }
0, 192, 0, /* green 8 0x00ff00 - */
{ }
255, 255, 0, /* yellow 9 0xffff00 - */
{ }
255, 204, 0, /* gold 10 0xffa500 0xffcc00 */
{ }
255, 102, 0, /* orange 11 0xff4500 0xff6600 */
{ }
255, 0, 0, /* red 12 0xff0000 - */
{ }
255, 153, 153, /* pink 13 0xff7256 0xff9999 */
{ }
255, 204, 204, /* pinktint 14 0xffaeb9 0xffcccc */
{ }
255, 255, 255, /* white 15 0xffffff -*/
{ }
0, 0, 0, /* black 16 0x000000 - */
{ }
204, 204, 255, /* bluetint 17 0xb0e2ff - 0xccccff*/
{ }
153, 255, 153, /* greentint 18 0x9aff9a - 0x99ff99 */
{ }
255, 255, 153, /* yellowtint 19 0xffec8b - 0xffff99 */
{ }
102, 102, 102, /* gray 20 0x7d7d7d 0x666666 */
{ }
153, 102, 51, /* brown 21 0x8b5742 01x996633 */
{ }
255, 0, 0, /* perm colors 22: red 0xff0000 - */
{ }
0, 255, 0, /* perm colors 23: green 0x00ff00 - */
{ }
255, 0, 255, /* perm colors 24: magenta 0xff00ff - */
{ }
00, 153, 255, /* perm colors 25: sky 0x1e90ff 0x0099ff */
{ }
153, 51, 255, /* perm colors 26: purple 0x9b30ff 0x9933ff */
{ }
0, 255, 0, /* SS colors 27: helix, green 0x00ff00 - */
{ }
255, 204, 0, /* SS colors 28: strand, gold 0xffa500 0xffcc00 */
{ }
255, 102, 0, /* SS colors 29: turn, orange 0xff4500 0xff6600 */
{ }
0, 255, 255, /* SS colors 30: coil, cyan ox00ffff - */
{ }
255, 255, 0, /* highlight colors 31: yellow 0xffff00 - */
{ }
0, 0, 0 /* background colors 32: black 0x000000 - */
{
};
}
ddvcreate.c: In function 'DDV_CreateDisplayFromIndex_1':
ddvcreate.c:493:17: 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:779:17: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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: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:1141:11: warning: 'halfBspLengthSeqL' may be used uninitialized in this function [-Wmaybe-uninitialized]
ubd->from=Start;
~~~~~~~~~^~~~~~
ddvcreate.c:1158:6: note: 'halfBspLengthSeqL' was declared here
Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
^~~~~~~~~~~~~~~~~
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: 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 -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:184:3: 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 -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:184:3: 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 -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:41:
/usr/include/features.h:184:3: 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:188:13: warning: variable 'hasLinkout' set but not used [-Wunused-but-set-variable]
Boolean hasLinkout=FALSE;
^~~~~~~~~~
txalign.c: In function 'addLinkoutForBioseq':
txalign.c:256:13: warning: variable 'hasLinkout' set but not used [-Wunused-but-set-variable]
Boolean hasLinkout=FALSE;
^~~~~~~~~~
txalign.c: In function 'DrawTextToBuffer':
txalign.c:1254:88: warning: format '%d' expects argument of type 'int', but argument 4 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
snprintf(checkboxBuf, 200, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%d\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%d', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb);
~^ ~~~~~~~~~~~~~~~~~~
%lld
txalign.c: In function 'load_align_sum_for_StdSeg':
txalign.c:2230:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (bsp = BioseqLockById(SeqLocId(ssp->loc->next))) {
^~~
txalign.c: In function 'ShowAlignNodeText2Ex':
txalign.c:3030:13: 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:4079:7: warning: unused variable 'seqid_length' [-Wunused-variable]
Int4 seqid_length = 0, total_length = 0;
^~~~~~~~~~~~
txalign.c: In function 'PrintDefLinesFromSeqAlignWithPath':
txalign.c:4494:39: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
} else if (bestid != NULL && !(options & TXALIGN_NO_DUMPGNL) || (options & TXALIGN_NO_ENTREZ))
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
txalign.c:4498:33: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (bsp = BioseqLockById(bestid)) {
^~~
txalign.c:4200:10: warning: unused variable 'ColumnDistance' [-Wunused-variable]
Int2 ColumnDistance=2, extraSpace=0, extraSpace2=0, strLen=0, maxEvalWidth=5, maxNWidth=2;
^~~~~~~~~~~~~~
txalign.c:4192:43: warning: unused variable 'sip_list' [-Wunused-variable]
SeqIdPtr bestid, gi_list, subject_id, sip_list=NULL, last_id;
^~~~~~~~
txalign.c:4188:17: 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:4817:25: warning: unused variable 't_adj' [-Wunused-variable]
Int4 m_adj = 0, t_adj = 0;
^~~~~
txalign.c:4816:29: warning: unused variable 'last_t_to' [-Wunused-variable]
Int4 last_m_to = 0, last_t_to = 0;
^~~~~~~~~
txalign.c: In function 'FSFPrintOneDefline':
txalign.c:4925:14: warning: variable 'seqid_len' set but not used [-Wunused-but-set-variable]
Int4 gi, seqid_len = 0;
^~~~~~~~~
txalign.c: In function 'FormatScoreFunc':
txalign.c:5142:13: warning: variable 'allocated' set but not used [-Wunused-but-set-variable]
Boolean allocated, first;
^~~~~~~~~
txalign.c: In function 'OOFShowSingleAlignment':
txalign.c:5808:27: warning: array subscript has type 'char' [-Wchar-subscripts]
else if(matrix[line1[line_index]][line2[line_index]] > 0)
^
txalign.c:5808:46: warning: array subscript has type 'char' [-Wchar-subscripts]
else if(matrix[line1[line_index]][line2[line_index]] > 0)
^
txalign.c:5575:13: 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:6063:33: warning: unused variable 'st' [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:6063:9: warning: unused variable 'tmp' [-Wunused-variable]
tmp[10] = " ", *st;
^~~
txalign.c: In function 'OOFDisplayTraceBack2':
txalign.c:6137:33: warning: unused variable 'st' [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c: In function 'FDGetTaxNamesFromBioseq':
txalign.c:6239:21: warning: variable 'bdsp' set but not used [-Wunused-but-set-variable]
BlastDefLinePtr bdsp;
^~~~
txalign.c: At top level:
txalign.c:310:19: 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:6137:33: warning: 'st' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:6063:9: warning: 'tmp' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~~
txalign.c:6063:33: warning: 'st' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:2915:1: warning: 'get_seq_id' defined but not used [-Wunused-function]
get_seq_id(SeqAlignPtr sap, Int2 index)
^~~~~~~~~~
txalign.c:1820:16: warning: 'has_hit_in_region' defined but not used [-Wunused-function]
static Boolean has_hit_in_region(Uint1Ptr all_frame)
^~~~~~~~~~~~~~~~~
txalign.c:112:16: 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:41:
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:1094:10: note: 'HTML_buffer' was declared here
CharPtr HTML_buffer;
^~~~~~~~~~~
txalign.c: In function 'OOFShowSingleAlignment.isra.15':
txalign.c:73:17: warning: 'dna_line_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define fprintf tx_fprintf
^~~~~~~~~~
txalign.c:5571:32: note: 'dna_line_start' was declared here
Int4 dna_index, pro_index, dna_line_start, pro_line_start;
^~~~~~~~~~~~~~
txalign.c:73:17: warning: 'pro_line_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define fprintf tx_fprintf
^~~~~~~~~~
txalign.c:5571:48: note: 'pro_line_start' was declared here
Int4 dna_index, pro_index, dna_line_start, pro_line_start;
^~~~~~~~~~~~~~
txalign.c: In function 'find_score_in_align':
txalign.c:2080:33: warning: 'smtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
stdaa_res = SeqMapTableConvert(smtp, t_res);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
txalign.c:1980:20: note: 'smtp' was declared here
SeqMapTablePtr smtp;
^~~~
txalign.c:1945:13: warning: 't_spp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqPortFree(t_spp);
^~~~~~~~~~~~~~~~~~
txalign.c:1876:23: note: 't_spp' was declared here
SeqPortPtr m_spp, t_spp;
^~~~~
txalign.c:1942:11: warning: 'm_spp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(m_spp == NULL)
^
txalign.c:1876:16: note: 'm_spp' was declared here
SeqPortPtr m_spp, t_spp;
^~~~~
txalign.c: In function 'ShowAlignNodeText2Ex.isra.16':
txalign.c:3025:10: warning: 'm_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 m_len; /*length of the master sequence*/
^~~~~
txalign.c: In function 'ShowTextAlignFromAnnot3':
txalign.c:949:12: 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 -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:184:3: 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 -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:242:
/usr/include/features.h:184:3: 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:885:13: warning: statement with no effect [-Wunused-value]
for (j; j<dsp->numseg && next == -1; j++)
^~~
alignmgr2.c: In function 'AlnMgr2CopySeg':
alignmgr2.c:2984:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (ldelta = ABS(s->beg - beg)) {
^~~~~~
alignmgr2.c: In function 'AlnMgr2AddInNewPairwiseSA':
alignmgr2.c:3221:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (a = AlnMgr2GetNextSeqPiece(a)) {
^
alignmgr2.c:3223:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (b = AlnMgr2GetNextLimitedSeqPiece(b, a)) {
^
alignmgr2.c:3233:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (A = AlnMgr2GetNextSeqPiece(A)) {
^
alignmgr2.c:3237:14: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (B = AlnMgr2GetNextLimitedSeqPiece(B, A)) {};
^
alignmgr2.c: In function 'AlnMgr2SetUnaln':
alignmgr2.c:5410:22: warning: variable 'dsp' set but not used [-Wunused-but-set-variable]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2PrintSeqAlign':
alignmgr2.c:5623:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (more = AlnMgr2GetNextAlnBit(sap, amp))
^~~~
alignmgr2.c: In function 'AlnMgr2GetNextAlnBit':
alignmgr2.c:5719:21: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
alignmgr2.c: In function 'AlnMgr2GetUnalignedInfo':
alignmgr2.c:6085:22: warning: variable 'saip' set but not used [-Wunused-but-set-variable]
SAIndex2Ptr saip;
^~~~
alignmgr2.c: In function 'AlnMgr2GetInterruptInfo':
alignmgr2.c:6331:7: warning: statement with no effect [-Wunused-value]
for (i; i<interrupt->segnum; i++)
^~~
alignmgr2.c: In function 'AlnMgr2GetAlnLength':
alignmgr2.c:6774:20: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (saip->unaln == FALSE || fill_in == FALSE)
^~
alignmgr2.c:6774:8: note: did you mean to dereference the pointer?
if (saip->unaln == FALSE || fill_in == FALSE)
^
alignmgr2.c: In function 'AlnMgr2ComputeScoreForSeqAlign':
alignmgr2.c:8341:17: warning: variable 'numseqs' set but not used [-Wunused-but-set-variable]
Int4 numseqs;
^~~~~~~
alignmgr2.c:8339:17: warning: variable 'mismatch' set but not used [-Wunused-but-set-variable]
Int4 mismatch;
^~~~~~~~
alignmgr2.c:8338:17: 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:242:
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:3557:13: warning: 'AlnMgr2AddInNewSA' defined but not used [-Wunused-function]
static void AlnMgr2AddInNewSA(SeqAlignPtr parent, SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~
alignmgr2.c:2368:18: warning: 'AlnMgr2GetEdgeList' defined but not used [-Wunused-function]
static AMEdgePtr AlnMgr2GetEdgeList(Int4 vertexnum, AMEdgePtr edge_head, AMEdgePtr already_used)
^~~~~~~~~~~~~~~~~~
alignmgr2.c:2140:13: warning: 'AlnMgr2SortVerticesByNumEdges' defined but not used [-Wunused-function]
static void AlnMgr2SortVerticesByNumEdges(AMVertexPtr PNTR vertexarray, Int4 numvertices)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:1061:13: warning: 'AlnMgr2UnpackSeqAlignChain' defined but not used [-Wunused-function]
static void AlnMgr2UnpackSeqAlignChain(SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetLongestSeqLoc':
alignmgr2.c:10131:15: warning: 'slp_longest' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqLocPtr slp_longest;
^~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2IndexLite':
alignmgr2.c:1001:33: warning: 'sap_segs_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap_segs_prev->next = (SeqAlignPtr)(sap_segs->segs);
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:968:17: note: 'sap_segs_prev' was declared here
SeqAlignPtr sap_segs_prev;
^~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetUnalignedInfo':
alignmgr2.c:6122:54: 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:7068:23: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (i=0; i<saip->srdp[row]->numunaln && !found; i++)
~~~~^~~~~~
alignmgr2.c:7077:19: 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:6353:16: warning: 'iip' may be used uninitialized in this function [-Wmaybe-uninitialized]
iip->strand = strand;
~~~~~~~~~~~~^~~~~~~~
alignmgr2.c:6182:19: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
trans = saip->srdp[saip->anchor-1]->sect;
~~~~^~~~~~
alignmgr2.c:6337:48: 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:6478:15: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
srdp = saip->srdp[n-1];
~~~~^~~~~~
alignmgr2.c:6489:57: 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:6550:20: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
*start = saip->aligncoords[i];
~~~~^~~~~~~~~~~~~
alignmgr2.c:6558:41: 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:6789:17: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
len += AlnMgr2GetMaxUnalignedLength(salp, i);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:6780:24: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
lastseg = saip->srdp[saip->anchor-1]->sect[saip->srdp[saip->anchor-1]->numsect-1];
~~~~^~~~~~
alignmgr2.c:6788:20: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
len += dsp->lens[i];
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetNextAlnBit':
alignmgr2.c:6025:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->anchor <= 0)
~~~~^~~~~~~~
alignmgr2.c:6006:17: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
len += dsp->lens[trans[i]];
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2IsSAPDiscAli':
alignmgr2.c:6813:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->numunaln > 0)
~~~~^~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetNumAlnBlocks':
alignmgr2.c:6836:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->numunaln >= 0)
~~~~^~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetNthBlockRange':
alignmgr2.c:6870:20: 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:6889:22: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAIndex2Ptr saip;
^~~~
alignmgr2.c:6936:65: 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:7019:26: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxseg = saip->unaln[*seg];
~~~~^~~~~~~
alignmgr2.c:7024:26: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
(*len) += dsp->lens[i];
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetNumSegsInRange':
alignmgr2.c:7185:62: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
start = binary_search_on_uint4_list(aligncoords, from, dsp->numseg);
~~~^~~~~~~~
alignmgr2.c:7150:21: warning: 'aligncoords' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint4Ptr aligncoords;
^~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2MapBioseqToSeqAlign':
alignmgr2.c:7652:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->anchor > 0)
~~~~^~~~~~~~
alignmgr2.c:7590:21: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2MapSeqAlignToBioseq':
alignmgr2.c:7715:11: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
sect = binary_search_on_uint4_list(saip->aligncoords, pos, saip->numseg);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:7730:36: 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:8036:7: warning: 'sap_real' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((a = AlnMgr2FindAnchor(sap_real)) > 0)
^
alignmgr2.c: In function 'AlnMgr2FillInUnaligned':
alignmgr2.c:9869:12: 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 -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 -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 -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 -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:184:3: 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);
^~~~~~~~~~~~~~~~~~~~~~
cdentrez.c: In function 'CdSeqSumAsnRead':
cdentrez.c:3424:34: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (cds, " cds%d", (int) proteins);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 6 and 11 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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[] = {
^
"", 0, 0,
{ }
"hca", MAGIC_hca, FORMAT_hca,
{ }
"sum", MAGIC_sum, FORMAT_sum,
{ }
"lnk", MAGIC_lnk, FORMAT_lnk,
{ }
"ofs", MAGIC_ofs, FORMAT_ofs,
{ }
"oix", MAGIC_oix, FORMAT_oix,
{ }
"trm", MAGIC_trm, FORMAT_trm,
{ }
"tix", MAGIC_tix, FORMAT_tix,
{ }
"pst", MAGIC_pst, FORMAT_pst,
{ }
"inf", MAGIC_inf, FORMAT_inf
{
};
}
cdnewlib.c:614:27: warning: missing braces around initializer [-Wmissing-braces]
struct CdDirInfo _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 '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 -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:184:3: 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 -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:184:3: 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:247:15: warning: statement with no effect [-Wunused-value]
#define FALSE ((Nlm_Boolean)0)
^
../include/ncbifile.h:144:76: 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:247:15: warning: statement with no effect [-Wunused-value]
#define FALSE ((Nlm_Boolean)0)
^
../include/ncbifile.h:145:76: 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:1257:45: warning: 'besttype' may be used uninitialized in this function [-Wmaybe-uninitialized]
besttype->fields[f].num_terms;
~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 were 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 -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:184:3: 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:354:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_RadioCallback':
vibbutns.c:373:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_SetButtonStatus':
vibbutns.c:694:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Nlm_Int2 val;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibfiles.c: In function 'Nlm_CardToStr':
vibfiles.c:715:19: warning: '%*u' directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=]
sprintf (temp, "%*u", length, (int)cardval);
^~~
vibfiles.c:715:18: note: directive argument in the range [0, 65535]
sprintf (temp, "%*u", length, (int)cardval);
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 32769 bytes into a destination of size 80
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vibfiles.c: In function 'Nlm_IntToStr':
vibfiles.c:725:19: warning: '%*d' directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=]
sprintf (temp, "%*d", length, intval);
^~~
vibfiles.c:725:18: note: directive argument in the range [-32768, 32767]
sprintf (temp, "%*d", length, intval);
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 32769 bytes into a destination of size 80
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:164:
/usr/include/features.h:184:3: 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:1121:15: 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 -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:184:3: 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:2006:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2005:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoice':
vibmenus.c:2072:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceGroup':
vibmenus.c:2122:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceItem':
vibmenus.c:2166:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2164:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableMenuItem':
vibmenus.c:2329:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2328:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoice':
vibmenus.c:2395:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoiceItem':
vibmenus.c:2489:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2487:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_RemoveSubMenu':
vibmenus.c:2627:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CountMenuItems':
vibmenus.c:3056:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetMenuItem':
vibmenus.c:3239:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetPopListTitle':
vibmenus.c:3349:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
Nlm_MenU m;
^
vibmenus.c: In function 'Nlm_AppendItems':
vibmenus.c:3978:17: warning: unused variable 'accel' [-Wunused-variable]
Nlm_Char accel;
^~~~~
vibmenus.c: In function 'Nlm_NewPopupList':
vibmenus.c:4969:19: warning: unused variable 'lbl' [-Wunused-variable]
Widget lbl;
^~~
vibmenus.c:4967:19: 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 -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:184:3: 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 -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:135:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:6800:13: warning: unused variable 'retval' [-Wunused-variable]
Nlm_Int2 retval;
^~~~~~
vibwndws.c: In function 'Nlm_RemoveDyingWindows':
vibwndws.c:6922:20: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:4419:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
document.c:4423:7: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -fPIC -D_PNG -I../include -DWIN_MOTIF shim3d.c
shim3d.c: In function 'Nlm_AddHalfWorm3D':
shim3d.c:3470:46: warning: unused variable 'tmp' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:40: warning: unused variable 'pCz' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:34: warning: unused variable 'pCy' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:28: warning: unused variable 'pCx' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:22: warning: unused variable 'pNz' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:16: warning: unused variable 'pNy' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:10: warning: unused variable 'pNx' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3469:47: warning: unused variable 'Cz' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3469:42: warning: unused variable 'Cy' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3469:37: warning: unused variable 'Cx' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3469:32: warning: unused variable 'Nz' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3469:27: warning: unused variable 'Ny' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3469:15: warning: unused variable 'Nx' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3468:21: warning: unused variable 'pi' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~
shim3d.c:3468:15: warning: unused variable 'sinj' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~~~
shim3d.c:3468:9: warning: unused variable 'cosj' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~~~
shim3d.c:3467:33: warning: unused variable 'prevlen' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~~~~~~
shim3d.c:3467:29: warning: unused variable 'Vz' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3467:25: warning: unused variable 'Vy' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3467:21: warning: unused variable 'Vx' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3467:17: warning: unused variable 'Hz' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3467:13: warning: unused variable 'Hy' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3467:9: warning: unused variable 'Hx' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3466:21: warning: unused variable 'dQtz' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3466:15: warning: unused variable 'dQty' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3466:9: warning: unused variable 'dQtx' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3464:14: warning: unused variable 'len' [-Wunused-variable]
GLdouble len, R1x, R1y, R1z, R2x, R2y, R2z, MG[4][3],
^~~
shim3d.c:3463:26: warning: unused variable 'offset' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^~~~~~
shim3d.c:3463:23: warning: unused variable 'm' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^
shim3d.c:3463:20: warning: unused variable 'k' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^
shim3d.c:3463:17: 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 -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:184:3: 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 -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:184:3: 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:354:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_RadioCallback':
vibbutns.c:373:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_SetButtonStatus':
vibbutns.c:694:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Nlm_Int2 val;
^~~
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 -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:184:3: 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 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibfiles.c: In function 'Nlm_CardToStr':
vibfiles.c:715:19: warning: '%*u' directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=]
sprintf (temp, "%*u", length, (int)cardval);
^~~
vibfiles.c:715:18: note: directive argument in the range [0, 65535]
sprintf (temp, "%*u", length, (int)cardval);
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 32769 bytes into a destination of size 80
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vibfiles.c: In function 'Nlm_IntToStr':
vibfiles.c:725:19: warning: '%*d' directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=]
sprintf (temp, "%*d", length, intval);
^~~
vibfiles.c:725:18: note: directive argument in the range [-32768, 32767]
sprintf (temp, "%*d", length, intval);
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 32769 bytes into a destination of size 80
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:184:3: 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 -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:184:3: 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 -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:164:
/usr/include/features.h:184:3: 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:1121:15: 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 -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:184:3: 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:2006:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2005:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoice':
vibmenus.c:2072:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceGroup':
vibmenus.c:2122:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceItem':
vibmenus.c:2166:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2164:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableMenuItem':
vibmenus.c:2329:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2328:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoice':
vibmenus.c:2395:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoiceItem':
vibmenus.c:2489:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2487:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_RemoveSubMenu':
vibmenus.c:2627:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CountMenuItems':
vibmenus.c:3056:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetMenuItem':
vibmenus.c:3239:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetPopListTitle':
vibmenus.c:3349:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
Nlm_MenU m;
^
vibmenus.c: In function 'Nlm_AppendItems':
vibmenus.c:3978:17: warning: unused variable 'accel' [-Wunused-variable]
Nlm_Char accel;
^~~~~
vibmenus.c: In function 'Nlm_NewPopupList':
vibmenus.c:4969:19: warning: unused variable 'lbl' [-Wunused-variable]
Widget lbl;
^~~
vibmenus.c:4967:19: 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 -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:184:3: 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 -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:135:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:6800:13: warning: unused variable 'retval' [-Wunused-variable]
Nlm_Int2 retval;
^~~~~~
vibwndws.c: In function 'Nlm_RemoveDyingWindows':
vibwndws.c:6922:20: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:4419:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
document.c:4423:7: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL shim3d.c
shim3d.c: In function 'OGL_AddCylinder3D':
shim3d.c:918:14: warning: unused variable 'iCount' [-Wunused-variable]
Nlm_Int4 iCount;
^~~~~~
shim3d.c: In function 'OGL_AddText3D':
shim3d.c:1210:22: warning: unused variable 'i' [-Wunused-variable]
Nlm_Int4 Length, i;
^
shim3d.c: In function 'OGL_Zoom_DragMA':
shim3d.c:1770:16: warning: unused variable 'OGL_Data' [-Wunused-variable]
TOGL_Data *OGL_Data = MAToOGL(ma);
^~~~~~~~
shim3d.c: In function 'OGL_Hit':
shim3d.c:2065:37: warning: left shift count >= width of type [-Wshift-count-overflow]
ZMinName = ZMinName << (sizeof(GLuint) * 8);
^~
shim3d.c: In function 'write_row_callback':
shim3d.c:2911:15: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
float start, end;
^~~~~
shim3d.c:2911:22: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
float start, end;
^~~
shim3d.c: In function 'SetOGLFont':
shim3d.c:2381:64: warning: 'closest' may be used uninitialized in this function [-Wmaybe-uninitialized]
fontInfo = XLoadQueryFont(Nlm_currentXDisplay, list[closest]);
^
shim3d.c:2376:37: warning: 'mindiff' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ii == 0 || diff < mindiff) {
~~~~~^~~~~~~~~
shim3d.c:2381:64: 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:3463:26: 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 -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:184:3: 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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
smdlg3.c: In function 'FeatureExtraDraw':
smdlg3.c:413:17: warning: 'y1' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 y0, y1, x0, x1, x2, x3;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:1943:8: warning: 'seglen' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 seglen;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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' [-Wdangling-else]
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' [-Wdangling-else]
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' [-Wdangling-else]
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 'PwDistanceItem':
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 -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:184:3: 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:3310:21: warning: unused variable 'dirty' [-Wunused-variable]
dirty = FALSE;
^~~~~
saled.c:3306:21: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:1444:25: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (tmp!='\0' && !isdigit (*tmp))
^~
salfiles.c:1444:22: note: did you mean to dereference the pointer?
while (tmp!='\0' && !isdigit (*tmp))
^
salfiles.c:1446:22: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (tmp!='\0')
^~
salfiles.c:1446:19: note: did you mean to dereference the pointer?
if (tmp!='\0')
^
salfiles.c:1455:25: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (tmp!='\0' && !isdigit (*tmp))
^~
salfiles.c:1455:22: note: did you mean to dereference the pointer?
while (tmp!='\0' && !isdigit (*tmp))
^
salfiles.c:1457:22: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (tmp!='\0')
^~
salfiles.c:1457:19: note: did you mean to dereference the pointer?
if (tmp!='\0')
^
salfiles.c:1536:25: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (tmp!='\0' && !isdigit (*tmp))
^~
salfiles.c:1536:22: note: did you mean to dereference the pointer?
while (tmp!='\0' && !isdigit (*tmp))
^
salfiles.c:1538:22: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (tmp!='\0')
^~
salfiles.c:1538:19: note: did you mean to dereference the pointer?
if (tmp!='\0')
^
salfiles.c:1547:25: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (tmp!='\0' && !isdigit (*tmp))
^~
salfiles.c:1547:22: note: did you mean to dereference the pointer?
while (tmp!='\0' && !isdigit (*tmp))
^
salfiles.c:1549:22: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (tmp!='\0')
^~
salfiles.c:1549:19: note: did you mean to dereference the pointer?
if (tmp!='\0')
^
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 were 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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:654:16: warning: 'seqstr' may be used uninitialized in this function [-Wmaybe-uninitialized]
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 -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:184:3: 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' [-Wdangling-else]
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:4674:15: warning: variable 'ppt' set but not used [-Wunused-but-set-variable]
PrompT ppt;
^~~
salpanel.c:4669:15: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
salpanel.c: In function 'OkToContinueWithFeatureApply':
salpanel.c:6103:14: warning: unused variable 'num_missing' [-Wunused-variable]
Int4 num_missing = 0, seq_num, start_num;
^~~~~~~~~~~
salpanel.c: In function 'DoApplyFeatureToAlignment':
salpanel.c:6219:31: warning: unused variable 'found_null' [-Wunused-variable]
Boolean found_null = FALSE;
^~~~~~~~~~
salpanel.c: In function 'ApplyFeatureToAlignment':
salpanel.c:6421:31: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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:5059:13: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:4976:23: warning: unused variable 'wdp' [-Wunused-variable]
SeqEditViewFormPtr wdp = NULL;
^~~
salsa.c:4974:23: warning: unused variable 'w' [-Wunused-variable]
WindoW w = NULL;
^
salsa.c: In function 'OldAlignmentEditor':
salsa.c:5106:16: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Int2 rval;
^~~~
salsa.c: In function 'LaunchAnnotAlignEditor':
salsa.c:5293:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignEditor':
salsa.c:5310:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignViewer':
salsa.c:5327:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop':
salsa.c:5342:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop2':
salsa.c:5359:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
salsa.c: In function 'InsertSeqProc':
salsa.c:5538:17: warning: variable 'cnclbt' set but not used [-Wunused-but-set-variable]
ButtoN insbt, cnclbt;
^~~~~~
salsa.c:5536:10: warning: variable 'insprt' set but not used [-Wunused-but-set-variable]
PrompT insprt;
^~~~~~
salsa.c: In function 'SeqAlignBestHit':
salsa.c:5605:22: warning: variable 'last' set but not used [-Wunused-but-set-variable]
Int4 last;
^~~~
salsa.c: In function 'SeqAlignStartUpdate':
salsa.c:5791:22: warning: variable 'k' set but not used [-Wunused-but-set-variable]
Int2 index, k, j;
^
salsa.c:5790:15: warning: variable 'start' set but not used [-Wunused-but-set-variable]
start;
^~~~~
salsa.c:5789:15: warning: variable 'len_sum' set but not used [-Wunused-but-set-variable]
Int4 len_sum,
^~~~~~~
salsa.c:5786:15: warning: variable 'lenp' set but not used [-Wunused-but-set-variable]
Int4Ptr lenp,
^~~~
salsa.c:5785:15: warning: variable 'pre' set but not used [-Wunused-but-set-variable]
SeqIdPtr pre, sip, next;
^~~
salsa.c: In function 'CCNormalizeSeqAlignId':
salsa.c:6746:23: warning: unused variable 'gi' [-Wunused-variable]
Int4 gi = 0;
^~
salsa.c:6745:17: 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:6744:17: 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:7106:16: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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:5973:13: warning: 'SWPrintFarpointerAln' defined but not used [-Wunused-function]
static void SWPrintFarpointerAln(SeqAlignPtr sap, FILE *fp)
^~~~~~~~~~~~~~~~~~~~
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:113:19: warning: 'fp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define FileClose Nlm_FileClose
^~~~~~~~~~~~~
salsa.c:6350:23: 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:113:19: warning: 'fp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define FileClose Nlm_FileClose
^~~~~~~~~~~~~
salsa.c:6318:23: note: 'fp' was declared here
FILE *fp;
^~
salsa.c: In function 'SeqAlignBestHit.isra.17':
salsa.c:5746:23: warning: 'nctr' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = nctr+beg+end;
~~~~^~~~
salsa.c:5748:24: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = -(beg+end);
~~~~^~~~~
salsa.c:5746:23: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:301:13: warning: 'CleanupGCFilterForm' defined but not used [-Wunused-function]
static void CleanupGCFilterForm (GraphiC g, VoidPtr data)
^~~~~~~~~~~~~~~~~~~
seqgrphx.c:152:25: warning: 'FilterMsgFunc' defined but not used [-Wunused-function]
static Int2 LIBCALLBACK FilterMsgFunc (OMMsgStructPtr ommsp)
^~~~~~~~~~~~~
seqgrphx.c:28:25: warning: 'MatrixMsgFunc' defined but not used [-Wunused-function]
static Int2 LIBCALLBACK MatrixMsgFunc (OMMsgStructPtr ommsp)
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:387:20: warning: 'MatrixSearch' defined but not used [-Wunused-function]
static SeqGraphPtr MatrixSearch (BioseqPtr bsp, Int2 matrixtype)
^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:1436:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (vsmp->title != NULL)
^~
vsm.c:1438:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (vsmp->aboutinfo != NULL)
^~
vsm.c: In function 'VSMAboutProc':
vsm.c:1466:8: warning: variable 'p' set but not used [-Wunused-but-set-variable]
PaneL p;
^
vsm.c: In function 'VSeqMgrCreateMainWindow':
vsm.c:1569:12: warning: variable 'omp' set but not used [-Wunused-but-set-variable]
ObjMgrPtr omp;
^~~
vsm.c: In function 'VSeqMgrPopulateMain':
vsm.c:1710:13: warning: variable 'atp' set but not used [-Wunused-but-set-variable]
AsnTypePtr atp;
^~~
vsm.c: In function 'VSMGatherPictProc':
vsm.c:2193:15: warning: variable 'bssp' set but not used [-Wunused-but-set-variable]
BioseqSetPtr bssp;
^~~~
vsm.c:2188:30: 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:2821:10: warning: variable 'ptr' set but not used [-Wunused-but-set-variable]
Pointer ptr;
^~~
vsm.c:2820:13: 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 -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:184:3: 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:1368:20: 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 -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:184:3: 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:1743:18: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Int2 val;
^~~
At top level:
vsmutil.c:1628:16: 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:2256:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2255:5: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'RevalidateProc':
vsmutil.c:2223:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2222:5: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'SetVerbosityAndRepopulate':
vsmutil.c:2297:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2296:5: 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:2620:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2619:9: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'ContinueProc':
vsmutil.c:2256:19: warning: array subscript is above array bounds [-Warray-bounds]
vep->counts [i] = 0;
~~~~~~~~~~~~^~~
vsmutil.c: In function 'RevalidateProc':
vsmutil.c:2223:19: warning: array subscript is above array bounds [-Warray-bounds]
vep->counts [i] = 0;
~~~~~~~~~~~~^~~
vsmutil.c: In function 'SetVerbosityAndRepopulate':
vsmutil.c:2297:19: warning: array subscript is above array bounds [-Warray-bounds]
vep->counts [i] = 0;
~~~~~~~~~~~~^~~
vsmutil.c: In function 'ClearValidateWindow':
vsmutil.c:613:21: warning: array subscript is above array bounds [-Warray-bounds]
vep->counts [sev] = 0;
~~~~~~~~~~~~^~~~~
vsmutil.c: In function 'CreateValidateWindowExExEx':
vsmutil.c:2620:23: warning: array subscript is above array bounds [-Warray-bounds]
vep->counts [i] = 0;
~~~~~~~~~~~~^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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:342:19: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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.part.21':
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:2561:45: warning: 'residue_names' may be used uninitialized in this function [-Wmaybe-uninitialized]
sBuf[c]=*residue_names[(int)*s];
^
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:2356:14: warning: 'q' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint1Ptr q;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:2962:8: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
dlgutil1.c: In function 'TestIntervalEditor':
dlgutil1.c:5324:20: warning: variable 'fuzz_to' set but not used [-Wunused-but-set-variable]
Int2 fuzz_to;
^~~~~~~
dlgutil1.c:5323:20: warning: variable 'fuzz_from' set but not used [-Wunused-but-set-variable]
Int2 fuzz_from;
^~~~~~~~~
dlgutil1.c:5322:41: warning: variable 'fuzz_before' set but not used [-Wunused-but-set-variable]
Boolean isInterval, isPoint, fuzz_before, fuzz_after;
^~~~~~~~~~~
dlgutil1.c: In function 'DbtagDialogToDbtagPtr':
dlgutil1.c:7254:16: warning: unused variable 'val' [-Wunused-variable]
long int val;
^~~
dlgutil1.c:7250:16: warning: unused variable 'ptr' [-Wunused-variable]
CharPtr ptr;
^~~
dlgutil1.c:7247:16: warning: unused variable 'num_digits' [-Wunused-variable]
Int2 num_digits;
^~~~~~~~~~
dlgutil1.c:7246:16: warning: unused variable 'notallzero' [-Wunused-variable]
Boolean notallzero;
^~~~~~~~~~
dlgutil1.c:7243:16: warning: unused variable 'leadingzero' [-Wunused-variable]
Boolean leadingzero;
^~~~~~~~~~~
dlgutil1.c:7238:16: warning: unused variable 'alldigits' [-Wunused-variable]
Boolean alldigits;
^~~~~~~~~
dlgutil1.c: In function 'CreateStandardEditMenu':
dlgutil1.c:9427:8: 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:8603:25: warning: 'GetNthNameValuePair' defined but not used [-Wunused-function]
static NameValuePairPtr GetNthNameValuePair (Int4 n, ValNodePtr list)
^~~~~~~~~~~~~~~~~~~
dlgutil1.c:8051:16: warning: 'ParseSpecimenVoucherOk' defined but not used [-Wunused-function]
static Boolean ParseSpecimenVoucherOk (CharPtr str)
^~~~~~~~~~~~~~~~~~~~~~
dlgutil1.c:1293:13: warning: 'GbqualsToVisStringDialog' defined but not used [-Wunused-function]
static void GbqualsToVisStringDialog (SeqFeatPtr sfp, DialoG d, CharPtr qual)
^~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:3552:11: warning: variable 'y' set but not used [-Wunused-but-set-variable]
Int4 x, y;
^
dlgutil2.c:3552:8: warning: variable 'x' set but not used [-Wunused-but-set-variable]
Int4 x, y;
^
dlgutil2.c: In function 'GetTableDisplayCell':
dlgutil2.c:3951:8: warning: variable 'start_row' set but not used [-Wunused-but-set-variable]
Int4 start_row, start_col;
^~~~~~~~~
dlgutil2.c: In function 'NewCreateInferenceDialog':
dlgutil2.c:7633:19: warning: variable 'fnt' set but not used [-Wunused-but-set-variable]
FonT fnt;
^~~
dlgutil2.c: In function 'ClickableListOnKey':
dlgutil2.c:10479:20: warning: variable 'clp' set but not used [-Wunused-but-set-variable]
ClickableListPtr clp;
^~~
dlgutil2.c: In function 'GetSelectedClickableListText':
dlgutil2.c:11151:36: 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:14210:36: warning: variable 's3' set but not used [-Wunused-but-set-variable]
SeqIntPtr s1, s2, s3;
^~
At top level:
dlgutil2.c:12342:16: warning: 'ParseMultiListQualOk' defined but not used [-Wunused-function]
static Boolean ParseMultiListQualOk (CharPtr val)
^~~~~~~~~~~~~~~~~~~~
dlgutil2.c:10336:13: warning: 'ClickClickableListItem' defined but not used [-Wunused-function]
static void ClickClickableListItem (DoC d, PoinT pt)
^~~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:10316:13: warning: 'DrawClickableListItem' defined but not used [-Wunused-function]
static void DrawClickableListItem (DoC d, RectPtr r, Int2 item, Int2 firstLine)
^~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:8854:13: warning: 'GetCategoryNumFromName' defined but not used [-Wunused-function]
static Int4 GetCategoryNumFromName (CharPtr category)
^~~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:1676:16: warning: 'GetNameForFeature' defined but not used [-Wunused-function]
static CharPtr GetNameForFeature (SeqFeatPtr sfp)
^~~~~~~~~~~~~~~~~
dlgutil2.c: In function 'PopulateDayPopup':
dlgutil2.c:11438:24: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (day, "%d", i);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:4402:28: warning: variable 'r' set but not used [-Wunused-but-set-variable]
RecT r;
^
asn2graphic.c: In function 'GphSentProc':
asn2graphic.c:4997:16: 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:4362:13: warning: 'SegmentTreeBot' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (! EnsureFeatureHasSegment (FPSP, featdeftype, SegmentTreeBot)) return 0;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2graphic.c:4354:24: warning: 'SegmentTreeMid' may be used uninitialized in this function [-Wmaybe-uninitialized]
SegmentTreeBot = CreateSegment (SegmentTreeMid, 0, 0);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2graphic.c:4350:24: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:1292:22: warning: variable 'doColors' set but not used [-Wunused-but-set-variable]
Boolean doColors;
^~~~~~~~
gbfview.c: In function 'PopulateFasta':
gbfview.c:1717:33: warning: left-hand operand of comma expression has no effect [-Wunused-value]
if (ISA_na (bsp->mol)) {TRUE,
^
gbfview.c:1649:20: warning: variable 'group_segs' set but not used [-Wunused-but-set-variable]
Uint1 group_segs;
^~~~~~~~~~
gbfview.c: In function 'PopulateAsnOrXML':
gbfview.c:1972:16: warning: variable 'lookupFar' set but not used [-Wunused-but-set-variable]
Boolean lookupFar = FALSE;
^~~~~~~~~
gbfview.c:1971:16: warning: variable 'lockFar' set but not used [-Wunused-but-set-variable]
Boolean lockFar = FALSE;
^~~~~~~
gbfview.c: In function 'PrintFlatFileFastaOrAsn':
gbfview.c:2494:5: 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:1234:13: warning: 'LookForFarProds' defined but not used [-Wunused-function]
static void LookForFarProds (
^~~~~~~~~~~~~~~
gbfview.c:1215:13: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:685:20: 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:673:20: 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:653:21: 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:653:21: 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:653:21: 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 -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:184:3: 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:8665:22: 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:626:12: 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:8665:26: 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:626:12: 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:8761:20: 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:626:12: 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:8761:24: 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:626:12: 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:9008:17: 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:535:22: 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 'SeqEdExportProc':
seqpanel.c:4329:13: 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 '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 '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 -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:184:3: 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 were 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:468:17: 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 were 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 -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:184:3: 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:272:10: 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:535:10: 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:1834:14: 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:2025:11: 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 were 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:652:16: 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:3206:39: 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 -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:184:3: 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:2814:7: 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:5353:17: warning: '%s' directive writing up to 299 bytes into a region of size 255 [-Wformat-overflow=]
sprintf(str, "%s", pfp->name);
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/asn2ff.h:113,
from ../include/ingenwin.h:58,
from ingenwin.c:45:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 1 and 300 bytes into a destination of size 255
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ingenwin.c:5229:37: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (i = last_pos; i <= exit; i += nchars_row){
~~^~~~~~~~~~~~~
ingenwin.c:5137:17: note: 'j' was declared here
Int4 i, j, k, row;
^
ingenwin.c: In function 'Ing_DoPropagate':
ingenwin.c:5625:26: warning: ' already exists. Do you still want to propagate it?' directive writing 51 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf (str_buf, "%s already exists. Do you still want to propagate it?", pfp->name);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/asn2ff.h:113,
from ../include/ingenwin.h:58,
from ingenwin.c:45:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 52 and 351 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:476:16: 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:476:16: 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:476:16: 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:476:16: 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:476:16: 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 -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:184:3: 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 'ExistingTextDialog':
macrodlg.c:1959:22: warning: variable 'ppt' set but not used [-Wunused-but-set-variable]
PrompT ppt;
^~~
macrodlg.c: In function 'EndDistanceToDialog':
macrodlg.c:3076:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", v->data.intvalue);
~^ ~~~~~~~~~~~~~~~~
%lld
macrodlg.c:3082:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", v->data.intvalue);
~^ ~~~~~~~~~~~~~~~~
%lld
macrodlg.c:3088:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", v->data.intvalue);
~^ ~~~~~~~~~~~~~~~~
%lld
macrodlg.c: In function 'SourceQualChoiceDialog':
macrodlg.c:3757:48: warning: variable 'b4' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3757:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3757:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3757:29: 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:3995:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:3995:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:3995:29: warning: variable 'b1' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c: In function 'CDSGeneProtQualConstraintDialog':
macrodlg.c:4309:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:4309:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:4309:29: warning: variable 'b1' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c: In function 'QuantityConstraintToDialog':
macrodlg.c:7368:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", vnp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c:7373:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", vnp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c:7378:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", vnp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c: In function 'TestApplyActionDialog':
macrodlg.c:12965:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'TestEditActionDialog':
macrodlg.c:13170:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'TestRemoveOutsideActionDialog':
macrodlg.c:13328:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'ApplyFeatureActionToDialog':
macrodlg.c:15186:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (num, "%d^", action->location->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c:15188:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (num, "%d", action->location->data.intvalue + 1);
~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c: In function 'AddMacroActions':
macrodlg.c:20523:25: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE;
^~~~
macrodlg.c: In function 'PointerToSampleDialog':
macrodlg.c:20659:19: 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:20779:53: 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:20779:42: 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:22071:33: warning: variable 'num_features' set but not used [-Wunused-but-set-variable]
Int4 num_fields, num_features;
^~~~~~~~~~~~
macrodlg.c:22071:21: warning: variable 'num_fields' set but not used [-Wunused-but-set-variable]
Int4 num_fields, num_features;
^~~~~~~~~~
macrodlg.c: In function 'LaunchMacroTemplateEditor':
macrodlg.c:23785:23: warning: variable 'bfp' set but not used [-Wunused-but-set-variable]
BaseFormPtr bfp;
^~~
macrodlg.c: In function 'SearchFuncToDialog':
macrodlg.c:25755:23: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", func->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c:25776:23: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", func->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~~
%lld
At top level:
macrodlg.c:20095:13: warning: 'ChangeMacroActionPopup' defined but not used [-Wunused-function]
static void ChangeMacroActionPopup (LisT t)
^~~~~~~~~~~~~~~~~~~~~~
macrodlg.c:20038:13: warning: 'GetPopupChoiceForActionChoice' defined but not used [-Wunused-function]
static Int2 GetPopupChoiceForActionChoice (Uint1 action_choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macrodlg.c:19715:13: warning: 'GetCategoryForActionChoice' defined but not used [-Wunused-function]
static Int2 GetCategoryForActionChoice (Uint1 action_choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~
macrodlg.c:19698:14: warning: 'GetActionChoiceForCategoryPopupChoice' defined but not used [-Wunused-function]
static Uint1 GetActionChoiceForCategoryPopupChoice (Int2 category, Int2 popup_choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macrodlg.c: In function 'ActionToSingleMacroActionForm':
macrodlg.c:22216:25: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 val, i;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 'CreateSimpleBioSourceDialog':
biosrc.c:2455:18: warning: variable 'indexerVersion' set but not used [-Wunused-but-set-variable]
Boolean indexerVersion;
^~~~~~~~~~~~~~
biosrc.c: In function 'CreateBioSourceDialog':
biosrc.c:3615:18: warning: variable 'y' set but not used [-Wunused-but-set-variable]
PrompT y;
^
At top level:
biosrc.c:3291:26: warning: 'EnumListFromQualNameAssoc' defined but not used [-Wunused-function]
static EnumFieldAssocPtr EnumListFromQualNameAssoc (Nlm_QualNameAssocPtr qp)
^~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:3100:16: warning: 'SubsourceDialogToSubSourcePtr' defined but not used [-Wunused-function]
static Pointer SubsourceDialogToSubSourcePtr (DialoG d)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2677:13: warning: 'SubSourcePtrToSubsourceDialog' defined but not used [-Wunused-function]
static void SubSourcePtrToSubsourceDialog (DialoG d, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2617:16: warning: 'OrgmodDialogToOrgModPtr' defined but not used [-Wunused-function]
static Pointer OrgmodDialogToOrgModPtr (DialoG d)
^~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2568:13: 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 -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:184:3: 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 'SetBestProteinFeature':
cdrgn.c:1003:21: warning: unused variable 'prp' [-Wunused-variable]
ProtRefPtr prp;
^~~
cdrgn.c: In function 'CdRegionPtrToForm':
cdrgn.c:1050:19: warning: unused variable 'vnp' [-Wunused-variable]
ValNodePtr vnp;
^~~
cdrgn.c: In function 'ProductToSeqLocPtr':
cdrgn.c:1293:19: warning: variable 'rfp' set but not used [-Wunused-but-set-variable]
RnaFormPtr rfp = NULL;
^~~
cdrgn.c: In function 'CreateCodeBreakAlist':
cdrgn.c:1926:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
cdrgn.c: In function 'CodeBreakPtrToCodeBreakDialog':
cdrgn.c:1977:19: warning: variable 'aa' set but not used [-Wunused-but-set-variable]
Uint1 aa;
^~
cdrgn.c: In function 'PopulateAAPopup':
cdrgn.c:7041:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
cdrgn.c: In function 'RnaRefPtrToForm':
cdrgn.c:7557:17: warning: unused variable 'is_iMet' [-Wunused-variable]
Boolean is_iMet = FALSE;
^~~~~~~
cdrgn.c:7556:17: warning: unused variable 'is_fMet' [-Wunused-variable]
Boolean is_fMet = FALSE;
^~~~~~~
At top level:
cdrgn.c:6851:13: warning: 'ConvertRnaRefNameToProductQual' defined but not used [-Wunused-function]
static void ConvertRnaRefNameToProductQual (SeqFeatPtr sfp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdrgn.c:6789:13: warning: 'RemoveQualByName' defined but not used [-Wunused-function]
static void RemoveQualByName (SeqFeatPtr sfp, CharPtr qual_name)
^~~~~~~~~~~~~~~~
cdrgn.c:6770:18: warning: 'FindOrAddQual' defined but not used [-Wunused-function]
static GBQualPtr FindOrAddQual (SeqFeatPtr sfp, CharPtr qual_name)
^~~~~~~~~~~~~
cdrgn.c:6323:15: warning: 'CreateMrnaUserObjectDialog' defined but not used [-Wunused-function]
static DialoG CreateMrnaUserObjectDialog (GrouP h, CharPtr label, SeqEntryPtr sep, BaseFormPtr bfp)
^~~~~~~~~~~~~~~~~~~~~~~~~~
cdrgn.c:6246:14: warning: 'check_rna_type' defined but not used [-Wunused-function]
static Uint1 check_rna_type (Uint1 type)
^~~~~~~~~~~~~~
cdrgn.c:3183:13: warning: 'SetComment' defined but not used [-Wunused-function]
static void SetComment (CharPtr new_comment, WindoW w)
^~~~~~~~~~
cdrgn.c:2149:13: warning: 'AccessionToGi' defined but not used [-Wunused-function]
static Int4 AccessionToGi (CharPtr string)
^~~~~~~~~~~~~
cdrgn.c:961:13: warning: 'FormToProtRef' defined but not used [-Wunused-function]
static void FormToProtRef(CdRgnFormPtr cfp, ProtRefPtr prp)
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
import.c:3776:22: warning: 'kDoNotEditTitle' initialized and declared 'extern'
extern const CharPtr kDoNotEditTitle = "You are manually editing a title. If you continue, the title will not be automatically updated if the taxonomy information changes. Are you sure you want to do this? It is a very bad idea.";
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 'MakeReplaceAuthorsForm':
pubdesc.c:4303:24: warning: variable 'pepp' set but not used [-Wunused-but-set-variable]
PubdescEditProcsPtr pepp;
^~~~
pubdesc.c: In function 'DisplayDocSum':
pubdesc.c:4865:9: warning: variable 'lineheight' set but not used [-Wunused-but-set-variable]
Int2 lineheight;
^~~~~~~~~~
At top level:
pubdesc.c:5377:13: warning: 'Quit' defined but not used [-Wunused-function]
static void Quit (ButtoN b)
^~~~
pubdesc.c:5113:14: warning: 'AddAll' defined but not used [-Wunused-function]
static void AddAll(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st)
^~~~~~
pubdesc.c: In function 'QueryFromForm':
pubdesc.c:5096:29: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (year_buf, "%d", year - 1);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pubdesc.c:5102:29: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (year_buf, "%d", year + 1);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:3152:7: warning: 'yac_num' may be used uninitialized in this function [-Wmaybe-uninitialized]
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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 were 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 '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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:2001:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiomolDescrFree':
objmmdb1.c:2139:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'BiomolDescrAsnRead':
objmmdb1.c:2189:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueGraphAsnRead':
objmmdb1.c:2446:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'MoleculeGraphAsnRead':
objmmdb1.c:2654:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'InterResidueBondAsnRead':
objmmdb1.c:2856:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:2855:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueAsnRead':
objmmdb1.c:3037:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3036:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueGraphPntrFree':
objmmdb1.c:3177:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'ResidueGraphPntrAsnRead':
objmmdb1.c:3212:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucGraphPntrAsnRead':
objmmdb1.c:3399:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3398:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucResidueGraphSetPntrAsnRead':
objmmdb1.c:3565:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3564:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomAsnRead':
objmmdb1.c:3732:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'IntraResidueBondAsnRead':
objmmdb1.c:3924:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3923:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ChiralCenterAsnRead':
objmmdb1.c:4097:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:4096:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomPntrAsnRead':
objmmdb1.c:4286:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:4285:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomPntrSetAsnRead':
objmmdb1.c:4441:16: 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 'BiostrucIdAsnRead':
objmmdb1.c:411:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
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:2284:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb1.c: In function 'BiostrucSourceAsnRead':
objmmdb1.c:1802:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb1.c:1752:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb1.c: In function 'ResidueGraphPntrAsnRead':
objmmdb1.c:3265:16: 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 -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:184:3: 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:242:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'ModelDescrAsnRead':
objmmdb2.c:289:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'ModelSpaceAsnRead':
objmmdb2.c:512:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:511:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'Coordinates_coordinatesFree':
objmmdb2.c:709:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'ModelCoordinateSetAsnRead':
objmmdb2.c:743:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'Coordinates_coordinatesAsnRead':
objmmdb2.c:831:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'ReferenceFrameAsnRead':
objmmdb2.c:1063:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:1062:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'CoordinatesFree':
objmmdb2.c:1193:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'CoordinatesAsnRead':
objmmdb2.c:1231:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'AtomicCoordinatesAsnRead':
objmmdb2.c:1420:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'Surface_surfaceFree':
objmmdb2.c:1640:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'SurfaceCoordinatesAsnRead':
objmmdb2.c:1686:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:1685:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'Surface_surfaceAsnRead':
objmmdb2.c:1766:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'DensityCoordinatesAsnRead':
objmmdb2.c:2030:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'ModelSpacePointsAsnRead':
objmmdb2.c:2263:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AtomicTemperatureFactorsFree':
objmmdb2.c:2404:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'AtomicTemperatureFactorsAsnRead':
objmmdb2.c:2439:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'AtomicOccupanciesAsnRead':
objmmdb2.c:2615:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AlternateConformationIdsAsnRead':
objmmdb2.c:2760:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'ConformationEnsembleAsnRead':
objmmdb2.c:2890:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'IsotropicTemperatureFactorsAsnRead':
objmmdb2.c:3054:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AnisotropicTemperatureFactorsAsnRead':
objmmdb2.c:3221:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'TMeshAsnRead':
objmmdb2.c:3426:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'TrianglesAsnRead':
objmmdb2.c:3626:16: 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:366:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'CoordinatesAsnRead':
objmmdb2.c:1281:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'AtomicTemperatureFactorsAsnRead':
objmmdb2.c:2485:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'ModelCoordinateSetAsnRead':
objmmdb2.c:877:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c:830:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb2.c: In function 'SurfaceCoordinatesAsnRead':
objmmdb2.c:1828:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c:1765:10: 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 -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:184:3: 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:220:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'AtomPntrsAsnRead':
objmmdb3.c:443:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ChemGraphAlignmentAsnRead':
objmmdb3.c:626:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ChemGraphInteractionAsnRead':
objmmdb3.c:824:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'SphereAsnRead':
objmmdb3.c:1024:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ConeAsnRead':
objmmdb3.c:1192:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'CylinderAsnRead':
objmmdb3.c:1372:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BrickAsnRead':
objmmdb3.c:1557:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'TransformAsnRead':
objmmdb3.c:1796:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucFeatureSetDescrFree':
objmmdb3.c:1921:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'Location_locationFree':
objmmdb3.c:2161:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'BiostrucFeatureAsnRead':
objmmdb3.c:2206:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'Property_propertyFree':
objmmdb3.c:2722:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'ColorPropAsnRead':
objmmdb3.c:2798:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'CameraAsnRead':
objmmdb3.c:2986:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucScriptAsnRead':
objmmdb3.c:3171:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionPntrsAsnRead':
objmmdb3.c:3330:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionSimilarityAsnRead':
objmmdb3.c:3648:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'OtherFeatureAsnRead':
objmmdb3.c:3825:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucMoleculePntrAsnRead':
objmmdb3.c:3999:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'MoleculePntrsAsnRead':
objmmdb3.c:4342:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ResidueExplicitPntrsAsnRead':
objmmdb3.c:4505:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ResidueIntervalPntrAsnRead':
objmmdb3.c:4673:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionCoordinatesAsnRead':
objmmdb3.c:4845:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionBoundaryFree':
objmmdb3.c:4981:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'AlignStatsAsnRead':
objmmdb3.c:5212:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RealValueAsnRead':
objmmdb3.c:5454:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ModelSpacePointAsnRead':
objmmdb3.c:5615:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'MoveFree':
objmmdb3.c:5759:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'RotMatrixAsnRead':
objmmdb3.c:5967:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'TransMatrixAsnRead':
objmmdb3.c:6200:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'GLMatrixAsnRead':
objmmdb3.c:6379:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucScriptStepAsnRead':
objmmdb3.c:6680:16: 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:307:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'BiostrucFeatureSetDescrAsnRead':
objmmdb3.c:2024:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'ResiduePntrsAsnRead':
objmmdb3.c:4213:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'RegionBoundaryAsnRead':
objmmdb3.c:5075:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'MoveAsnRead':
objmmdb3.c:5839:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'RegionPntrsAsnRead':
objmmdb3.c:3464:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c:3409:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb3.c: In function 'BiostrucFeatureAsnRead':
objmmdb3.c:2691:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c:2626:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb3.c:2370:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c:2308:10: 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 -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:184:3: 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:605:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:604:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dGeneralStyleAsnRead':
objcn3d.c:789:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:788:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dBackboneLabelStyleAsnRead':
objcn3d.c:972:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:971:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dStyleSettingsAsnRead':
objcn3d.c:1175:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1174:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dStyleSettingsSetAsnRead':
objcn3d.c:1578:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dStyleTableItemAsnRead':
objcn3d.c:1707:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1706:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dResidueRangeAsnRead':
objcn3d.c:1872:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1871:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dMoleculeLocationAsnRead':
objcn3d.c:2035:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dObjectLocationAsnRead':
objcn3d.c:2198:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dUserAnnotationAsnRead':
objcn3d.c:2363:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dGLMatrixAsnRead':
objcn3d.c:2555:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:2554:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dVectorAsnRead':
objcn3d.c:2843:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:2842:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dViewSettingsAsnRead':
objcn3d.c:3016:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:3015:12: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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' [-Wdangling-else]
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 -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:184:3: 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 were guarded by the 'if'
src = orgstring;
^~~
mmdbapi3.c:840:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
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 -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:184:3: 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 -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:184:3: 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 -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 -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:184:3: 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:559:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (vnp = ValNodeFindNext(currentbp->descr, NULL, BiomolDescr_name))
^~~
prunebsc.c:574:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (vnp = ValNodeFindNext(het->descr, NULL, BiomolDescr_name))
^~~
prunebsc.c:663:9: 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:695:16: warning: 'mol_id' may be used uninitialized in this function [-Wmaybe-uninitialized]
bsmpHead = PruneModel(bsmp, pvnIds, mol_id);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prunebsc.c:591:26: warning: 'currenthet' may be used uninitialized in this function [-Wmaybe-uninitialized]
currenthet->next = het;
~~~~~~~~~~~~~~~~~^~~~~
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 -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:184:3: 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 'CddAsnRead':
objcdd.c:402:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddSetAsnRead':
objcdd.c:798:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:795:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddTreeAsnRead':
objcdd.c:935:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:934:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddTreeSetAsnRead':
objcdd.c:1147:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1144:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddPrefNodesAsnRead':
objcdd.c:1281:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1280:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddProjectAsnRead':
objcdd.c:1478:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddOrgRefAsnRead':
objcdd.c:1668:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1667:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddOrgRefSetAsnRead':
objcdd.c:1838:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1835:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddPrefNodeDescrFree':
objcdd.c:1932:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'CddPrefNodeDescrAsnRead':
objcdd.c:1967:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddPrefNodeDescrSetAsnRead':
objcdd.c:2130:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2127:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'GlobalIdAsnRead':
objcdd.c:2263:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2262:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddRepeatAsnRead':
objcdd.c:2450:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2449:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddBookRefAsnRead':
objcdd.c:2627:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2626:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddDescrSetAsnRead':
objcdd.c:3183:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:3180:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'MatrixAsnRead':
objcdd.c:3315:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'TriangleAsnRead':
objcdd.c:3504:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'UpdateCommentFree':
objcdd.c:3641:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'UpdateCommentAsnRead':
objcdd.c:3685:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'UpdateAlignAsnRead':
objcdd.c:3889:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'RejectIdAsnRead':
objcdd.c:4064:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'FeatureEvidenceFree':
objcdd.c:4188:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'FeatureEvidenceAsnRead':
objcdd.c:4232:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'AlignAnnotAsnRead':
objcdd.c:4437:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'AlignAnnotSetAsnRead':
objcdd.c:4606:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4603:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'DomainParentAsnRead':
objcdd.c:4738:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4737:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'SequenceTreeAsnRead':
objcdd.c:4919:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4918:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'AlgorithmTypeAsnRead':
objcdd.c:5107:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5106:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'SeqTreeNodeAsnRead':
objcdd.c:5410:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5409:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'Children_footprintAsnRead':
objcdd.c:5595:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5594:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'NodeAnnotationAsnRead':
objcdd.c:5887:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5886:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddViewerRectAsnRead':
objcdd.c:6053:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:6052:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddViewerAsnRead':
objcdd.c:6235:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddScriptAsnRead':
objcdd.c:6410:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:6409:12: 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 'CddIdAsnRead':
objcdd.c:134:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c: In function 'CddPrefNodeDescrAsnRead':
objcdd.c:2016:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c: In function 'CddDescrAsnRead':
objcdd.c:3007:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c: In function 'UpdateCommentAsnRead':
objcdd.c:3746:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c: In function 'FeatureEvidenceAsnRead':
objcdd.c:4293:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c: In function 'SeqTreeNodeAsnRead':
objcdd.c:5561:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c:5510:10: 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 -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:184:3: 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 were 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 were 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;
~~~~~~~~~~~~~~^~~~~~~~
In file included from ../include/ncbi.h:59:0,
from cddutil.c:336:
cddutil.c: In function 'CddCalculateTriangle':
../include/ncbimem.h:232:23: warning: 'buffer1' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
cddutil.c:3415:19: note: 'buffer1' was declared here
Uint1Ptr buffer1, buffer2, buffer3;
^~~~~~~
cddutil.c:3524:22: warning: 'pscTail' may be used uninitialized in this function [-Wmaybe-uninitialized]
pscTail->next = psc; pscTail = psc; psc = NULL;
~~~~~~~~~~~~~~^~~~~
cddutil.c: In function 'CddDenDiagCposComp2KBP':
cddutil.c:4974:11: warning: 'pssm' may be used uninitialized in this function [-Wmaybe-uninitialized]
return(pssm);
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 * 4)) + (sizetype)((unsigned int)a * 4))' 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:829:10: warning: 'Sigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (Sigma > 0) {
^
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 -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:76:
/usr/include/features.h:184:3: 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:126:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'NcbiMimeAsn1AsnRead':
objmime.c:173:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'Data_dataFree':
objmime.c:382:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'EntrezGeneralAsnRead':
objmime.c:428:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c:427:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'Data_dataAsnRead':
objmime.c:522:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'BiostrucAlignAsnRead':
objmime.c:801:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucAlignSeqAsnRead':
objmime.c:1027:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucSeqAsnRead':
objmime.c:1220:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucSeqsAsnRead':
objmime.c:1415:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'SeqAlignData_seq_align_dataFree':
objmime.c:1613:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'BiostrucSeqsAlignsCddAsnRead':
objmime.c:1647:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'SeqAlignData_seq_align_dataAsnRead':
objmime.c:1734:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'BundleSeqsAlignsAsnRead':
objmime.c:1973:16: 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:81:
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: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/mapmime.h:6:0,
from objmime.c:81:
../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:235:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c: In function 'EntrezGeneralAsnRead':
objmime.c:584:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c:521:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmime.c: In function 'BiostrucSeqsAlignsCddAsnRead':
objmime.c:1780:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c:1733:10: 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 -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:184:3: 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 -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 -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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 -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:64:5: warning: 'nt' may be used uninitialized in this function [-Wmaybe-uninitialized]
int nt; /* Number of threads within specified ensemble cutoff */
^~
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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 were 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 were 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 were 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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:184:3: 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:165:2:
2,-2, 0, 0,-2,-1, 0, 1,-1,-1,-2,-1,-1,-3, 1, 1, 1,-5,-3, 0, 1, 1, 0,
{ }
-2, 5, 0,-1,-3, 1,-1,-3, 1,-2,-2, 2, 0,-3, 0, 0,-1, 1,-4,-2, 0, 1, 0,
{ }
0, 0, 2, 2,-3, 0, 1, 0, 1,-1,-2, 1,-2,-2, 0, 1, 0,-4,-1,-2, 3, 2, 0,
{ }
0,-1, 2, 3,-4, 1, 3, 0, 0,-2,-3, 0,-2,-4,-1, 0, 0,-6,-3,-2, 4, 3, 0,
{ }
-2,-3,-3,-4, 8,-4,-4,-3,-3,-2,-5,-4,-4,-4,-2, 0,-2,-6, 0,-2,-3,-3, 0,
{ }
-1, 1, 0, 1,-4, 4, 2,-1, 2,-2,-1, 0,-1,-4, 0,-1,-1,-4,-3,-2, 2, 4, 0,
{ }
0,-1, 1, 3,-4, 2, 3, 0, 0,-2,-3, 0,-2,-4, 0, 0, 0,-6,-3,-2, 3, 4, 0,
{ }
1,-3, 0, 0,-3,-1, 0, 4,-2,-2,-3,-2,-3,-3,-1, 1, 0,-5,-4,-1, 1, 0, 0,
{ }
-1, 1, 1, 0,-3, 2, 0,-2, 5,-2,-2, 0,-2,-1, 0,-1,-1,-3, 0,-2, 2, 2, 0,
{ }
-1,-2,-1,-2,-2,-2,-2,-2,-2, 4, 2,-1, 2, 1,-2,-1, 0,-5,-1, 3,-1,-1, 0,
{ }
-2,-2,-2,-3,-5,-1,-3,-3,-2, 2, 4,-2, 3, 1,-2,-2,-1,-4,-1, 1,-2,-1, 0,
{ }
-1, 2, 1, 0,-4, 0, 0,-2, 0,-1,-2, 4, 1,-4,-1, 0, 0,-3,-4,-2, 1, 1, 0,
{ }
-1, 0,-2,-2,-4,-1,-2,-3,-2, 2, 3, 1, 5, 0,-2,-1, 0,-4,-2, 1,-1, 0, 0,
{ }
-3,-3,-2,-4,-4,-4,-4,-3,-1, 1, 1,-4, 0, 7,-4,-2,-2, 0, 5,-1,-2,-3, 0,
{ }
1, 0, 0,-1,-2, 0, 0,-1, 0,-2,-2,-1,-2,-4, 5, 1, 0,-5,-4,-1, 0, 1, 0,
{ }
1, 0, 1, 0, 0,-1, 0, 1,-1,-1,-2, 0,-1,-2, 1, 2, 1,-2,-2,-1, 1, 1, 0,
{ }
1,-1, 0, 0,-2,-1, 0, 0,-1, 0,-1, 0, 0,-2, 0, 1, 3,-4,-2, 0, 1, 0, 0,
{ }
-5, 1,-4,-6,-6,-4,-6,-5,-3,-5,-4,-3,-4, 0,-5,-2,-4,12, 0,-6,-3,-4, 0,
{ }
-3,-4,-1,-3, 0,-3,-3,-4, 0,-1,-1,-4,-2, 5,-4,-2,-2, 0, 7,-2,-1,-2, 0,
{ }
0,-2,-2,-2,-2,-2,-2,-1,-2, 3, 1,-2, 1,-1,-1,-1, 0,-6,-2, 4,-1,-1, 0,
{ }
1, 0, 3, 4,-3, 2, 3, 1, 2,-1,-2, 1,-1,-2, 0, 1, 1,-3,-1,-1, 4, 4, 0,
{ }
1, 1, 2, 3,-3, 4, 4, 0, 2,-1,-1, 1, 0,-3, 1, 1, 0,-4,-2,-1, 4, 5, 0,
{ }
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
{
};
}
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' [-Wdangling-else]
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 $";
^~~~~
csim.c: In function 'SIM':
csim.c:1071:62: warning: 'dj' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~^~~~
csim.c:928:23: note: 'dj' was declared here
register Int4 di, dj; /* end-point associated with d */
^~
csim.c:1071:51: warning: 'di' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~^~~~
csim.c:928:19: note: 'di' was declared here
register Int4 di, dj; /* end-point associated with d */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF db_slist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/list.h:56,
from db_slist.c:97:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
db_slist.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: db_slist.c,v 6.2 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF dust.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from dust.c:102:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dust.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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 -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:184:3: 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:668:7: 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:710:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = diag_prev[len1+len2-1-pos]) {
^~
falign.c:719:7: 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:881:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = diag_prev[len1+se2-pos]) {
^~
falign.c:889:7: 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:1547:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = diag_prev[ocur_diag]) {
^~
falign.c: In function 'enterS':
falign.c:1897:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (s = findS(f->bgf)) {
^
falign.c: In function 'local':
falign.c:1958:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = diag_prev[cur_diag]) {
^~
falign.c: In function 'align':
falign.c:1999:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = cdiag_prev[cur_diag]) {
^~
falign.c: In function 'calign':
falign.c:2054:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = cdiag_prev[cur_diag]) {
^~
falign.c: In function 'malign':
falign.c:2109:6: 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 $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF g_any.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from g_any.c:89:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
g_any.c: In function 'k_align':
g_any.c:212:10: warning: array subscript has type 'char' [-Wchar-subscripts]
va = vv[A[i+1]];
^
g_any.c:229:26: warning: array subscript has type 'char' [-Wchar-subscripts]
if (j < J2) c = s + va[B[j+1]];
^
g_any.c:319:10: warning: array subscript has type 'char' [-Wchar-subscripts]
b2 = PP[t1][b1];
^
g_any.c:322:10: warning: array subscript has type 'char' [-Wchar-subscripts]
t2 = PT[t1][b1];
^
g_any.c: In function 'z_ALIGN':
g_any.c:367:7: warning: variable 'check_score' set but not used [-Wunused-but-set-variable]
Int4 check_score;
^~~~~~~~~~~
g_any.c: In function 'CHECK_SCORE':
g_any.c:492:13: warning: array subscript has type 'char' [-Wchar-subscripts]
score = vv[A[++i]][B[++j]] + score;
^
g_any.c:492:21: warning: array subscript has type 'char' [-Wchar-subscripts]
score = vv[A[++i]][B[++j]] + score;
^
At top level:
g_any.c:428:35: warning: 'CLINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:428:24: warning: 'BLINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:428:13: warning: 'ALINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: g_any.c,v 6.5 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF sim2.c
sim2.c: In function 'SIM2':
sim2.c:19:16: warning: unused variable 'compB' [-Wunused-variable]
CharPtr A, B, compB = NULL;
^~~~~
sim2.c:17:26: warning: unused variable 'sapC' [-Wunused-variable]
SeqAlignPtr sap = NULL, sapC=NULL, out_sap, out_sapC;
^~~~
At top level:
sim2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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 -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:184:3: 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:630:9: 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' [-Wdangling-else]
if (row == 0 && col == 0)
^
sim4.c:1794:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (row == 0)
^
sim4.c:1838:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (col == 0)
^
sim4.c:1962:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (row == m && col == n)
^
sim4.c:1991:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (row == m)
^
sim4.c:2037:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
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.13':
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 -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:184:3: 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 $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF slist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/list.h:56,
from slist.c:101:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
slist.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: slist.c,v 6.2 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF sec.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from sec.c:67:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sec.c: In function 'Region':
sec.c:268:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:268:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:292:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:292:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:321:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:321:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:345:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:345:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:428:35: warning: array subscript has type 'char' [-Wchar-subscripts]
diag_score = diag_score + V[seq1[i]][seq2[j]];
^
sec.c:428:44: warning: array subscript has type 'char' [-Wchar-subscripts]
diag_score = diag_score + V[seq1[i]][seq2[j]];
^
At top level:
sec.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -fPIC -D_PNG -I../include -DWIN_MOTIF tfuns.c
tfuns.c: In function 'find_orf':
tfuns.c:866:26: warning: unused variable 'into' [-Wunused-variable]
IntFuzzPtr infrom=NULL, into=NULL;
^~~~
tfuns.c:866:13: warning: unused variable 'infrom' [-Wunused-variable]
IntFuzzPtr infrom=NULL, into=NULL;
^~~~~~
At top level:
tfuns.c:977:13: 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 6.17 2015/08/17 17:15:09 bollin Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:169,
from toasn3.c:10:
/usr/include/features.h:184:3: 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:1444:17: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
toasn3.c: In function 'CheckQualsWithComm':
toasn3.c:1731:18: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toasn3.c: In function 'CheckQuals':
toasn3.c:1768:18: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toasn3.c: In function 'CountSourceFeat':
toasn3.c:2570:13: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
toasn3.c:2561:19: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
toasn3.c: In function 'TASNTrimInternalSemicolons':
toasn3.c:4155:12: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
CharPtr tmp;
^~~
toasn3.c: In function 'ImpFeatToProtRef':
toasn3.c:4861:13: warning: variable 'lfree' set but not used [-Wunused-but-set-variable]
Boolean lfree = FALSE, partial5, partial3;
^~~~~
toasn3.c: In function 'RemovePeptideImpFeats':
toasn3.c:5160:24: warning: variable 'ifp' set but not used [-Wunused-but-set-variable]
ImpFeatPtr ifp;
^~~
At top level:
toasn3.c:1711:16: 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 6.150 2016/11/02 23:36:09 kans Exp $";
^~~~~
toasn3.c: In function 'FixNucProtSet':
toasn3.c:2204:21: 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 -fPIC -D_PNG -I../include -DWIN_MOTIF toporg.c
toporg.c: In function 'ChkSegset':
toporg.c:64:51: warning: variable 'is_title' set but not used [-Wunused-but-set-variable]
Boolean is_org = FALSE, is_modif = FALSE, is_title = FALSE;
^~~~~~~~
toporg.c:63:17: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toporg.c:60:17: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
toporg.c:55:17: 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:608:51: 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:1330:17: warning: variable 'empty' set but not used [-Wunused-but-set-variable]
Boolean empty;
^~~~~
toporg.c:1329:17: warning: variable 'bsmp' set but not used [-Wunused-but-set-variable]
BSMapPtr bsmp;
^~~~
toporg.c:1328:29: warning: variable 'set_vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr descr, vnp, set_vnp;
^~~~~~~
toporg.c: In function 'MapsToGenref':
toporg.c:2021:17: warning: variable 'loc' set but not used [-Wunused-but-set-variable]
SeqLocPtr loc;
^~~
toporg.c:2016:17: warning: variable 'descr' set but not used [-Wunused-but-set-variable]
ValNodePtr descr = NULL, head, last, vnp;
^~~~~
toporg.c: In function 'FindOldLineage':
toporg.c:2606:17: warning: variable 'lineage' set but not used [-Wunused-but-set-variable]
CharPtr lineage;
^~~~~~~
toporg.c: In function 'ArePubsMergeableForFig':
toporg.c:4796:36: 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:4796:12: note: add parentheses around left hand side expression to silence this warning
|| !cgp_fig->serial_number != cgp_nofig->serial_number) {
^~~~~~~~~~~~~~~~~~~~~~~
( )
toporg.c: In function 'StripBadTitleFromProteinProducts':
toporg.c:5311:22: warning: variable 'tech' set but not used [-Wunused-but-set-variable]
Uint1 tech;
^~~~
toporg.c: In function 'FindPubWithFig':
toporg.c:5647:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
Int4 a = 0;
^
toporg.c: In function 'AddMissingGeneXref':
toporg.c:5955:22: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
toporg.c: In function 'ConvertSegSetToDeltaSeqInt':
toporg.c:7093:18: warning: unused variable 'str' [-Wunused-variable]
CharPtr str, ttl = NULL;
^~~
toporg.c:7086:18: warning: unused variable 'ovp' [-Wunused-variable]
ObjValNodePtr ovp;
^~~
At top level:
toporg.c:5475:13: warning: 'SynchronizePseudogenesProc' defined but not used [-Wunused-function]
static void SynchronizePseudogenesProc (
^~~~~~~~~~~~~~~~~~~~~~~~~~
toporg.c:3119:13: 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 6.251 2016/11/02 23:36:10 kans Exp $";
^~~~~
toporg.c: In function 'MergeEquivCitSubs':
toporg.c:3905:7: warning: 'csp1' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (DateMatch (csp1->date, csp2->date, FALSE) != 0) return FALSE;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
toporg.c:3925:18: note: 'csp1' was declared here
CitSubPtr csp1, csp2;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF suggest.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from suggest.c:199:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
suggest.c: In function 'get_frames':
suggest.c:458:12: warning: array subscript has type 'char' [-Wchar-subscripts]
val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]];
^
suggest.c:458:26: warning: array subscript has type 'char' [-Wchar-subscripts]
val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]];
^
At top level:
suggest.c:1331:13: warning: 'ReportSuggestIntervalsError' defined but not used [-Wunused-function]
static void ReportSuggestIntervalsError (SeqRecPtr srp, CharPtr gen_txt)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
suggest.c:1222:1: warning: 'fprintf_m_stk_entry' defined but not used [-Wunused-function]
fprintf_m_stk_entry(FILE *fp, Int4 index, char *msg)
^~~~~~~~~~~~~~~~~~~
suggest.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: suggest.c,v 6.14 2009/04/10 17:22:14 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF suggslp.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from suggslp.c:53:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
suggslp.c: In function 'MakeReverseSequence':
suggslp.c:190:11: warning: array subscript has type 'char' [-Wchar-subscripts]
*t++ = r[*--s];
^
At top level:
suggslp.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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:3179:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (virtual_oidlist = rdfp_chain->oidlist) {
^~~~~~~~~~~~~~~
blast.c: In function 'BlastGetDbChunk':
blast.c:3210:13: 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 were 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' [-Wdangling-else]
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 $";
^~~~~
blast.c: In function 'BLASTMergeHitLists.isra.4':
blast.c:6256:24: warning: 'op_type' may be used uninitialized in this function [-Wmaybe-uninitialized]
esp2->op_type = op_type;
~~~~~~~~~~~~~~^~~~~~~~~
blast.c:6058:10: note: 'op_type' was declared here
Uint1 op_type;
^~~~~~~
blast.c: In function 'blastMergeFilterLocs':
blast.c:3985:16: warning: 'dup_slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
dup_slp = (SeqLocPtr) dup_slp->data.ptrvalue;
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast.c: In function 'BlastLinkHsps':
blast.c:10455:41: warning: 'orig_hitlist' may be used uninitialized in this function [-Wmaybe-uninitialized]
search->current_hitlist = orig_hitlist;
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blastutl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastutl.c:1836:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastutl.c: In function 'BlastSeqLocFilterEx':
blastutl.c:7554:11: warning: statement with no effect [-Wunused-value]
stop_timer("after repeat filtering");
^
blastutl.c: In function 'BlastPreliminaryGappedScore':
blastutl.c:9853:30: warning: variable 'query_length' set but not used [-Wunused-but-set-variable]
Int4 index, max_offset = 0, query_length, min_score;
^~~~~~~~~~~~
blastutl.c: In function 'BlastGetGappedScore':
blastutl.c:10282:11: warning: statement with no effect [-Wunused-value]
stop_timer("after BlastGappedScoreInternal");
^
At top level:
blastutl.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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:11522:43: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 loop_increment, loop_increment2, stop;
^~~~
blastutl.c:11711:18: warning: 'start_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score2 += matrix[(Int4) *(str+index2)][*(words+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_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score2 += posMatrix[offset+index2][*(words+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:9377:56: warning: 'seqalign_array' may be used uninitialized in this function [-Wmaybe-uninitialized]
seqalign_array[index2] =
~~~~~~~~~~~~~~~~~~~~~~~^
SeqAlignFree(seqalign_array[index2]);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:184:3: 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 were 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 $";
^~~~~
blastool.c: In function 'BlastCreateVirtualOIDList':
blastool.c:2556:24: warning: 'gilist' may be used uninitialized in this function [-Wmaybe-uninitialized]
BlastDoubleInt4Ptr gilist, real_gilist = NULL, *real_gilist_ptrs = NULL;
^~~~~~
blastool.c: In function 'BlastInsertList2Heap':
blastool.c:3595:31: warning: 'query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
context = hsp->query_offset / query_length;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
blastool.c: In function 'BlastFreeHeap':
blastool.c:3687:31: warning: 'query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
context = hsp->query_offset / query_length;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
blastool.c: In function 'BLASTFilterOverlapRegions':
blastool.c:4531:24: warning: 'next_tail' may be used uninitialized in this function [-Wmaybe-uninitialized]
tail->next = seqalign;
~~~~~~~~~~~^~~~~~~~~~
blastool.c: In function 'BlastPrintAlignInfo':
blastool.c:4800:23: warning: 'sap' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap->next = SeqAlignNew();
~~~~~~~~~~^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blastconcat.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastconcat.c:89:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastconcat.c: In function 'BlastMakeFakeBspConcat':
blastconcat.c:648:12: warning: variable 'slp' set but not used [-Wunused-but-set-variable]
SeqLocPtr slp = NULL;
^~~
At top level:
blastconcat.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastconcat.c,v 1.14 2007/05/07 13:30:54 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF splutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from splutil.c:52:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
splutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: splutil.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF gapxdrop.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/gapxdrop.h:150,
from gapxdrop.c:368:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gapxdrop.c: In function 'ALIGN_EX':
gapxdrop.c:864:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (s == 1)
^
gapxdrop.c:867:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (s == 2)
^
At top level:
gapxdrop.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: gapxdrop.c,v 6.76 2003/11/07 21:52:52 dondosha Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg0.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg0.c:36:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg0.c: In function 'g_band0_align':
bandalg0.c:273:9: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if(leftd >= 1)
^
At top level:
bandalg0.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg0.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg1.c:36:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg1.c: In function 'gband_quadratic':
bandalg1.c:54:14: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int4 c, i, j;
^
bandalg1.c: In function 'g_band1_align':
bandalg1.c:205:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if(leftd >= 1)
^
At top level:
bandalg1.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg1.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg2.c:36:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg2.c: In function 'gb_linear_align':
bandalg2.c:208:24: warning: variable 'misma' set but not used [-Wunused-but-set-variable]
register Int4 match, misma;
^~~~~
bandalg2.c:208:17: warning: variable 'match' set but not used [-Wunused-but-set-variable]
register Int4 match, misma;
^~~~~
bandalg2.c:207:18: warning: variable 'AA' set but not used [-Wunused-but-set-variable]
register Uint1 AA;
^~
At top level:
bandalg2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg2.c,v 6.5 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
bandalg2.c: In function 'gb_linear_align':
bandalg2.c:202:38: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 rmid, k =0, l=0, r, v, kt, X, Y;
^
In file included from bandalg2.c:36:0:
../include/bandalgn.h:140:76: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
data->last = (data->last < 0) ? (data->sapp[-1] -= (k)) : (*data->sapp++ = -(k));
^
bandalg2.c:202:35: note: 'X' was declared here
Int4 rmid, k =0, l=0, r, v, kt, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg3.c:37:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg3.c: In function 'gband_linear_qgap':
bandalg3.c:54:14: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int4 c, i, j;
^
At top level:
bandalg3.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg3.c,v 6.4 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
bandalg3.c: In function 'gband_linear_qgap':
bandalg3.c:314:16: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
else if(Y != rightd) _INS(rightd-Y)
^
bandalg3.c:185:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
bandalg3.c:313:21: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(X != M) _DEL(M - X)
^
bandalg3.c:185:25: note: 'X' was declared here
Int4 ib, best=MININT, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg4.c:37:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg4.c: In function 'g_band4_align_small':
bandalg4.c:826:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (e == 1)
^
bandalg4.c:829:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (e == 2)
^
bandalg4.c:630:8: warning: variable 'band' set but not used [-Wunused-but-set-variable]
Int4 band, j;
^~~~
At top level:
bandalg4.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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:562:7: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
g_band4_align(A, B, r - 1, r + rmid, rmid + 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MIN(up, r + rmid), tb, 1, legA, legB, 1, 1, data);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bandalg4.c:824:27: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
k = (t=data->state[i][j]) %5;
^
bandalg4.c:640:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
bandalg4.c:824:24: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
k = (t=data->state[i][j]) %5;
^
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 -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:184:3: 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' [-Wdangling-else]
if (e == 1)
^
bandalg5.c:295:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
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 $";
^~~~~
bandalg5.c: In function 'gband_q3gap':
bandalg5.c:320:6: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (Y != rightd) _INS(rightd - Y);
^
bandalg5.c:146:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
bandalg5.c:319:22: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (X != M) _DEL(M - X);
^
bandalg5.c:146:25: note: 'X' was declared here
Int4 ib, best=MININT, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalgn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from bandalgn.c:118:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalgn.c: In function 'ExtendSeqAlign':
bandalgn.c:1113:22: warning: variable 'ddp' set but not used [-Wunused-but-set-variable]
DenseDiagPtr ddp;
^~~
bandalgn.c: In function 'CC_ExtendSeqAlign':
bandalgn.c:1188:22: warning: variable 'ddp' set but not used [-Wunused-but-set-variable]
DenseDiagPtr ddp;
^~~
At top level:
bandalgn.c:699:14: warning: 'HSblastna_to_ncbi4na' defined but not used [-Wunused-variable]
static Uint1 HSblastna_to_ncbi4na[] = { 1, /* A, 0 */
^~~~~~~~~~~~~~~~~~~~
bandalgn.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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:1055:10: warning: 'maxdi' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxy = maxdi + width;
~~~~~^~~~~~~~~~~~~~~
bandalgn.c:1056:10: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 * 4)) + (sizetype)((unsigned int)a * 4))' 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 -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:184:3: 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 -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:2057:
/usr/include/features.h:184:3: 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:2503:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (**filenames == '"')
^
readdb.c: In function 's_GetBlastDirInfo':
readdb.c:2734:32: 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:3320:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (rdfp->cih)
^~
readdb.c:3326:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (rdbap->first_oid > 0) {
^~
readdb.c:3400:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (rdfp->cih && rdfp->aliasfilebit == 0)
^~
readdb.c:3406:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (rdbap->first_oid > 0) {
^~
readdb.c: In function 'FindBlastDBFileEx':
readdb.c:3480:33: warning: unused variable 'envp' [-Wunused-variable]
CharPtr buffer, buffer1, envp = NULL;
^~~~
readdb.c: In function 'readdb_new_internalEx':
readdb.c:3558:25: warning: unused variable 'envp' [-Wunused-variable]
CharPtr charptr, envp = NULL;
^~~~
readdb.c: In function 'readdb_get_link':
readdb.c:4752:12: warning: variable 'loaded_new' set but not used [-Wunused-but-set-variable]
Boolean loaded_new = FALSE;
^~~~~~~~~~
readdb.c:4751:24: 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:4896:38: 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:5236:22: warning: unused variable 'dummy_gi' [-Wunused-variable]
Int4 dummy_gi = 0; /* Not used, should have been handled above. */
^~~~~~~~
readdb.c:5180:13: warning: unused variable 'chptr' [-Wunused-variable]
CharPtr chptr = NULL;
^~~~~
readdb.c: In function 'FDBuildOldStyleDefline':
readdb.c:6366:33: 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 'PrintDbInformationWithRID':
readdb.c:7571:14: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (rdfp == FALSE)
^~
readdb.c:7571:9: note: did you mean to dereference the pointer?
if (rdfp == FALSE)
^
readdb.c: In function 'FDBLoadMembershipsTable':
readdb.c:8265:21: warning: variable 'fn_name' set but not used [-Wunused-but-set-variable]
const char* fn_name = NULL;
^~~~~~~
readdb.c: In function 'SeqIdE2Index':
readdb.c:8613:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((tsip->version > 0) && (tsip->release == NULL))
^~
readdb.c:8615:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
break;
^~~~~
readdb.c:8618:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (tsip->version > 0)
^~
readdb.c:8620:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
break;
^~~~~
readdb.c:8577:13: warning: unused variable 'tmp' [-Wunused-variable]
CharPtr tmp, ptr=NULL;
^~~
readdb.c:8576:11: warning: unused variable 'tmptype' [-Wunused-variable]
Uint1 tmptype;
^~~~~~~
readdb.c: In function 'SeqIdSetE2Index':
readdb.c:8881:14: warning: variable 'oldanp' set but not used [-Wunused-but-set-variable]
SeqIdPtr oldanp;
^~~~~~
readdb.c: In function 'FindDBbyGI':
readdb.c:11397:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (gi > cih->maxgi)
^~
readdb.c:11400:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cigi = cih->ci + gi;
^~~~
readdb.c: In function 'Fastacmd_Search_ex':
readdb.c:12080:22: warning: variable 'guess_gi' set but not used [-Wunused-but-set-variable]
Int4 guess_gi = -1;
^~~~~~~~
readdb.c: In function 'DumpOneSequence':
readdb.c:12407:20: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
fprintf(fp, "%d\n", gi->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~
%lld
readdb.c:12417:14: 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:2067:
readdb.c: At top level:
../include/objentgene.h:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
readdb.c:12829:1: 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:2060:0:
../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 6.549 2016/09/02 15:04:59 ucko Exp $";
^~~~~
readdb.c: In function 'ReadDBOpenMHdrAndSeqFiles':
readdb.c:2259:27: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%chr", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:2277:27: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:2296:27: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%chr", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:2252:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:2252:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c: In function 'readdb_get_taxonomy_names':
readdb.c:5679:28: 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:6668:44: 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 'readdb_new_internalEx':
readdb.c:3671:25: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%cin", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3811:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%cnd", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3812:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer1, "%s.%cni", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3825:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%csd", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3826:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer1, "%s.%csi", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3845:29: warning: '.ppd' directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
sprintf(buffer, "%s.ppd", rdfp->full_filename);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3846:29: warning: '.ppi' directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
sprintf(buffer1, "%s.ppi", rdfp->full_filename);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c: In function 'GetAccList':
readdb.c:11821:29: warning: 'AccListLast' may be used uninitialized in this function [-Wmaybe-uninitialized]
AccListLast->next = AccListTmp;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
readdb.c: In function 'FD_ConstructMultivolumeDBList':
readdb.c:12688:31: warning: '%02ld' directive writing between 2 and 10 bytes into a region of size 9 [-Wformat-overflow=]
sprintf(numstr, ".%02ld ", (long) i);
^~~~~
readdb.c:12688:29: note: directive argument in the range [0, 2147483647]
sprintf(numstr, ".%02ld ", (long) i);
^~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:12690:31: warning: '%03ld' directive writing between 3 and 10 bytes into a region of size 9 [-Wformat-overflow=]
sprintf(numstr, ".%03ld ", (long) i);
^~~~~
readdb.c:12690:29: note: directive argument in the range [0, 2147483647]
sprintf(numstr, ".%03ld ", (long) i);
^~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 6 and 13 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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;
^~~~~~~~~~
ncbisam.c:1070:23: warning: 'KeyDataSamples' may be used uninitialized in this function [-Wmaybe-uninitialized]
KeyDataSamples[SampleCount].key = SwapUint4(UINT4_MAX);
^
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 -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:86:
/usr/include/features.h:184:3: 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:699:12: warning: type defaults to 'int' in declaration of 'tmpa' [-Wimplicit-int]
register tmpa = UCHAR(*a), tmpb = UCHAR(*b);
^~~~
ncbisort.c:699:30: warning: type defaults to 'int' in declaration of 'tmpb' [-Wimplicit-int]
register tmpa = UCHAR(*a), tmpb = UCHAR(*b);
^~~~
In file included from ncbisort.c:86:0:
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 6.9 2012/08/22 23:02:39 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF salign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salign.h:10,
from salign.c:45:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salign.c: In function 'BandAlignTwoSeqLocsFunc':
salign.c:173:13: warning: variable 'is_prot' set but not used [-Wunused-but-set-variable]
Boolean is_prot;
^~~~~~~
salign.c: In function 'SortBlastHits':
salign.c:391:15: warning: variable 'totalvalmax' set but not used [-Wunused-but-set-variable]
totalvalmax = INT4_MAX,
^~~~~~~~~~~
salign.c: In function 'link_solution':
salign.c:1188:15: warning: unused variable 'first' [-Wunused-variable]
Boolean first = TRUE;
^~~~~
At top level:
salign.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: salign.c,v 6.11 2009/01/21 17:09:18 bollin Exp $";
^~~~~
salign.c: In function 'SortBlastHits':
salign.c:455:6: warning: 'salpdup' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAlignSetFree (salpdup);
^~~~~~~~~~~~~~~~~~~~~~~~~
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.5':
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 -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:184:3: 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 were 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 were 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 were 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 were 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF urkutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from urkutil.c:59:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkutil.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF urkpcc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkpcc.h:54,
from urkpcc.c:56:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkpcc.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkpcc.c,v 6.13 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF urkptpf.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from urkptpf.c:65:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkptpf.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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 $";
^~~~~
urkepi.c: In function 'FilterEpi':
urkepi.c:1053:21: warning: 'right' may be used uninitialized in this function [-Wmaybe-uninitialized]
cfap->right = right;
~~~~~~~~~~~~^~~~~~~
urkepi.c:936:56: note: 'right' was declared here
Int4 i, n, j, k, start, stop, loop, fact, left, right;
^~~~~
urkepi.c:1052:20: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized]
cfap->left = left;
~~~~~~~~~~~^~~~~~
urkepi.c:936:50: note: 'left' was declared here
Int4 i, n, j, k, start, stop, loop, fact, left, right;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF urkfltr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkfltr.h:51,
from urkfltr.c:56:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkfltr.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkfltr.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF urkdust.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkdust.h:51,
from urkdust.c:56:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkdust.c: In function 'DustMe_h':
urkdust.c:196:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(dcvp->curlevel <= newlevel) && dcvp->curend == loop+1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
urkdust.c: In function 'DustForGraph':
urkdust.c:776:17: warning: variable 'drphead' set but not used [-Wunused-but-set-variable]
DustRegionPtr drphead;
^~~~~~~
At top level:
urkdust.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkdust.c,v 6.10 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF urksigu.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urksigu.h:57,
from urksigu.c:59:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urksigu.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urksigu.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF seg.c
seg.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seg.c,v 6.19 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
seg.c: In function 'getprob':
seg.c:935:15: warning: 'ans2' may be used uninitialized in this function [-Wmaybe-uninitialized]
ans = ans1 + ans2 - totseq;
~~~~~^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF urkbias.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from urkbias.c:56:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkbias.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkbias.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF urkcnsrt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkcnsrt.h:60,
from urkcnsrt.c:80:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkcnsrt.c:1203:13: warning: 'ScanFrame' defined but not used [-Wunused-function]
static void ScanFrame (BioseqPtr bsp, SeqLocPtr slp, Int4 frame,
^~~~~~~~~
urkcnsrt.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkcnsrt.c,v 6.21 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
urkcnsrt.c: In function 'Scan3Frames':
urkcnsrt.c:1385:5: warning: 'length' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (i = n; i < length; i++)
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF urktree.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urktree.h:51,
from urktree.c:53:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urktree.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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:507:12: 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 -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:184:3: 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:534:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) {
^~~
pattern1.c:547:7: 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:750:11: 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' [-Wdangling-else]
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 were 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 $";
^~~~~
pattern1.c: In function 'get_patL':
pattern1.c:1348:42: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
*end = wordIndex*BITS_PACKED_PER_WORD+j;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
pattern1.c: In function 'align':
pattern1.c:1158:8: warning: 'CDrow' may be used uninitialized in this function [-Wmaybe-uninitialized]
score = (CDrow-1)->CC;
~~~~~~^~~~~~~~~~~~~~~
pattern1.c: In function 'get_patLL':
pattern1.c:1393:5: warning: 'pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j = 0; j < pos; j+= wordIndex) {
^~~
pattern1.c: In function 'init_pattern':
pattern1.c:192:11: warning: 'tj' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 tj; /*temporary copy of j*/
^~
pattern1.c: In function 'align_of_pattern':
pattern1.c:1562:19: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized]
local_score += ALIGN_B(querySeq-1, dbSeq-1, queryMatchOffset, dbMatchOffset,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BAND_LOW, BAND_HIGH, matrix, gap_open, gap_extend, alignScript, data);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF impatool.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from impatool.c:73:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
impatool.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: impatool.c,v 6.16 2006/06/30 18:44:40 camacho Exp $";
^~~~~
impatool.c: In function 'IMPALAPrintHelp':
impatool.c:301:20: warning: 'ret_buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
ret_buffer = MemFree(ret_buffer);
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF posit2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from posit2.c:78:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
posit2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: posit2.c,v 6.12 2006/09/18 20:54:27 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF mbalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/mbalign.h:4,
from mbalign.c:176:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mbalign.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: mbalign.c,v 6.43 2006/02/02 17:57:34 papadopo Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF vecscrn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vecscrn.h:74,
from vecscrn.c:103:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vecscrn.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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 -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:184:3: 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 'SaveUntilChar':
rpsutil.c:2190:13: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (ptr != NULLB)
^~
rpsutil.c:2190:9: note: did you mean to dereference the pointer?
if (ptr != NULLB)
^
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 'RPSInitEx':
rpsutil.c:451:28: warning: '.rps' directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
sprintf(rps_matrix, "%s.rps", rpsinfo->rdfp->full_filename);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/rpsutil.h:128,
from rpsutil.c:281:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:452:28: warning: '.loo' directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
sprintf(rps_lookup, "%s.loo", rpsinfo->rdfp->full_filename);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/rpsutil.h:128,
from rpsutil.c:281:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:453:25: warning: '.aux' directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
sprintf(rps_aux, "%s.aux", rpsinfo->rdfp->full_filename);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/rpsutil.h:128,
from rpsutil.c:281:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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;
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
In file included from ../include/ncbi.h:62:0,
from ../include/rpsutil.h:128,
from rpsutil.c:281:
rpsutil.c: In function 'RPSBgetCddHits':
../include/ncbistr.h:284:20: warning: 'dbname' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Nlm_StrCmp strcmp
^~~~~~
rpsutil.c:2212:21: note: 'dbname' was declared here
CharPtr dbname;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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;
^
At top level:
kappa.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: kappa.c,v 6.94 2013/11/04 15:42:10 boratyng Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF xmlblast.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/xmlblast.h:89,
from xmlblast.c:171:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
xmlblast.c: In function 'PSIXmlInit':
xmlblast.c:1239:13: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = FALSE;
^~~~~~
At top level:
xmlblast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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 -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:184:3: 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] = {
^
4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4,
{ }
-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4,
{ }
-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4,
{ }
-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4,
{ }
0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4,
{ }
-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4,
{ }
-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4,
{ }
0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4,
{ }
-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4,
{ }
-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4,
{ }
-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4,
{ }
-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4,
{ }
-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4,
{ }
-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4,
{ }
-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4,
{ }
1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4,
{ }
0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4,
{ }
-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4,
{ }
-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4,
{ }
0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4,
{ }
-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4,
{ }
-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4,
{ }
0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4,
{ }
-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1
{
};
}
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 -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:263:
/usr/include/features.h:184:3: 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:1740:21: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
Int4 offset;
^~~~~~
spidey.c: In function 'SPI_AlnSinglemRNAToPieces':
spidey.c:2854:19: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if (spot->from == spot->to == 0)
~~~~~~~~~~~^~~~~~~~~~~
spidey.c: In function 'SPI_FillInLastmRNAHoles':
spidey.c:6299:21: warning: variable 'internal' set but not used [-Wunused-but-set-variable]
Boolean internal;
^~~~~~~~
spidey.c: In function 'SPI_FindBestAlnByDotPlot':
spidey.c:6445:20: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
spidey.c:6444:20: warning: variable 'start2' set but not used [-Wunused-but-set-variable]
Int4 start2;
^~~~~~
spidey.c:6443:20: warning: variable 'start1' set but not used [-Wunused-but-set-variable]
Int4 start1;
^~~~~~
spidey.c: In function 'SPI_ConnectAlnPieces':
spidey.c:7814:30: warning: variable 'tmparray' set but not used [-Wunused-but-set-variable]
SPI_FragPtr PNTR tmparray;
^~~~~~~~
spidey.c:7800:25: warning: variable 'sfpprev' set but not used [-Wunused-but-set-variable]
SPI_FragPtr sfpprev;
^~~~~~~
spidey.c: In function 'SPI_AdjustSplicesInPieces':
spidey.c:8448:23: warning: variable 'minus' set but not used [-Wunused-but-set-variable]
Boolean minus;
^~~~~
spidey.c: In function 'SPI_CheckMrnaOrder':
spidey.c:10296:35: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if ((ival->strand == Seq_strand_plus == ival2->strand
spidey.c:10300:38: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
|| (ival->strand == Seq_strand_minus == ival2->strand
spidey.c:10313:35: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if ((ival->strand == Seq_strand_plus == ival2->strand
spidey.c:10315:38: 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:263:
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 6.74 2016/09/02 14:57:38 ucko Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF motif.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/motif.h:45,
from motif.c:47:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
motif.c: In function 'MOT_FindPolyA':
motif.c:86:18: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
Uint1 buf[MOT_WINSIZE];
^~~
motif.c: In function 'MOT_FindKozak':
motif.c:216:18: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
Uint1 buf[MOT_WINSIZE];
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from ../include/motif.h:48,
from motif.c:47:
motif.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
motif.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: motif.c,v 6.7 2007/05/07 13:30:54 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blfmtutl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blfmtutl.c:175:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blfmtutl.c: In function 'CBStatisticsGetReference':
blfmtutl.c:593:4: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
} else
^~~~
blfmtutl.c:595:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
add_string_to_bufferEx("Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,", &ret_buffer, &ret_buffer_length, TRUE);
^~~~~~~~~~~~~~~~~~~~~~
blfmtutl.c: In function 'BlastPrintTabularResults':
blfmtutl.c:1281:16: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for (index=1; ssp->next; index++)
^~~
blfmtutl.c:1283:20: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
num_gap_opens = index / 2;
^~~~~~~~~~~~~
At top level:
blfmtutl.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blfmtutl.c,v 1.44 2012/10/10 14:05:50 fongah2 Exp $";
^~~~~
blfmtutl.c: In function 'BlastPrintTabularResults':
blfmtutl.c:1117:13: warning: 'alignments_count' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (--alignments_count < 0)
^
blfmtutl.c:1353:19: warning: 's_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
s_end += s_shift;
~~~~~~^~~~~~~~~~
blfmtutl.c:1352:21: warning: 's_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
s_start += s_shift;
~~~~~~~~^~~~~~~~~~
blfmtutl.c:1351:19: warning: 'q_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
q_end += q_shift;
~~~~~~^~~~~~~~~~
blfmtutl.c:1350:21: warning: 'q_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
q_start += q_shift;
~~~~~~~~^~~~~~~~~~
blfmtutl.c:1081:24: 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:1413:26: 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 -fPIC -D_PNG -I../include -DWIN_MOTIF matrix_frequency_data.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF compo_mode_condition.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF composition_adjustment.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF nlm_linear_algebra.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF optimize_target_freq.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF compo_heap.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF smith_waterman.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF redo_alignment.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF unified_pvalues.c
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 -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:61,
from ../include/gifgen.h:115,
from gdfontg.c:1:
/usr/include/features.h:184:3: 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 -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:61,
from ../include/gifgen.h:115,
from gdfontmb.c:1:
/usr/include/features.h:184:3: 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 -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:61,
from ../include/gifgen.h:115,
from gdfontt.c:1:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:61,
from ../include/gifgen.h:115,
from gdfontl.c:1:
/usr/include/features.h:184:3: 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 -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:61,
from ../include/gifgen.h:115,
from gdfonts.c:1:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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:3448:15: warning: 'fZCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fZCen += fZt / l;
~~~~~~^~~~~~~~~~
algorend.c:3447:15: warning: 'fYCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYCen += fYt / l;
~~~~~~^~~~~~~~~~
algorend.c:3446:15: warning: 'fXCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXCen += fXt / l;
~~~~~~^~~~~~~~~~
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:3449:77: warning: 'fYTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fYCen - fYFrom) * (fZCen - fZTo) - (fZCen - fZFrom) * (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:3449:22: warning: 'fYFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fYCen - fYFrom) * (fZCen - fZTo) - (fZCen - fZFrom) * (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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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]
{
^
255, 255, 255, /* default 0 */
{ }
255, 20, 147, /* hotpink 1 */
{ }
255, 0, 255, /* magenta 2 */
{ }
155, 48, 255, /* purple 3 */
{ }
0, 0, 255, /* blue 4 */
{ }
30, 144, 255, /* sky 5 */
{ }
0, 255, 255, /* cyan 6 */
{ }
0, 255, 127, /* sea 7 */
{ }
0, 255, 0, /* green 8 */
{ }
255, 255, 0, /* yellow 9 */
{ }
255, 165, 0, /* gold 10 */
{ }
255, 69, 0, /* orange 11 */
{ }
255, 0, 0, /* red 12 */
{ }
255, 114, 86, /* pink 13 */
{ }
255, 174, 185, /* pinktint 14 */
{ }
255, 255, 255, /* white 15 */
{ }
0, 0, 0, /* black 16 */
{ }
176, 226, 255, /* bluetint 17 */
{ }
154, 255, 154, /* greentint 18 */
{ }
255, 236, 139, /* yellowtint 19 */
{ }
125, 125, 125, /* gray 20 */
{ }
139, 87, 66, /* brown 21 */
{ }
255, 0, 0, /* perm colors 22: red */
{ }
0, 255, 0, /* perm colors 23: green */
{ }
255, 0, 255, /* perm colors 24: magenta */
{ }
30, 144, 255, /* perm colors 25: sky */
{ }
155, 48, 255, /* perm colors 26: purple */
{ }
0, 255, 0, /* SS colors 27: helix, green */
{ }
255, 165, 0, /* SS colors 28: strand, gold */
{ }
255, 69, 0, /* SS colors 29: turn, orange */
{ }
0, 255, 255, /* SS colors 30: coil, cyan */
{ }
255, 255, 0, /* highlight colors 31: yellow */
{ }
0, 0, 0, /* background colors 32: black */
{ }
160, 82, 45, /* sienna 33 */
{ }
240, 230, 140, /* khaki 34 */
{ }
171, 130, 255, /* light purple 35 */
{ }
255, 200, 0, /* orange yellow 36 */
{ }
117, 128, 160, /* 37 */
{ }
5, 53, 239, /* 38 */
{ }
27, 62, 255, /* 39 */
{ }
84, 110, 203, /* 40 */
{ }
216, 77, 84, /* 41 */
{ }
125, 128, 135, /* 42 */
{ }
237, 29, 61, /* 43 */
{ }
184, 118, 120, /* 44 */
{ }
155, 9, 0, /* 45 */
{ }
155, 119, 107, /* 46 */
{ }
80, 110, 196, /* 47 */
{ }
122, 127, 157, /* 48 */
{ }
50, 85, 241, /* 49 */
{ }
201, 93, 91, /* 50 */
{ }
254, 0, 5, /* 51 */
{ }
155, 137, 133, /* 52 */
{ }
3, 53, 246 /* 53 */
{
};
}
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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));
^~~~~~~~~~~~~~~
cn3dmodl.c: In function 'Cn3D_ListDomainProc':
cn3dmodl.c:410:34: warning: ' ' directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=]
sprintf(MolName, "%4s %2s", domaindata[iCount]->pcPDBName,
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 9 and 24 bytes into a destination of size 20
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmodl.c:413:34: warning: ' ' directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=]
sprintf(MolName, "%4s %2s %2d",
^~
cn3dmodl.c:413:30: note: directive argument in the range [-32768, 32767]
sprintf(MolName, "%4s %2s %2d",
^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 13 and 32 bytes into a destination of size 20
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:1295:29: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
pars->PBBRender = 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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]
{
^
255, 255, 255, /* default 0 */
{ }
255, 20, 147, /* hotpink 1 */
{ }
255, 0, 255, /* magenta 2 */
{ }
155, 48, 255, /* purple 3 */
{ }
0, 0, 255, /* blue 4 */
{ }
30, 144, 255, /* sky 5 */
{ }
0, 255, 255, /* cyan 6 */
{ }
0, 255, 127, /* sea 7 */
{ }
0, 255, 0, /* green 8 */
{ }
255, 255, 0, /* yellow 9 */
{ }
255, 165, 0, /* gold 10 */
{ }
255, 69, 0, /* orange 11 */
{ }
255, 0, 0, /* red 12 */
{ }
255, 114, 86, /* pink 13 */
{ }
255, 174, 185, /* pinktint 14 */
{ }
255, 255, 255, /* white 15 */
{ }
0, 0, 0, /* black 16 */
{ }
176, 226, 255, /* bluetint 17 */
{ }
154, 255, 154, /* greentint 18 */
{ }
255, 236, 139, /* yellowtint 19 */
{ }
125, 125, 125, /* gray 20 */
{ }
139, 87, 66, /* brown 21 */
{ }
255, 0, 0, /* perm colors 22: red */
{ }
0, 255, 0, /* perm colors 23: green */
{ }
255, 0, 255, /* perm colors 24: magenta */
{ }
30, 144, 255, /* perm colors 25: sky */
{ }
155, 48, 255, /* perm colors 26: purple */
{ }
0, 255, 0, /* SS colors 27: helix, green */
{ }
255, 165, 0, /* SS colors 28: strand, gold */
{ }
255, 69, 0, /* SS colors 29: turn, orange */
{ }
0, 255, 255, /* SS colors 30: coil, cyan */
{ }
255, 255, 0, /* highlight colors 31: yellow */
{ }
0, 0, 0, /* background colors 32: black */
{ }
160, 82, 45, /* sienna 33 */
{ }
240, 230, 140, /* khaki 34 */
{ }
171, 130, 255, /* light purple 35 */
{ }
255, 200, 0, /* orange yellow 36 */
{ }
117, 128, 160, /* 37 */
{ }
5, 53, 239, /* 38 */
{ }
27, 62, 255, /* 39 */
{ }
84, 110, 203, /* 40 */
{ }
216, 77, 84, /* 41 */
{ }
125, 128, 135, /* 42 */
{ }
237, 29, 61, /* 43 */
{ }
184, 118, 120, /* 44 */
{ }
155, 9, 0, /* 45 */
{ }
155, 119, 107, /* 46 */
{ }
80, 110, 196, /* 47 */
{ }
122, 127, 157, /* 48 */
{ }
50, 85, 241, /* 49 */
{ }
201, 93, 91, /* 50 */
{ }
254, 0, 5, /* 51 */
{ }
155, 137, 133, /* 52 */
{ }
3, 53, 246 /* 53 */
{
};
}
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'; did you mean 'Nlm_InitAppContext'? [-Wimplicit-function-declaration]
Nlm_SetOGLContext(NULL, NULL, NULL, NULL);
^~~~~~~~~~~~~~~~~
Nlm_InitAppContext
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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));
^~~~~~~~~~~~~~~
cn3dmodl.c: In function 'Cn3D_ListDomainProc':
cn3dmodl.c:410:34: warning: ' ' directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=]
sprintf(MolName, "%4s %2s", domaindata[iCount]->pcPDBName,
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 9 and 24 bytes into a destination of size 20
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmodl.c:413:34: warning: ' ' directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=]
sprintf(MolName, "%4s %2s %2d",
^~
cn3dmodl.c:413:30: note: directive argument in the range [-32768, 32767]
sprintf(MolName, "%4s %2s %2d",
^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 13 and 32 bytes into a destination of size 20
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:184:3: 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: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 */
^~~
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++) {
^~~
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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -fPIC -D_PNG -I../include -DWIN_MOTIF aa_ungapped.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_diagnostics.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_engine.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_extend.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_filter.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_gapalign.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_hits.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_itree.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_lookup.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_message.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_options.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seg.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seqsrc.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_sw.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_setup.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_stat.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_traceback.c
blast_traceback.c: In function 'BLAST_ComputeTraceback_MT':
blast_traceback.c:1500:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for default(none) num_threads(actual_num_threads) schedule(guided) if (actual_num_threads > 1) \
blast_traceback.c:1524:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(retval)
blast_traceback.c:1530:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush(has_been_interrupted)
blast_traceback.c:1561:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(tback_gen_code)
blast_traceback.c:1591:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(retval)
blast_traceback.c:1631:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(tback_gen_code)
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_util.c
blast_util.c: In function 'BlastProgram2Number':
blast_util.c:306:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (strcasecmp("mapper", program) == 0)
^~
blast_util.c:309:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return 0;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF gapinfo.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF greedy_align.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF link_hsps.c
link_hsps.c: In function 's_FwdCompareHSPs':
link_hsps.c:133:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (h1->context > h2->context)
^~
link_hsps.c:136:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (h1->query.offset < h2->query.offset)
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF lookup_wrap.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF na_ungapped.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_math.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_std.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF pattern.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF phi_extend.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF phi_lookup.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF lookup_util.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_encoding.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_psi.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_psi_priv.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_kappa.c
blast_kappa.c: In function 'Blast_RedoAlignmentCore_MT':
blast_kappa.c:3407:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel \
blast_kappa.c:3426:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
#pragma omp for schedule(static)
blast_kappa.c:3428:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush(interrupt)
blast_kappa.c:3489:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(intrpt)
blast_kappa.c:3491:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush(interrupt)
blast_kappa.c:3504:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(intrpt)
blast_kappa.c:3506:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush(interrupt)
blast_kappa.c:3722:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(intrpt)
blast_kappa.c:3724:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush(interrupt)
blast_kappa.c:3730:0: warning: ignoring #pragma omp barrier [-Wunknown-pragmas]
#pragma omp barrier
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF matrix_freq_ratios.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_hspstream.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_parameters.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_posit.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF phi_gapalign.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_program.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_query_info.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_tune.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_aalookup.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_nalookup.c
blast_nalookup.c: In function 's_NaHashLookupScanSubjectForWordCounts':
blast_nalookup.c:1850:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for if (num_threads > 1) num_threads(num_threads) \
blast_nalookup.c:1858:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical (get_sequence_for_word_counts)
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_aascan.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_nascan.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_dynarray.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF split_query.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF gencode_singleton.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fPIC -D_PNG -I../include -DWIN_MOTIF hspfilter_collector.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_hspstream_mt_utils.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_traceback_mt_priv.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF boost_erf.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF jumper.c
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 blast_hspstream_mt_utils.o blast_traceback_mt_priv.o boost_erf.o jumper.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 -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:184:3: 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 -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:88,
from blast_input.c:34:
/usr/include/features.h:184:3: 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 $";
^~~~~
blast_input.c: In function 'BLAST_GetQuerySeqLoc':
blast_input.c:98:21: warning: '%ld' directive writing between 1 and 7 bytes into a region of size 4 [-Wformat-overflow=]
sprintf(prefix, "%ld", (long) (*ctr/MAX_NUM_QUERIES));
^~~
blast_input.c:98:20: note: directive argument in the range [-131080, 131080]
sprintf(prefix, "%ld", (long) (*ctr/MAX_NUM_QUERIES));
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:88,
from blast_input.c:34:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 8 bytes into a destination of size 4
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 1.120 2012/10/10 14:07:01 fongah2 Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_mtlock.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:61,
from ../include/ncbithr.h:87,
from blast_mtlock.c:39:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_mtlock.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_options_api.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_prelim.c
blast_prelim.c: In function 'Blast_PrelimSearchThreadRun':
blast_prelim.c:100:9: warning: variable 'status' set but not used [-Wunused-but-set-variable]
Int2 status = 0;
^~~~~~
At top level:
blast_prelim.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_prelim.c,v 1.8 2006/05/24 21:17:50 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_returns.c
blast_returns.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_returns.c,v 1.39 2010/06/10 13:44:46 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from blast_seq.c:34:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_seq.c: In function 's_SeqLocFillSequenceBuffer':
blast_seq.c:529:10: warning: variable 'seq_code' set but not used [-Wunused-but-set-variable]
Uint1 seq_code, strand;
^~~~~~~~
At top level:
blast_seq.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_seq.c,v 1.89 2008/06/09 17:29:14 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seqalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from ../include/algo/blast/api/blast_seqalign.h:42,
from blast_seqalign.c:35:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_seqalign.c: In function 's_HSPListToSeqAlignUngapped':
blast_seqalign.c:343:26: warning: variable 'hspset_cnt_old' set but not used [-Wunused-but-set-variable]
Int4 hsp_cnt, index2, hspset_cnt_old;
^~~~~~~~~~~~~~
At top level:
blast_seqalign.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_seqalign.c,v 1.64 2010/02/12 20:54:54 maning Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_tabular.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/algo/blast/api/blast_tabular.h:42,
from blast_tabular.c:35:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_tabular.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_tabular.c,v 1.41 2009/06/01 14:33:38 maning Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF repeats_filter.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:88,
from ../include/algo/blast/api/repeats_filter.h:41,
from repeats_filter.c:41:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
repeats_filter.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: repeats_filter.c,v 1.19 2007/12/19 21:56:48 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF seqsrc_multiseq.c
seqsrc_multiseq.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seqsrc_multiseq.c,v 1.28 2011/05/26 20:59:45 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF seqsrc_readdb.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from ../include/algo/blast/api/seqsrc_readdb.h:38,
from seqsrc_readdb.c:35:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqsrc_readdb.c: In function 's_ReaddbGetNextChunk':
seqsrc_readdb.c:375:11: warning: variable 'real_readdb_entries' set but not used [-Wunused-but-set-variable]
Uint4 real_readdb_entries;
^~~~~~~~~~~~~~~~~~~
At top level:
seqsrc_readdb.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:88,
from ../include/algo/blast/api/dust_filter.h:41,
from dust_filter.c:41:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:61,
from ../include/ncbithr.h:87,
from hspfilter_queue.c:41:
/usr/include/features.h:184:3: 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;
^~~~~~
hspfilter_queue.c: In function 's_BlastHSPQueueNew':
hspfilter_queue.c:157:24: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
writer->InitFnPtr = &s_BlastHSPQueueInit;
^
hspfilter_queue.c:158:24: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
writer->FinalFnPtr = &s_BlastHSPQueueFinal;
^
hspfilter_queue.c: In function 'BlastHSPQueueInfoNew':
hspfilter_queue.c:189:26: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
writer_info->NewFnPtr = &s_BlastHSPQueueNew;
^
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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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:184:3: 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 'AsnCodeGenEnumDefines':
asncode.c:736:28: warning: format '%d' expects argument of type 'int', but argument 4 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (iter->buf, "%s %d\n", AsnCodeCleanName (avtp->name, lclbuf,
~^
%lld
CLEAN_FOR_SLOT, iter -> acip -> maxDefineLength), avtp->intvalue);
~~~~~~~~~~~~~~
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' [-Wdangling-else]
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:4238:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (iter->atp != NULL)
^
asncode.c: In function 'AsnCode':
asncode.c:4317:48: 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:1211: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" GNUTLS_INCLUDE=-DHAVE_LIBGNUTLS 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 -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:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/taxonomy/client/*.c .
set: No match.
makenet.unx:475: 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:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/id0arch/client/*.c .
set: No match.
makenet.unx:475: 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:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/misc/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/misc/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ssparse/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ssparse/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libparsn/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libparsn/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/smart/smartnet/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/smart/smartnet/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/www/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/www/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/query/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/query/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/ctlib/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/ctlib/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/oslib/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/oslib/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/idloadlib/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/idloadlib/*.h ../include
set: No match.
makenet.unx:475: 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/export_cmt.c .
./ln-if-absent ../internal/parser/flat2asn.c .
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./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:475: 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 -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:184:3: 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 -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:184:3: 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 -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:125:
/usr/include/features.h:184:3: 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:201:19: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 were 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 -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:184:3: 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] = {
^
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
9, 7, 4, 3,
{ }
9, 8, 5, 3,
{ }
10, 9, 5, 3,
{ }
10, 10, 5, 3,
{ }
11, 10, 5, 3,
{ }
11, 11, 5, 3,
{ }
12, 11, 5, 3,
{ }
12, 11, 5, 3,
{ }
12, 11, 5, 3
{
};
}
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 were 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 -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:184:3: 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] = {
^
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
9, 7, 4, 3,
{ }
9, 8, 5, 3,
{ }
10, 9, 5, 3,
{ }
10, 10, 5, 3,
{ }
11, 10, 5, 3,
{ }
11, 11, 5, 3,
{ }
12, 11, 5, 3,
{ }
12, 11, 5, 3,
{ }
12, 11, 5, 3
{
};
}
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 were 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netcnfg.c: In function 'ShowNetConfigForm':
netcnfg.c:319:23: warning: variable 'ppt1' set but not used [-Wunused-but-set-variable]
PrompT ppt0, ppt1;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:495:27: 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
medutil.c: In function 'FixPubEquiv':
medutil.c:1134:16: warning: variable 'got' set but not used [-Wunused-but-set-variable]
Boolean got;
^~~
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 -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:184:3: 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 -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:184:3: 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 'SubmitRequest':
netblap3.c:1763:18: warning: 'bllist' may be used uninitialized in this function [-Wmaybe-uninitialized]
bllist->next = blresp;
~~~~~~~~~~~~~^~~~~~~~
netblap3.c:1698:19: note: 'bllist' was declared here
BlastResponsePtr bllist, blresp, head;
^~~~~~
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 -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:184:3: 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:92:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1InfoAsnRead':
objtax1.c:502:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:501:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1ErrorAsnRead':
objtax1.c:1131:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1130:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1NameAsnRead':
objtax1.c:1296:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1295:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1DataAsnRead':
objtax1.c:1482:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1481:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon2DataAsnRead':
objtax1.c:1670:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c: In function 'Taxon1ReqAsnRead':
objtax1.c:284:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax1.c: In function 'Taxon1RespAsnRead':
objtax1.c:920:16: 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 -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:184:3: 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 -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:1611:22: warning: 'lst' may be used uninitialized in this function [-Wmaybe-uninitialized]
lst->next= dst= OrgModNew();
~~~~~~~~~^~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:73,
from parttree.c:79:
/usr/include/features.h:184:3: 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 -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 -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:161:
/usr/include/features.h:184:3: 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:1359:37: warning: variable 'linlines' set but not used [-Wunused-but-set-variable]
Int2 numtaxa, numorgs, numhits, linlines, longname;
^~~~~~~~
taxblast.c: In function 'RDTaxLookupReset':
taxblast.c:2050:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
At top level:
taxblast.c:1967:13: 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 6.31 2015/07/06 19:25:47 madden Exp $";
^~~~~
taxblast.c: In function 'TXBGetTargetGi.isra.3':
taxblast.c:504:12: 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 -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:184:3: 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 -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:184:3: 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);
^
id1arch.c:558:65: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(repl_date,"%-20s",shp->replace_date->str);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output 21 or more bytes into a destination of size 20
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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.6.1.20170106 \
-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.6.1.20170106 \
-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:1211: warning: the use of `tempnam' is dangerous, better use `mkstemp'
gcc -shared -Wl,-soname=libblast.so.6 -o libblast.so.6.1.20170106 \
-Wl,--whole-archive libblast.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libblastcompadj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm
ln -s libblast.so.6.1.20170106 libblast.so.6
ln -s libblast.so.6.1.20170106 libblast.so
gcc -shared -Wl,-soname=libncbiobj.so.6 -o libncbiobj.so.6.1.20170106 \
-Wl,--whole-archive libncbiobj.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbi.so.6.1.20170106 -lm
gcc -shared -Wl,-soname=libncbitool.so.6 -o libncbitool.so.6.1.20170106 \
-Wl,--whole-archive libncbitool.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libblastcompadj.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm
gcc -shared -Wl,-soname=libblastapi.so.6 -o libblastapi.so.6.1.20170106 \
-Wl,--whole-archive libblastapi.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libblast.so.6.1.20170106 libncbitool.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm
ln -s libblastapi.so.6.1.20170106 libblastapi.so.6
ln -s libblastapi.so.6.1.20170106 libblastapi.so
ln -s libblastcompadj.so.6.1.20170106 libblastcompadj.so.6
ln -s libblastcompadj.so.6.1.20170106 libblastcompadj.so
gcc -shared -Wl,-soname=libconnssl.so.6 -o libconnssl.so.6.1.20170106 \
-Wl,--whole-archive libconnssl.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbi.so.6.1.20170106 -lgnutls
ln -s libconnssl.so.6.1.20170106 libconnssl.so.6
ln -s libconnssl.so.6.1.20170106 libconnssl.so
gcc -shared -Wl,-soname=libnetcli.so.6 -o libnetcli.so.6.1.20170106 \
-Wl,--whole-archive libnetcli.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbi.so.6.1.20170106
gcc -shared -Wl,-soname=libncbiid1.so.6 -o libncbiid1.so.6.1.20170106 \
-Wl,--whole-archive libncbiid1.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiobj.so.6.1.20170106 libnetcli.so.6.1.20170106 libncbi.so.6.1.20170106
gcc -shared -Wl,-soname=libncbimmdb.so.6 -o libncbimmdb.so.6.1.20170106 \
-Wl,--whole-archive libncbimmdb.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiid1.so.6.1.20170106 libncbitool.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm
gcc -shared -Wl,-soname=libvibrantOGL.so.6 -o libvibrantOGL.so.6.1.20170106 \
-Wl,--whole-archive libvibrantOGL.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lGLU -lGL -lpng -lXm -lXmu -lXt -lX11 -lm
gcc -shared -Wl,-soname=libncbidesk.so.6 -o libncbidesk.so.6.1.20170106 \
-Wl,--whole-archive libncbidesk.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libblastapi.so.6.1.20170106 libncbimmdb.so.6.1.20170106 libncbitool.so.6.1.20170106 libvibrantOGL.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm
gcc -shared -Wl,-soname=libddvlib.so.6 -o libddvlib.so.6.1.20170106 \
-Wl,--whole-archive libddvlib.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbidesk.so.6.1.20170106 libvibrantOGL.so.6.1.20170106 libncbitool.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106
ln -s libddvlib.so.6.1.20170106 libddvlib.so.6
ln -s libddvlib.so.6.1.20170106 libddvlib.so
ln -s libncbi.so.6.1.20170106 libncbi.so.6
ln -s libncbi.so.6.1.20170106 libncbi.so
ln -s libncbiNacc.so.6.1.20170106 libncbiCacc.so.6.1.20170106
ln -s libncbiCacc.so.6.1.20170106 libncbiCacc.so.6
ln -s libncbiCacc.so.6.1.20170106 libncbiCacc.so
gcc -shared -Wl,-soname=libncbicdr.so.6 -o libncbicdr.so.6.1.20170106 \
-Wl,--whole-archive libncbicdr.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106
gcc -shared -Wl,-soname=libncbiNacc.so.6 -o libncbiNacc.so.6.1.20170106 \
-Wl,--whole-archive libncbiNacc.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbicdr.so.6.1.20170106 libnetentr.a libnetcli.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm
ln -s libncbiNacc.so.6.1.20170106 libncbiNacc.so.6
ln -s libncbiNacc.so.6.1.20170106 libncbiNacc.so
ln -s libncbiNacc.so.6.1.20170106 libncbiacc.so.6.1.20170106
ln -s libncbiacc.so.6.1.20170106 libncbiacc.so.6
ln -s libncbiacc.so.6.1.20170106 libncbiacc.so
ln -s libncbicdr.so.6.1.20170106 libncbicdr.so.6
ln -s libncbicdr.so.6.1.20170106 libncbicdr.so
ln -s libncbicn3dOGL.so.6.1.20170106 libncbicn3d.so.6.1.20170106
ln -s libncbicn3d.so.6.1.20170106 libncbicn3d.so.6
ln -s libncbicn3d.so.6.1.20170106 libncbicn3d.so
gcc -shared -Wl,-soname=libncbicn3dOGL.so.6 -o libncbicn3dOGL.so.6.1.20170106 \
-Wl,--whole-archive libncbicn3dOGL.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiNacc.so.6.1.20170106 libddvlib.so.6.1.20170106 libncbidesk.so.6.1.20170106 libncbimmdb.so.6.1.20170106 libncbitool.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 libvibrantOGL.so.6.1.20170106 -lm
ln -s libncbicn3dOGL.so.6.1.20170106 libncbicn3dOGL.so.6
ln -s libncbicn3dOGL.so.6.1.20170106 libncbicn3dOGL.so
ln -s libncbidesk.so.6.1.20170106 libncbidesk.so.6
ln -s libncbidesk.so.6.1.20170106 libncbidesk.so
ln -s libncbiid1.so.6.1.20170106 libncbiid1.so.6
ln -s libncbiid1.so.6.1.20170106 libncbiid1.so
gcc -shared -Wl,-soname=libncbimla.so.6 -o libncbimla.so.6.1.20170106 \
-Wl,--whole-archive libncbimla.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiobj.so.6.1.20170106 libnetcli.so.6.1.20170106 libncbi.so.6.1.20170106
ln -s libncbimla.so.6.1.20170106 libncbimla.so.6
ln -s libncbimla.so.6.1.20170106 libncbimla.so
ln -s libncbimmdb.so.6.1.20170106 libncbimmdb.so.6
ln -s libncbimmdb.so.6.1.20170106 libncbimmdb.so
ln -s libncbiobj.so.6.1.20170106 libncbiobj.so.6
ln -s libncbiobj.so.6.1.20170106 libncbiobj.so
ln -s libncbitool.so.6.1.20170106 libncbitool.so.6
ln -s libncbitool.so.6.1.20170106 libncbitool.so
gcc -shared -Wl,-soname=libncbitxc2.so.6 -o libncbitxc2.so.6.1.20170106 \
-Wl,--whole-archive libncbitxc2.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbitool.so.6.1.20170106 libnetcli.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm
ln -s libncbitxc2.so.6.1.20170106 libncbitxc2.so.6
ln -s libncbitxc2.so.6.1.20170106 libncbitxc2.so
gcc -shared -Wl,-soname=libnetblast.so.6 -o libnetblast.so.6.1.20170106 \
-Wl,--whole-archive libnetblast.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbitool.so.6.1.20170106 libnetcli.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106
ln -s libnetblast.so.6.1.20170106 libnetblast.so.6
ln -s libnetblast.so.6.1.20170106 libnetblast.so
ln -s libnetcli.so.6.1.20170106 libnetcli.so.6
ln -s libnetcli.so.6.1.20170106 libnetcli.so
ln -s libncbiNacc.so.6.1.20170106 libnetentr.so.6.1.20170106
ln -s libnetentr.so.6.1.20170106 libnetentr.so.6
ln -s libnetentr.so.6.1.20170106 libnetentr.so
gcc -shared -Wl,-soname=libvibgif.so.6 -o libvibgif.so.6.1.20170106 \
-Wl,--whole-archive libvibgif.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbi.so.6.1.20170106 -lm
ln -s libvibgif.so.6.1.20170106 libvibgif.so.6
ln -s libvibgif.so.6.1.20170106 libvibgif.so
gcc -shared -Wl,-soname=libvibnet.so.6 -o libvibnet.so.6.1.20170106 \
-Wl,--whole-archive libvibnet.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now \
libncbiNacc.so.6.1.20170106 libncbidesk.so.6.1.20170106 libncbimmdb.so.6.1.20170106 libvibrantOGL.so.6.1.20170106 libncbitool.so.6.1.20170106 libncbicdr.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106
ln -s libvibnet.so.6.1.20170106 libvibnet.so.6
ln -s libvibnet.so.6.1.20170106 libvibnet.so
ln -s libvibrantOGL.so.6.1.20170106 libvibrant.so.6.1.20170106
ln -s libvibrant.so.6.1.20170106 libvibrant.so.6
ln -s libvibrant.so.6.1.20170106 libvibrant.so
ln -s libvibrantOGL.so.6.1.20170106 libvibrantOGL.so.6
ln -s libvibrantOGL.so.6.1.20170106 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" GNUTLS_INCLUDE=-DHAVE_LIBGNUTLS 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 -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_lbos.h .
./ln-if-absent ../connect/ncbi_lbosp.h .
./ln-if-absent ../connect/parson.h .
./ln-if-absent ../connect/ncbi_lbsm.h .
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../connect/ncbi_lbsm_ipc.h .
makefile:686: 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:686: 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:686: 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:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/compr/*.h ../include
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libindx/*.c .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libindx/*.h ../include
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libpars/*.c .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libpars/*.h ../include
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/*.c .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/*.dat .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideochr*.h ../include
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideoorgs.h .
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.c .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.dat .
set: No match.
makefile:686: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.h ../include
set: No match.
makefile:686: 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 -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:61,
from ncbithr.c:289:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:310:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
ncbimath.c: In function 'general_lngamma':
ncbimath.c:230:5: warning: 'y[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
++y[0];
~^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:46:
/usr/include/features.h:184:3: 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 -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:184:3: 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:2966:58: 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 -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:184:3: 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 -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:184:3: 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 -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:83:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:565:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
asndebin.c:568:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
if (atp == NULL)
^~
asndebin.c:634:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* empty sequence written */
^~~~
asndebin.c:636:7: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:45:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:54:
/usr/include/features.h:184:3: 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:698:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* use alternative write function */
^~~~
asnio.c:701:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:52:
/usr/include/features.h:184:3: 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:198:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((token == END_STRUCT) && ((isa == SEQ_TYPE) || (isa == SET_TYPE)))
^~
asnlex.c:201:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (token != IDENT)
^~
asnlex.c: In function 'AsnTxtReadVal':
asnlex.c:345:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else /* empty sequence written */
^~~~
asnlex.c:347:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
while (atp2 != NULL)
^~~~~
At top level:
asnlex.c:1290:13: 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 -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:184:3: 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 -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:184:3: 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 were 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 were 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 were 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 were 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 -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:184:3: 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:1774:7: warning: variable 'isa' set but not used [-Wunused-but-set-variable]
Int2 isa;
^~~
asnprint.c: In function 'AsnPrintModuleXMLInc':
asnprint.c:2095:10: 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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:61,
from ncbithrs.c:289:
/usr/include/features.h:184:3: 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 -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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:75:
/usr/include/features.h:184:3: 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:440:50: 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:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:116:12: 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:2572:73: 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:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:208:12: 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 's_CreateOnTop':
ncbi_socket.c:4435:35: 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:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:130:12: 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:4471:43: 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:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:116:12: 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_CreateListening':
ncbi_socket.c:4865:48: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
error = getsockname(x_lsock, &addr.sa, &addrlen) != 0
^
In file included from ncbi_socketp.h:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:116:12: 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:5105:49: 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:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:232:12: 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_RecvMsg':
ncbi_socket.c:5409:52: 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:269:0,
from ncbi_socketp.h:54,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/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,
^~~~~~~~
ncbi_socket.c: In function 'TRIGGER_Create':
ncbi_socket.c:5661:18: warning: unused variable 'x_id' [-Wunused-variable]
unsigned int x_id = ++s_ID_Counter;
^~~~
ncbi_socket.c: In function 'DSOCK_Bind':
ncbi_socket.c:7390:51: warning: pointer targets in passing argument 3 of 'getsockname' differ in signedness [-Wpointer-sign]
error = getsockname(sock->sock, &addr.sa, &addrlen) != 0
^
In file included from ncbi_socketp.h:54:0,
from ncbi_connssl.h:37,
from ncbi_socket.c:76:
/usr/include/arm-linux-gnueabihf/sys/socket.h:116:12: 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,
^~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF ncbi_buffer.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_buffer.c:33:
/usr/include/features.h:184:3: 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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:61,
from ncbi_priv.c:33:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:61,
from ncbi_connection.c:34:
/usr/include/features.h:184:3: 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 -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:61,
from ncbi_connector.c:34:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:61,
from ncbi_heapmgr.c:115:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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 -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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:49:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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 -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 -D_PNG -I../include -DWIN_MOTIF ncbi_lbos.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_lbos.c:36:
/usr/include/features.h:184:3: 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_lbos.c: In function 's_LBOS_ReadLbosresolver':
ncbi_lbos.c:756:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (s_LBOS_Lbosresolver == NULL)
^~
ncbi_lbos.c:759:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
s_LBOS_Lbosresolver = strdup(str + 7);
^~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF parson.c
parson.c: In function 'remove_comments':
parson.c:281:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for (i = 0; i < (ptr - string) + end_token_len; i++)
^~~
parson.c:283:12: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
string = ptr + end_token_len - 1;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF ncbi_ipv6.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_ipv6.c:33:
/usr/include/features.h:184:3: 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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 ncbi_lbos.o parson.o ncbi_ipv6.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 -D_PNG -I../include -DWIN_MOTIF -DHAVE_LIBGNUTLS ncbi_gnutls.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_gnutls.c:33:
/usr/include/features.h:184:3: 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_gnutls.c: In function 's_GnuTlsCreate':
ncbi_gnutls.c:293:5: warning: 'gnutls_connection_end_t' is deprecated [-Wdeprecated-declarations]
gnutls_connection_end_t end = (side == eSOCK_Client
^~~~~~~~~~~~~~~~~~~~~~~
In file included from ncbi_gnutls.c:35:0:
ncbi_gnutls.c: In function 's_GnuTlsInit':
ncbi_priv.h:217:33: warning: 'version' may be used uninitialized in this function [-Wmaybe-uninitialized]
_mess.message = NcbiMessagePlusError(&_mess.dynamic, \
^~~~~~~~~~~~~~~~~~~~
ncbi_gnutls.c:582:17: note: 'version' was declared here
const char* version;
^~~~~~~
rm -f libconnssl.a
ar cru libconnssl.a ncbi_gnutls.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -p libconnssl.a ../lib
ranlib ../lib/libconnssl.a
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:65:
/usr/include/features.h:184:3: 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:140:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:143:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (lsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objacces.c: In function 'LinkSetAsnRead':
objacces.c:216:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:219:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
lsp = LinkSetNew();
^~~
objacces.c:220:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (lsp == NULL)
^~
objacces.c:223:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objacces.c:226:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objacces.c:228:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:184:3: 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:597:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:600:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
sap = SeqAlignNew();
^~~
objalign.c:601:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sap == NULL)
^~
objalign.c:604:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'DenseDiagAsnWrite':
objalign.c:1020:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1023:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ddp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c: In function 'DenseDiagAsnRead':
objalign.c:1112:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1115:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ddp = DenseDiagNew();
^~~
objalign.c:1116:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ddp == NULL)
^~
objalign.c:1119:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'DenseSegAsnWrite':
objalign.c:1268:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1271:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (dsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c: In function 'DenseSegAsnRead':
objalign.c:1374:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1377:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
dsp = DenseSegNew();
^~~
objalign.c:1378:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dsp == NULL)
^~
objalign.c:1381:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'StdSegAsnWrite':
objalign.c:1559:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1562:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c:1581:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! SeqLocSetAsnWrite(ssp->loc, aip, STD_SEG_loc, STD_SEG_loc_E))
^~
objalign.c:1584:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ssp->scores != NULL)
^~
objalign.c: In function 'StdSegAsnRead':
objalign.c:1626:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1629:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ssp = StdSegNew();
^~~
objalign.c:1630:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ssp == NULL)
^~
objalign.c:1633:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'SeqAlignSetAsnWrite':
objalign.c:1704:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1708:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
oldsap = sap;
^~~~~~
objalign.c: In function 'PackSegAsnWrite':
objalign.c:1892:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:1895:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (psp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objalign.c:1926:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnCloseStruct(aip, PACKED_SEG_starts, (Pointer)psp->starts))
^~
objalign.c:1929:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
av.ptrvalue = psp->present;
^~
objalign.c: In function 'PackSegAsnRead':
objalign.c:1999:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objalign.c:2002:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
psp = PackSegNew();
^~~
objalign.c:2003:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (psp == NULL)
^~
objalign.c:2006:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */
^~
objalign.c: In function 'SplicedSegAsnRead':
objalign.c:2179:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseSegAsnRead':
objalign.c:2422:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedExonAsnRead':
objalign.c:2614:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedSegModifierFree':
objalign.c:2875:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'ProductPosFree':
objalign.c:3050:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'SplicedExonChunkFree':
objalign.c:3225:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalign.c: In function 'SpliceSiteAsnRead':
objalign.c:3469:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'ProtPosAsnRead':
objalign.c:3626:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseAlignAsnRead':
objalign.c:3798:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SparseSegExtAsnRead':
objalign.c:4020:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalign.c: In function 'SplicedSegModifierAsnRead':
objalign.c:2955:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objalign.c: In function 'SplicedExonChunkAsnRead':
objalign.c:3326:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objalign.c: In function 'ProductPosAsnRead':
objalign.c:3130:16: 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 -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:184:3: 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 -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:113:
/usr/include/features.h:184:3: 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:208:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:211:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
afp = AffilNew();
^~~
objbibli.c: In function 'AffilAsnWrite':
objbibli.c:296:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:299:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (afp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'AuthListFree':
objbibli.c:458:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (alp->affil != NULL)
^~
objbibli.c:460:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return (AuthListPtr)MemFree(alp);
^~~~~~
objbibli.c: In function 'AuthListAsnRead':
objbibli.c:489:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:492:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
alp = AuthListNew();
^~~
objbibli.c: In function 'AuthListAsnWrite':
objbibli.c:583:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:586:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (alp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:590:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)alp)) /* open AuthList SEQUENCE */
^~
objbibli.c:593:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
av.ptrvalue = alp->names;
^~
objbibli.c: In function 'AuthorFree':
objbibli.c:677:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ap->affil != NULL)
^~
objbibli.c:679:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return (AuthorPtr)MemFree(ap);
^~~~~~
objbibli.c: In function 'AuthorAsnRead':
objbibli.c:707:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:710:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ap = AuthorNew();
^~
objbibli.c: In function 'AuthorAsnWrite':
objbibli.c:779:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:782:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ap == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitArtAsnRead':
objbibli.c:925:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:928:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cap = CitArtNew();
^~~
objbibli.c: In function 'CitArtAsnWrite':
objbibli.c:1027:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1030:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cap == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1034:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)cap)) /* open the SEQUENCE */
^~
objbibli.c:1037:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cap->title != NULL)
^~
objbibli.c: In function 'ImprintAsnRead':
objbibli.c:1152:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1155:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ip = ImprintNew();
^~
objbibli.c: In function 'ImprintAsnWrite':
objbibli.c:1251:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1254:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitRetractAsnRead':
objbibli.c:1391:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1394:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
crp = CitRetractNew();
^~~
objbibli.c: In function 'CitRetractAsnWrite':
objbibli.c:1445:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1448:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (crp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitJourAsnRead':
objbibli.c:1524:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1527:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cjp = CitJourNew();
^~~
objbibli.c: In function 'CitJourAsnWrite':
objbibli.c:1576:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1579:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cjp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1585:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! ImprintAsnWrite(cjp->imp, aip, CIT_JOUR_imp))
^~
objbibli.c:1587:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cjp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitBookAsnRead':
objbibli.c:1676:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1679:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cbp = CitBookNew();
^~~
objbibli.c: In function 'CitBookAsnWrite':
objbibli.c:1744:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1747:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1760:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! ImprintAsnWrite(cbp->imp, aip, CIT_BOOK_imp))
^~
objbibli.c:1762:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cbp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitProcAsnWrite':
objbibli.c:1879:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1882:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:1901:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnCloseStruct(aip, CIT_PROC_meet, (Pointer)cpp->otherdata))
^~
objbibli.c:1903:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! AsnCloseStruct(aip, atp, (Pointer)cpp)) /* end SEQUENCE */
^~
objbibli.c: In function 'CitLetAsnWrite':
objbibli.c:1995:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:1998:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (clp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitPatAsnRead':
objbibli.c:2091:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2094:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cpp = CitPatNew();
^~~
objbibli.c: In function 'CitPatAsnWrite':
objbibli.c:2213:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2216:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'IdPatAsnRead':
objbibli.c:2346:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2349:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
idp = IdPatNew();
^~~
objbibli.c: In function 'IdPatAsnWrite':
objbibli.c:2412:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2415:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (idp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitGenAsnRead':
objbibli.c:2546:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2549:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cgp = CitGenNew();
^~~
objbibli.c: In function 'CitGenAsnWrite':
objbibli.c:2627:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2630:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cgp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'TitleAsnWrite':
objbibli.c:2825:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2828:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (tp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'CitSubFree':
objbibli.c:2909:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (csp == NULL)
^~
objbibli.c:2912:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
AuthListFree(csp->authors);
^~~~~~~~~~~~
objbibli.c: In function 'CitSubAsnRead':
objbibli.c:2943:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2946:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
csp = CitSubNew();
^~~
objbibli.c:2958:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:2961:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (atp == CIT_SUB_imp)
^~
objbibli.c: In function 'CitSubAsnWrite':
objbibli.c:3029:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3032:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (csp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c:3038:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AuthListAsnWrite(csp->authors, aip, CIT_SUB_authors))
^~
objbibli.c:3041:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (csp->imp != NULL)
^~
objbibli.c: In function 'PatPrioritySetAsnRead':
objbibli.c:3694:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ppp == NULL)
^~
objbibli.c:3697:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (head == NULL)
^~
objbibli.c:3715:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3717:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ppp->date = DateAsnRead(aip, atp);
^~~
objbibli.c: In function 'PatPrioritySetAsnWrite':
objbibli.c:3755:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, set, (Pointer)ppp)) /* open the SEQUENCE OF */
^~
objbibli.c:3758:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
for (tmp = ppp; tmp != NULL; tmp = tmp->next)
^~~
objbibli.c: In function 'ArticleIdAsnRead':
objbibli.c:3849:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3852:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
aidp = ArticleIdNew();
^~~~
objbibli.c: In function 'ArticleIdAsnWrite':
objbibli.c:3925:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:3928:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (aidp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objbibli.c: In function 'PubStatusDateAsnRead':
objbibli.c:4039:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:4042:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
psdp = PubStatusDateNew();
^~~~
objbibli.c: In function 'PubStatusDateAsnWrite':
objbibli.c:4091:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objbibli.c:4094:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:184:3: 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:1500:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ExperimentSupportAsnRead':
objfeat.c:1748:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ProgramIdAsnRead':
objfeat.c:1933:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'EvidenceBasisAsnRead':
objfeat.c:2103:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'InferenceSupportAsnRead':
objfeat.c:2267:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ModelEvidenceItemAsnRead':
objfeat.c:2483:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SeqFeatSupportAsnRead':
objfeat.c:2688:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAQualAsnRead':
objfeat.c:4244:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAQualSetAsnRead':
objfeat.c:4396:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'RNAGenAsnRead':
objfeat.c:4524:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'GeneNomenclatureAsnRead':
objfeat.c:4707:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'OrgNameMatch':
objfeat.c:5957:28: warning: self-comparison always evaluates to false [-Wtautological-compare]
|| onp2->mgcode != onp2->mgcode
^~
objfeat.c: In function 'TaxElementAsnWrite':
objfeat.c:7399:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)tep))
^~
objfeat.c:7402:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
av.intvalue = (Int4)(tep->fixed_level);
^~
objfeat.c: In function 'PCRPrimerAsnRead':
objfeat.c:8276:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRPrimerSetAsnRead':
objfeat.c:8421:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRReactionAsnRead':
objfeat.c:8542:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PCRReactionSetAsnRead':
objfeat.c:8685:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneRefAsnRead':
objfeat.c:8812:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneSeqSetAsnRead':
objfeat.c:9005:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'CloneSeqAsnRead':
objfeat.c:9135:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SomaticOriginAsnRead':
objfeat.c:9487:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'SomaticOriginConditionAsnRead':
objfeat.c:9566:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'VariationRefAsnRead':
objfeat.c:9645:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_loss_of_heterozygosityAsnRead':
objfeat.c:10687:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_frameshiftAsnRead':
objfeat.c:10765:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'VarRefDataFree':
objfeat.c:10865:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'VarRefDataSetAsnRead':
objfeat.c:10918:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Consequence_elementFree':
objfeat.c:11112:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'VariationInstAsnRead':
objfeat.c:11241:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: At top level:
objfeat.c:11393:1: warning: "/*" within comment [-Wcomment]
/**************************************************
objfeat.c: In function 'VariantPropertiesAsnRead':
objfeat.c:11422:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PhenotypeAsnRead':
objfeat.c:11746:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'PopulationDataAsnRead':
objfeat.c:11945:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'ExtLocAsnRead':
objfeat.c:12161:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objfeat.c: In function 'Seq_seqFree':
objfeat.c:12327:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objfeat.c: In function 'DeltaItemAsnRead':
objfeat.c:12360:16: 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 -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:184:3: 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 were 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 were guarded by the 'if'
if (dp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'DateAsnRead':
objgen.c:494:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:497:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
dp = DateNew();
^~
objgen.c:498:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dp == NULL)
^~
objgen.c:501:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */
^~
objgen.c: In function 'DbtagFree':
objgen.c:752:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt == NULL)
^~
objgen.c:755:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
dbt->tag = ObjectIdFree(dbt->tag);
^~~
objgen.c: In function 'DbtagAsnRead':
objgen.c:784:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:787:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
dbt = DbtagNew();
^~~
objgen.c:788:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt == NULL)
^~
objgen.c:791:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */
^~
objgen.c:799:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (dbt->tag == NULL)
^~
objgen.c:802:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
atp = AsnReadId(aip, amp, atp); if (atp == NULL) goto erret; /* END_STRUCT */
^~~
objgen.c: In function 'DbtagAsnWrite':
objgen.c:833:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:836:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (dbt == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'ObjectIdAsnRead':
objgen.c:980:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:983:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */
^~
objgen.c:989:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oid == NULL)
^~
objgen.c:991:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (atp == OBJECT_ID_id)
^~
objgen.c: In function 'ObjectIdAsnWrite':
objgen.c:1024:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1027:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (oid == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'NameStdFree':
objgen.c:1174:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (nsp == NULL)
^~
objgen.c:1177:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
for (i = 0; i < 7; i++)
^~~
objgen.c: In function 'NameStdAsnRead':
objgen.c:1208:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1211:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
nsp = NameStdNew();
^~~
objgen.c:1212:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (nsp == NULL)
^~
objgen.c:1215:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */
^~
objgen.c: In function 'NameStdAsnWrite':
objgen.c:1271:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1274:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (nsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'PersonIdFree':
objgen.c:1368:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pid == NULL)
^~
objgen.c:1371:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (pid->choice == 1) /* Dbtag */
^~
objgen.c: In function 'PersonIdAsnWrite':
objgen.c:1464:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1467:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (pid == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objgen.c: In function 'IntFuzzAsnRead':
objgen.c:1682:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1685:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ifp = IntFuzzNew();
^~~
objgen.c:1686:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ifp == NULL)
^~
objgen.c:1689:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE (nothing) */
^~
objgen.c: In function 'UserFieldAsnRead':
objgen.c:1944:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:1947:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ufp = UserFieldNew();
^~~
objgen.c: In function 'UserObjectAsnRead':
objgen.c:2434:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objgen.c:2437:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
uop = UserObjectNew();
^~~
objgen.c:2438:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (uop == NULL)
^~
objgen.c:2441:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:88,
from objloc.c:43:
/usr/include/features.h:184:3: 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 were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqIdAsnRead':
objloc.c:443:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:446:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
anp = ValNodeNew(NULL);
^~~
objloc.c: In function 'SeqIdDup':
objloc.c:587:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oldid == NULL)
^~
objloc.c:590:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
newid = ValNodeNew(NULL);
^~~~~
objloc.c: In function 'SeqIdSetAsnRead':
objloc.c:752:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, atp, &av) <= 0) /* end struct */
^~
objloc.c:754:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (first == NULL)
^~
objloc.c: In function 'SeqIdSetAsnWrite':
objloc.c:786:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp2 == NULL)
^~
objloc.c:789:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, settype); goto erret; }
^~
objloc.c: In function 'TextSeqIdAsnWrite':
objloc.c:864:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:867:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (tsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'TextSeqIdAsnRead':
objloc.c:934:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:937:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
tsip = TextSeqIdNew();
^~~~
objloc.c:938:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (tsip == NULL)
^~
objloc.c:941:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PatentSeqIdAsnWrite':
objloc.c:1018:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1021:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (psip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PatentSeqIdAsnRead':
objloc.c:1068:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1071:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
psip = PatentSeqIdNew();
^~~~
objloc.c:1072:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (psip == NULL)
^~
objloc.c:1075:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'GiimAsnWrite':
objloc.c:1151:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1154:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (gip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'GiimAsnRead':
objloc.c:1216:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (gip == NULL)
^~
objloc.c:1219:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PDBSeqIdAsnWrite':
objloc.c:1305:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1308:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (pdbsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PDBSeqIdAsnRead':
objloc.c:1374:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1377:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
pdbsip = PDBSeqIdNew();
^~~~~~
objloc.c:1378:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pdbsip == NULL)
^~
objloc.c:1381:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'SeqLocAsnWrite':
objloc.c:1528:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1531:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocAsnRead':
objloc.c:1624:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1627:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
anp = ValNodeNew(NULL);
^~~
objloc.c:1628:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (anp == NULL)
^~
objloc.c:1631:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the CHOICE value (nothing) */
^~
objloc.c: In function 'SeqLocMixAsnWrite':
objloc.c:1738:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1741:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocEquivAsnWrite':
objloc.c:1805:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:1808:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqLocSetAsnWrite':
objloc.c:1873:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp2 == NULL)
^~
objloc.c:1876:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL) { AsnNullValueMsg(aip, set); goto erret; }
^~
objloc.c: In function 'SeqLocSetAsnRead':
objloc.c:1940:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, atp, &av) <= 0) /* read END_STRUCT */
^~
objloc.c:1942:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (first == NULL)
^~
objloc.c: In function 'SeqIntAsnWrite':
objloc.c:2022:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2025:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (sip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqIntAsnRead':
objloc.c:2095:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2098:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
sip = SeqIntNew();
^~~
objloc.c:2099:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sip == NULL)
^~
objloc.c:2102:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PackSeqIntAsnWrite':
objloc.c:2179:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2181:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
oldsip = sip;
^~~~~~
objloc.c:2185:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)oldsip))
^~
objloc.c:2187:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
for ( ;sip != NULL; sip = sip->next)
^~~
objloc.c: In function 'SeqPntAsnWrite':
objloc.c:2309:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2312:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (spp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqPntAsnRead':
objloc.c:2374:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2377:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
spp = SeqPntNew();
^~~
objloc.c:2378:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (spp == NULL)
^~
objloc.c:2381:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'PackSeqPntAsnWrite':
objloc.c:2479:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2482:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (pspp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'PackSeqPntAsnRead':
objloc.c:2553:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2556:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
pspp = PackSeqPntNew();
^~~~
objloc.c:2557:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (pspp == NULL)
^~
objloc.c:2560:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */
^~
objloc.c: In function 'SeqBondAsnWrite':
objloc.c:2724:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2727:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objloc.c: In function 'SeqBondAsnRead':
objloc.c:2776:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objloc.c:2779:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
sbp = SeqBondNew();
^~~
objloc.c:2780:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sbp == NULL)
^~
objloc.c:2783:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:104:
/usr/include/features.h:184:3: 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:248:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objmedli.c:251:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
mmp = MedlineMeshNew();
^~~
objmedli.c: In function 'DocRefFree':
objmedli.c:1190:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (drp == NULL)
^~
objmedli.c:1193:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:125:
/usr/include/features.h:184:3: 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:831:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, settype, &av) <= 0) /* read START_STRUCT */
^~
objpub.c:834:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (settype == PUB_SET_pub)
^~
objpub.c:901:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnReadVal(aip, settype, &av) <= 0) /* read END_STRUCT for SET OF */
^~
objpub.c:903:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (anp == NULL)
^~
objpub.c: In function 'PubLabelUnique':
objpub.c:1360:17: warning: unused variable 'pmid' [-Wunused-variable]
Int4 muid = 0, pmid = 0;
^~~~
objpub.c:1360:7: warning: unused variable 'muid' [-Wunused-variable]
Int4 muid = 0, pmid = 0;
^~~~
objpub.c: In function 'PubSetAsnRead':
objpub.c:876:13: warning: 'func' may be used uninitialized in this function [-Wmaybe-uninitialized]
pnt = (* func)(aip, atp);
~~~~^~~~~~~~~~~~~~~~~~~~
objpub.c:887:25: 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 -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:84:
/usr/include/features.h:184:3: 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 -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:184:3: 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:339:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmFinalDataAsnRead':
objscoremat.c:548:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmParametersAsnRead':
objscoremat.c:766:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'PssmWithParametersAsnRead':
objscoremat.c:946:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'BlockPropertyAsnRead':
objscoremat.c:1113:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'CoreBlockAsnRead':
objscoremat.c:1289:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'LoopConstraintAsnRead':
objscoremat.c:1480:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'CoreDefAsnRead':
objscoremat.c:1646:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objscoremat.c: In function 'FormatRpsDbParametersAsnRead':
objscoremat.c:1817:16: 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 -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:184:3: 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:1609:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objseq.c: In function 'SeqGapAsnRead':
objseq.c:1764:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objseq.c: In function 'SeqDescrAsnWriteExtra':
objseq.c:2035:48: 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:4841:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:4843:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
break;
^~~~~
objseq.c:4849:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:4851:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
break;
^~~~~
objseq.c: In function 'AnnotDescAsnWrite':
objseq.c:5226:9: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
objseq.c:5228:12: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:74:
/usr/include/features.h:184:3: 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:900:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ebp == NULL)
^~
objblock.c:903:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -D_PNG -I../include -DWIN_MOTIF objcode.c
objcode.c:48:51: 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:105:
/usr/include/features.h:184:3: 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 -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:184:3: 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 were guarded by the 'if'
if (bsp->idx.parentptr == NULL || bsp->idx.parenttype == OBJ_SEQSUB) {
^~
objsset.c: In function 'SeqEntryFree':
objsset.c:878:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (sep->choice == 2)
^~
objsset.c:881:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return (SeqEntryPtr)MemFree(sep);
^~~~~~
objsset.c: In function 'SeqEntryFreeComponents':
objsset.c:898:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (sep->choice == 2)
^~
objsset.c:901:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return sep;
^~~~~~
objsset.c: In function 'SeqEntryAsnGet':
objsset.c:1075:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (retcode == 1) /* just after a Bioseq */
^~
objsset.c:1077:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:84:
/usr/include/features.h:184:3: 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:341:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (loaded)
^~
objsub.c:344:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! SeqSetAsnLoad ())
^~
objsub.c:347:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (AsnLoad())
^~
objsub.c:350:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ObjMgrTypeLoad(OBJ_SEQSUB, "Seq-submit", seqsubtypename, "Sequence Data Submission",
^~~~~~~~~~~~~~
objsub.c: In function 'SeqSubmitAsnWrite':
objsub.c:455:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:458:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:462:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)ssp))
^~
objsub.c:465:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! SubmitBlockAsnWrite(ssp->sub, aip, SEQ_SUBMIT_sub)) goto erret;
^~
objsub.c: In function 'SeqSubmitAsnRead':
objsub.c:539:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:542:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ssp = SeqSubmitNew();
^~~
objsub.c:543:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ssp == NULL)
^~
objsub.c:546:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objsub.c: In function 'SubmitBlockAsnWrite':
objsub.c:682:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:685:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:689:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)sbp))
^~
objsub.c:692:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (! ContactInfoAsnWrite(sbp->contact, aip, SUBMIT_BLOCK_contact))
^~
objsub.c: In function 'SubmitBlockAsnRead':
objsub.c:770:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:773:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
oldatp = atp;
^~~~~~
objsub.c:775:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (sbp == NULL)
^~
objsub.c:778:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */
^~
objsub.c: In function 'ContactInfoAsnWrite':
objsub.c:942:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:945:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cip == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
^~
objsub.c:949:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (! AsnOpenStruct(aip, atp, (Pointer)cip))
^~
objsub.c:952:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (cip->name != NULL)
^~
objsub.c: In function 'ContactInfoAsnRead':
objsub.c:1068:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (atp == NULL)
^~
objsub.c:1070:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
oldatp = atp;
^~~~~~
objsub.c:1073:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (cip == NULL)
^~
objsub.c:1076:2: note: ...this statement, but the latter is misleadingly indented as if it were 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 -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:81:
/usr/include/features.h:184:3: 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:836:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ptr == NULL) return NULL;
^
objprt.c:853:22: note: 'ptr' was declared here
PrintFormBooleanPtr ptr;
^~~
objprt.c: In function 'PrintFormEnumAsnRead':
objprt.c:952:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ptr == NULL) return NULL;
^
objprt.c:969:19: note: 'ptr' was declared here
PrintFormEnumPtr ptr;
^~~
objprt.c: In function 'PrintFormTextAsnRead':
objprt.c:1070:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ptr == NULL) return NULL;
^
objprt.c:1086:19: note: 'ptr' was declared here
PrintFormTextPtr ptr;
^~~
objprt.c: In function 'UserFormatAsnRead':
objprt.c:1175:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ptr == NULL) return NULL;
^
objprt.c:1192:16: note: 'ptr' was declared here
UserFormatPtr ptr;
^~~
objprt.c: In function 'PrintFormAsnRead':
objprt.c:600:6: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
vnp = PrintFormFree(vnp);
~~~~^~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormatAsnRead':
objprt.c:356:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (head_ptr == NULL) return NULL;
^
objprt.c:379:17: note: 'ptr' was declared here
PrintFormatPtr ptr;
^~~
objprt.c: In function 'PrintTemplateAsnRead':
objprt.c:250:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr=PrintTemplateFree(ptr);
~~~^~~~~~~~~~~~~~~~~~~~~~~
objprt.c: In function 'PrintFormBlockAsnRead':
objprt.c:690:5: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ptr == NULL) return NULL;
^
objprt.c:707:20: note: 'ptr' was declared here
PrintFormBlockPtr ptr;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:527:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objalignloc.c: In function 'AlignIdAsnRead':
objalignloc.c:559:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignBoxAsnRead':
objalignloc.c:750:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:749:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignRowsAsnRead':
objalignloc.c:932:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:931:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignColumnsAsnRead':
objalignloc.c:1096:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objalignloc.c:1095:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objalignloc.c: In function 'AlignIdAsnRead':
objalignloc.c:615:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objalignloc.c: In function 'AlignLocAsnRead':
objalignloc.c:370:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objalignloc.c:312:10: 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 -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:184:3: 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:269:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c:268:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtable.c: In function 'SeqTableAsnRead':
objtable.c:474:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'CommonStringTableAsnRead':
objtable.c:657:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'CommonBytesTableAsnRead':
objtable.c:819:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtable.c: In function 'SeqTableSingleDataFree':
objtable.c:1225:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtable.c: In function 'SeqTableSingleDataAsnRead':
objtable.c:1269:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtable.c: In function 'SeqTableMultiDataAsnRead':
objtable.c:1111:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtable.c: In function 'SeqTableSingleDataAsnRead':
objtable.c:1354:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtable.c: In function 'SeqTableSparseIndexAsnRead':
objtable.c:1559:16: 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 -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:184:3: 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:288:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objpubme.c:287:12: 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 -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:184:3: 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:259:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmdrs.c:258:12: 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 -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:184:3: 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:720:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objproj.c: In function 'ProjdescFree':
objproj.c:857:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objproj.c: In function 'ProjdescAsnRead':
objproj.c:898:12: 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:958:16: 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 -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:184:3: 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:69:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:66:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objgbseq.c: In function 'GBSeqAsnRead':
objgbseq.c:235:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBReferenceAsnRead':
objgbseq.c:742:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBCommentAsnRead':
objgbseq.c:983:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBStrucCommentAsnRead':
objgbseq.c:1150:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBFeatureAsnRead':
objgbseq.c:1321:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBFeatureSetAsnRead':
objgbseq.c:1548:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBAltSeqDataAsnRead':
objgbseq.c:1715:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c: In function 'GBXrefAsnRead':
objgbseq.c:1882:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:1881:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objgbseq.c: In function 'GBStrucCommentItemAsnRead':
objgbseq.c:2053:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:2052:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objgbseq.c: In function 'GBIntervalAsnRead':
objgbseq.c:2233:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:2232:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objgbseq.c: In function 'GBQualifierAsnRead':
objgbseq.c:2447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:2446:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objgbseq.c: In function 'GBAltSeqItemAsnRead':
objgbseq.c:2622:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objgbseq.c:2621:12: 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 -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:184:3: 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:325:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtseq.c: In function 'BioseqToTSeq':
objtseq.c:452:8: warning: variable 'seqcode' set but not used [-Wunused-but-set-variable]
Uint1 seqcode;
^~~~~~~
objtseq.c: In function 'BioseqToMiniTSeq':
objtseq.c:564:8: 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 -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:184:3: 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:69:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:66:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objinsdseq.c: In function 'INSDSeqAsnRead':
objinsdseq.c:235:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDReferenceAsnRead':
objinsdseq.c:742:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDCommentAsnRead':
objinsdseq.c:983:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDStrucCommentAsnRead':
objinsdseq.c:1150:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDFeatureAsnRead':
objinsdseq.c:1321:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDFeatureSetAsnRead':
objinsdseq.c:1548:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDAltSeqDataAsnRead':
objinsdseq.c:1715:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c: In function 'INSDXrefAsnRead':
objinsdseq.c:1882:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:1881:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objinsdseq.c: In function 'INSDStrucCommentItemAsnRead':
objinsdseq.c:2053:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:2052:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objinsdseq.c: In function 'INSDIntervalAsnRead':
objinsdseq.c:2233:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:2232:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objinsdseq.c: In function 'INSDQualifierAsnRead':
objinsdseq.c:2447:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:2446:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objinsdseq.c: In function 'INSDAltSeqItemAsnRead':
objinsdseq.c:2622:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objinsdseq.c:2621:12: 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 -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:184:3: 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:272:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:271:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MacroActionListAsnRead':
objmacro.c:478:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:475:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SuspectRuleSetAsnRead':
objmacro.c:595:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:592:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'WordSubstitutionAsnRead':
objmacro.c:731:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c: In function 'WordSubstitutionSetAsnRead':
objmacro.c:899:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:896:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'StringConstraintAsnRead':
objmacro.c:1045:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1044:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StringConstraintSetAsnRead':
objmacro.c:1307:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1304:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'LocationPosConstraintFree':
objmacro.c:1403:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationPosConstraintAsnRead':
objmacro.c:1432:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationConstraintAsnRead':
objmacro.c:1633:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1632:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalValAsnRead':
objmacro.c:1849:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:1848:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalValChoiceFree':
objmacro.c:1979:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FeatQualLegalValChoiceAsnRead':
objmacro.c:2011:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatQualLegalSetAsnRead':
objmacro.c:2165:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2162:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'FeatQualChoiceFree':
objmacro.c:2261:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FeatQualChoiceAsnRead':
objmacro.c:2293:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldAsnRead':
objmacro.c:2474:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2473:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldLegalAsnRead':
objmacro.c:2641:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2640:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FeatureFieldPairAsnRead':
objmacro.c:2807:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:2806:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaFeatTypeFree':
objmacro.c:2950:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'RnaFeatTypeAsnRead':
objmacro.c:2982:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaQualAsnRead':
objmacro.c:3232:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3231:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RnaQualPairAsnRead':
objmacro.c:3400:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3399:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualPairAsnRead':
objmacro.c:3576:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3575:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualChoiceFree':
objmacro.c:3704:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SourceQualChoiceAsnRead':
objmacro.c:3733:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualTextValAsnRead':
objmacro.c:3950:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:3949:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualValChoiceFree':
objmacro.c:4080:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SourceQualValChoiceAsnRead':
objmacro.c:4112:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualValSetAsnRead':
objmacro.c:4310:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4307:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'CDSGeneProtFieldPairAsnRead':
objmacro.c:4442:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4441:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldFree':
objmacro.c:4570:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MolinfoFieldAsnRead':
objmacro.c:4599:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoMoleculePairAsnRead':
objmacro.c:4826:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4825:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoTechniquePairAsnRead':
objmacro.c:4990:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:4989:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoCompletednessPairAsnRead':
objmacro.c:5154:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5153:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoMolClassPairAsnRead':
objmacro.c:5318:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5317:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoTopologyPairAsnRead':
objmacro.c:5482:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5481:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoStrandPairAsnRead':
objmacro.c:5646:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:5645:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldPairFree':
objmacro.c:5774:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MolinfoFieldPairAsnRead':
objmacro.c:5821:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoFieldListAsnRead':
objmacro.c:6015:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6012:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'MolinfoFieldConstraintAsnRead':
objmacro.c:6149:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6148:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StructuredCommentFieldFree':
objmacro.c:6280:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'StructuredCommentFieldAsnRead':
objmacro.c:6312:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'StructuredCommentFieldPairAsnRead':
objmacro.c:6508:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6507:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'DBLinkFieldPairAsnRead':
objmacro.c:6678:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6677:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldConstraintAsnRead':
objmacro.c:6843:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:6842:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeFree':
objmacro.c:6974:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeAsnRead':
objmacro.c:7003:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintAsnRead':
objmacro.c:7220:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7219:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PublicationConstraintAsnRead':
objmacro.c:7389:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7388:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceConstraintAsnRead':
objmacro.c:7571:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7570:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtPseudoConstraintAsnRead':
objmacro.c:7763:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:7762:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtConstraintFieldFree':
objmacro.c:7891:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'CDSGeneProtConstraintFieldAsnRead':
objmacro.c:7920:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CDSGeneProtQualConstraintAsnRead':
objmacro.c:8095:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:8094:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldConstraintAsnRead':
objmacro.c:8279:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:8278:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldTypeFree':
objmacro.c:8413:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FieldTypeAsnRead':
objmacro.c:8457:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintFree':
objmacro.c:8666:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintAsnRead':
objmacro.c:8695:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'QuantityConstraintFree':
objmacro.c:8875:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'QuantityConstraintAsnRead':
objmacro.c:8904:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceConstraintAsnRead':
objmacro.c:9104:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9103:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TranslationConstraintAsnRead':
objmacro.c:9332:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9331:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConstraintChoiceFree':
objmacro.c:9487:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConstraintChoiceAsnRead':
objmacro.c:9549:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConstraintChoiceSetAsnRead':
objmacro.c:9783:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:9780:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'TextMarkerFree':
objmacro.c:9879:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TextMarkerAsnRead':
objmacro.c:9911:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TextPortionAsnRead':
objmacro.c:10109:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10108:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldEditAsnRead':
objmacro.c:10328:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10327:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FieldPairTypeFree':
objmacro.c:10478:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FieldPairTypeAsnRead':
objmacro.c:10528:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyActionAsnRead':
objmacro.c:10747:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10746:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditActionAsnRead':
objmacro.c:10927:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:10926:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TextTransformFree':
objmacro.c:11061:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TextTransformAsnRead':
objmacro.c:11096:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TextTransformSetAsnRead':
objmacro.c:11269:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11266:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'ConvertActionAsnRead':
objmacro.c:11405:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11404:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CopyActionAsnRead':
objmacro.c:11600:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11599:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SwapActionAsnRead':
objmacro.c:11768:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11767:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AECRParseActionAsnRead':
objmacro.c:11932:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:11931:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveActionAsnRead':
objmacro.c:12151:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:12150:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveOutsideActionAsnRead':
objmacro.c:12312:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:12311:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ActionChoiceFree':
objmacro.c:12455:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ActionChoiceAsnRead':
objmacro.c:12508:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcOrgChoiceFree':
objmacro.c:12697:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcOrgChoiceAsnRead':
objmacro.c:12726:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcOrgAsnRead':
objmacro.c:12911:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:12910:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcGeneralIdFree':
objmacro.c:13042:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcGeneralIdAsnRead':
objmacro.c:13074:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseSrcFree':
objmacro.c:13232:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseSrcAsnRead':
objmacro.c:13270:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseDstOrgAsnRead':
objmacro.c:13526:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:13525:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ParseDestFree':
objmacro.c:13657:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ParseDestAsnRead':
objmacro.c:13695:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationIntervalAsnRead':
objmacro.c:13905:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:13904:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationChoiceFree':
objmacro.c:14033:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationChoiceAsnRead':
objmacro.c:14065:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SequenceListAsnRead':
objmacro.c:14241:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14238:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objmacro.c: In function 'SequenceListChoiceFree':
objmacro.c:14337:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SequenceListChoiceAsnRead':
objmacro.c:14369:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyFeatureActionAsnRead':
objmacro.c:14560:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14559:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveFeatureActionAsnRead':
objmacro.c:14827:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14826:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFromCDSOptionsAsnRead':
objmacro.c:14994:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:14993:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureSrcOptionsFree':
objmacro.c:15131:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConvertFeatureSrcOptionsAsnRead':
objmacro.c:15163:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RegionTypeAsnRead':
objmacro.c:15332:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15331:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureDstOptionsFree':
objmacro.c:15451:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ConvertFeatureDstOptionsAsnRead':
objmacro.c:15486:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ConvertFeatureActionAsnRead':
objmacro.c:15702:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15701:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditLocationStrandAsnRead':
objmacro.c:15911:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:15910:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'Partial5SetActionAsnRead':
objmacro.c:16075:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16074:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'Partial3SetActionAsnRead':
objmacro.c:16239:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16238:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'PartialBothSetActionAsnRead':
objmacro.c:16403:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16402:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ExtendToFeatureAsnRead':
objmacro.c:16568:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:16567:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'LocationEditTypeFree':
objmacro.c:16708:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'LocationEditTypeAsnRead':
objmacro.c:16755:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'EditFeatureLocationActionAsnRead':
objmacro.c:17032:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17031:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MolinfoBlockAsnRead':
objmacro.c:17232:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17231:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveDescriptorActionAsnRead':
objmacro.c:17415:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17414:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AutodefActionAsnRead':
objmacro.c:17584:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c: In function 'FixPubCapsActionAsnRead':
objmacro.c:17758:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17757:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SortFieldsActionAsnRead':
objmacro.c:17963:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:17962:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixAuthorCapsAsnRead':
objmacro.c:18142:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18141:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixCapsActionFree':
objmacro.c:18261:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixCapsActionAsnRead':
objmacro.c:18296:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixFormatActionFree':
objmacro.c:18470:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixFormatActionAsnRead':
objmacro.c:18499:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveDuplicateFeatureActionAsnRead':
objmacro.c:18705:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18704:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'GeneXrefTypeAsnRead':
objmacro.c:18899:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:18898:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'XrefTypeFree':
objmacro.c:19036:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'XrefTypeAsnRead':
objmacro.c:19068:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveXrefsActionAsnRead':
objmacro.c:19239:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19238:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MakeGeneXrefActionAsnRead':
objmacro.c:19410:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19409:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AuthorFixActionAsnRead':
objmacro.c:19578:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19577:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'UpdateSequencesActionAsnRead':
objmacro.c:19747:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:19746:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CreateTSAIdsSrcFree':
objmacro.c:19877:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'CreateTSAIdsSrcAsnRead':
objmacro.c:19909:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'CreateTSAIdsActionAsnRead':
objmacro.c:20092:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:20091:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AutofixActionAsnRead':
objmacro.c:20274:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:20273:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'FixSetsActionFree':
objmacro.c:20395:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'FixSetsActionAsnRead':
objmacro.c:20424:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TableMatchTypeFree':
objmacro.c:20582:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'TableMatchTypeAsnRead':
objmacro.c:20614:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'TableMatchAsnRead':
objmacro.c:20873:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:20872:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyTableExtraDataFree':
objmacro.c:21004:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ApplyTableExtraDataAsnRead':
objmacro.c:21033:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ApplyTableActionAsnRead':
objmacro.c:21210:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21209:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AddFileActionAsnRead':
objmacro.c:21411:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21410:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AddDescriptorListActionAsnRead':
objmacro.c:21582:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21581:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RemoveSequencesActionAsnRead':
objmacro.c:21753:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21752:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'UpdateReplacedEcNumbersActionAsnRead':
objmacro.c:21911:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:21910:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'RetranslateCdsActionAsnRead':
objmacro.c:22084:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:22083:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'AdjustFeaturesForGapsActionAsnRead':
objmacro.c:22239:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:22238:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'MacroActionChoiceFree':
objmacro.c:22412:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'MacroActionChoiceAsnRead':
objmacro.c:22522:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SearchFuncFree':
objmacro.c:23116:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'SearchFuncAsnRead':
objmacro.c:23154:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SimpleReplaceAsnRead':
objmacro.c:23425:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:23424:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ReplaceFuncFree':
objmacro.c:23564:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmacro.c: In function 'ReplaceFuncAsnRead':
objmacro.c:23599:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'ReplaceRuleAsnRead':
objmacro.c:23781:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:23780:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SuspectRuleAsnRead':
objmacro.c:23955:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmacro.c:23954:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmacro.c: In function 'SourceQualChoiceAsnRead':
objmacro.c:3806:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SourceQualValChoiceAsnRead':
objmacro.c:4182:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MolinfoFieldAsnRead':
objmacro.c:4679:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MolinfoFieldPairAsnRead':
objmacro.c:5883:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'StructuredCommentFieldAsnRead':
objmacro.c:6371:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FieldTypeAsnRead':
objmacro.c:8543:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ConstraintChoiceAsnRead':
objmacro.c:9631:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'TextTransformAsnRead':
objmacro.c:11149:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcGeneralIdAsnRead':
objmacro.c:13133:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixCapsActionAsnRead':
objmacro.c:18363:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixFormatActionAsnRead':
objmacro.c:18565:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FixSetsActionAsnRead':
objmacro.c:20483:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'MacroActionChoiceAsnRead':
objmacro.c:22829:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationPosConstraintAsnRead':
objmacro.c:1491:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FeatQualChoiceAsnRead':
objmacro.c:2342:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'RnaFeatTypeAsnRead':
objmacro.c:3076:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'PubFieldSpecialConstraintTypeAsnRead':
objmacro.c:7076:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SequenceConstraintMolTypeConstraintAsnRead':
objmacro.c:8768:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'QuantityConstraintAsnRead':
objmacro.c:8963:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'TextMarkerAsnRead':
objmacro.c:9970:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'FieldPairTypeAsnRead':
objmacro.c:10594:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ActionChoiceAsnRead':
objmacro.c:12578:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcOrgChoiceAsnRead':
objmacro.c:12778:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseSrcAsnRead':
objmacro.c:13365:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ParseDestAsnRead':
objmacro.c:13762:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationChoiceAsnRead':
objmacro.c:14121:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SequenceListChoiceAsnRead':
objmacro.c:14418:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ConvertFeatureDstOptionsAsnRead':
objmacro.c:15556:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'LocationEditTypeAsnRead':
objmacro.c:16859:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'CreateTSAIdsSrcAsnRead':
objmacro.c:19958:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'TableMatchTypeAsnRead':
objmacro.c:20712:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'SearchFuncAsnRead':
objmacro.c:23259:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmacro.c: In function 'ReplaceFuncAsnRead':
objmacro.c:23648:16: 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 -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:184:3: 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:277:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2BooleanElementFree':
objent2.c:416:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'Entrez2BooleanElementAsnRead':
objent2.c:457:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LimitsAsnRead':
objent2.c:666:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:665:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2BooleanTermAsnRead':
objent2.c:844:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:843:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2RequestAsnRead':
objent2.c:1041:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1040:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'E2RequestFree':
objent2.c:1203:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'E2RequestAsnRead':
objent2.c:1256:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2EvalBooleanAsnRead':
objent2.c:1493:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1492:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermQueryAsnRead':
objent2.c:1670:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1669:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermPosAsnRead':
objent2.c:1849:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:1848:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2HierQueryAsnRead':
objent2.c:2036:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2035:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2GetLinksAsnRead':
objent2.c:2224:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2223:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2IdAsnRead':
objent2.c:2419:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2418:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DtFilterAsnRead':
objent2.c:2584:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2583:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2ReplyAsnRead':
objent2.c:2762:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:2761:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'E2ReplyFree':
objent2.c:2935:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objent2.c: In function 'E2ReplyAsnRead':
objent2.c:2991:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2InfoAsnRead':
objent2.c:3237:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2BooleanReplyAsnRead':
objent2.c:3409:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:3408:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumListAsnRead':
objent2.c:3587:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2TermListAsnRead':
objent2.c:3749:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2HierNodeAsnRead':
objent2.c:3922:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2LinkSetAsnRead':
objent2.c:4122:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4121:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkCountListAsnRead':
objent2.c:4299:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2DbInfoAsnRead':
objent2.c:4466:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2FieldInfoAsnRead':
objent2.c:4706:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4705:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkInfoAsnRead':
objent2.c:4950:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:4949:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumFieldInfoAsnRead':
objent2.c:5149:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5148:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2DocsumAsnRead':
objent2.c:5325:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c: In function 'Entrez2DocsumDataAsnRead':
objent2.c:5488:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5487:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2TermAsnRead':
objent2.c:5655:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5654:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2LinkCountAsnRead':
objent2.c:5838:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objent2.c:5837:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objent2.c: In function 'Entrez2BooleanElementAsnRead':
objent2.c:524:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objent2.c: In function 'E2RequestAsnRead':
objent2.c:1333:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objent2.c: In function 'E2ReplyAsnRead':
objent2.c:3075:16: 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 -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:184:3: 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 -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:184:3: 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:2813:24: warning: 'SortByInt4' defined but not used [-Wunused-function]
static int LIBCALLBACK SortByInt4 (VoidPtr vp1, VoidPtr vp2)
^~~~~~~~~~
pmfapi.c: In function 'ConfirmAccStrInSep':
pmfapi.c:1314:3: warning: 'tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqIdFree (tmp);
^~~~~~~~~~~~~~~
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:1479:58: 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:1663:58: 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:1744:58: 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:1817:61: 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:1869:60: 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:1920:63: 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:1971:62: 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:2021:60: 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 -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:184:3: 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:1072:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'Value_valueFree':
objtax3.c:1253:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objtax3.c: In function 'T3StatusFlagsAsnRead':
objtax3.c:1283:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax3.c: In function 'T3RefreshFlagsAsnRead':
objtax3.c:1608:16: 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:1421:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax3.c:1362:10: 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 -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:184:3: 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:189:27: warning: variable 't3' set but not used [-Wunused-but-set-variable]
time_t t1, t2, t3;
^~
tax3api.c: In function 'CheckSuggestedFixes':
tax3api.c:1030:20: warning: variable 'tep' set but not used [-Wunused-but-set-variable]
T3ErrorPtr tep;
^~~
tax3api.c: In function 'TryNewSuggestedFixes':
tax3api.c:1142:20: warning: variable 'tep' set but not used [-Wunused-but-set-variable]
T3ErrorPtr tep;
^~~
tax3api.c: In function 'RemoveSpeciesSpecific':
tax3api.c:1398:13: warning: unused variable 'cp' [-Wunused-variable]
CharPtr cp;
^~
At top level:
tax3api.c:3399:13: warning: 'AddBioSourcesToChecklist' defined but not used [-Wunused-function]
static void AddBioSourcesToChecklist (ValNodePtr biop_list, ValNodePtr check_list)
^~~~~~~~~~~~~~~~~~~~~~~~
tax3api.c:2699:16: warning: 'MatchesGenBankSynonym' defined but not used [-Wunused-function]
static Boolean MatchesGenBankSynonym (CharPtr txt, OrgRefPtr response_org)
^~~~~~~~~~~~~~~~~~~~~
tax3api.c:2682:16: warning: 'MatchesSynonym' defined but not used [-Wunused-function]
static Boolean MatchesSynonym (CharPtr txt, OrgRefPtr response_org)
^~~~~~~~~~~~~~
tax3api.c:2273:16: warning: 'EndsWithSp' defined but not used [-Wunused-function]
static Boolean EndsWithSp (CharPtr str)
^~~~~~~~~~
tax3api.c:990:19: warning: 'MakeTaxFixRequestList' defined but not used [-Wunused-function]
static ValNodePtr MakeTaxFixRequestList (ValNodePtr biop_list)
^~~~~~~~~~~~~~~~~~~~~
tax3api.c:362:16: warning: 'HasMisspellingFlag' defined but not used [-Wunused-function]
static Boolean HasMisspellingFlag (T3DataPtr t)
^~~~~~~~~~~~~~~~~~
tax3api.c:298:13: 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 -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:184:3: 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 -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:184:3: 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:412:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:409:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objentgene.c: In function 'GeneTrackAsnRead':
objentgene.c:547:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c: In function 'GeneCommentaryAsnRead':
objentgene.c:768:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c: In function 'Method_methodFree':
objentgene.c:1073:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objentgene.c: In function 'MapsAsnRead':
objentgene.c:1104:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1103:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'Method_methodAsnRead':
objentgene.c:1184:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'GeneSourceAsnRead':
objentgene.c:1426:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1425:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'XtraTermsAsnRead':
objentgene.c:1641:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1640:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'OtherSourceAsnRead':
objentgene.c:1812:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objentgene.c:1811:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objentgene.c: In function 'MapsAsnRead':
objentgene.c:1236:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objentgene.c:1183:10: 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 -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:184:3: 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:613:16: 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:904:16: 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 -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:184:3: 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 -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:123:
/usr/include/features.h:184:3: 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:262:15: warning: variable 'waiting' set but not used [-Wunused-but-set-variable]
Boolean waiting = FALSE;
^~~~~~~
qblastapi.c: In function 'BLASTGetSeqAnnotByRIDEx':
qblastapi.c:826:18: warning: variable 'status' set but not used [-Wunused-but-set-variable]
EIO_Status status;
^~~~~~
qblastapi.c: In function 'BLASTGetQueryBioseqByRIDEx':
qblastapi.c:871:18: warning: variable 'status' set but not used [-Wunused-but-set-variable]
EIO_Status status;
^~~~~~
qblastapi.c: In function 'QBlastCheckQueue':
qblastapi.c:688:36: warning: '&FORMAT_OBJECT=Alignment&FORMAT_TYPE=ASN.1
' directive writing 43 bytes into a region of size between 5 and 68 [-Wformat-overflow=]
sprintf (str, "CMD=Get&RID=%s&FORMAT_OBJECT=Alignment&FORMAT_TYPE=ASN.1\n", curr->rid);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from qblastapi.c:123:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 56 and 119 bytes into a destination of size 80
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:448:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimCitAsnRead':
objmim.c:909:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:908:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimTextAsnRead':
objmim.c:1096:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:1095:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimEditItemAsnRead':
objmim.c:1276:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:1275:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimAllelicVariantAsnRead':
objmim.c:1448:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimIndexTermAsnRead':
objmim.c:1640:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimReferenceAsnRead':
objmim.c:1819:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c: In function 'MimLinkAsnRead':
objmim.c:2195:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2194:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimAuthorAsnRead':
objmim.c:2369:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2368:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmim.c: In function 'MimPageAsnRead':
objmim.c:2535:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmim.c:2534:12: 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 -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:184:3: 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:259:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:256:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'DependentFieldRuleAsnRead':
objvalid.c:396:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:395:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objvalid.c: In function 'DependentFieldSetAsnRead':
objvalid.c:582:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:579:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'CommentRuleAsnRead':
objvalid.c:721:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:720:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objvalid.c: In function 'CommentSetAsnRead':
objvalid.c:926:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:923:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objvalid.c: In function 'PhraseListAsnRead':
objvalid.c:1043:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objvalid.c:1040:12: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:4260:13: warning: variable 'is_cdregion' set but not used [-Wunused-but-set-variable]
Boolean is_cdregion = FALSE;
^~~~~~~~~~~
seqport.c: In function 'NaLocFromNaInterval':
seqport.c:4590:8: 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:4706:18: warning: variable 'cds_right' set but not used [-Wunused-but-set-variable]
Int4 cds_left, cds_right;
^~~~~~~~~
seqport.c:4706:8: warning: variable 'cds_left' set but not used [-Wunused-but-set-variable]
Int4 cds_left, cds_right;
^~~~~~~~
seqport.c: In function 'DeltaRevComp':
seqport.c:5388:21: warning: variable 'dspnext' set but not used [-Wunused-but-set-variable]
DeltaSeqPtr dsp, dspnext;
^~~~~~~
seqport.c: In function 'SeqSearchEnterNucWord':
seqport.c:6943:18: warning: variable 'patLen' set but not used [-Wunused-but-set-variable]
Int2 next, patLen, state;
^~~~~~
seqport.c: In function 'ProtSearchEnterProtWord':
seqport.c:7817:18: 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 -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:184:3: 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:7994:11: warning: variable 'first_strand' set but not used [-Wunused-but-set-variable]
Uint1 first_strand, last_strand;
^~~~~~~~~~~~
sequtil.c: In function 'SeqPointWriteEx':
sequtil.c:8532:15: warning: variable 'fuzzlen' set but not used [-Wunused-but-set-variable]
Int4 fuzzlen, id_len;
^~~~~~~
sequtil.c: In function 'TaxNameFromCommon':
sequtil.c:8687:42: warning: missing braces around initializer [-Wmissing-braces]
static Nlm_TaxCommon taxcommon[40] = {
^
"Chinese hamsters", "Cricetulus sp."
{
,"Syrian golden hamsters", "Mesocricetus auratus"
}{
,"Syrian hamsters", "Mesocricetus sp."
}{
,"barley", "Hordeum sp."
}{
,"carrots", "Daucus sp."
}{
,"cats", "Felis sp."
}{
,"cattles", "Bos sp."
}{
,"chickens", "Gallus sp."
}{
,"chimpanzees", "Pan sp."
}{
,"chimpanzes", "Pan sp."
}{
,"corn", "Zea sp."
}{
,"cucumber", "Cucumis sativus"
}{
,"dogs", "Canis sp."
}{
,"goats", "Capra sp."
}{
,"gorillas", "Gorilla sp."
}{
,"guinea pigs", "Cavia sp."
}{
,"hamsters", "Cricetidae gen. sp."
}{
,"horses", "Equus sp."
}{
,"humans", "Homo sapiens"
}{
,"maize", "Zea sp."
}{
,"mice", "Mus sp."
}{
,"mouse", "Mus sp."
}{
,"peas", "Pisum sp."
}{
,"potatoes", "Solanum sp."
}{
,"potato", "Solanum sp."
}{
,"quails", "Phasianidae gen. sp."
}{
,"rabbits", "Oryctolagus sp."
}{
,"rats", "Rattus sp."
}{
,"rices", "Oryza sp."
}{
,"sheeps", "Ovis sp."
}{
,"sorghums", "Sorghum sp."
}{
,"soybeans", "Glycine sp."
}{
,"spinach", "Spinacia sp."
}{
,"swine", "Sus sp."
}{
,"tobacco", "Nicotiania sp."
}{
,"tomatoes", "Lycopersicon sp."
}{
,"tomato", "Lycopersicon sp."
}{
,"turkeys", "Meleagris sp."
}{
,"wheat", "Triticum sp."
}{
,"zebrafish", "Brachydanio sp."
}{
};
}
sequtil.c: In function 'GetBestScoreAndEvalueFromScorePtr':
sequtil.c:9510:48: 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:10110:38: warning: variable 'sip2' set but not used [-Wunused-but-set-variable]
SeqIdPtr sip2;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:7293:0: warning: "RNA_QUAL" redefined
#define RNA_QUAL &at[2254]
../include/all.h:5823:0: note: this is the location of the previous definition
#define RNA_QUAL &at[1025]
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:1461:22: warning: variable 'gene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr gene = NULL;
^~~~
tofasta.c: In function 'FastaIdEx':
tofasta.c:3100:15: warning: variable 'sip' set but not used [-Wunused-but-set-variable]
SeqIdPtr sip;
^~~
tofasta.c: In function 'CreateDefLineExEx':
tofasta.c:4991:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (vnp != NULL)
^~
tofasta.c:4993:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (title != NULL) {
^~
tofasta.c: In function 'x_SetSuffix':
tofasta.c:8313:24: warning: variable 'buf2' set but not used [-Wunused-but-set-variable]
Char buf1 [512], buf2 [256];
^~~~
tofasta.c: In function 'FastaToSeqEntryInternalExEx':
tofasta.c:2838:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(buffer+1, BuffSize, fd);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tofasta.c:2863:13: 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:8058:17: warning: 'x_StringInList' defined but not used [-Wunused-function]
static Boolean x_StringInList (
^~~~~~~~~~~~~~
tofasta.c:3661:19: warning: 'GatherGenesForCDS' defined but not used [-Wunused-function]
static ValNodePtr GatherGenesForCDS(SeqLocPtr slp)
^~~~~~~~~~~~~~~~~
tofasta.c:3627:19: warning: 'GatherSeqFeatProt' defined but not used [-Wunused-function]
static SeqFeatPtr GatherSeqFeatProt(BioseqPtr bsp)
^~~~~~~~~~~~~~~~~
tofasta.c:3541:19: warning: 'GetCDSProtUnindexed' defined but not used [-Wunused-function]
static SeqFeatPtr GetCDSProtUnindexed (
^~~~~~~~~~~~~~~~~~~
tofasta.c:3378:19: warning: 'IndexedGatherDescrOnBioseq' defined but not used [-Wunused-function]
static ValNodePtr IndexedGatherDescrOnBioseq (ItemInfoPtr iip, BioseqPtr bsp, Uint1 choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~
tofasta.c:3283:16: warning: 'get_descr' defined but not used [-Wunused-function]
static Boolean get_descr (GatherContextPtr gcp)
^~~~~~~~~
tofasta.c:3254:16: 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:2713:27: warning: 'mask_to' may be used uninitialized in this function [-Wmaybe-uninitialized]
mask_sint->to = mask_to;
~~~~~~~~~~~~~~^~~~~~~~~
tofasta.c: In function 'FastaToSeqEntryInternalExEx':
tofasta.c:2774:25: 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 -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:184:3: 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 -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:153:
/usr/include/features.h:184:3: 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 -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:184:3: 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 'GetUserFieldValueString':
valid.c:2212:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", ufp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
valid.c: In function 'ValidateSeqIdCase':
valid.c:3574:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'ValidateGenProdSet':
valid.c:6046:19: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'CountAdjacentProc':
valid.c:6730:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'CheckBioseqEndsForNAndGap':
valid.c:7040:44: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (str [0] == 'n' || str [0] == 'N' && begin_n != NULL) {
^
valid.c:7061:56: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (str [len - 1] == 'n' || str [len - 1] == 'N' && end_n != NULL) {
^
valid.c: In function 'ValidateBioseqInst':
valid.c:7341:19: warning: variable 'tech' set but not used [-Wunused-but-set-variable]
Uint1 tech;
^~~~
valid.c:7278:19: warning: variable 'prot' set but not used [-Wunused-but-set-variable]
SeqFeatPtr prot;
^~~~
valid.c: In function 'FixOrgModVoucher':
valid.c:13882:22: warning: unused variable 'allowed_type' [-Wunused-variable]
Uint1 type = 0, allowed_type = 0;
^~~~~~~~~~~~
valid.c: In function 'ValidateBioSource':
valid.c:15514:19: warning: variable 'isMicrosporidia' set but not used [-Wunused-but-set-variable]
Boolean isMicrosporidia = FALSE;
^~~~~~~~~~~~~~~
valid.c:15512:19: warning: variable 'isEukaryote' set but not used [-Wunused-but-set-variable]
Boolean isEukaryote = FALSE;
^~~~~~~~~~~
valid.c:15503:19: warning: variable 'id' set but not used [-Wunused-but-set-variable]
Int4 id;
^~
valid.c: In function 'ValidateDblink':
valid.c:16786:21: warning: variable 'gcp' set but not used [-Wunused-but-set-variable]
GatherContextPtr gcp;
^~~
valid.c: In function 'ValidateSeqDescrCommon':
valid.c:16883:19: warning: variable 'pdp' set but not used [-Wunused-but-set-variable]
PubdescPtr pdp;
^~~
valid.c: In function 'GetFeatsInGaps':
valid.c:18858:21: warning: variable 'realBases' set but not used [-Wunused-but-set-variable]
Int4 realBases;
^~~~~~~~~
valid.c:18857:21: warning: variable 'plusses' set but not used [-Wunused-but-set-variable]
Int4 plusses;
^~~~~~~
valid.c:18854:21: warning: variable 'Ns' set but not used [-Wunused-but-set-variable]
Int4 Ns;
^~
valid.c:18851:21: warning: variable 'dashes' set but not used [-Wunused-but-set-variable]
Int4 dashes;
^~~~~~
valid.c: In function 'ValidateBioseqContextIndexed':
valid.c:20267:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (bvsp->is_mrna || cdscount == 1 && genecount < 2) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
valid.c:19476:65: warning: variable 'cdsmgene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr utr5pgene, cdspgene, utr3pgene, utr5mgene, cdsmgene, utr3mgene;
^~~~~~~~
valid.c:19476:33: warning: variable 'cdspgene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr utr5pgene, cdspgene, utr3pgene, utr5mgene, cdsmgene, utr3mgene;
^~~~~~~~
valid.c:19475:51: warning: variable 'utr5minus' set but not used [-Wunused-but-set-variable]
SeqFeatPtr utr5plus, cdsplus, utr3plus, utr5minus, cdsminus, utr3minus;
^~~~~~~~~
valid.c:19475:41: warning: variable 'utr3plus' set but not used [-Wunused-but-set-variable]
SeqFeatPtr utr5plus, cdsplus, utr3plus, utr5minus, cdsminus, utr3minus;
^~~~~~~~
valid.c:19442:41: warning: variable 'utr3gene' set but not used [-Wunused-but-set-variable]
SeqFeatPtr cdsgene, utr5gene, utr3gene;
^~~~~~~~
valid.c: In function 'ReportBadWGSGap':
valid.c:21153:18: warning: unused variable 'is_wgs' [-Wunused-variable]
Boolean is_wgs = FALSE;
^~~~~~
valid.c: In function 'ValidateBarcodeIndexNumber':
valid.c:21432:21: warning: variable 'bin_len' set but not used [-Wunused-but-set-variable]
Int4 bin_len;
^~~~~~~
valid.c: In function 'ValidateRptUnit':
valid.c:23411:32: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean badchars, found, just_nuc_letters, multi_rpt_unit, in_range;
^~~~~
valid.c: In function 'CheckForCommonCDSProduct':
valid.c:25628:19: warning: variable 'is_nw' set but not used [-Wunused-but-set-variable]
Boolean is_nw = FALSE;
^~~~~
valid.c:25625:19: warning: variable 'is_nc' set but not used [-Wunused-but-set-variable]
Boolean is_nc = FALSE;
^~~~~
valid.c: In function 'CheckForIllegalDbxref':
valid.c:26017:16: warning: variable 'id' set but not used [-Wunused-but-set-variable]
Int4 id;
^~
valid.c: In function 'ValidateAnticodon':
valid.c:26781:53: warning: variable 'circular' set but not used [-Wunused-but-set-variable]
ordered = TRUE, adjacent = FALSE, circular = FALSE, exception = FALSE;
^~~~~~~~
valid.c:26780:19: 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:28000:17: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
valid.c: In function 'ValidateSeqFeat':
valid.c:28328:19: warning: unused variable 'is_nc' [-Wunused-variable]
Boolean is_nc = FALSE;
^~~~~
valid.c:28308:19: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
valid.c:28286:19: warning: variable 'pdp' set but not used [-Wunused-but-set-variable]
PubdescPtr pdp;
^~~
valid.c: In function 'CdTransCheck':
valid.c:30490:19: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'SpliceCheckEx':
valid.c:31313:19: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
valid.c: In function 'CdsProductIdCheck':
valid.c:31689:15: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
valid.c: In function 'ValidateSeqLoc':
valid.c:31754:19: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = TRUE, tmpval, mixed_strand = FALSE, unmarked_strand = FALSE,
^~~~~~
valid.c:31753:24: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
SeqLocPtr tmp, prev;
^~~~
valid.c: In function 'SortSeqGraphProc':
valid.c:32156:26: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (gip2->right < gip2->right) {
^
At top level:
valid.c:30138:13: warning: 'ValidateTranslExcept' defined but not used [-Wunused-function]
static void ValidateTranslExcept (
^~~~~~~~~~~~~~~~~~~~
valid.c:27650:16: warning: 'CouldExtendPartial' defined but not used [-Wunused-function]
static Boolean CouldExtendPartial (SeqLocPtr slp, Boolean partial5)
^~~~~~~~~~~~~~~~~~
valid.c:20878:28: warning: 'MultiGeneOverlapFree' defined but not used [-Wunused-function]
static MultiGeneOverlapPtr MultiGeneOverlapFree (MultiGeneOverlapPtr m)
^~~~~~~~~~~~~~~~~~~~
valid.c:20828:19: warning: 'ListFeaturesContainedInLocation' defined but not used [-Wunused-function]
static ValNodePtr ListFeaturesContainedInLocation (BioseqPtr bsp, SeqLocPtr slp, Uint1 seqfeatChoice, Uint1 featdefChoice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
valid.c:17541:16: warning: 'IsEMBLAccn' defined but not used [-Wunused-function]
static Boolean IsEMBLAccn (SeqEntryPtr sep, SeqLocPtr location)
^~~~~~~~~~
valid.c:14642:16: warning: 'CountryIsClosestToLatLon' defined but not used [-Wunused-function]
static Boolean CountryIsClosestToLatLon (
^~~~~~~~~~~~~~~~~~~~~~~~
valid.c:14545:16: warning: 'LatLonInRange' defined but not used [-Wunused-function]
static Boolean LatLonInRange (
^~~~~~~~~~~~~
valid.c:13478:16: warning: 'LatLonIsValid' defined but not used [-Wunused-function]
static Boolean LatLonIsValid (CharPtr name)
^~~~~~~~~~~~~
valid.c:10462:16: warning: 'ConsistentWithC' defined but not used [-Wunused-function]
static Boolean ConsistentWithC (Char ch)
^~~~~~~~~~~~~~~
valid.c:6952:13: warning: 'ReportLongSeqId' defined but not used [-Wunused-function]
static void ReportLongSeqId (SeqIdPtr sip, ValidStructPtr vsp, Int4 max_len)
^~~~~~~~~~~~~~~
valid.c:5932:13: warning: 'CheckMutSetSources' defined but not used [-Wunused-function]
static void CheckMutSetSources (BioSourcePtr biop, Pointer userdata)
^~~~~~~~~~~~~~~~~~
valid.c:4360:13: warning: 'FindLongIdsThatCollideWhenTruncated' defined but not used [-Wunused-function]
static void FindLongIdsThatCollideWhenTruncated (SeqEntryPtr sep, ValidStructPtr vsp, Int4 trunc_len)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
valid.c:1511:16: 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 -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:184:3: 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:263:15: warning: variable 'errstr' set but not used [-Wunused-but-set-variable]
const char *errstr;
^~~~~~
valapi.c: In function 'DoesFieldValueMatchExpression':
valapi.c:292:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", ufp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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_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 '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 '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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:748:3: warning: 'cLineType' may be used uninitialized in this function [-Wmaybe-uninitialized]
fprintf(stderr,"%04d: 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 -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:184:3: 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 -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:184:3: 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:1267:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if(stptrtemp[j+i*aligndim]+lenptrtemp[i]>bslen)
^
alignval.c: In function 'PercentStringMatch':
alignval.c:1579:32: 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:2004:12: warning: variable 'aln_len' set but not used [-Wunused-but-set-variable]
Int4 aln_len, start, stop;
^~~~~~~
alignval.c: In function 'ValidateSeqAlign':
alignval.c:2125:16: warning: variable 'ans' set but not used [-Wunused-but-set-variable]
MsgAnswer ans;
^~~
alignval.c: In function 'GetAlignmentColumnPercentIdentities':
alignval.c:2511:14: 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:2002:13: warning: 'CheckAlnSeqLens' defined but not used [-Wunused-function]
static void CheckAlnSeqLens (SeqAlignPtr salp)
^~~~~~~~~~~~~~~
alignval.c:1560:16: warning: 'IsSipContainedInStdseg' defined but not used [-Wunused-function]
static Boolean IsSipContainedInStdseg(SeqIdPtr sip, StdSegPtr ssp)
^~~~~~~~~~~~~~~~~~~~~~
alignval.c:602:13: 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 -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:184:3: 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:2012:18: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
sqnutil1.c: In function 'ParseAnticodon':
sqnutil1.c:3494:14: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil1.c: In function 'ParseCodeBreak':
sqnutil1.c:3617:17: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil1.c: In function 'CleanUpPubdescAuthors':
sqnutil1.c:9093:20: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
ValNodePtr PNTR prev;
^~~~
sqnutil1.c: In function 'FixWrongFuzzOnPlusStrand':
sqnutil1.c:11948:15: warning: unused variable 'spp' [-Wunused-variable]
SeqPntPtr spp;
^~~
sqnutil1.c: In function 'FixWrongFuzzOnMinusStrand':
sqnutil1.c:12007:15: warning: unused variable 'spp' [-Wunused-variable]
SeqPntPtr spp;
^~~
sqnutil1.c: In function 'ConsolidateBioSourceNotes':
sqnutil1.c:13250:21: warning: variable 'note_mod' set but not used [-Wunused-but-set-variable]
OrgModPtr mod, note_mod;
^~~~~~~~
sqnutil1.c:13249:21: warning: variable 'note_ssp' set but not used [-Wunused-but-set-variable]
SubSourcePtr ssp, note_ssp;
^~~~~~~~
sqnutil1.c: In function 'RemoveUnnecessaryGeneXrefs':
sqnutil1.c:15059:24: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil1.c: In function 'LinkTwoFeatures':
sqnutil1.c:17930:25: warning: variable 'prev_xref' set but not used [-Wunused-but-set-variable]
SeqFeatXrefPtr xref, prev_xref, next_xref;
^~~~~~~~~
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:10386:16: warning: 'CleanUpSgml' defined but not used [-Wunused-function]
static CharPtr CleanUpSgml (
^~~~~~~~~~~
sqnutil1.c:10272:13: warning: 'SortGoTermsSfp' defined but not used [-Wunused-function]
static void SortGoTermsSfp (
^~~~~~~~~~~~~~
sqnutil1.c:7405:16: warning: 'IsStringSingleToken' defined but not used [-Wunused-function]
static Boolean IsStringSingleToken (CharPtr str)
^~~~~~~~~~~~~~~~~~~
sqnutil1.c:4942:13: warning: 'CleanupConsSplice' defined but not used [-Wunused-function]
static void CleanupConsSplice (GBQualPtr gbq)
^~~~~~~~~~~~~~~~~
sqnutil1.c:2007:16: 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 -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:184:3: 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:5223:11: warning: variable 'last' set but not used [-Wunused-but-set-variable]
Uint1 last;
^~~~
sqnutil2.c: In function 'ReadFeatureTableEx':
sqnutil2.c:7254:18: warning: variable 'isnote' set but not used [-Wunused-but-set-variable]
Boolean isnote;
^~~~~~
sqnutil2.c:7246:18: warning: variable 'endsinspace' set but not used [-Wunused-but-set-variable]
Boolean endsinspace;
^~~~~~~~~~~
sqnutil2.c: In function 'SeqEntryCopyReplace':
sqnutil2.c:9270:8: warning: variable 'type' set but not used [-Wunused-but-set-variable]
Uint1 type = 0;
^~~~
sqnutil2.c: In function 'StreamingReadBioseq':
sqnutil2.c:10095:10: warning: variable 'level' set but not used [-Wunused-but-set-variable]
Int2 level;
^~~~~
sqnutil2.c: In function 'StreamAsnForDescriptors':
sqnutil2.c:10328:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (rval = StreamingReadSeqEntry (aip, sp, &sr)) {
^~~~
sqnutil2.c: In function 'WriteAsnWithReplacedDescriptors':
sqnutil2.c:10749:12: 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:11700:18: warning: variable 'begin' set but not used [-Wunused-but-set-variable]
Int4 begin;
^~~~~
sqnutil2.c: In function 'ReadFastaOnly':
sqnutil2.c:11894:18: warning: variable 'seqid' set but not used [-Wunused-but-set-variable]
Char seqid [2048];
^~~~~
sqnutil2.c: In function 'ReadDeltaFastaWithEmptyDefline':
sqnutil2.c:12446:29: warning: variable 'seqid' set but not used [-Wunused-but-set-variable]
Char line [4096], seqid [2048];
^~~~~
sqnutil2.c: In function 'SortSeqGraphProc':
sqnutil2.c:13002:26: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (gip2->right < gip2->right) {
^
sqnutil2.c: In function 'PrintQualityScoresToBuffer':
sqnutil2.c:13052:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil2.c: In function 'GetScoresbySeqId':
sqnutil2.c:13461:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil2.c: In function 'RemoveGapsFromDeltaLocation':
sqnutil2.c:15480:15: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil2.c: In function 'IsStringInSpanInList':
sqnutil2.c:16693:11: warning: variable 'str_val' set but not used [-Wunused-but-set-variable]
Int4 str_val;
^~~~~~~
sqnutil2.c:16691:27: 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:18415:35: 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:18779:14: warning: variable 'target_strand' set but not used [-Wunused-but-set-variable]
Uint1 target_strand;
^~~~~~~~~~~~~
sqnutil2.c:18778:14: warning: variable 'seq_len' set but not used [-Wunused-but-set-variable]
Int4 seq_len;
^~~~~~~
sqnutil2.c: In function 'AdjustForConsensusSpliceCallback':
sqnutil2.c:20313:33: 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:20926:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
sqnutil2.c: In function 'RemoveBadCodonRecognizedCallback':
sqnutil2.c:22812:13: warning: variable 'rcodon' set but not used [-Wunused-but-set-variable]
Uint1 rcodon [4];
^~~~~~
sqnutil2.c: In function 'CompareStructuredComment':
sqnutil2.c:25151:23: warning: variable 'ovp2' set but not used [-Wunused-but-set-variable]
ObjValNodePtr ovp1, ovp2;
^~~~
sqnutil2.c:25151:17: warning: variable 'ovp1' set but not used [-Wunused-but-set-variable]
ObjValNodePtr ovp1, ovp2;
^~~~
sqnutil2.c: In function 'UniqueAndCountValNodeCS':
sqnutil2.c:25546:17: warning: variable 'curr' set but not used [-Wunused-but-set-variable]
ValNodePtr curr;
^~~~
sqnutil2.c: In function 'PerformArticleQuery':
sqnutil2.c:25810:20: warning: variable 'debug_mode' set but not used [-Wunused-but-set-variable]
Boolean debug_mode = FALSE;
^~~~~~~~~~
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:18065:19: warning: 'AuthAffilListFree' defined but not used [-Wunused-function]
static ValNodePtr AuthAffilListFree (ValNodePtr list)
^~~~~~~~~~~~~~~~~
sqnutil2.c:18044:21: warning: 'AuthAffilNew' defined but not used [-Wunused-function]
static AuthAffilPtr AuthAffilNew (CharPtr affil)
^~~~~~~~~~~~
sqnutil2.c:16282:19: warning: 'MakeTranscriptomeIDTokensFromLine' defined but not used [-Wunused-function]
static ValNodePtr MakeTranscriptomeIDTokensFromLine (CharPtr line)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil2.c:16188:13: warning: 'RevCompFeatsOnBioseq' defined but not used [-Wunused-function]
static void RevCompFeatsOnBioseq (BioseqPtr bsp)
^~~~~~~~~~~~~~~~~~~~
sqnutil2.c:8333:16: warning: 'DoesSeqEntryAccessionMatchList' defined but not used [-Wunused-function]
static Boolean DoesSeqEntryAccessionMatchList (SeqEntryPtr sep, ValNodePtr accn_list)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil2.c:4684:16: 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 -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:184:3: 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:528:22: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil3.c: In function 'CautiousSeqEntryCleanup':
sqnutil3.c:2178:16: warning: variable 'taxserver' set but not used [-Wunused-but-set-variable]
Boolean taxserver;
^~~~~~~~~
sqnutil3.c: In function 'AddGapSeqLit':
sqnutil3.c:3127:19: warning: unused variable 'gap_chars' [-Wunused-variable]
CharPtr gap_chars = "NNNNNNNNNN"
^~~~~~~~~
sqnutil3.c: In function 'ConvertSegSetsToDeltaSequencesInt':
sqnutil3.c:3382:26: 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:4797:32: warning: variable 'num_sets' set but not used [-Wunused-but-set-variable]
Int4 index, curr_seg, num_sets;
^~~~~~~~
sqnutil3.c:4791:26: warning: variable 'salp_last' set but not used [-Wunused-but-set-variable]
SeqAlignPtr salp_list, salp_last;
^~~~~~~~~
sqnutil3.c:4791:15: warning: variable 'salp_list' set but not used [-Wunused-but-set-variable]
SeqAlignPtr salp_list, salp_last;
^~~~~~~~~
sqnutil3.c: In function 'ConvertContainedCDSToMiscFeat':
sqnutil3.c:12824:14: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
sqnutil3.c: In function 'OrgNameMatchExceptOldName':
sqnutil3.c:13713:28: warning: self-comparison always evaluates to false [-Wtautological-compare]
|| onp2->mgcode != onp2->mgcode
^~
sqnutil3.c: In function 'FindMismatchedCitSubAffiliations':
sqnutil3.c:19281:14: warning: variable 'has_seq_submit' set but not used [-Wunused-but-set-variable]
Boolean has_seq_submit = TRUE;
^~~~~~~~~~~~~~
sqnutil3.c: In function 'GetCDSformRNA':
sqnutil3.c:20267:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sqnutil3.c: In function 'FindTextInFlatfileOncaller':
sqnutil3.c:22140:19: warning: variable 'okay' set but not used [-Wunused-but-set-variable]
Boolean okay;
^~~~
sqnutil3.c: In function 'CheckForTitleAuthorConflicts':
sqnutil3.c:23168:14: warning: variable 'author_conflict' set but not used [-Wunused-but-set-variable]
Boolean author_conflict = FALSE;
^~~~~~~~~~~~~~~
sqnutil3.c: In function 'SortVnpByBspProjectId':
sqnutil3.c:26956:31: 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:31033:21: warning: variable 'special_flag' set but not used [-Wunused-but-set-variable]
Boolean special_flag = FALSE;
^~~~~~~~~~~~
sqnutil3.c: In function 'CollectionDateIsInTheFuture':
sqnutil3.c:34586:20: warning: variable 'time' set but not used [-Wunused-but-set-variable]
CharPtr str, time;
^~~~
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:35189:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
sqnutil3.c:36777:13: warning: 'TestLatLonFormatting' defined but not used [-Wunused-function]
static void TestLatLonFormatting (FILE *fp)
^~~~~~~~~~~~~~~~~~~~
sqnutil3.c:34406:22: warning: 'BetterDateFree' defined but not used [-Wunused-function]
static BetterDatePtr BetterDateFree (BetterDatePtr dp)
^~~~~~~~~~~~~~
sqnutil3.c:33998:16: warning: 'GetColon' defined but not used [-Wunused-function]
static CharPtr GetColon (CharPtr str)
^~~~~~~~
sqnutil3.c:17224:24: warning: 'IntervalPairFree' defined but not used [-Wunused-function]
static IntervalPairPtr IntervalPairFree (IntervalPairPtr i)
^~~~~~~~~~~~~~~~
sqnutil3.c:10883:16: warning: 'IsMitochondrionBioseq' defined but not used [-Wunused-function]
static Boolean IsMitochondrionBioseq(BioseqPtr bsp)
^~~~~~~~~~~~~~~~~~~~~
sqnutil3.c: In function 'LinkCDSmRNAbyLabelAndLocationCallback':
sqnutil3.c:876:23: warning: 'best_diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (diff < best_diff) {
^
sqnutil3.c: In function 'tRNASameStrandBioseqCallback':
sqnutil3.c:16769:8: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (strand == Seq_strand_minus) {
^
sqnutil3.c: In function 'CheckForDivConflicts':
sqnutil3.c:8132:15: warning: 'sfp' may be used uninitialized in this function [-Wmaybe-uninitialized]
else ValNodeAddPointer(&(grp_sdp_sfp[num_grp]), OBJ_SEQFEAT, sfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c:8131:13: warning: 'sdp' may be used uninitialized in this function [-Wmaybe-uninitialized]
ValNodeAddPointer(&(grp_sdp_sfp[num_grp]), OBJ_SEQDESC, sdp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil3.c: In function 'FindMismatchedComments':
sqnutil3.c:26612:47: warning: 'sdp' may be used uninitialized in this function [-Wmaybe-uninitialized]
sprintf (fmt, sub_fmt, (CharPtr) sdp->data.ptrvalue);
~~~~~~~~~^~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:8566:43: warning: variable 'twobefore' set but not used [-Wunused-but-set-variable]
FeatureClausePtr thisclause, onebefore, twobefore, oneafter, twoafter;
^~~~~~~~~
sqnutil4.c: In function 'SmashOneTallClause':
sqnutil4.c:9900:20: warning: variable 'subclause_featlist' set but not used [-Wunused-but-set-variable]
ValNodePtr subclause_featlist;
^~~~~~~~~~~~~~~~~~
sqnutil4.c: In function 'GetFeatureClauseForSeg':
sqnutil4.c:10787:21: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start, stop;
^~~~~
sqnutil4.c: In function 'RemoveAutodefObjectsForDesc':
sqnutil4.c:13618:18: warning: unused variable 'bssp' [-Wunused-variable]
BioseqSetPtr bssp;
^~~~
sqnutil4.c:13617:15: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp;
^~~
sqnutil4.c: In function 'ConvertProtToImpFunc':
sqnutil4.c:15072:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sqnutil4.c: In function 'ExtraCDSCreationActions':
sqnutil4.c:15989:28: warning: variable 'nsep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr psep, nsep;
^~~~
sqnutil4.c: In function 'TESTDisplayQualCombo':
sqnutil4.c:17099:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Int4 val;
^~~
sqnutil4.c: In function 'ConvertCDSToMatPeptideForOverlappingCDS':
sqnutil4.c:18589:15: warning: variable 'crp' set but not used [-Wunused-but-set-variable]
CdRegionPtr crp;
^~~
sqnutil4.c: In function 'AddNewUniqueAnnotations':
sqnutil4.c:18780:39: 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:19443:27: warning: variable 'vnp_last' set but not used [-Wunused-but-set-variable]
ValNodePtr list, vnp, vnp_last = NULL;
^~~~~~~~
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:64:
../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:17248:13: warning: 'TESTDisplayList' defined but not used [-Wunused-function]
static void TESTDisplayList (ValNodePtr new_list)
^~~~~~~~~~~~~~~
sqnutil4.c:17219:19: warning: 'ExpandOneComboListUsingAllPresentQuals' defined but not used [-Wunused-function]
static ValNodePtr ExpandOneComboListUsingAllPresentQuals (QualComboPtr q)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil4.c:16930:16: warning: 'RemoveFieldFromUniqBioSrcGrpList' defined but not used [-Wunused-function]
static Boolean RemoveFieldFromUniqBioSrcGrpList (ValNodePtr list, FieldTypePtr field)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sqnutil4.c:10029:19: warning: 'RemoveAllButLastCDS' defined but not used [-Wunused-function]
static ValNodePtr RemoveAllButLastCDS (
^~~~~~~~~~~~~~~~~~~
sqnutil4.c:9998:13: warning: 'SmashTallClauses' defined but not used [-Wunused-function]
static void SmashTallClauses (
^~~~~~~~~~~~~~~~
sqnutil4.c:9834:13: warning: 'RemoveFeats' defined but not used [-Wunused-function]
static void RemoveFeats (
^~~~~~~~~~~
sqnutil4.c:5211:13: warning: 'CountFeatures' defined but not used [-Wunused-function]
static Int4 CountFeatures (
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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;
^~~
subutil.c: In function 'MakeRNAFeature':
subutil.c:3639:29: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (AA_for_tRNA != '\0')
^~
subutil.c:3639:17: note: did you mean to dereference the pointer?
if (AA_for_tRNA != '\0')
^
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 -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:184:3: 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 -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:184:3: 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:50,
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 'print_taxinfo':
asn2ff1.c:4356:19: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(tmp, "%d", gcode);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 4 bytes into a destination of size 3
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:169,
from asn2ff2.c:216:
/usr/include/features.h:184:3: 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:50,
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 -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:48,
from asn2ff3.c:39:
/usr/include/features.h:184:3: 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:1073:26: warning: unused variable 'qual_temp' [-Wunused-variable]
GBQualPtr gbqual, qual, qual_temp=NULL, qual_gene=NULL;
^~~~~~~~~
asn2ff3.c:1072:10: warning: unused variable 'still_looking' [-Wunused-variable]
Boolean still_looking=TRUE;
^~~~~~~~~~~~~
asn2ff3.c: In function 'mRNAEvidenceComment':
asn2ff3.c:1157:9: warning: unused variable 'Locus_id' [-Wunused-variable]
Int4 Locus_id = 0;
^~~~~~~~
asn2ff3.c: In function 'Add_gene_id':
asn2ff3.c:2717:24: 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);
~^ ~~~~~~~~~~~~~~~~~~
%p
asn2ff3.c: In function 'Add_trid':
asn2ff3.c:3142:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf(buf, "%ld", sip->data.intvalue);
~~^ ~~~~~~~~~~~~~~~~~~
%lld
asn2ff3.c:3123:9: warning: unused variable 'gi' [-Wunused-variable]
BIG_ID gi = -1;
^~
asn2ff3.c: In function 'AddPID':
asn2ff3.c:3185:21: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf(buf, "%ld", sip->data.intvalue);
~~^ ~~~~~~~~~~~~~~~~~~
%lld
At top level:
asn2ff3.c:2702:13: 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:50,
from asn2ff3.c:39:
../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:48,
from asn2ff3.c:39:
asn2ff3.c: In function 'Add_dbxref.isra.1':
../include/ncbimem.h:232:23: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
asn2ff3.c:216:10: note: 'val' was declared here
CharPtr val;
^~~
asn2ff3.c: In function 'GettRNAaa':
asn2ff3.c:1619:9: warning: 'seq_code' may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr = Get3LetterSymbol(seq_code, table, trna->aa, error_msgs);
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2ff3.c: In function 'ConvertToNAImpFeat':
asn2ff3.c:2254:23: warning: '%ld' directive writing between 1 and 3 bytes into a region of size 2 [-Wformat-overflow=]
sprintf(buf_ptr, "%ld", (long) (cdr->frame));
^~~
asn2ff3.c:2254:22: note: directive argument in the range [1, 255]
sprintf(buf_ptr, "%ld", (long) (cdr->frame));
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:48,
from asn2ff3.c:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 4 bytes into a destination of size 2
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:48,
from asn2ff4.c:273:
/usr/include/features.h:184:3: 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' [-Wdangling-else]
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 were 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 were guarded by the 'if'
gsc.seglevels = 1;
^~~
In file included from ../include/asn2ff6.h:142:0,
from ../include/asn2ffp.h:50,
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)) {
^~~~~~~~~~~~~~
asn2ff4.c: In function 'CreateImpFeatFromProt':
asn2ff4.c:1723:18: warning: '%d' directive writing between 1 and 3 bytes into a region of size 2 [-Wformat-overflow=]
sprintf(buf, "%d", cdr->frame);
^~
asn2ff4.c:1723:17: note: directive argument in the range [1, 255]
sprintf(buf, "%d", cdr->frame);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/asn2ffg.h:200,
from ../include/asn2ffp.h:48,
from asn2ff4.c:273:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 4 bytes into a destination of size 2
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:48,
from asn2ff5.c:177:
/usr/include/features.h:184:3: 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' [-Wdangling-else]
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:50,
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 -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:184:3: 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 were 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 -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:184:3: 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:2202:19: warning: variable 'right' set but not used [-Wunused-but-set-variable]
Boolean left, right;
^~~~~
asn2gnb1.c: In function 's_LocusGetBaseName':
asn2gnb1.c:2350:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
asn2gnb1.c:2352:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
newLength = segNameLen - deleteChars;
^~~~~~~~~
asn2gnb1.c: In function 'DoOneSection':
asn2gnb1.c:2522:24: warning: variable 'iasp' set but not used [-Wunused-but-set-variable]
IntAsn2gbSectPtr iasp;
^~~~
asn2gnb1.c:2514:24: warning: variable 'bkmask' set but not used [-Wunused-but-set-variable]
BlockMask bkmask;
^~~~~~
asn2gnb1.c: In function 'Count2Seg':
asn2gnb1.c:3438:18: warning: variable 'to' set but not used [-Wunused-but-set-variable]
Int4 to;
^~
asn2gnb1.c:3436:18: warning: variable 'parent' set but not used [-Wunused-but-set-variable]
BioseqPtr parent;
^~~~~~
asn2gnb1.c: At top level:
asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces]
static ModeFlags flagTable [] = {
^
asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces]
asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces]
asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces]
asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces]
asn2gnb1.c: In function 'SeqIdWriteForTable':
asn2gnb1.c:5808:13: warning: variable 'pdb' set but not used [-Wunused-but-set-variable]
pdb = NULL, general = NULL, gi = NULL;
^~~
asn2gnb1.c:5807:40: 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:255:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb1.c:6951:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb1.c:6930:20: 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:255:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb1.c:7072:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb1.c: In function 'asn2gnbk_cleanup':
asn2gnb1.c:7118:21: warning: variable 'iasp' set but not used [-Wunused-but-set-variable]
IntAsn2gbSectPtr iasp;
^~~~
asn2gnb1.c: In function 'SeqEntryToGnbk':
asn2gnb1.c:7304:22: warning: variable 'userdata' set but not used [-Wunused-but-set-variable]
Pointer userdata = NULL;
^~~~~~~~
asn2gnb1.c:7299:22: 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 -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:184:3: 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:217:11: warning: variable 'ch' set but not used [-Wunused-but-set-variable]
Char ch;
^~
asn2gnb2.c: In function 'AddLocusBlock':
asn2gnb2.c:1361:66: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
} else if ((moltype >= 2 && moltype <= 8) || moltype >= 10 && moltype <= 11) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
asn2gnb2.c: In function 'IsSuccessor':
asn2gnb2.c:1742:15: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (accp != '\0' && prevp != '\0') {
^~
asn2gnb2.c:1742:10: note: did you mean to dereference the pointer?
while (accp != '\0' && prevp != '\0') {
^
asn2gnb2.c:1742:34: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (accp != '\0' && prevp != '\0') {
^~
asn2gnb2.c:1742:28: note: did you mean to dereference the pointer?
while (accp != '\0' && prevp != '\0') {
^
asn2gnb2.c: In function 'IsProjectAccn':
asn2gnb2.c:1767:38: warning: comparison between pointer and zero character constant [-Wpointer-compare]
for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr); ++ptr, ++letters) continue;
^~
asn2gnb2.c:1767:34: note: did you mean to dereference the pointer?
for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr); ++ptr, ++letters) continue;
^
asn2gnb2.c: In function 'AddDblinkBlock':
asn2gnb2.c:2892:22: warning: variable 'parentID' set but not used [-Wunused-but-set-variable]
Int4 parentID;
^~~~~~~~
asn2gnb2.c: In function 'AddSPBlock':
asn2gnb2.c:3409:14: warning: implicit declaration of function 'PrintDate'; did you mean 'truncate'? [-Wimplicit-function-declaration]
string = PrintDate (spb->created);
^~~~~~~~~
truncate
asn2gnb2.c:3409:12: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
string = PrintDate (spb->created);
^
asn2gnb2.c:3417:12: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
string = PrintDate (spb->sequpd);
^
asn2gnb2.c:3424:12: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
string = PrintDate (spb->annotupd);
^
asn2gnb2.c: In function 'AddSourceOrganismBlock':
asn2gnb2.c:5056:22: warning: variable 'common' set but not used [-Wunused-but-set-variable]
CharPtr common;
^~~~~~
asn2gnb2.c: In function 'GetRefsOnBioseq':
asn2gnb2.c:5893:22: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
asn2gnb2.c:5890:22: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb2.c:5884:22: warning: variable 'right' set but not used [-Wunused-but-set-variable]
Int4 right;
^~~~~
asn2gnb2.c:5878:22: warning: variable 'left' set but not used [-Wunused-but-set-variable]
Int4 left;
^~~~
asn2gnb2.c: In function 'AddLocusBlock':
asn2gnb2.c:244:25: warning: '%0*d' directive writing between 1 and 32768 bytes into a region of size 4 [-Wformat-overflow=]
sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg);
^~~~
asn2gnb2.c:244:23: note: directive argument in the range [0, 65535]
sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg);
^~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 3 and 32770 bytes into a destination of size 5
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:246:24: warning: '%0*d' directive writing between 1 and 32768 bytes into a region of size 5 [-Wformat-overflow=]
sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg);
^~~~
asn2gnb2.c:246:23: note: directive argument in the range [0, 65535]
sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg);
^~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 32769 bytes into a destination of size 5
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:1514:48: warning: '" title="Jump to the comment section of this record">Comment</a></li>' directive writing 69 bytes into a region of size between 66 and 106 [-Wformat-overflow=]
sprintf (sect, "<li><a href=\"#comment_%s\" title=\"Jump to the comment section of this record\">Comment</a></li>",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 92 and 132 bytes into a destination of size 128
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:1518:46: warning: '" title="Jump to the feature table of this record">Features</a></li>' directive writing 68 bytes into a region of size between 66 and 106 [-Wformat-overflow=]
sprintf (sect, "<li><a href=\"#feature_%s\" title=\"Jump to the feature table of this record\">Features</a></li>",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 91 and 131 bytes into a destination of size 128
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:1527:117: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (sect, "<li><a href=\"#genome_%s\" title=\"Jump to the genome section of this record\">Genome</a></li>",
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 89 and 129 bytes into a destination of size 128
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:1532:117: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (sect, "<li><a href=\"#contig_%s\" title=\"Jump to the contig section of this record\">Contig</a></li>",
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from asn2gnb2.c:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 89 and 129 bytes into a destination of size 128
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:796:22: warning: variable 'urf' set but not used [-Wunused-but-set-variable]
UserFieldPtr ufp, urf = NULL;
^~~
asn2gnb3.c: In function 'AddCommentBlock':
asn2gnb3.c:2656:22: warning: variable 'is_wgs' set but not used [-Wunused-but-set-variable]
Boolean is_wgs = FALSE;
^~~~~~
asn2gnb3.c: In function 'GetSourcesOnBioseq':
asn2gnb3.c:5472:22: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
asn2gnb3.c:5470:22: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start;
^~~~~
asn2gnb3.c:5468:22: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb3.c: In function 'AddSourceFeatBlock':
asn2gnb3.c:5989:22: warning: unused variable 'sip' [-Wunused-variable]
SeqIdPtr sip;
^~~
asn2gnb3.c: In function 'GetFeatsOnCdsProduct':
asn2gnb3.c:6446:22: warning: variable 'isRefSeq' set but not used [-Wunused-but-set-variable]
Boolean isRefSeq;
^~~~~~~~
asn2gnb3.c: In function 'GetRemoteFeatsOnCdsProduct':
asn2gnb3.c:6595:20: warning: variable 'lastsfp' set but not used [-Wunused-but-set-variable]
SeqFeatPtr lastsfp;
^~~~~~~
asn2gnb3.c:6594:20: warning: variable 'lastsap' set but not used [-Wunused-but-set-variable]
SeqAnnotPtr lastsap;
^~~~~~~
asn2gnb3.c:6593:20: warning: variable 'lastright' set but not used [-Wunused-but-set-variable]
Int4 lastright;
^~~~~~~~~
asn2gnb3.c:6592:20: warning: variable 'lastleft' set but not used [-Wunused-but-set-variable]
Int4 lastleft;
^~~~~~~~
asn2gnb3.c:6591:20: warning: variable 'isRefSeq' set but not used [-Wunused-but-set-variable]
Boolean isRefSeq;
^~~~~~~~
asn2gnb3.c: In function 'GetFeatsOnBioseq':
asn2gnb3.c:6895:22: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start;
^~~~~
asn2gnb3.c:6866:22: 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));
^~~~~~~~~~~~~~~
asn2gnb3.c:1582:16: warning: 'nsWGSGapsString' defined but not used [-Wunused-variable]
static CharPtr nsWGSGapsString = "The strings of n's in this record represent gaps between contigs or uncallable bases.";
^~~~~~~~~~~~~~~
asn2gnb3.c:1581:16: warning: 'nsAreGapsString' defined but not used [-Wunused-variable]
static CharPtr nsAreGapsString = "The strings of n's in this record represent gaps between contigs, and the length of each string corresponds to the length of the gap.";
^~~~~~~~~~~~~~~
asn2gnb3.c: In function 'AddCommentBlock':
asn2gnb3.c:3429:29: warning: 'nm' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (IS_protdb_accession (nm)) {
^~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:3723:50: warning: "/*" within comment [-Wcomment]
StringChr (str + 1, '(') == NULL /* && StringChr (str, ',') != NULL */) {
asn2gnb4.c:3101:24: warning: variable 'split' set but not used [-Wunused-but-set-variable]
Boolean split;
^~~~~
asn2gnb4.c:3042:24: warning: variable 'at_end' set but not used [-Wunused-but-set-variable]
Boolean at_end = FALSE;
^~~~~~
asn2gnb4.c: In function 'FF_asn2gb_www_featkey_Ex':
asn2gnb4.c:5325:16: warning: variable 'prefix' set but not used [-Wunused-but-set-variable]
CharPtr prefix = "?";
^~~~~~
asn2gnb4.c: In function 'FormatFeatureBlockEx':
asn2gnb4.c:6572:22: 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:255:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb4.c:8796:19: note: in expansion of macro 'MAX'
max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
^~~
asn2gnb4.c: In function 'FormatFeatureQuals':
../include/ncbistd.h:255:22: warning: comparison between 'enum <anonymous>' and 'enum <anonymous>' [-Wenum-compare]
#define MAX(a,b) ((a)>=(b)?(a):(b))
^
asn2gnb4.c:8869:19: 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:7695:24: 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 -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:184:3: 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:2108:16: 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 -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:184:3: 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:2546:27: 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:5701:20: warning: variable 'dspnext' set but not used [-Wunused-but-set-variable]
DeltaSeqPtr dspnext;
^~~~~~~
asn2gnb6.c: In function 'ProcessGapSpecialFormat':
asn2gnb6.c:6041:13: warning: unused variable 'sip' [-Wunused-variable]
SeqIdPtr sip;
^~~
asn2gnb6.c: In function 'FormatSequenceBlock':
asn2gnb6.c:6168:21: 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));
^~~~~~~~~~~~~~~
asn2gnb6.c:76:16: warning: 'link_lat_lon' defined but not used [-Wunused-variable]
static CharPtr link_lat_lon = "https://www.ncbi.nlm.nih.gov/projects/Sequin/latlonview.html?";
^~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -D_PNG -I../include -DWIN_MOTIF gbfeat.c
gbfeat.c: In function 'CkLabelType':
gbfeat.c:1465:33: 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 -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 -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:102:
/usr/include/features.h:184:3: 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:2134:24: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (*current_col != '\0')
^
gbparint.c: In function 'Nlm_gbparselex_ver':
gbparint.c:2520:24: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
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 -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] = {
^
"Ala", 'A',
{ }
"Asx", 'B',
{ }
"Cys", 'C',
{ }
"Asp", 'D',
{ }
"Glu", 'E',
{ }
"Phe", 'F',
{ }
"Gly", 'G',
{ }
"His", 'H',
{ }
"Ile", 'I',
{ }
"Xle", 'J', /* was - notice no 'J', breaks naive meaning of index -Karl */
{ }
"Lys", 'K',
{ }
"Leu", 'L',
{ }
"Met", 'M',
{ }
"Asn", 'N',
{ }
"Pyl", 'O', /* was - no 'O' */
{ }
"Pro", 'P',
{ }
"Gln", 'Q',
{ }
"Arg", 'R',
{ }
"Ser", 'S',
{ }
"Thr", 'T',
{ }
"Val", 'V',
{ }
"Trp", 'W',
{ }
"Sec", 'U', /* was - not in iupacaa */
{ }
"Xxx", 'X',
{ }
"Tyr", 'Y',
{ }
"Glx", 'Z',
{ }
"TERM", '*', /* not in iupacaa */ /*changed by Tatiana 06.07.95?`*/
{ }
"OTHER", 'X'};
{ }
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:48,
from ffprint.c:127:
/usr/include/features.h:184:3: 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:50,
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 -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:184:3: 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:50,
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";
^~~~~~~~~~~
wprint.c: In function 'PrintDate':
wprint.c:188:20: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(day, "%d", (int) (date -> data[3] ));
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from wprint.c:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 4 bytes into a destination of size 3
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
wprint.c: In function 'www_db_xref':
wprint.c:969:20: warning: '%d' directive writing between 1 and 6 bytes into a region of size between 4 and 9 [-Wformat-overflow=]
sprintf(id, "%d%d", id1, id2);
^~
wprint.c:969:17: note: directive argument in the range [-32768, 32767]
sprintf(id, "%d%d", id1, id2);
^~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from wprint.c:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 3 and 13 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:184:3: 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 -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:53:
/usr/include/features.h:184:3: 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:311:13: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
seqmgr.c: In function 'ClearBioseqFindCache':
seqmgr.c:897:14: 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 were 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:5657:14: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
SeqLocPtr prev, tmp;
^~~~
seqmgr.c: In function 'SeqEntryAsnOut':
seqmgr.c:11799:41: warning: variable 'aopp_desc' set but not used [-Wunused-but-set-variable]
AsnOptionPtr aopp_feat = NULL, aopp_desc = NULL;
^~~~~~~~~
seqmgr.c:11799:23: 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:63:
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));
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 were 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 were 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 -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:169,
from gather.c:44:
/usr/include/features.h:184:3: 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:4827:30: 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)));
^
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:169,
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:2280:11: 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:2280:12: 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:2470:58: 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:2218:10: warning: 'mag_val' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 mag_val; /*the magnification value */
^~~~~~~
gather.c: In function 'GatherBioseqFunc':
gather.c:3307:53: warning: 'tlen' may be used uninitialized in this function [-Wmaybe-uninitialized]
rdp->right = offset + tlen - 1;
~~~~~~~^~~~~~
gather.c:3280:39: warning: 'trunc_r' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (trunc_r)
^
gather.c:3285:40: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 'coll_align_data':
jzcoll.c:2631:20: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf(buf, "%d", gilist->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~~~~
%lld
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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:4463:23: 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:6981:27: warning: variable 'does_match' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE, does_match, do_remove;
^~~~~~~~~~
macroapi.c: In function 'ParseCodonsRecognizedFromCommaDelimitedList':
macroapi.c:7726:41: warning: pointer targets in passing argument 1 of 'ExpandWobbleCodon' differ in signedness [-Wpointer-sign]
wobble_list = ExpandWobbleCodon(codon);
^~~~~
macroapi.c:7636:19: note: expected 'Nlm_CharPtr {aka char *}' but argument is of type 'Nlm_Uint1 * {aka unsigned char *}'
static ValNodePtr ExpandWobbleCodon (CharPtr codon)
^~~~~~~~~~~~~~~~~
macroapi.c: In function 'GetQualFromFeatureAnyType':
macroapi.c:8537:8: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (str == NULL
~~~~~~~~~~~
&& (field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_pseudo)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:8681:23: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", vnp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'SetNameInPrimerList':
macroapi.c:10682:21: warning: variable 'prev_pp' set but not used [-Wunused-but-set-variable]
PCRPrimerPtr pp, prev_pp = NULL;
^~~~~~~
macroapi.c: In function 'SetSeqInPrimerList':
macroapi.c:10703:21: warning: variable 'prev_pp' set but not used [-Wunused-but-set-variable]
PCRPrimerPtr pp, prev_pp = NULL;
^~~~~~~
macroapi.c: In function 'GetGenomeProjectIdFromBioseq':
macroapi.c:12881:27: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", ufp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'RemoveGenomeProjectIdFromBioseq':
macroapi.c:12916:27: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", ufp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'SetGenomeProjectIdOnBioseq':
macroapi.c:12957:27: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", ufp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'GetPubFieldFromPub':
macroapi.c:15043:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (str, "%d", the_pub->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'GetCitListsForSeqEntry':
macroapi.c:15825:19: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
macroapi.c:15823:19: warning: variable 'okay' set but not used [-Wunused-but-set-variable]
Boolean okay;
^~~~
macroapi.c: In function 'GetPubclassQualFromPub':
macroapi.c:18324:11: warning: unused variable 'str' [-Wunused-variable]
CharPtr str = NULL;
^~~
macroapi.c: In function 'GetPubMLStatus':
macroapi.c:18681:14: warning: variable 'csp' set but not used [-Wunused-but-set-variable]
CitSubPtr csp;
^~~
macroapi.c: In function 'CollectDBLinkObjectsForApply':
macroapi.c:20029:72: warning: unused variable 'tmp_tail' [-Wunused-variable]
ValNodePtr target_list = NULL, bsp_list = NULL, tmp_list = NULL, tmp_tail = NULL, vnp;
^~~~~~~~
macroapi.c:20029:55: warning: unused variable 'tmp_list' [-Wunused-variable]
ValNodePtr target_list = NULL, bsp_list = NULL, tmp_list = NULL, tmp_tail = NULL, vnp;
^~~~~~~~
macroapi.c: In function 'DoConvertActionToObjectListEx':
macroapi.c:20844:20: warning: unused variable 'already_added' [-Wunused-variable]
Boolean already_added, field_change;
^~~~~~~~~~~~~
macroapi.c: In function 'ApplyPartial5SetActionToSeqFeat':
macroapi.c:25749:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'ApplyPartial3SetActionToSeqFeat':
macroapi.c:25872:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'ApplyPartialBothSetActionToSeqFeat':
macroapi.c:25939:16: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
macroapi.c: In function 'FindPosBeforeFeat':
macroapi.c:26236:15: warning: variable 'regulator' set but not used [-Wunused-but-set-variable]
SeqFeatPtr regulator = NULL, candidate;
^~~~~~~~~
macroapi.c: In function 'PerformAutofixInSeqEntry':
macroapi.c:29471:8: warning: unused variable 'num_created' [-Wunused-variable]
Int4 num_created = 0;
^~~~~~~~~~~
macroapi.c: In function 'AddFileDescriptors':
macroapi.c:29871:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (sdp = SeqDescAsnRead (aip, NULL)) {
^~~
macroapi.c: In function 'ApplyMacroToSeqEntryExEx':
macroapi.c:31907:28: warning: too many arguments for format [-Wformat-extra-args]
fprintf (log_fp, "Instantiated protein titles\n", num);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'PreprocessAddDescriptorListMacro':
macroapi.c:32020:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (sdp = SeqDescAsnRead (aip, NULL)) {
^~~
macroapi.c: In function 'FieldTypeFromString':
macroapi.c:32370:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if (ft == NULL && StringsAreEquivalent(str, "location") || StringsAreEquivalent(str, "genome")) {
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'SummarizeRemoveOutsideAction':
macroapi.c:32939:11: warning: unused variable 'case_insensitive' [-Wunused-variable]
CharPtr case_insensitive = " (case insensitive)";
^~~~~~~~~~~~~~~~
macroapi.c: In function 'GetObjectTableForTabTable':
macroapi.c:37508:63: 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 'FormatMultipleDestinationErrorMessage':
macroapi.c:37987:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", vnp->data.intvalue + 1);
~^ ~~~~~~~~~~~~~~~~~~~~~~
%lld
macroapi.c: In function 'CheckObjTableForExistingText':
macroapi.c:38084:14: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
macroapi.c: In function 'FixSuspectProductNamesInEntrezGene':
macroapi.c:40352:18: warning: variable 'prefix' set but not used [-Wunused-but-set-variable]
CharPtr prefix = NULL;
^~~~~~
In file included from ../include/tax3api.h:51:0,
from macroapi.c:67:
macroapi.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));
^~~~~~~~~~~~~~~~~~~
macroapi.c:37233:16: warning: 'IsFieldTypeProteinDesc' defined but not used [-Wunused-function]
static Boolean IsFieldTypeProteinDesc (FieldTypePtr ft)
^~~~~~~~~~~~~~~~~~~~~~
macroapi.c:27097:13: warning: 'GetDescriptorTypeFromDescriptorChoice' defined but not used [-Wunused-function]
static Int4 GetDescriptorTypeFromDescriptorChoice (Uint1 descriptor_choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:21298:13: warning: 'GetFieldsFromAECR' defined but not used [-Wunused-function]
static void GetFieldsFromAECR (AECRActionPtr act, FieldTypePtr PNTR pField, ValNodePtr PNTR pFieldPair)
^~~~~~~~~~~~~~~~~
macroapi.c:20787:16: warning: 'NoFieldChange' defined but not used [-Wunused-function]
static Boolean NoFieldChange (CharPtr new_val, ValNodePtr vnp, FieldTypePtr field_from, StringConstraintPtr scp, BatchExtraPtr batch_extra)
^~~~~~~~~~~~~
macroapi.c:16014:13: warning: 'InitBatchExtraForAECRActionAndObjectList' defined but not used [-Wunused-function]
static void InitBatchExtraForAECRActionAndObjectList (BatchExtraPtr batch_extra, AECRActionPtr action, ValNodePtr object_list)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:10389:16: warning: 'HasMultiplePrimerSets' defined but not used [-Wunused-function]
static Boolean HasMultiplePrimerSets (CharPtr value)
^~~~~~~~~~~~~~~~~~~~~
macroapi.c:5482:16: warning: 'DoesLocationMatchConstraint' defined but not used [-Wunused-function]
static Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:4590:13: warning: 'TestAdvancedStringMatch' defined but not used [-Wunused-function]
static void TestAdvancedStringMatch (void)
^~~~~~~~~~~~~~~~~~~~~~~
macroapi.c:2806:13: warning: 'OriginFromOriginName' defined but not used [-Wunused-function]
static Int4 OriginFromOriginName (CharPtr origin_name)
^~~~~~~~~~~~~~~~~~~~
macroapi.c:1200:16: warning: 'IsObjectAppropriateForFieldPair' defined but not used [-Wunused-function]
static Boolean IsObjectAppropriateForFieldPair (Uint1 choice, Pointer data, FieldPairTypePtr fieldpair)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'GetSourceQualFromBioSource':
macroapi.c:11026:25: warning: 'subfield' may be used uninitialized in this function [-Wmaybe-uninitialized]
str = GetThreeFieldSubfield (ssp->name, subfield);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'GetMultipleSourceQualsFromBioSource':
macroapi.c:11174:23: warning: 'subfield' may be used uninitialized in this function [-Wmaybe-uninitialized]
str = GetThreeFieldSubfield (ssp->name, subfield);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'RemoveSourceQualFromBioSource':
macroapi.c:11278:50: warning: 'subfield' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 orgmod_subtype = -1, subsrc_subtype = -1, subfield;
^~~~~~~~
macroapi.c: In function 'ReadNameListFromString':
macroapi.c:14037:14: warning: 'ch_r1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*p_repl1 = ch_r1;
~~~~~~~~~^~~~~~~
macroapi.c:13946:11: note: 'ch_r1' was declared here
Char ch_r1, ch_r2, ch_r3;
^~~~~
macroapi.c: In function 'SetAuthorListFromString':
macroapi.c:14298:17: warning: 'vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
name_list = FreeNameList (1, vnp);
^~~~~~~~~~~~~~~~~~~~~
macroapi.c: In function 'AlsoChangeMrnaForObject':
macroapi.c:20637:10: warning: 'mrna' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (mrna != NULL) {
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:363:33: warning: 'spp_1' may be used uninitialized in this function [-Wmaybe-uninitialized]
res_1 = SeqPortGetResidue(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 -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:184:3: 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 -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:184:3: 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 were 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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:1662:29: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j=0; j < numseg*dim && strandp!=NULL; j++, strandp++)
~~~~~~^~~~
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 -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:184:3: 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 'prot_to_rputprot':
salstruc.c:734:18: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (strptmp == '\0') break;
^~
salstruc.c:734:10: note: did you mean to dereference the pointer?
if (strptmp == '\0') break;
^
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 'data_collect_arrange':
salstruc.c:920:20: warning: 'entityID' may be used uninitialized in this function [-Wmaybe-uninitialized]
bspssp = new_seledstruct (entityID, itemID, OBJ_(tdp->feattype), 0,itemID,
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
from + adp->bufferstart, to + adp->bufferstart,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bspsip, Seq_strand_plus, TRUE, NULL, (Pointer) tdp, 0, 1);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:184:3: 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' [-Wdangling-else]
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:753:19: warning: 'PosFeat' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 BeginLines=0,PosFeat,StartLetter,StopLetter;
^~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -D_PNG -I../include -DWIN_MOTIF pgppop.c
pgppop.c:58:2: warning: missing braces around initializer [-Wmissing-braces]
{
^
pgppop.c:60:4:
255, 255, 255, /* default 0 0xffffff - */
{ }
255, 00, 153, /* hotpink 1 0xff1493 0xff0099 */
{ }
255, 0, 255, /* magenta 2 0xff00ff - */
{ }
153, 51, 255, /* purple 3 0x9b30ff 0x9933ff */
{ }
0, 0, 255, /* blue 4 0x0000ff - */
{ }
00, 153, 255, /* sky 5 0x1e90ff 0x0099ff */
{ }
0, 255, 255, /* cyan 6 0x00ffff - */
{ }
0, 255, 153, /* sea 7 0x00ff8f 0x00ff99 */
{ }
0, 255, 0, /* green 8 0x00ff00 - */
{ }
255, 255, 0, /* yellow 9 0xffff00 - */
{ }
255, 204, 0, /* gold 10 0xffa500 0xffcc00 */
{ }
255, 102, 0, /* orange 11 0xff4500 0xff6600 */
{ }
255, 0, 0, /* red 12 0xff0000 - */
{ }
255, 153, 153, /* pink 13 0xff7256 0xff9999 */
{ }
255, 204, 204, /* pinktint 14 0xffaeb9 0xffcccc */
{ }
255, 255, 255, /* white 15 0xffffff -*/
{ }
0, 0, 0, /* black 16 0x000000 - */
{ }
204, 204, 255, /* bluetint 17 0xb0e2ff - 0xccccff*/
{ }
153, 255, 153, /* greentint 18 0x9aff9a - 0x99ff99 */
{ }
255, 255, 153, /* yellowtint 19 0xffec8b - 0xffff99 */
{ }
102, 102, 102, /* gray 20 0x7d7d7d 0x666666 */
{ }
153, 102, 51, /* brown 21 0x8b5742 01x996633 */
{ }
255, 0, 0, /* perm colors 22: red 0xff0000 - */
{ }
0, 255, 0, /* perm colors 23: green 0x00ff00 - */
{ }
255, 0, 255, /* perm colors 24: magenta 0xff00ff - */
{ }
00, 153, 255, /* perm colors 25: sky 0x1e90ff 0x0099ff */
{ }
153, 51, 255, /* perm colors 26: purple 0x9b30ff 0x9933ff */
{ }
0, 255, 0, /* SS colors 27: helix, green 0x00ff00 - */
{ }
255, 204, 0, /* SS colors 28: strand, gold 0xffa500 0xffcc00 */
{ }
255, 102, 0, /* SS colors 29: turn, orange 0xff4500 0xff6600 */
{ }
0, 255, 255, /* SS colors 30: coil, cyan ox00ffff - */
{ }
255, 255, 0, /* highlight colors 31: yellow 0xffff00 - */
{ }
0, 0, 0 /* background colors 32: black 0x000000 - */
{
};
}
pgppop.c: In function 'DDV_WWW_get_CDS_minus':
pgppop.c:329:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
pgppop.c:327:5: warning: variable 'numivals2' set but not used [-Wunused-but-set-variable]
numivals2=0;
^~~~~~~~~
pgppop.c: In function 'DDV_WWW_get_CDS_plus':
pgppop.c:451:9: warning: variable 'bGiForProductOk' set but not used [-Wunused-but-set-variable]
Boolean bGiForProductOk=FALSE;
^~~~~~~~~~~~~~~
pgppop.c: In function 'DDV_DisplayTopScale':
pgppop.c:1300:7: warning: unused variable 'szBlank' [-Wunused-variable]
Char szBlank[TABLE_LEFT_MARGIN+5]={""};
^~~~~~~
pgppop.c: In function 'DDV_GetBLASTCompLine_1':
pgppop.c:1736:31: warning: array subscript has type 'char' [-Wchar-subscripts]
if (matrix[s][q]>0){
^
pgppop.c:1736:34: warning: array subscript has type 'char' [-Wchar-subscripts]
if (matrix[s][q]>0){
^
pgppop.c: In function 'DDV_DisplayDefaultAlign':
pgppop.c:3169:13: warning: unused variable 'sabp' [-Wunused-variable]
SABlockPtr sabp=NULL;/*indexed SeqAlign*/
^~~~
pgppop.c: In function 'DDV_ShowSeqAlign':
pgppop.c:3512:10: warning: unused variable 'szPopSetAuth' [-Wunused-variable]
Char szPopSetAuth[INFO_SIZE+1]={""};
^~~~~~~~~~~~
pgppop.c:3510:10: 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:3683:9: 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:49:
pgppop.c: At top level:
../include/objentgene.h:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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: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));
^~~~~~~~~~~~~~~
pgppop.c:2664:13: warning: 'DDV_PrintFastaGappedSequence' defined but not used [-Wunused-function]
static void DDV_PrintFastaGappedSequence(CharPtr szSequence,FILE *fp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pgppop.c:2617:13: warning: 'DDV_GetGappedSequence' defined but not used [-Wunused-function]
static void DDV_GetGappedSequence(SegmentPtr segp,CharPtr szSequence,
^~~~~~~~~~~~~~~~~~~~~
pgppop.c:1841:13: warning: 'DDV_HideMaskedLetters' defined but not used [-Wunused-function]
static void DDV_HideMaskedLetters(CharPtr szSeqMaster,ParaGPtr pgp,ValNodePtr mask)
^~~~~~~~~~~~~~~~~~~~~
pgppop.c:314:13: 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: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";
^~~~~~~~~~~
pgppop.c: In function 'DDV_GetPubValues':
pgppop.c:2873:20: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(szBuf,"%d",year);
^
In file included from /usr/include/stdio.h:862:0,
from pgppop.c:41:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 7 bytes into a destination of size 6
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pgppop.c: In function 'DDV_PopDisplay2':
pgppop.c:997:23: warning: 'pgp2' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (pgp2 && ((pgp2->StopLetter-pgp2->StartLetter+1)>=AbsLengthAli)) {
~~~~^~~~~~~~~~~~
pgppop.c:1004:14: 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 -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:61,
from ../include/samutil.h:230,
from samutil.c:42:
/usr/include/features.h:184:3: 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:796:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((a == NULL) || (b == NULL))
^~
samutil.c:799:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
choice = a->choice;
^~~~~~
samutil.c: In function 'SAM_AlignIdDup':
samutil.c:852:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (oldid == NULL)
^~
samutil.c:855:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
newid = ValNodeNew(NULL);
^~~~~
samutil.c: In function 'DDE_FreeStack':
samutil.c:1556:11: warning: operation on 'Index' may be undefined [-Wsequence-point]
Index = ++Index % DDE_STACK_SIZE;
samutil.c: In function 'DDE_Add':
samutil.c:1611:22: warning: operation on 'pStack->StackMin' may be undefined [-Wsequence-point]
pStack->StackMin = ++pStack->StackMin % DDE_STACK_SIZE;
samutil.c:1622:22: 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:1686:22: 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:1717:22: 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:1984:26: 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:3106:41: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr ptxtList, last_vnp, vnp;
^~~
samutil.c: In function 'DDE_RightAddNode':
samutil.c:3707:33: 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:3757:24: warning: variable 'RetVal2' set but not used [-Wunused-but-set-variable]
Boolean RetVal1, RetVal2, IsLeftAlignedGap, NodeDeleted;
^~~~~~~
samutil.c: In function 'DDE_RightMergeAndAddNodeList':
samutil.c:3813:38: 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:4592:41: 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:5028:22: 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:3143:9: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
return(last_vnp);
^
samutil.c: In function 'DDE_GetNumResidues':
samutil.c:3166:13: 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:42:
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:3137:15: note: 'last_vnp' was declared here
ValNodePtr last_vnp;
^~~~~~~~
samutil.c:3034:15: 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:2685:14: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
tail = DDE_AddMsaTxtNode(tail, GapIndex, GapIndex, TRUE, TRUE, FALSE);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c: In function 'DDE_AddGapToEndOfAllRows':
samutil.c:3118:9: 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:3923:8: 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:2325:13: 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:2854:8: 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:2356:8: 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:4210:8: 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:4210:8: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
msap = (MsaTxtDispPtr) vnp->data.ptrvalue;
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c:3137:15: note: 'last_vnp' was declared here
ValNodePtr last_vnp;
^~~~~~~~
samutil.c: In function 'DDE_ShiftRightBoundaryRight1':
samutil.c:4210:8: warning: 'last_vnp' may be used uninitialized in this function [-Wmaybe-uninitialized]
msap = (MsaTxtDispPtr) vnp->data.ptrvalue;
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samutil.c:3137:15: note: 'last_vnp' was declared here
ValNodePtr last_vnp;
^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:292:4:
255, 255, 255, /* default 0 0xffffff - */
{ }
255, 0, 153, /* hotpink 1 0xff1493 0xff0099 */
{ }
255, 0, 255, /* magenta 2 0xff00ff - */
{ }
153, 51, 255, /* purple 3 0x9b30ff 0x9933ff */
{ }
0, 0, 255, /* blue 4 0x0000ff - */
{ }
00, 153, 255, /* sky 5 0x1e90ff 0x0099ff */
{ }
0, 255, 255, /* cyan 6 0x00ffff - */
{ }
0, 255, 153, /* sea 7 0x00ff8f 0x00ff99 */
{ }
0, 192, 0, /* green 8 0x00ff00 - */
{ }
255, 255, 0, /* yellow 9 0xffff00 - */
{ }
255, 204, 0, /* gold 10 0xffa500 0xffcc00 */
{ }
255, 102, 0, /* orange 11 0xff4500 0xff6600 */
{ }
255, 0, 0, /* red 12 0xff0000 - */
{ }
255, 153, 153, /* pink 13 0xff7256 0xff9999 */
{ }
255, 204, 204, /* pinktint 14 0xffaeb9 0xffcccc */
{ }
255, 255, 255, /* white 15 0xffffff -*/
{ }
0, 0, 0, /* black 16 0x000000 - */
{ }
204, 204, 255, /* bluetint 17 0xb0e2ff - 0xccccff*/
{ }
153, 255, 153, /* greentint 18 0x9aff9a - 0x99ff99 */
{ }
255, 255, 153, /* yellowtint 19 0xffec8b - 0xffff99 */
{ }
102, 102, 102, /* gray 20 0x7d7d7d 0x666666 */
{ }
153, 102, 51, /* brown 21 0x8b5742 01x996633 */
{ }
255, 0, 0, /* perm colors 22: red 0xff0000 - */
{ }
0, 255, 0, /* perm colors 23: green 0x00ff00 - */
{ }
255, 0, 255, /* perm colors 24: magenta 0xff00ff - */
{ }
00, 153, 255, /* perm colors 25: sky 0x1e90ff 0x0099ff */
{ }
153, 51, 255, /* perm colors 26: purple 0x9b30ff 0x9933ff */
{ }
0, 255, 0, /* SS colors 27: helix, green 0x00ff00 - */
{ }
255, 204, 0, /* SS colors 28: strand, gold 0xffa500 0xffcc00 */
{ }
255, 102, 0, /* SS colors 29: turn, orange 0xff4500 0xff6600 */
{ }
0, 255, 255, /* SS colors 30: coil, cyan ox00ffff - */
{ }
255, 255, 0, /* highlight colors 31: yellow 0xffff00 - */
{ }
0, 0, 0 /* background colors 32: black 0x000000 - */
{
};
}
ddvcreate.c: In function 'DDV_CreateDisplayFromIndex_1':
ddvcreate.c:493:17: 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:779:17: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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: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:1141:11: warning: 'halfBspLengthSeqL' may be used uninitialized in this function [-Wmaybe-uninitialized]
ubd->from=Start;
~~~~~~~~~^~~~~~
ddvcreate.c:1158:6: note: 'halfBspLengthSeqL' was declared here
Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
^~~~~~~~~~~~~~~~~
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: 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 -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:184:3: 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 -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:184:3: 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 -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:41:
/usr/include/features.h:184:3: 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:188:13: warning: variable 'hasLinkout' set but not used [-Wunused-but-set-variable]
Boolean hasLinkout=FALSE;
^~~~~~~~~~
txalign.c: In function 'addLinkoutForBioseq':
txalign.c:256:13: warning: variable 'hasLinkout' set but not used [-Wunused-but-set-variable]
Boolean hasLinkout=FALSE;
^~~~~~~~~~
txalign.c: In function 'DrawTextToBuffer':
txalign.c:1254:88: warning: format '%d' expects argument of type 'int', but argument 4 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
snprintf(checkboxBuf, 200, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%d\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%d', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb);
~^ ~~~~~~~~~~~~~~~~~~
%lld
txalign.c: In function 'load_align_sum_for_StdSeg':
txalign.c:2230:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (bsp = BioseqLockById(SeqLocId(ssp->loc->next))) {
^~~
txalign.c: In function 'ShowAlignNodeText2Ex':
txalign.c:3030:13: 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:4079:7: warning: unused variable 'seqid_length' [-Wunused-variable]
Int4 seqid_length = 0, total_length = 0;
^~~~~~~~~~~~
txalign.c: In function 'PrintDefLinesFromSeqAlignWithPath':
txalign.c:4494:39: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
} else if (bestid != NULL && !(options & TXALIGN_NO_DUMPGNL) || (options & TXALIGN_NO_ENTREZ))
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
txalign.c:4498:33: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (bsp = BioseqLockById(bestid)) {
^~~
txalign.c:4200:10: warning: unused variable 'ColumnDistance' [-Wunused-variable]
Int2 ColumnDistance=2, extraSpace=0, extraSpace2=0, strLen=0, maxEvalWidth=5, maxNWidth=2;
^~~~~~~~~~~~~~
txalign.c:4192:43: warning: unused variable 'sip_list' [-Wunused-variable]
SeqIdPtr bestid, gi_list, subject_id, sip_list=NULL, last_id;
^~~~~~~~
txalign.c:4188:17: 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:4817:25: warning: unused variable 't_adj' [-Wunused-variable]
Int4 m_adj = 0, t_adj = 0;
^~~~~
txalign.c:4816:29: warning: unused variable 'last_t_to' [-Wunused-variable]
Int4 last_m_to = 0, last_t_to = 0;
^~~~~~~~~
txalign.c: In function 'FSFPrintOneDefline':
txalign.c:4925:14: warning: variable 'seqid_len' set but not used [-Wunused-but-set-variable]
Int4 gi, seqid_len = 0;
^~~~~~~~~
txalign.c: In function 'FormatScoreFunc':
txalign.c:5142:13: warning: variable 'allocated' set but not used [-Wunused-but-set-variable]
Boolean allocated, first;
^~~~~~~~~
txalign.c: In function 'OOFShowSingleAlignment':
txalign.c:5808:27: warning: array subscript has type 'char' [-Wchar-subscripts]
else if(matrix[line1[line_index]][line2[line_index]] > 0)
^
txalign.c:5808:46: warning: array subscript has type 'char' [-Wchar-subscripts]
else if(matrix[line1[line_index]][line2[line_index]] > 0)
^
txalign.c:5575:13: 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:6063:33: warning: unused variable 'st' [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:6063:9: warning: unused variable 'tmp' [-Wunused-variable]
tmp[10] = " ", *st;
^~~
txalign.c: In function 'OOFDisplayTraceBack2':
txalign.c:6137:33: warning: unused variable 'st' [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c: In function 'FDGetTaxNamesFromBioseq':
txalign.c:6239:21: warning: variable 'bdsp' set but not used [-Wunused-but-set-variable]
BlastDefLinePtr bdsp;
^~~~
txalign.c: At top level:
txalign.c:310:19: 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:6137:33: warning: 'st' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:6063:9: warning: 'tmp' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~~
txalign.c:6063:33: warning: 'st' defined but not used [-Wunused-variable]
tmp[10] = " ", *st;
^~
txalign.c:2915:1: warning: 'get_seq_id' defined but not used [-Wunused-function]
get_seq_id(SeqAlignPtr sap, Int2 index)
^~~~~~~~~~
txalign.c:1820:16: warning: 'has_hit_in_region' defined but not used [-Wunused-function]
static Boolean has_hit_in_region(Uint1Ptr all_frame)
^~~~~~~~~~~~~~~~~
txalign.c:112:16: 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:41:
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:1094:10: note: 'HTML_buffer' was declared here
CharPtr HTML_buffer;
^~~~~~~~~~~
txalign.c: In function 'OOFShowSingleAlignment.isra.15':
txalign.c:73:17: warning: 'dna_line_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define fprintf tx_fprintf
^~~~~~~~~~
txalign.c:5571:32: note: 'dna_line_start' was declared here
Int4 dna_index, pro_index, dna_line_start, pro_line_start;
^~~~~~~~~~~~~~
txalign.c:73:17: warning: 'pro_line_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define fprintf tx_fprintf
^~~~~~~~~~
txalign.c:5571:48: note: 'pro_line_start' was declared here
Int4 dna_index, pro_index, dna_line_start, pro_line_start;
^~~~~~~~~~~~~~
txalign.c: In function 'find_score_in_align':
txalign.c:2080:33: warning: 'smtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
stdaa_res = SeqMapTableConvert(smtp, t_res);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
txalign.c:1980:20: note: 'smtp' was declared here
SeqMapTablePtr smtp;
^~~~
txalign.c:1945:13: warning: 't_spp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqPortFree(t_spp);
^~~~~~~~~~~~~~~~~~
txalign.c:1876:23: note: 't_spp' was declared here
SeqPortPtr m_spp, t_spp;
^~~~~
txalign.c:1942:11: warning: 'm_spp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(m_spp == NULL)
^
txalign.c:1876:16: note: 'm_spp' was declared here
SeqPortPtr m_spp, t_spp;
^~~~~
txalign.c: In function 'ShowAlignNodeText2Ex.isra.16':
txalign.c:3025:10: warning: 'm_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 m_len; /*length of the master sequence*/
^~~~~
txalign.c: In function 'ShowTextAlignFromAnnot3':
txalign.c:949:12: 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 -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:184:3: 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 -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:242:
/usr/include/features.h:184:3: 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:885:13: warning: statement with no effect [-Wunused-value]
for (j; j<dsp->numseg && next == -1; j++)
^~~
alignmgr2.c: In function 'AlnMgr2CopySeg':
alignmgr2.c:2984:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (ldelta = ABS(s->beg - beg)) {
^~~~~~
alignmgr2.c: In function 'AlnMgr2AddInNewPairwiseSA':
alignmgr2.c:3221:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (a = AlnMgr2GetNextSeqPiece(a)) {
^
alignmgr2.c:3223:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (b = AlnMgr2GetNextLimitedSeqPiece(b, a)) {
^
alignmgr2.c:3233:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (A = AlnMgr2GetNextSeqPiece(A)) {
^
alignmgr2.c:3237:14: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (B = AlnMgr2GetNextLimitedSeqPiece(B, A)) {};
^
alignmgr2.c: In function 'AlnMgr2SetUnaln':
alignmgr2.c:5410:22: warning: variable 'dsp' set but not used [-Wunused-but-set-variable]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2PrintSeqAlign':
alignmgr2.c:5623:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (more = AlnMgr2GetNextAlnBit(sap, amp))
^~~~
alignmgr2.c: In function 'AlnMgr2GetNextAlnBit':
alignmgr2.c:5719:21: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
alignmgr2.c: In function 'AlnMgr2GetUnalignedInfo':
alignmgr2.c:6085:22: warning: variable 'saip' set but not used [-Wunused-but-set-variable]
SAIndex2Ptr saip;
^~~~
alignmgr2.c: In function 'AlnMgr2GetInterruptInfo':
alignmgr2.c:6331:7: warning: statement with no effect [-Wunused-value]
for (i; i<interrupt->segnum; i++)
^~~
alignmgr2.c: In function 'AlnMgr2GetAlnLength':
alignmgr2.c:6774:20: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (saip->unaln == FALSE || fill_in == FALSE)
^~
alignmgr2.c:6774:8: note: did you mean to dereference the pointer?
if (saip->unaln == FALSE || fill_in == FALSE)
^
alignmgr2.c: In function 'AlnMgr2ComputeScoreForSeqAlign':
alignmgr2.c:8341:17: warning: variable 'numseqs' set but not used [-Wunused-but-set-variable]
Int4 numseqs;
^~~~~~~
alignmgr2.c:8339:17: warning: variable 'mismatch' set but not used [-Wunused-but-set-variable]
Int4 mismatch;
^~~~~~~~
alignmgr2.c:8338:17: 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:242:
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:3557:13: warning: 'AlnMgr2AddInNewSA' defined but not used [-Wunused-function]
static void AlnMgr2AddInNewSA(SeqAlignPtr parent, SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~
alignmgr2.c:2368:18: warning: 'AlnMgr2GetEdgeList' defined but not used [-Wunused-function]
static AMEdgePtr AlnMgr2GetEdgeList(Int4 vertexnum, AMEdgePtr edge_head, AMEdgePtr already_used)
^~~~~~~~~~~~~~~~~~
alignmgr2.c:2140:13: warning: 'AlnMgr2SortVerticesByNumEdges' defined but not used [-Wunused-function]
static void AlnMgr2SortVerticesByNumEdges(AMVertexPtr PNTR vertexarray, Int4 numvertices)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:1061:13: warning: 'AlnMgr2UnpackSeqAlignChain' defined but not used [-Wunused-function]
static void AlnMgr2UnpackSeqAlignChain(SeqAlignPtr sap)
^~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetLongestSeqLoc':
alignmgr2.c:10131:15: warning: 'slp_longest' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqLocPtr slp_longest;
^~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2IndexLite':
alignmgr2.c:1001:33: warning: 'sap_segs_prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap_segs_prev->next = (SeqAlignPtr)(sap_segs->segs);
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:968:17: note: 'sap_segs_prev' was declared here
SeqAlignPtr sap_segs_prev;
^~~~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetUnalignedInfo':
alignmgr2.c:6122:54: 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:7068:23: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (i=0; i<saip->srdp[row]->numunaln && !found; i++)
~~~~^~~~~~
alignmgr2.c:7077:19: 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:6353:16: warning: 'iip' may be used uninitialized in this function [-Wmaybe-uninitialized]
iip->strand = strand;
~~~~~~~~~~~~^~~~~~~~
alignmgr2.c:6157:22: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAIndex2Ptr saip;
^~~~
alignmgr2.c:6337:48: 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:6478:15: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
srdp = saip->srdp[n-1];
~~~~^~~~~~
alignmgr2.c:6449:21: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2GetNthRowSpanInSA':
alignmgr2.c:6550:20: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
*start = saip->aligncoords[i];
~~~~^~~~~~~~~~~~~
alignmgr2.c:6558:41: 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:6789:17: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
len += AlnMgr2GetMaxUnalignedLength(salp, i);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:6780:24: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
lastseg = saip->srdp[saip->anchor-1]->sect[saip->srdp[saip->anchor-1]->numsect-1];
~~~~^~~~~~
alignmgr2.c:6788:20: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
len += dsp->lens[i];
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetNextAlnBit':
alignmgr2.c:6025:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->anchor <= 0)
~~~~^~~~~~~~
alignmgr2.c:6006:17: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
len += dsp->lens[trans[i]];
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2IsSAPDiscAli':
alignmgr2.c:6813:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->numunaln > 0)
~~~~^~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetNumAlnBlocks':
alignmgr2.c:6836:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->numunaln >= 0)
~~~~^~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2GetNthBlockRange':
alignmgr2.c:6870:20: 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:6889:22: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
SAIndex2Ptr saip;
^~~~
alignmgr2.c:6887:22: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2GetNextLengthBit':
alignmgr2.c:7019:26: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxseg = saip->unaln[*seg];
~~~~^~~~~~~
alignmgr2.c:7024:26: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
(*len) += dsp->lens[i];
~~~^~~~~~
alignmgr2.c: In function 'AlnMgr2GetNumSegsInRange':
alignmgr2.c:7185:62: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
start = binary_search_on_uint4_list(aligncoords, from, dsp->numseg);
~~~^~~~~~~~
alignmgr2.c:7150:21: warning: 'aligncoords' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint4Ptr aligncoords;
^~~~~~~~~~~
alignmgr2.c: In function 'AlnMgr2MapBioseqToSeqAlign':
alignmgr2.c:7652:12: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (saip->anchor > 0)
~~~~^~~~~~~~
alignmgr2.c:7590:21: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2MapSeqAlignToBioseq':
alignmgr2.c:7715:11: warning: 'saip' may be used uninitialized in this function [-Wmaybe-uninitialized]
sect = binary_search_on_uint4_list(saip->aligncoords, pos, saip->numseg);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alignmgr2.c:7685:21: warning: 'dsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
DenseSegPtr dsp;
^~~
alignmgr2.c: In function 'AlnMgr2GetSubAlign':
alignmgr2.c:7554:26: warning: 'sap_real' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (sap == NULL || sap->saip == NULL)
~~~^~~~~~
alignmgr2.c:7999:21: note: 'sap_real' was declared here
SeqAlignPtr sap_real;
^~~~~~~~
alignmgr2.c: In function 'AlnMgr2FillInUnaligned':
alignmgr2.c:9869:12: 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 -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 -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 -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 -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:184:3: 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);
^~~~~~~~~~~~~~~~~~~~~~
cdentrez.c: In function 'CdSeqSumAsnRead':
cdentrez.c:3424:34: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (cds, " cds%d", (int) proteins);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 6 and 11 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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[] = {
^
"", 0, 0,
{ }
"hca", MAGIC_hca, FORMAT_hca,
{ }
"sum", MAGIC_sum, FORMAT_sum,
{ }
"lnk", MAGIC_lnk, FORMAT_lnk,
{ }
"ofs", MAGIC_ofs, FORMAT_ofs,
{ }
"oix", MAGIC_oix, FORMAT_oix,
{ }
"trm", MAGIC_trm, FORMAT_trm,
{ }
"tix", MAGIC_tix, FORMAT_tix,
{ }
"pst", MAGIC_pst, FORMAT_pst,
{ }
"inf", MAGIC_inf, FORMAT_inf
{
};
}
cdnewlib.c:614:27: warning: missing braces around initializer [-Wmissing-braces]
struct CdDirInfo _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 '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 -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:184:3: 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 -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:184:3: 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:247:15: warning: statement with no effect [-Wunused-value]
#define FALSE ((Nlm_Boolean)0)
^
../include/ncbifile.h:144:76: 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:247:15: warning: statement with no effect [-Wunused-value]
#define FALSE ((Nlm_Boolean)0)
^
../include/ncbifile.h:145:76: 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:1257:45: warning: 'besttype' may be used uninitialized in this function [-Wmaybe-uninitialized]
besttype->fields[f].num_terms;
~~~~~~~~^~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 were 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 -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:184:3: 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:354:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_RadioCallback':
vibbutns.c:373:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_SetButtonStatus':
vibbutns.c:694:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Nlm_Int2 val;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibfiles.c: In function 'Nlm_CardToStr':
vibfiles.c:715:19: warning: '%*u' directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=]
sprintf (temp, "%*u", length, (int)cardval);
^~~
vibfiles.c:715:18: note: directive argument in the range [0, 65535]
sprintf (temp, "%*u", length, (int)cardval);
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 32769 bytes into a destination of size 80
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vibfiles.c: In function 'Nlm_IntToStr':
vibfiles.c:725:19: warning: '%*d' directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=]
sprintf (temp, "%*d", length, intval);
^~~
vibfiles.c:725:18: note: directive argument in the range [-32768, 32767]
sprintf (temp, "%*d", length, intval);
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 32769 bytes into a destination of size 80
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:164:
/usr/include/features.h:184:3: 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:1121:15: 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 -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:184:3: 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:2006:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2005:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoice':
vibmenus.c:2072:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceGroup':
vibmenus.c:2122:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceItem':
vibmenus.c:2166:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2164:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableMenuItem':
vibmenus.c:2329:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2328:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoice':
vibmenus.c:2395:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoiceItem':
vibmenus.c:2489:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2487:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_RemoveSubMenu':
vibmenus.c:2627:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CountMenuItems':
vibmenus.c:3056:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetMenuItem':
vibmenus.c:3239:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetPopListTitle':
vibmenus.c:3349:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
Nlm_MenU m;
^
vibmenus.c: In function 'Nlm_AppendItems':
vibmenus.c:3978:17: warning: unused variable 'accel' [-Wunused-variable]
Nlm_Char accel;
^~~~~
vibmenus.c: In function 'Nlm_NewPopupList':
vibmenus.c:4969:19: warning: unused variable 'lbl' [-Wunused-variable]
Widget lbl;
^~~
vibmenus.c:4967:19: 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 -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:184:3: 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 -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:135:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:6800:13: warning: unused variable 'retval' [-Wunused-variable]
Nlm_Int2 retval;
^~~~~~
vibwndws.c: In function 'Nlm_RemoveDyingWindows':
vibwndws.c:6922:20: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:4419:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
document.c:4423:7: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -D_PNG -I../include -DWIN_MOTIF shim3d.c
shim3d.c: In function 'Nlm_AddHalfWorm3D':
shim3d.c:3470:46: warning: unused variable 'tmp' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:40: warning: unused variable 'pCz' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:34: warning: unused variable 'pCy' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:28: warning: unused variable 'pCx' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:22: warning: unused variable 'pNz' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:16: warning: unused variable 'pNy' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3470:10: warning: unused variable 'pNx' [-Wunused-variable]
*pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL;
^~~
shim3d.c:3469:47: warning: unused variable 'Cz' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3469:42: warning: unused variable 'Cy' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3469:37: warning: unused variable 'Cx' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3469:32: warning: unused variable 'Nz' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3469:27: warning: unused variable 'Ny' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3469:15: warning: unused variable 'Nx' [-Wunused-variable]
GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz,
^~
shim3d.c:3468:21: warning: unused variable 'pi' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~
shim3d.c:3468:15: warning: unused variable 'sinj' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~~~
shim3d.c:3468:9: warning: unused variable 'cosj' [-Wunused-variable]
cosj, sinj, pi = 3.14159265358979323846;
^~~~
shim3d.c:3467:33: warning: unused variable 'prevlen' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~~~~~~
shim3d.c:3467:29: warning: unused variable 'Vz' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3467:25: warning: unused variable 'Vy' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3467:21: warning: unused variable 'Vx' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3467:17: warning: unused variable 'Hz' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3467:13: warning: unused variable 'Hy' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3467:9: warning: unused variable 'Hx' [-Wunused-variable]
Hx, Hy, Hz, Vx, Vy, Vz, prevlen,
^~
shim3d.c:3466:21: warning: unused variable 'dQtz' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3466:15: warning: unused variable 'dQty' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3466:9: warning: unused variable 'dQtx' [-Wunused-variable]
dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/
^~~~
shim3d.c:3464:14: warning: unused variable 'len' [-Wunused-variable]
GLdouble len, R1x, R1y, R1z, R2x, R2y, R2z, MG[4][3],
^~~
shim3d.c:3463:26: warning: unused variable 'offset' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^~~~~~
shim3d.c:3463:23: warning: unused variable 'm' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^
shim3d.c:3463:20: warning: unused variable 'k' [-Wunused-variable]
Nlm_Int4 i, j, k, m, offset;
^
shim3d.c:3463:17: 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 -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:184:3: 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 -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:184:3: 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:354:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_RadioCallback':
vibbutns.c:373:20: warning: variable 'c' set but not used [-Wunused-but-set-variable]
Nlm_ControlTool c;
^
vibbutns.c: In function 'Nlm_SetButtonStatus':
vibbutns.c:694:20: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Nlm_Int2 val;
^~~
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 -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:184:3: 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 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vibfiles.c: In function 'Nlm_CardToStr':
vibfiles.c:715:19: warning: '%*u' directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=]
sprintf (temp, "%*u", length, (int)cardval);
^~~
vibfiles.c:715:18: note: directive argument in the range [0, 65535]
sprintf (temp, "%*u", length, (int)cardval);
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 32769 bytes into a destination of size 80
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vibfiles.c: In function 'Nlm_IntToStr':
vibfiles.c:725:19: warning: '%*d' directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=]
sprintf (temp, "%*d", length, intval);
^~~
vibfiles.c:725:18: note: directive argument in the range [-32768, 32767]
sprintf (temp, "%*d", length, intval);
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/vibtypes.h:94,
from vibfiles.c:54:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 32769 bytes into a destination of size 80
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:184:3: 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 -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:184:3: 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 -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:164:
/usr/include/features.h:184:3: 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:1121:15: 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 -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:184:3: 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:2006:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2005:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoice':
vibmenus.c:2072:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceGroup':
vibmenus.c:2122:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_EnableChoiceItem':
vibmenus.c:2166:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2164:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableMenuItem':
vibmenus.c:2329:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2328:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoice':
vibmenus.c:2395:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_DisableChoiceItem':
vibmenus.c:2489:17: warning: variable 'itm' set but not used [-Wunused-but-set-variable]
Nlm_Int2 itm;
^~~
vibmenus.c:2487:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_RemoveSubMenu':
vibmenus.c:2627:20: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_CountMenuItems':
vibmenus.c:3056:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetMenuItem':
vibmenus.c:3239:17: warning: variable 'h' set but not used [-Wunused-but-set-variable]
Nlm_MenuTool h;
^
vibmenus.c: In function 'Nlm_GetPopListTitle':
vibmenus.c:3349:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
Nlm_MenU m;
^
vibmenus.c: In function 'Nlm_AppendItems':
vibmenus.c:3978:17: warning: unused variable 'accel' [-Wunused-variable]
Nlm_Char accel;
^~~~~
vibmenus.c: In function 'Nlm_NewPopupList':
vibmenus.c:4969:19: warning: unused variable 'lbl' [-Wunused-variable]
Widget lbl;
^~~
vibmenus.c:4967:19: 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 -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:184:3: 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 -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:135:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:6800:13: warning: unused variable 'retval' [-Wunused-variable]
Nlm_Int2 retval;
^~~~~~
vibwndws.c: In function 'Nlm_RemoveDyingWindows':
vibwndws.c:6922:20: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:4419:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
document.c:4423:7: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL shim3d.c
shim3d.c: In function 'OGL_AddCylinder3D':
shim3d.c:918:14: warning: unused variable 'iCount' [-Wunused-variable]
Nlm_Int4 iCount;
^~~~~~
shim3d.c: In function 'OGL_AddText3D':
shim3d.c:1210:22: warning: unused variable 'i' [-Wunused-variable]
Nlm_Int4 Length, i;
^
shim3d.c: In function 'OGL_Zoom_DragMA':
shim3d.c:1770:16: warning: unused variable 'OGL_Data' [-Wunused-variable]
TOGL_Data *OGL_Data = MAToOGL(ma);
^~~~~~~~
shim3d.c: In function 'OGL_Hit':
shim3d.c:2065:37: warning: left shift count >= width of type [-Wshift-count-overflow]
ZMinName = ZMinName << (sizeof(GLuint) * 8);
^~
shim3d.c: In function 'write_row_callback':
shim3d.c:2911:15: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
float start, end;
^~~~~
shim3d.c:2911:22: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
float start, end;
^~~
shim3d.c: In function 'SetOGLFont':
shim3d.c:2381:64: warning: 'closest' may be used uninitialized in this function [-Wmaybe-uninitialized]
fontInfo = XLoadQueryFont(Nlm_currentXDisplay, list[closest]);
^
shim3d.c:2376:37: warning: 'mindiff' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ii == 0 || diff < mindiff) {
~~~~~^~~~~~~~~
shim3d.c:2381:64: 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:3463:26: 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 -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:184:3: 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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
smdlg3.c: In function 'FeatureExtraDraw':
smdlg3.c:413:17: warning: 'y1' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 y0, y1, x0, x1, x2, x3;
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:1943:8: warning: 'seglen' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 seglen;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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' [-Wdangling-else]
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' [-Wdangling-else]
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' [-Wdangling-else]
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 'PwDistanceItem':
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 -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:184:3: 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:3310:21: warning: unused variable 'dirty' [-Wunused-variable]
dirty = FALSE;
^~~~~
saled.c:3306:21: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:1444:25: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (tmp!='\0' && !isdigit (*tmp))
^~
salfiles.c:1444:22: note: did you mean to dereference the pointer?
while (tmp!='\0' && !isdigit (*tmp))
^
salfiles.c:1446:22: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (tmp!='\0')
^~
salfiles.c:1446:19: note: did you mean to dereference the pointer?
if (tmp!='\0')
^
salfiles.c:1455:25: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (tmp!='\0' && !isdigit (*tmp))
^~
salfiles.c:1455:22: note: did you mean to dereference the pointer?
while (tmp!='\0' && !isdigit (*tmp))
^
salfiles.c:1457:22: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (tmp!='\0')
^~
salfiles.c:1457:19: note: did you mean to dereference the pointer?
if (tmp!='\0')
^
salfiles.c:1536:25: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (tmp!='\0' && !isdigit (*tmp))
^~
salfiles.c:1536:22: note: did you mean to dereference the pointer?
while (tmp!='\0' && !isdigit (*tmp))
^
salfiles.c:1538:22: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (tmp!='\0')
^~
salfiles.c:1538:19: note: did you mean to dereference the pointer?
if (tmp!='\0')
^
salfiles.c:1547:25: warning: comparison between pointer and zero character constant [-Wpointer-compare]
while (tmp!='\0' && !isdigit (*tmp))
^~
salfiles.c:1547:22: note: did you mean to dereference the pointer?
while (tmp!='\0' && !isdigit (*tmp))
^
salfiles.c:1549:22: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (tmp!='\0')
^~
salfiles.c:1549:19: note: did you mean to dereference the pointer?
if (tmp!='\0')
^
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 were 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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:654:16: warning: 'seqstr' may be used uninitialized in this function [-Wmaybe-uninitialized]
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 -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:184:3: 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' [-Wdangling-else]
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:4674:15: warning: variable 'ppt' set but not used [-Wunused-but-set-variable]
PrompT ppt;
^~~
salpanel.c:4669:15: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
salpanel.c: In function 'OkToContinueWithFeatureApply':
salpanel.c:6103:14: warning: unused variable 'num_missing' [-Wunused-variable]
Int4 num_missing = 0, seq_num, start_num;
^~~~~~~~~~~
salpanel.c: In function 'DoApplyFeatureToAlignment':
salpanel.c:6219:31: warning: unused variable 'found_null' [-Wunused-variable]
Boolean found_null = FALSE;
^~~~~~~~~~
salpanel.c: In function 'ApplyFeatureToAlignment':
salpanel.c:6421:31: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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:5059:13: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:4976:23: warning: unused variable 'wdp' [-Wunused-variable]
SeqEditViewFormPtr wdp = NULL;
^~~
salsa.c:4974:23: warning: unused variable 'w' [-Wunused-variable]
WindoW w = NULL;
^
salsa.c: In function 'OldAlignmentEditor':
salsa.c:5106:16: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Int2 rval;
^~~~
salsa.c: In function 'LaunchAnnotAlignEditor':
salsa.c:5293:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignEditor':
salsa.c:5310:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignViewer':
salsa.c:5327:20: warning: variable 'handled' set but not used [-Wunused-but-set-variable]
Int2 handled;
^~~~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop':
salsa.c:5342:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
salsa.c: In function 'LaunchAlignEditorFromDesktop2':
salsa.c:5359:20: warning: variable 'ompcp' set but not used [-Wunused-but-set-variable]
OMProcControlPtr ompcp;
^~~~~
salsa.c: In function 'InsertSeqProc':
salsa.c:5538:17: warning: variable 'cnclbt' set but not used [-Wunused-but-set-variable]
ButtoN insbt, cnclbt;
^~~~~~
salsa.c:5536:10: warning: variable 'insprt' set but not used [-Wunused-but-set-variable]
PrompT insprt;
^~~~~~
salsa.c: In function 'SeqAlignBestHit':
salsa.c:5605:22: warning: variable 'last' set but not used [-Wunused-but-set-variable]
Int4 last;
^~~~
salsa.c: In function 'SeqAlignStartUpdate':
salsa.c:5791:22: warning: variable 'k' set but not used [-Wunused-but-set-variable]
Int2 index, k, j;
^
salsa.c:5790:15: warning: variable 'start' set but not used [-Wunused-but-set-variable]
start;
^~~~~
salsa.c:5789:15: warning: variable 'len_sum' set but not used [-Wunused-but-set-variable]
Int4 len_sum,
^~~~~~~
salsa.c:5786:15: warning: variable 'lenp' set but not used [-Wunused-but-set-variable]
Int4Ptr lenp,
^~~~
salsa.c:5785:15: warning: variable 'pre' set but not used [-Wunused-but-set-variable]
SeqIdPtr pre, sip, next;
^~~
salsa.c: In function 'CCNormalizeSeqAlignId':
salsa.c:6746:23: warning: unused variable 'gi' [-Wunused-variable]
Int4 gi = 0;
^~
salsa.c:6745:17: 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:6744:17: 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:7106:16: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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:5973:13: warning: 'SWPrintFarpointerAln' defined but not used [-Wunused-function]
static void SWPrintFarpointerAln(SeqAlignPtr sap, FILE *fp)
^~~~~~~~~~~~~~~~~~~~
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:113:19: warning: 'fp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define FileClose Nlm_FileClose
^~~~~~~~~~~~~
salsa.c:6350:23: 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:113:19: warning: 'fp' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define FileClose Nlm_FileClose
^~~~~~~~~~~~~
salsa.c:6318:23: note: 'fp' was declared here
FILE *fp;
^~
salsa.c: In function 'SeqAlignBestHit.isra.17':
salsa.c:5746:23: warning: 'nctr' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = nctr+beg+end;
~~~~^~~~
salsa.c:5748:24: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = -(beg+end);
~~~~^~~~~
salsa.c:5746:23: warning: 'beg' may be used uninitialized in this function [-Wmaybe-uninitialized]
*nonly = nctr+beg+end;
~~~~^~~~
salsa.c: In function 'SkipThisWindowProc':
salsa.c:4574:22: warning: 'salp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAlignPtr salp;
^~~~
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)
~~~^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:301:13: warning: 'CleanupGCFilterForm' defined but not used [-Wunused-function]
static void CleanupGCFilterForm (GraphiC g, VoidPtr data)
^~~~~~~~~~~~~~~~~~~
seqgrphx.c:152:25: warning: 'FilterMsgFunc' defined but not used [-Wunused-function]
static Int2 LIBCALLBACK FilterMsgFunc (OMMsgStructPtr ommsp)
^~~~~~~~~~~~~
seqgrphx.c:28:25: warning: 'MatrixMsgFunc' defined but not used [-Wunused-function]
static Int2 LIBCALLBACK MatrixMsgFunc (OMMsgStructPtr ommsp)
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:387:20: warning: 'MatrixSearch' defined but not used [-Wunused-function]
static SeqGraphPtr MatrixSearch (BioseqPtr bsp, Int2 matrixtype)
^~~~~~~~~~~~
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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:1436:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (vsmp->title != NULL)
^~
vsm.c:1438:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (vsmp->aboutinfo != NULL)
^~
vsm.c: In function 'VSMAboutProc':
vsm.c:1466:8: warning: variable 'p' set but not used [-Wunused-but-set-variable]
PaneL p;
^
vsm.c: In function 'VSeqMgrCreateMainWindow':
vsm.c:1569:12: warning: variable 'omp' set but not used [-Wunused-but-set-variable]
ObjMgrPtr omp;
^~~
vsm.c: In function 'VSeqMgrPopulateMain':
vsm.c:1710:13: warning: variable 'atp' set but not used [-Wunused-but-set-variable]
AsnTypePtr atp;
^~~
vsm.c: In function 'VSMGatherPictProc':
vsm.c:2193:15: warning: variable 'bssp' set but not used [-Wunused-but-set-variable]
BioseqSetPtr bssp;
^~~~
vsm.c:2188:30: 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:2821:10: warning: variable 'ptr' set but not used [-Wunused-but-set-variable]
Pointer ptr;
^~~
vsm.c:2820:13: 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 -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:184:3: 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:1368:20: 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 -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:184:3: 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:1743:18: warning: variable 'val' set but not used [-Wunused-but-set-variable]
Int2 val;
^~~
At top level:
vsmutil.c:1628:16: 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:2256:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2255:5: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'RevalidateProc':
vsmutil.c:2223:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2222:5: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'SetVerbosityAndRepopulate':
vsmutil.c:2297:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2296:5: 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:2620:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations]
vep->counts [i] = 0;
~~~~~~~~~~~~~~~~^~~
vsmutil.c:2619:9: note: within this loop
for (i = SEV_NONE; i <= SEV_MAX; i++) {
^~~
vsmutil.c: In function 'ContinueProc':
vsmutil.c:2256:19: warning: array subscript is above array bounds [-Warray-bounds]
vep->counts [i] = 0;
~~~~~~~~~~~~^~~
vsmutil.c: In function 'RevalidateProc':
vsmutil.c:2223:19: warning: array subscript is above array bounds [-Warray-bounds]
vep->counts [i] = 0;
~~~~~~~~~~~~^~~
vsmutil.c: In function 'SetVerbosityAndRepopulate':
vsmutil.c:2297:19: warning: array subscript is above array bounds [-Warray-bounds]
vep->counts [i] = 0;
~~~~~~~~~~~~^~~
vsmutil.c: In function 'ClearValidateWindow':
vsmutil.c:613:21: warning: array subscript is above array bounds [-Warray-bounds]
vep->counts [sev] = 0;
~~~~~~~~~~~~^~~~~
vsmutil.c: In function 'CreateValidateWindowExExEx':
vsmutil.c:2620:23: warning: array subscript is above array bounds [-Warray-bounds]
vep->counts [i] = 0;
~~~~~~~~~~~~^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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:342:19: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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.part.21':
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:2561:45: warning: 'residue_names' may be used uninitialized in this function [-Wmaybe-uninitialized]
sBuf[c]=*residue_names[(int)*s];
^
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:2356:14: warning: 'q' may be used uninitialized in this function [-Wmaybe-uninitialized]
Uint1Ptr q;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:2962:8: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
dlgutil1.c: In function 'TestIntervalEditor':
dlgutil1.c:5324:20: warning: variable 'fuzz_to' set but not used [-Wunused-but-set-variable]
Int2 fuzz_to;
^~~~~~~
dlgutil1.c:5323:20: warning: variable 'fuzz_from' set but not used [-Wunused-but-set-variable]
Int2 fuzz_from;
^~~~~~~~~
dlgutil1.c:5322:41: warning: variable 'fuzz_before' set but not used [-Wunused-but-set-variable]
Boolean isInterval, isPoint, fuzz_before, fuzz_after;
^~~~~~~~~~~
dlgutil1.c: In function 'DbtagDialogToDbtagPtr':
dlgutil1.c:7254:16: warning: unused variable 'val' [-Wunused-variable]
long int val;
^~~
dlgutil1.c:7250:16: warning: unused variable 'ptr' [-Wunused-variable]
CharPtr ptr;
^~~
dlgutil1.c:7247:16: warning: unused variable 'num_digits' [-Wunused-variable]
Int2 num_digits;
^~~~~~~~~~
dlgutil1.c:7246:16: warning: unused variable 'notallzero' [-Wunused-variable]
Boolean notallzero;
^~~~~~~~~~
dlgutil1.c:7243:16: warning: unused variable 'leadingzero' [-Wunused-variable]
Boolean leadingzero;
^~~~~~~~~~~
dlgutil1.c:7238:16: warning: unused variable 'alldigits' [-Wunused-variable]
Boolean alldigits;
^~~~~~~~~
dlgutil1.c: In function 'CreateStandardEditMenu':
dlgutil1.c:9427:8: 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:8603:25: warning: 'GetNthNameValuePair' defined but not used [-Wunused-function]
static NameValuePairPtr GetNthNameValuePair (Int4 n, ValNodePtr list)
^~~~~~~~~~~~~~~~~~~
dlgutil1.c:8051:16: warning: 'ParseSpecimenVoucherOk' defined but not used [-Wunused-function]
static Boolean ParseSpecimenVoucherOk (CharPtr str)
^~~~~~~~~~~~~~~~~~~~~~
dlgutil1.c:1293:13: warning: 'GbqualsToVisStringDialog' defined but not used [-Wunused-function]
static void GbqualsToVisStringDialog (SeqFeatPtr sfp, DialoG d, CharPtr qual)
^~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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:3552:11: warning: variable 'y' set but not used [-Wunused-but-set-variable]
Int4 x, y;
^
dlgutil2.c:3552:8: warning: variable 'x' set but not used [-Wunused-but-set-variable]
Int4 x, y;
^
dlgutil2.c: In function 'GetTableDisplayCell':
dlgutil2.c:3951:8: warning: variable 'start_row' set but not used [-Wunused-but-set-variable]
Int4 start_row, start_col;
^~~~~~~~~
dlgutil2.c: In function 'NewCreateInferenceDialog':
dlgutil2.c:7633:19: warning: variable 'fnt' set but not used [-Wunused-but-set-variable]
FonT fnt;
^~~
dlgutil2.c: In function 'ClickableListOnKey':
dlgutil2.c:10479:20: warning: variable 'clp' set but not used [-Wunused-but-set-variable]
ClickableListPtr clp;
^~~
dlgutil2.c: In function 'GetSelectedClickableListText':
dlgutil2.c:11151:36: 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:14210:36: warning: variable 's3' set but not used [-Wunused-but-set-variable]
SeqIntPtr s1, s2, s3;
^~
At top level:
dlgutil2.c:12342:16: warning: 'ParseMultiListQualOk' defined but not used [-Wunused-function]
static Boolean ParseMultiListQualOk (CharPtr val)
^~~~~~~~~~~~~~~~~~~~
dlgutil2.c:10336:13: warning: 'ClickClickableListItem' defined but not used [-Wunused-function]
static void ClickClickableListItem (DoC d, PoinT pt)
^~~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:10316:13: warning: 'DrawClickableListItem' defined but not used [-Wunused-function]
static void DrawClickableListItem (DoC d, RectPtr r, Int2 item, Int2 firstLine)
^~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:8854:13: warning: 'GetCategoryNumFromName' defined but not used [-Wunused-function]
static Int4 GetCategoryNumFromName (CharPtr category)
^~~~~~~~~~~~~~~~~~~~~~
dlgutil2.c:1676:16: warning: 'GetNameForFeature' defined but not used [-Wunused-function]
static CharPtr GetNameForFeature (SeqFeatPtr sfp)
^~~~~~~~~~~~~~~~~
dlgutil2.c: In function 'PopulateDayPopup':
dlgutil2.c:11438:24: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (day, "%d", i);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:4402:28: warning: variable 'r' set but not used [-Wunused-but-set-variable]
RecT r;
^
asn2graphic.c: In function 'GphSentProc':
asn2graphic.c:4997:16: 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:4362:13: warning: 'SegmentTreeBot' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (! EnsureFeatureHasSegment (FPSP, featdeftype, SegmentTreeBot)) return 0;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2graphic.c:4354:24: warning: 'SegmentTreeMid' may be used uninitialized in this function [-Wmaybe-uninitialized]
SegmentTreeBot = CreateSegment (SegmentTreeMid, 0, 0);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
asn2graphic.c:4350:24: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:1292:22: warning: variable 'doColors' set but not used [-Wunused-but-set-variable]
Boolean doColors;
^~~~~~~~
gbfview.c: In function 'PopulateFasta':
gbfview.c:1717:33: warning: left-hand operand of comma expression has no effect [-Wunused-value]
if (ISA_na (bsp->mol)) {TRUE,
^
gbfview.c:1649:20: warning: variable 'group_segs' set but not used [-Wunused-but-set-variable]
Uint1 group_segs;
^~~~~~~~~~
gbfview.c: In function 'PopulateAsnOrXML':
gbfview.c:1972:16: warning: variable 'lookupFar' set but not used [-Wunused-but-set-variable]
Boolean lookupFar = FALSE;
^~~~~~~~~
gbfview.c:1971:16: warning: variable 'lockFar' set but not used [-Wunused-but-set-variable]
Boolean lockFar = FALSE;
^~~~~~~
gbfview.c: In function 'PrintFlatFileFastaOrAsn':
gbfview.c:2494:5: 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:1234:13: warning: 'LookForFarProds' defined but not used [-Wunused-function]
static void LookForFarProds (
^~~~~~~~~~~~~~~
gbfview.c:1215:13: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:685:20: 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:673:20: 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:653:21: 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:653:21: 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:653:21: 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 -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:184:3: 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:8665:22: 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:626:12: 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:8665:26: 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:626:12: 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:8761:20: 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:626:12: 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:8761:24: 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:626:12: 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:9008:17: 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:535:22: 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 'SeqEdExportProc':
seqpanel.c:4329:13: 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 '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 '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 -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:184:3: 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 were 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:468:17: 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 were 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 -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:184:3: 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:272:10: 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:535:10: 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:1834:14: 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:2025:11: 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 were 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:652:16: 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:3206:39: 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 -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:184:3: 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:2814:7: 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:5353:17: warning: '%s' directive writing up to 299 bytes into a region of size 255 [-Wformat-overflow=]
sprintf(str, "%s", pfp->name);
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/asn2ff.h:113,
from ../include/ingenwin.h:58,
from ingenwin.c:45:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 1 and 300 bytes into a destination of size 255
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ingenwin.c:5229:37: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (i = last_pos; i <= exit; i += nchars_row){
~~^~~~~~~~~~~~~
ingenwin.c:5137:17: note: 'j' was declared here
Int4 i, j, k, row;
^
ingenwin.c: In function 'Ing_DoPropagate':
ingenwin.c:5625:26: warning: ' already exists. Do you still want to propagate it?' directive writing 51 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf (str_buf, "%s already exists. Do you still want to propagate it?", pfp->name);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/asn2ff.h:113,
from ../include/ingenwin.h:58,
from ingenwin.c:45:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 52 and 351 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:476:16: 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:476:16: 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:476:16: 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:476:16: 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:476:16: 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 -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:184:3: 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 'ExistingTextDialog':
macrodlg.c:1959:22: warning: variable 'ppt' set but not used [-Wunused-but-set-variable]
PrompT ppt;
^~~
macrodlg.c: In function 'EndDistanceToDialog':
macrodlg.c:3076:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", v->data.intvalue);
~^ ~~~~~~~~~~~~~~~~
%lld
macrodlg.c:3082:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", v->data.intvalue);
~^ ~~~~~~~~~~~~~~~~
%lld
macrodlg.c:3088:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", v->data.intvalue);
~^ ~~~~~~~~~~~~~~~~
%lld
macrodlg.c: In function 'SourceQualChoiceDialog':
macrodlg.c:3757:48: warning: variable 'b4' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3757:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3757:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3 = NULL, b4 = NULL;
^~
macrodlg.c:3757:29: 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:3995:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:3995:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:3995:29: warning: variable 'b1' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c: In function 'CDSGeneProtQualConstraintDialog':
macrodlg.c:4309:37: warning: variable 'b3' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:4309:33: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c:4309:29: warning: variable 'b1' set but not used [-Wunused-but-set-variable]
ButtoN b1, b2, b3;
^~
macrodlg.c: In function 'QuantityConstraintToDialog':
macrodlg.c:7368:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", vnp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c:7373:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", vnp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c:7378:21: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", vnp->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c: In function 'TestApplyActionDialog':
macrodlg.c:12965:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'TestEditActionDialog':
macrodlg.c:13170:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'TestRemoveOutsideActionDialog':
macrodlg.c:13328:8: warning: variable 'field_type' set but not used [-Wunused-but-set-variable]
Int2 field_type = 0;
^~~~~~~~~~
macrodlg.c: In function 'ApplyFeatureActionToDialog':
macrodlg.c:15186:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (num, "%d^", action->location->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c:15188:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (num, "%d", action->location->data.intvalue + 1);
~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c: In function 'AddMacroActions':
macrodlg.c:20523:25: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE;
^~~~
macrodlg.c: In function 'PointerToSampleDialog':
macrodlg.c:20659:19: 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:20779:53: 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:20779:42: 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:22071:33: warning: variable 'num_features' set but not used [-Wunused-but-set-variable]
Int4 num_fields, num_features;
^~~~~~~~~~~~
macrodlg.c:22071:21: warning: variable 'num_fields' set but not used [-Wunused-but-set-variable]
Int4 num_fields, num_features;
^~~~~~~~~~
macrodlg.c: In function 'LaunchMacroTemplateEditor':
macrodlg.c:23785:23: warning: variable 'bfp' set but not used [-Wunused-but-set-variable]
BaseFormPtr bfp;
^~~
macrodlg.c: In function 'SearchFuncToDialog':
macrodlg.c:25755:23: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", func->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~~
%lld
macrodlg.c:25776:23: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (buf, "%d", func->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~~~
%lld
At top level:
macrodlg.c:20095:13: warning: 'ChangeMacroActionPopup' defined but not used [-Wunused-function]
static void ChangeMacroActionPopup (LisT t)
^~~~~~~~~~~~~~~~~~~~~~
macrodlg.c:20038:13: warning: 'GetPopupChoiceForActionChoice' defined but not used [-Wunused-function]
static Int2 GetPopupChoiceForActionChoice (Uint1 action_choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macrodlg.c:19715:13: warning: 'GetCategoryForActionChoice' defined but not used [-Wunused-function]
static Int2 GetCategoryForActionChoice (Uint1 action_choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~
macrodlg.c:19698:14: warning: 'GetActionChoiceForCategoryPopupChoice' defined but not used [-Wunused-function]
static Uint1 GetActionChoiceForCategoryPopupChoice (Int2 category, Int2 popup_choice)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
macrodlg.c: In function 'ActionToSingleMacroActionForm':
macrodlg.c:22216:25: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int2 val, i;
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 'CreateSimpleBioSourceDialog':
biosrc.c:2455:18: warning: variable 'indexerVersion' set but not used [-Wunused-but-set-variable]
Boolean indexerVersion;
^~~~~~~~~~~~~~
biosrc.c: In function 'CreateBioSourceDialog':
biosrc.c:3615:18: warning: variable 'y' set but not used [-Wunused-but-set-variable]
PrompT y;
^
At top level:
biosrc.c:3291:26: warning: 'EnumListFromQualNameAssoc' defined but not used [-Wunused-function]
static EnumFieldAssocPtr EnumListFromQualNameAssoc (Nlm_QualNameAssocPtr qp)
^~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:3100:16: warning: 'SubsourceDialogToSubSourcePtr' defined but not used [-Wunused-function]
static Pointer SubsourceDialogToSubSourcePtr (DialoG d)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2677:13: warning: 'SubSourcePtrToSubsourceDialog' defined but not used [-Wunused-function]
static void SubSourcePtrToSubsourceDialog (DialoG d, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2617:16: warning: 'OrgmodDialogToOrgModPtr' defined but not used [-Wunused-function]
static Pointer OrgmodDialogToOrgModPtr (DialoG d)
^~~~~~~~~~~~~~~~~~~~~~~
biosrc.c:2568:13: 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 -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:184:3: 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 'SetBestProteinFeature':
cdrgn.c:1003:21: warning: unused variable 'prp' [-Wunused-variable]
ProtRefPtr prp;
^~~
cdrgn.c: In function 'CdRegionPtrToForm':
cdrgn.c:1050:19: warning: unused variable 'vnp' [-Wunused-variable]
ValNodePtr vnp;
^~~
cdrgn.c: In function 'ProductToSeqLocPtr':
cdrgn.c:1293:19: warning: variable 'rfp' set but not used [-Wunused-but-set-variable]
RnaFormPtr rfp = NULL;
^~~
cdrgn.c: In function 'CreateCodeBreakAlist':
cdrgn.c:1926:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
cdrgn.c: In function 'CodeBreakPtrToCodeBreakDialog':
cdrgn.c:1977:19: warning: variable 'aa' set but not used [-Wunused-but-set-variable]
Uint1 aa;
^~
cdrgn.c: In function 'PopulateAAPopup':
cdrgn.c:7041:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
cdrgn.c: In function 'RnaRefPtrToForm':
cdrgn.c:7557:17: warning: unused variable 'is_iMet' [-Wunused-variable]
Boolean is_iMet = FALSE;
^~~~~~~
cdrgn.c:7556:17: warning: unused variable 'is_fMet' [-Wunused-variable]
Boolean is_fMet = FALSE;
^~~~~~~
At top level:
cdrgn.c:6851:13: warning: 'ConvertRnaRefNameToProductQual' defined but not used [-Wunused-function]
static void ConvertRnaRefNameToProductQual (SeqFeatPtr sfp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdrgn.c:6789:13: warning: 'RemoveQualByName' defined but not used [-Wunused-function]
static void RemoveQualByName (SeqFeatPtr sfp, CharPtr qual_name)
^~~~~~~~~~~~~~~~
cdrgn.c:6770:18: warning: 'FindOrAddQual' defined but not used [-Wunused-function]
static GBQualPtr FindOrAddQual (SeqFeatPtr sfp, CharPtr qual_name)
^~~~~~~~~~~~~
cdrgn.c:6323:15: warning: 'CreateMrnaUserObjectDialog' defined but not used [-Wunused-function]
static DialoG CreateMrnaUserObjectDialog (GrouP h, CharPtr label, SeqEntryPtr sep, BaseFormPtr bfp)
^~~~~~~~~~~~~~~~~~~~~~~~~~
cdrgn.c:6246:14: warning: 'check_rna_type' defined but not used [-Wunused-function]
static Uint1 check_rna_type (Uint1 type)
^~~~~~~~~~~~~~
cdrgn.c:3183:13: warning: 'SetComment' defined but not used [-Wunused-function]
static void SetComment (CharPtr new_comment, WindoW w)
^~~~~~~~~~
cdrgn.c:2149:13: warning: 'AccessionToGi' defined but not used [-Wunused-function]
static Int4 AccessionToGi (CharPtr string)
^~~~~~~~~~~~~
cdrgn.c:961:13: warning: 'FormToProtRef' defined but not used [-Wunused-function]
static void FormToProtRef(CdRgnFormPtr cfp, ProtRefPtr prp)
^~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
import.c:3776:22: warning: 'kDoNotEditTitle' initialized and declared 'extern'
extern const CharPtr kDoNotEditTitle = "You are manually editing a title. If you continue, the title will not be automatically updated if the taxonomy information changes. Are you sure you want to do this? It is a very bad idea.";
^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 'MakeReplaceAuthorsForm':
pubdesc.c:4303:24: warning: variable 'pepp' set but not used [-Wunused-but-set-variable]
PubdescEditProcsPtr pepp;
^~~~
pubdesc.c: In function 'DisplayDocSum':
pubdesc.c:4865:9: warning: variable 'lineheight' set but not used [-Wunused-but-set-variable]
Int2 lineheight;
^~~~~~~~~~
At top level:
pubdesc.c:5377:13: warning: 'Quit' defined but not used [-Wunused-function]
static void Quit (ButtoN b)
^~~~
pubdesc.c:5113:14: warning: 'AddAll' defined but not used [-Wunused-function]
static void AddAll(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st)
^~~~~~
pubdesc.c: In function 'QueryFromForm':
pubdesc.c:5096:29: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (year_buf, "%d", year - 1);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pubdesc.c:5102:29: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf (year_buf, "%d", year + 1);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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:3152:7: warning: 'yac_num' may be used uninitialized in this function [-Wmaybe-uninitialized]
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 -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:184:3: 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 were 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 were 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 '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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:2001:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'BiomolDescrFree':
objmmdb1.c:2139:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'BiomolDescrAsnRead':
objmmdb1.c:2189:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueGraphAsnRead':
objmmdb1.c:2446:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'MoleculeGraphAsnRead':
objmmdb1.c:2654:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'InterResidueBondAsnRead':
objmmdb1.c:2856:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:2855:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueAsnRead':
objmmdb1.c:3037:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3036:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ResidueGraphPntrFree':
objmmdb1.c:3177:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb1.c: In function 'ResidueGraphPntrAsnRead':
objmmdb1.c:3212:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucGraphPntrAsnRead':
objmmdb1.c:3399:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3398:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'BiostrucResidueGraphSetPntrAsnRead':
objmmdb1.c:3565:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3564:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomAsnRead':
objmmdb1.c:3732:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c: In function 'IntraResidueBondAsnRead':
objmmdb1.c:3924:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:3923:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'ChiralCenterAsnRead':
objmmdb1.c:4097:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:4096:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomPntrAsnRead':
objmmdb1.c:4286:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb1.c:4285:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb1.c: In function 'AtomPntrSetAsnRead':
objmmdb1.c:4441:16: 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 'BiostrucIdAsnRead':
objmmdb1.c:411:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
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:2284:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb1.c: In function 'BiostrucSourceAsnRead':
objmmdb1.c:1802:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb1.c:1752:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb1.c: In function 'ResidueGraphPntrAsnRead':
objmmdb1.c:3265:16: 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 -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:184:3: 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:242:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'ModelDescrAsnRead':
objmmdb2.c:289:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'ModelSpaceAsnRead':
objmmdb2.c:512:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:511:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'Coordinates_coordinatesFree':
objmmdb2.c:709:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'ModelCoordinateSetAsnRead':
objmmdb2.c:743:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'Coordinates_coordinatesAsnRead':
objmmdb2.c:831:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'ReferenceFrameAsnRead':
objmmdb2.c:1063:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:1062:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'CoordinatesFree':
objmmdb2.c:1193:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'CoordinatesAsnRead':
objmmdb2.c:1231:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'AtomicCoordinatesAsnRead':
objmmdb2.c:1420:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'Surface_surfaceFree':
objmmdb2.c:1640:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'SurfaceCoordinatesAsnRead':
objmmdb2.c:1686:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c:1685:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'Surface_surfaceAsnRead':
objmmdb2.c:1766:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'DensityCoordinatesAsnRead':
objmmdb2.c:2030:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'ModelSpacePointsAsnRead':
objmmdb2.c:2263:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AtomicTemperatureFactorsFree':
objmmdb2.c:2404:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb2.c: In function 'AtomicTemperatureFactorsAsnRead':
objmmdb2.c:2439:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmmdb2.c: In function 'AtomicOccupanciesAsnRead':
objmmdb2.c:2615:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AlternateConformationIdsAsnRead':
objmmdb2.c:2760:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'ConformationEnsembleAsnRead':
objmmdb2.c:2890:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'IsotropicTemperatureFactorsAsnRead':
objmmdb2.c:3054:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'AnisotropicTemperatureFactorsAsnRead':
objmmdb2.c:3221:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'TMeshAsnRead':
objmmdb2.c:3426:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb2.c: In function 'TrianglesAsnRead':
objmmdb2.c:3626:16: 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:366:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'CoordinatesAsnRead':
objmmdb2.c:1281:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'AtomicTemperatureFactorsAsnRead':
objmmdb2.c:2485:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c: In function 'ModelCoordinateSetAsnRead':
objmmdb2.c:877:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c:830:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb2.c: In function 'SurfaceCoordinatesAsnRead':
objmmdb2.c:1828:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb2.c:1765:10: 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 -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:184:3: 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:220:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'AtomPntrsAsnRead':
objmmdb3.c:443:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ChemGraphAlignmentAsnRead':
objmmdb3.c:626:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ChemGraphInteractionAsnRead':
objmmdb3.c:824:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'SphereAsnRead':
objmmdb3.c:1024:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ConeAsnRead':
objmmdb3.c:1192:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'CylinderAsnRead':
objmmdb3.c:1372:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BrickAsnRead':
objmmdb3.c:1557:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'TransformAsnRead':
objmmdb3.c:1796:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucFeatureSetDescrFree':
objmmdb3.c:1921:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'Location_locationFree':
objmmdb3.c:2161:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'BiostrucFeatureAsnRead':
objmmdb3.c:2206:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'Property_propertyFree':
objmmdb3.c:2722:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'ColorPropAsnRead':
objmmdb3.c:2798:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'CameraAsnRead':
objmmdb3.c:2986:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucScriptAsnRead':
objmmdb3.c:3171:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionPntrsAsnRead':
objmmdb3.c:3330:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionSimilarityAsnRead':
objmmdb3.c:3648:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'OtherFeatureAsnRead':
objmmdb3.c:3825:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucMoleculePntrAsnRead':
objmmdb3.c:3999:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'MoleculePntrsAsnRead':
objmmdb3.c:4342:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ResidueExplicitPntrsAsnRead':
objmmdb3.c:4505:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ResidueIntervalPntrAsnRead':
objmmdb3.c:4673:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionCoordinatesAsnRead':
objmmdb3.c:4845:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RegionBoundaryFree':
objmmdb3.c:4981:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'AlignStatsAsnRead':
objmmdb3.c:5212:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'RealValueAsnRead':
objmmdb3.c:5454:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'ModelSpacePointAsnRead':
objmmdb3.c:5615:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'MoveFree':
objmmdb3.c:5759:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmmdb3.c: In function 'RotMatrixAsnRead':
objmmdb3.c:5967:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'TransMatrixAsnRead':
objmmdb3.c:6200:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'GLMatrixAsnRead':
objmmdb3.c:6379:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmmdb3.c: In function 'BiostrucScriptStepAsnRead':
objmmdb3.c:6680:16: 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:307:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'BiostrucFeatureSetDescrAsnRead':
objmmdb3.c:2024:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'ResiduePntrsAsnRead':
objmmdb3.c:4213:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'RegionBoundaryAsnRead':
objmmdb3.c:5075:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'MoveAsnRead':
objmmdb3.c:5839:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c: In function 'RegionPntrsAsnRead':
objmmdb3.c:3464:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c:3409:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb3.c: In function 'BiostrucFeatureAsnRead':
objmmdb3.c:2691:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c:2626:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmmdb3.c:2370:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmmdb3.c:2308:10: 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 -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:184:3: 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:605:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:604:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dGeneralStyleAsnRead':
objcn3d.c:789:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:788:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dBackboneLabelStyleAsnRead':
objcn3d.c:972:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:971:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dStyleSettingsAsnRead':
objcn3d.c:1175:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1174:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dStyleSettingsSetAsnRead':
objcn3d.c:1578:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dStyleTableItemAsnRead':
objcn3d.c:1707:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1706:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dResidueRangeAsnRead':
objcn3d.c:1872:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:1871:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dMoleculeLocationAsnRead':
objcn3d.c:2035:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dObjectLocationAsnRead':
objcn3d.c:2198:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dUserAnnotationAsnRead':
objcn3d.c:2363:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c: In function 'Cn3dGLMatrixAsnRead':
objcn3d.c:2555:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:2554:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dVectorAsnRead':
objcn3d.c:2843:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:2842:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcn3d.c: In function 'Cn3dViewSettingsAsnRead':
objcn3d.c:3016:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcn3d.c:3015:12: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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' [-Wdangling-else]
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 -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:184:3: 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 were guarded by the 'if'
src = orgstring;
^~~
mmdbapi3.c:840:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
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 -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:184:3: 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 -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:184:3: 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 -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 -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:184:3: 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:559:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (vnp = ValNodeFindNext(currentbp->descr, NULL, BiomolDescr_name))
^~~
prunebsc.c:574:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (vnp = ValNodeFindNext(het->descr, NULL, BiomolDescr_name))
^~~
prunebsc.c:663:9: 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:695:16: warning: 'mol_id' may be used uninitialized in this function [-Wmaybe-uninitialized]
bsmpHead = PruneModel(bsmp, pvnIds, mol_id);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prunebsc.c:591:26: warning: 'currenthet' may be used uninitialized in this function [-Wmaybe-uninitialized]
currenthet->next = het;
~~~~~~~~~~~~~~~~~^~~~~
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 -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:184:3: 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 'CddAsnRead':
objcdd.c:402:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddSetAsnRead':
objcdd.c:798:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:795:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddTreeAsnRead':
objcdd.c:935:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:934:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddTreeSetAsnRead':
objcdd.c:1147:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1144:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddPrefNodesAsnRead':
objcdd.c:1281:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1280:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddProjectAsnRead':
objcdd.c:1478:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddOrgRefAsnRead':
objcdd.c:1668:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1667:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddOrgRefSetAsnRead':
objcdd.c:1838:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:1835:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'CddPrefNodeDescrFree':
objcdd.c:1932:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'CddPrefNodeDescrAsnRead':
objcdd.c:1967:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddPrefNodeDescrSetAsnRead':
objcdd.c:2130:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2127:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'GlobalIdAsnRead':
objcdd.c:2263:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2262:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddRepeatAsnRead':
objcdd.c:2450:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2449:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddBookRefAsnRead':
objcdd.c:2627:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:2626:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddDescrSetAsnRead':
objcdd.c:3183:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:3180:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'MatrixAsnRead':
objcdd.c:3315:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'TriangleAsnRead':
objcdd.c:3504:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'UpdateCommentFree':
objcdd.c:3641:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'UpdateCommentAsnRead':
objcdd.c:3685:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'UpdateAlignAsnRead':
objcdd.c:3889:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'RejectIdAsnRead':
objcdd.c:4064:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'FeatureEvidenceFree':
objcdd.c:4188:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objcdd.c: In function 'FeatureEvidenceAsnRead':
objcdd.c:4232:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'AlignAnnotAsnRead':
objcdd.c:4437:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'AlignAnnotSetAsnRead':
objcdd.c:4606:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4603:12: warning: unused variable 'av' [-Wunused-variable]
DataVal av;
^~
objcdd.c: In function 'DomainParentAsnRead':
objcdd.c:4738:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4737:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'SequenceTreeAsnRead':
objcdd.c:4919:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:4918:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'AlgorithmTypeAsnRead':
objcdd.c:5107:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5106:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'SeqTreeNodeAsnRead':
objcdd.c:5410:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5409:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'Children_footprintAsnRead':
objcdd.c:5595:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5594:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'NodeAnnotationAsnRead':
objcdd.c:5887:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:5886:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddViewerRectAsnRead':
objcdd.c:6053:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:6052:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objcdd.c: In function 'CddViewerAsnRead':
objcdd.c:6235:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c: In function 'CddScriptAsnRead':
objcdd.c:6410:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objcdd.c:6409:12: 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 'CddIdAsnRead':
objcdd.c:134:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c: In function 'CddPrefNodeDescrAsnRead':
objcdd.c:2016:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c: In function 'CddDescrAsnRead':
objcdd.c:3007:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c: In function 'UpdateCommentAsnRead':
objcdd.c:3746:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c: In function 'FeatureEvidenceAsnRead':
objcdd.c:4293:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c: In function 'SeqTreeNodeAsnRead':
objcdd.c:5561:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objcdd.c:5510:10: 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 -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:184:3: 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 were 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 were 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;
~~~~~~~~~~~~~~^~~~~~~~
In file included from ../include/ncbi.h:59:0,
from cddutil.c:336:
cddutil.c: In function 'CddCalculateTriangle':
../include/ncbimem.h:232:23: warning: 'buffer1' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define MemFree Nlm_MemFree
^~~~~~~~~~~
cddutil.c:3415:19: note: 'buffer1' was declared here
Uint1Ptr buffer1, buffer2, buffer3;
^~~~~~~
cddutil.c:3524:22: warning: 'pscTail' may be used uninitialized in this function [-Wmaybe-uninitialized]
pscTail->next = psc; pscTail = psc; psc = NULL;
~~~~~~~~~~~~~~^~~~~
cddutil.c: In function 'CddDenDiagCposComp2KBP':
cddutil.c:4974:11: warning: 'pssm' may be used uninitialized in this function [-Wmaybe-uninitialized]
return(pssm);
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 * 4)) + (sizetype)((unsigned int)a * 4))' 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:829:10: warning: 'Sigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (Sigma > 0) {
^
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 -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:76:
/usr/include/features.h:184:3: 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:126:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'NcbiMimeAsn1AsnRead':
objmime.c:173:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'Data_dataFree':
objmime.c:382:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'EntrezGeneralAsnRead':
objmime.c:428:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c:427:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'Data_dataAsnRead':
objmime.c:522:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'BiostrucAlignAsnRead':
objmime.c:801:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucAlignSeqAsnRead':
objmime.c:1027:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucSeqAsnRead':
objmime.c:1220:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'BiostrucSeqsAsnRead':
objmime.c:1415:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'SeqAlignData_seq_align_dataFree':
objmime.c:1613:12: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
objmime.c: In function 'BiostrucSeqsAlignsCddAsnRead':
objmime.c:1647:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objmime.c: In function 'SeqAlignData_seq_align_dataAsnRead':
objmime.c:1734:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objmime.c: In function 'BundleSeqsAlignsAsnRead':
objmime.c:1973:16: 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:81:
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: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/mapmime.h:6:0,
from objmime.c:81:
../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:235:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c: In function 'EntrezGeneralAsnRead':
objmime.c:584:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c:521:10: note: 'choice' was declared here
Uint1 choice;
^~~~~~
objmime.c: In function 'BiostrucSeqsAlignsCddAsnRead':
objmime.c:1780:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objmime.c:1733:10: 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 -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:184:3: 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 -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 -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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 were 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 -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:64:5: warning: 'nt' may be used uninitialized in this function [-Wmaybe-uninitialized]
int nt; /* Number of threads within specified ensemble cutoff */
^~
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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 were 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 were 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 were 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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:184:3: 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:165:2:
2,-2, 0, 0,-2,-1, 0, 1,-1,-1,-2,-1,-1,-3, 1, 1, 1,-5,-3, 0, 1, 1, 0,
{ }
-2, 5, 0,-1,-3, 1,-1,-3, 1,-2,-2, 2, 0,-3, 0, 0,-1, 1,-4,-2, 0, 1, 0,
{ }
0, 0, 2, 2,-3, 0, 1, 0, 1,-1,-2, 1,-2,-2, 0, 1, 0,-4,-1,-2, 3, 2, 0,
{ }
0,-1, 2, 3,-4, 1, 3, 0, 0,-2,-3, 0,-2,-4,-1, 0, 0,-6,-3,-2, 4, 3, 0,
{ }
-2,-3,-3,-4, 8,-4,-4,-3,-3,-2,-5,-4,-4,-4,-2, 0,-2,-6, 0,-2,-3,-3, 0,
{ }
-1, 1, 0, 1,-4, 4, 2,-1, 2,-2,-1, 0,-1,-4, 0,-1,-1,-4,-3,-2, 2, 4, 0,
{ }
0,-1, 1, 3,-4, 2, 3, 0, 0,-2,-3, 0,-2,-4, 0, 0, 0,-6,-3,-2, 3, 4, 0,
{ }
1,-3, 0, 0,-3,-1, 0, 4,-2,-2,-3,-2,-3,-3,-1, 1, 0,-5,-4,-1, 1, 0, 0,
{ }
-1, 1, 1, 0,-3, 2, 0,-2, 5,-2,-2, 0,-2,-1, 0,-1,-1,-3, 0,-2, 2, 2, 0,
{ }
-1,-2,-1,-2,-2,-2,-2,-2,-2, 4, 2,-1, 2, 1,-2,-1, 0,-5,-1, 3,-1,-1, 0,
{ }
-2,-2,-2,-3,-5,-1,-3,-3,-2, 2, 4,-2, 3, 1,-2,-2,-1,-4,-1, 1,-2,-1, 0,
{ }
-1, 2, 1, 0,-4, 0, 0,-2, 0,-1,-2, 4, 1,-4,-1, 0, 0,-3,-4,-2, 1, 1, 0,
{ }
-1, 0,-2,-2,-4,-1,-2,-3,-2, 2, 3, 1, 5, 0,-2,-1, 0,-4,-2, 1,-1, 0, 0,
{ }
-3,-3,-2,-4,-4,-4,-4,-3,-1, 1, 1,-4, 0, 7,-4,-2,-2, 0, 5,-1,-2,-3, 0,
{ }
1, 0, 0,-1,-2, 0, 0,-1, 0,-2,-2,-1,-2,-4, 5, 1, 0,-5,-4,-1, 0, 1, 0,
{ }
1, 0, 1, 0, 0,-1, 0, 1,-1,-1,-2, 0,-1,-2, 1, 2, 1,-2,-2,-1, 1, 1, 0,
{ }
1,-1, 0, 0,-2,-1, 0, 0,-1, 0,-1, 0, 0,-2, 0, 1, 3,-4,-2, 0, 1, 0, 0,
{ }
-5, 1,-4,-6,-6,-4,-6,-5,-3,-5,-4,-3,-4, 0,-5,-2,-4,12, 0,-6,-3,-4, 0,
{ }
-3,-4,-1,-3, 0,-3,-3,-4, 0,-1,-1,-4,-2, 5,-4,-2,-2, 0, 7,-2,-1,-2, 0,
{ }
0,-2,-2,-2,-2,-2,-2,-1,-2, 3, 1,-2, 1,-1,-1,-1, 0,-6,-2, 4,-1,-1, 0,
{ }
1, 0, 3, 4,-3, 2, 3, 1, 2,-1,-2, 1,-1,-2, 0, 1, 1,-3,-1,-1, 4, 4, 0,
{ }
1, 1, 2, 3,-3, 4, 4, 0, 2,-1,-1, 1, 0,-3, 1, 1, 0,-4,-2,-1, 4, 5, 0,
{ }
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
{
};
}
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' [-Wdangling-else]
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 $";
^~~~~
csim.c: In function 'SIM':
csim.c:1071:62: warning: 'dj' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~^~~~
csim.c:928:23: note: 'dj' was declared here
register Int4 di, dj; /* end-point associated with d */
^~
csim.c:1071:51: warning: 'di' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl
~~~^~~~
csim.c:928:19: note: 'di' was declared here
register Int4 di, dj; /* end-point associated with d */
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF db_slist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/list.h:56,
from db_slist.c:97:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
db_slist.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: db_slist.c,v 6.2 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF dust.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from dust.c:102:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
dust.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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 -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:184:3: 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:668:7: 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:710:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = diag_prev[len1+len2-1-pos]) {
^~
falign.c:719:7: 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:881:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (df = diag_prev[len1+se2-pos]) {
^~
falign.c:889:7: 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:1547:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = diag_prev[ocur_diag]) {
^~
falign.c: In function 'enterS':
falign.c:1897:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (s = findS(f->bgf)) {
^
falign.c: In function 'local':
falign.c:1958:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = diag_prev[cur_diag]) {
^~
falign.c: In function 'align':
falign.c:1999:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = cdiag_prev[cur_diag]) {
^~
falign.c: In function 'calign':
falign.c:2054:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (pf = cdiag_prev[cur_diag]) {
^~
falign.c: In function 'malign':
falign.c:2109:6: 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 $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF g_any.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from g_any.c:89:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
g_any.c: In function 'k_align':
g_any.c:212:10: warning: array subscript has type 'char' [-Wchar-subscripts]
va = vv[A[i+1]];
^
g_any.c:229:26: warning: array subscript has type 'char' [-Wchar-subscripts]
if (j < J2) c = s + va[B[j+1]];
^
g_any.c:319:10: warning: array subscript has type 'char' [-Wchar-subscripts]
b2 = PP[t1][b1];
^
g_any.c:322:10: warning: array subscript has type 'char' [-Wchar-subscripts]
t2 = PT[t1][b1];
^
g_any.c: In function 'z_ALIGN':
g_any.c:367:7: warning: variable 'check_score' set but not used [-Wunused-but-set-variable]
Int4 check_score;
^~~~~~~~~~~
g_any.c: In function 'CHECK_SCORE':
g_any.c:492:13: warning: array subscript has type 'char' [-Wchar-subscripts]
score = vv[A[++i]][B[++j]] + score;
^
g_any.c:492:21: warning: array subscript has type 'char' [-Wchar-subscripts]
score = vv[A[++i]][B[++j]] + score;
^
At top level:
g_any.c:428:35: warning: 'CLINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:428:24: warning: 'BLINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:428:13: warning: 'ALINE' defined but not used [-Wunused-variable]
static Char ALINE[51], BLINE[51], CLINE[51];
^~~~~
g_any.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: g_any.c,v 6.5 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF sim2.c
sim2.c: In function 'SIM2':
sim2.c:19:16: warning: unused variable 'compB' [-Wunused-variable]
CharPtr A, B, compB = NULL;
^~~~~
sim2.c:17:26: warning: unused variable 'sapC' [-Wunused-variable]
SeqAlignPtr sap = NULL, sapC=NULL, out_sap, out_sapC;
^~~~
At top level:
sim2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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 -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:184:3: 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:630:9: 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' [-Wdangling-else]
if (row == 0 && col == 0)
^
sim4.c:1794:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (row == 0)
^
sim4.c:1838:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (col == 0)
^
sim4.c:1962:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (row == m && col == n)
^
sim4.c:1991:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (row == m)
^
sim4.c:2037:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
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.13':
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 -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:184:3: 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 $";
^~~~~
simutil.c: In function 'sort_align_list':
simutil.c:602:20: warning: 'score2' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (score2 > score1) { /* swap */
^
simutil.c:602:20: warning: 'score1' may be used uninitialized in this function [-Wmaybe-uninitialized]
simutil.c: In function 'get_top_K_alignment':
simutil.c:659:16: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (score < cut_off) break;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF slist.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/list.h:56,
from slist.c:101:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
slist.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: slist.c,v 6.2 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF sec.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/simutil.h:77,
from sec.c:67:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
sec.c: In function 'Region':
sec.c:268:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:268:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:292:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:292:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:321:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:321:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:345:19: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:345:28: warning: array subscript has type 'char' [-Wchar-subscripts]
ext_score += V[seq1[i]][seq2[j]];
^
sec.c:428:35: warning: array subscript has type 'char' [-Wchar-subscripts]
diag_score = diag_score + V[seq1[i]][seq2[j]];
^
sec.c:428:44: warning: array subscript has type 'char' [-Wchar-subscripts]
diag_score = diag_score + V[seq1[i]][seq2[j]];
^
At top level:
sec.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -D_PNG -I../include -DWIN_MOTIF tfuns.c
tfuns.c: In function 'find_orf':
tfuns.c:866:26: warning: unused variable 'into' [-Wunused-variable]
IntFuzzPtr infrom=NULL, into=NULL;
^~~~
tfuns.c:866:13: warning: unused variable 'infrom' [-Wunused-variable]
IntFuzzPtr infrom=NULL, into=NULL;
^~~~~~
At top level:
tfuns.c:977:13: 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 6.17 2015/08/17 17:15:09 bollin Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:169,
from toasn3.c:10:
/usr/include/features.h:184:3: 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:1444:17: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
toasn3.c: In function 'CheckQualsWithComm':
toasn3.c:1731:18: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toasn3.c: In function 'CheckQuals':
toasn3.c:1768:18: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toasn3.c: In function 'CountSourceFeat':
toasn3.c:2570:13: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
toasn3.c:2561:19: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
toasn3.c: In function 'TASNTrimInternalSemicolons':
toasn3.c:4155:12: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
CharPtr tmp;
^~~
toasn3.c: In function 'ImpFeatToProtRef':
toasn3.c:4861:13: warning: variable 'lfree' set but not used [-Wunused-but-set-variable]
Boolean lfree = FALSE, partial5, partial3;
^~~~~
toasn3.c: In function 'RemovePeptideImpFeats':
toasn3.c:5160:24: warning: variable 'ifp' set but not used [-Wunused-but-set-variable]
ImpFeatPtr ifp;
^~~
At top level:
toasn3.c:1711:16: 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 6.150 2016/11/02 23:36:09 kans Exp $";
^~~~~
toasn3.c: In function 'FixNucProtSet':
toasn3.c:2204:21: 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 -D_PNG -I../include -DWIN_MOTIF toporg.c
toporg.c: In function 'ChkSegset':
toporg.c:64:51: warning: variable 'is_title' set but not used [-Wunused-but-set-variable]
Boolean is_org = FALSE, is_modif = FALSE, is_title = FALSE;
^~~~~~~~
toporg.c:63:17: warning: variable 'orp' set but not used [-Wunused-but-set-variable]
OrgRefPtr orp;
^~~
toporg.c:60:17: warning: variable 'pnt' set but not used [-Wunused-but-set-variable]
Pointer pnt;
^~~
toporg.c:55:17: 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:608:51: 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:1330:17: warning: variable 'empty' set but not used [-Wunused-but-set-variable]
Boolean empty;
^~~~~
toporg.c:1329:17: warning: variable 'bsmp' set but not used [-Wunused-but-set-variable]
BSMapPtr bsmp;
^~~~
toporg.c:1328:29: warning: variable 'set_vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr descr, vnp, set_vnp;
^~~~~~~
toporg.c: In function 'MapsToGenref':
toporg.c:2021:17: warning: variable 'loc' set but not used [-Wunused-but-set-variable]
SeqLocPtr loc;
^~~
toporg.c:2016:17: warning: variable 'descr' set but not used [-Wunused-but-set-variable]
ValNodePtr descr = NULL, head, last, vnp;
^~~~~
toporg.c: In function 'FindOldLineage':
toporg.c:2606:17: warning: variable 'lineage' set but not used [-Wunused-but-set-variable]
CharPtr lineage;
^~~~~~~
toporg.c: In function 'ArePubsMergeableForFig':
toporg.c:4796:36: 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:4796:12: note: add parentheses around left hand side expression to silence this warning
|| !cgp_fig->serial_number != cgp_nofig->serial_number) {
^~~~~~~~~~~~~~~~~~~~~~~
( )
toporg.c: In function 'StripBadTitleFromProteinProducts':
toporg.c:5311:22: warning: variable 'tech' set but not used [-Wunused-but-set-variable]
Uint1 tech;
^~~~
toporg.c: In function 'FindPubWithFig':
toporg.c:5647:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
Int4 a = 0;
^
toporg.c: In function 'AddMissingGeneXref':
toporg.c:5955:22: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
toporg.c: In function 'ConvertSegSetToDeltaSeqInt':
toporg.c:7093:18: warning: unused variable 'str' [-Wunused-variable]
CharPtr str, ttl = NULL;
^~~
toporg.c:7086:18: warning: unused variable 'ovp' [-Wunused-variable]
ObjValNodePtr ovp;
^~~
At top level:
toporg.c:5475:13: warning: 'SynchronizePseudogenesProc' defined but not used [-Wunused-function]
static void SynchronizePseudogenesProc (
^~~~~~~~~~~~~~~~~~~~~~~~~~
toporg.c:3119:13: 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 6.251 2016/11/02 23:36:10 kans Exp $";
^~~~~
toporg.c: In function 'MergeEquivCitSubs':
toporg.c:3905:7: warning: 'csp1' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (DateMatch (csp1->date, csp2->date, FALSE) != 0) return FALSE;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
toporg.c:3925:18: note: 'csp1' was declared here
CitSubPtr csp1, csp2;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF suggest.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from suggest.c:199:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
suggest.c: In function 'get_frames':
suggest.c:458:12: warning: array subscript has type 'char' [-Wchar-subscripts]
val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]];
^
suggest.c:458:26: warning: array subscript has type 'char' [-Wchar-subscripts]
val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]];
^
At top level:
suggest.c:1331:13: warning: 'ReportSuggestIntervalsError' defined but not used [-Wunused-function]
static void ReportSuggestIntervalsError (SeqRecPtr srp, CharPtr gen_txt)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
suggest.c:1222:1: warning: 'fprintf_m_stk_entry' defined but not used [-Wunused-function]
fprintf_m_stk_entry(FILE *fp, Int4 index, char *msg)
^~~~~~~~~~~~~~~~~~~
suggest.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: suggest.c,v 6.14 2009/04/10 17:22:14 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF suggslp.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from suggslp.c:53:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
suggslp.c: In function 'MakeReverseSequence':
suggslp.c:190:11: warning: array subscript has type 'char' [-Wchar-subscripts]
*t++ = r[*--s];
^
At top level:
suggslp.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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:3179:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (virtual_oidlist = rdfp_chain->oidlist) {
^~~~~~~~~~~~~~~
blast.c: In function 'BlastGetDbChunk':
blast.c:3210:13: 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 were 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' [-Wdangling-else]
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 $";
^~~~~
blast.c: In function 'BLASTMergeHitLists.isra.4':
blast.c:6256:24: warning: 'op_type' may be used uninitialized in this function [-Wmaybe-uninitialized]
esp2->op_type = op_type;
~~~~~~~~~~~~~~^~~~~~~~~
blast.c:6058:10: note: 'op_type' was declared here
Uint1 op_type;
^~~~~~~
blast.c: In function 'blastMergeFilterLocs':
blast.c:3985:16: warning: 'dup_slp' may be used uninitialized in this function [-Wmaybe-uninitialized]
dup_slp = (SeqLocPtr) dup_slp->data.ptrvalue;
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast.c: In function 'BlastLinkHsps':
blast.c:10455:41: warning: 'orig_hitlist' may be used uninitialized in this function [-Wmaybe-uninitialized]
search->current_hitlist = orig_hitlist;
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blastutl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastutl.c:1836:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastutl.c: In function 'BlastSeqLocFilterEx':
blastutl.c:7554:11: warning: statement with no effect [-Wunused-value]
stop_timer("after repeat filtering");
^
blastutl.c: In function 'BlastPreliminaryGappedScore':
blastutl.c:9853:30: warning: variable 'query_length' set but not used [-Wunused-but-set-variable]
Int4 index, max_offset = 0, query_length, min_score;
^~~~~~~~~~~~
blastutl.c: In function 'BlastGetGappedScore':
blastutl.c:10282:11: warning: statement with no effect [-Wunused-value]
stop_timer("after BlastGappedScoreInternal");
^
At top level:
blastutl.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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:11522:43: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 loop_increment, loop_increment2, stop;
^~~~
blastutl.c:11711:18: warning: 'start_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score2 += matrix[(Int4) *(str+index2)][*(words+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_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
start_score2 += posMatrix[offset+index2][*(words+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:9377:56: warning: 'seqalign_array' may be used uninitialized in this function [-Wmaybe-uninitialized]
seqalign_array[index2] =
~~~~~~~~~~~~~~~~~~~~~~~^
SeqAlignFree(seqalign_array[index2]);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:184:3: 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 were 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 $";
^~~~~
blastool.c: In function 'BlastCreateVirtualOIDList':
blastool.c:2556:24: warning: 'gilist' may be used uninitialized in this function [-Wmaybe-uninitialized]
BlastDoubleInt4Ptr gilist, real_gilist = NULL, *real_gilist_ptrs = NULL;
^~~~~~
blastool.c: In function 'BlastInsertList2Heap':
blastool.c:3595:31: warning: 'query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
context = hsp->query_offset / query_length;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
blastool.c: In function 'BlastFreeHeap':
blastool.c:3687:31: warning: 'query_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
context = hsp->query_offset / query_length;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
blastool.c: In function 'BLASTFilterOverlapRegions':
blastool.c:4531:24: warning: 'next_tail' may be used uninitialized in this function [-Wmaybe-uninitialized]
tail->next = seqalign;
~~~~~~~~~~~^~~~~~~~~~
blastool.c: In function 'BlastPrintAlignInfo':
blastool.c:4800:23: warning: 'sap' may be used uninitialized in this function [-Wmaybe-uninitialized]
sap->next = SeqAlignNew();
~~~~~~~~~~^~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blastconcat.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blastconcat.c:89:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blastconcat.c: In function 'BlastMakeFakeBspConcat':
blastconcat.c:648:12: warning: variable 'slp' set but not used [-Wunused-but-set-variable]
SeqLocPtr slp = NULL;
^~~
At top level:
blastconcat.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blastconcat.c,v 1.14 2007/05/07 13:30:54 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF splutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from splutil.c:52:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
splutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: splutil.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF gapxdrop.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/gapxdrop.h:150,
from gapxdrop.c:368:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
gapxdrop.c: In function 'ALIGN_EX':
gapxdrop.c:864:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (s == 1)
^
gapxdrop.c:867:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (s == 2)
^
At top level:
gapxdrop.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: gapxdrop.c,v 6.76 2003/11/07 21:52:52 dondosha Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF bandalg0.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg0.c:36:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg0.c: In function 'g_band0_align':
bandalg0.c:273:9: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if(leftd >= 1)
^
At top level:
bandalg0.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg0.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF bandalg1.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg1.c:36:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg1.c: In function 'gband_quadratic':
bandalg1.c:54:14: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int4 c, i, j;
^
bandalg1.c: In function 'g_band1_align':
bandalg1.c:205:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if(leftd >= 1)
^
At top level:
bandalg1.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg1.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF bandalg2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg2.c:36:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg2.c: In function 'gb_linear_align':
bandalg2.c:208:24: warning: variable 'misma' set but not used [-Wunused-but-set-variable]
register Int4 match, misma;
^~~~~
bandalg2.c:208:17: warning: variable 'match' set but not used [-Wunused-but-set-variable]
register Int4 match, misma;
^~~~~
bandalg2.c:207:18: warning: variable 'AA' set but not used [-Wunused-but-set-variable]
register Uint1 AA;
^~
At top level:
bandalg2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg2.c,v 6.5 2003/05/30 17:25:35 coulouri Exp $";
^~~~~
bandalg2.c: In function 'gb_linear_align':
bandalg2.c:202:38: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 rmid, k =0, l=0, r, v, kt, X, Y;
^
In file included from bandalg2.c:36:0:
../include/bandalgn.h:140:76: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
data->last = (data->last < 0) ? (data->sapp[-1] -= (k)) : (*data->sapp++ = -(k));
^
bandalg2.c:202:35: note: 'X' was declared here
Int4 rmid, k =0, l=0, r, v, kt, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF bandalg3.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg3.c:37:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg3.c: In function 'gband_linear_qgap':
bandalg3.c:54:14: warning: variable 'j' set but not used [-Wunused-but-set-variable]
Int4 c, i, j;
^
At top level:
bandalg3.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: bandalg3.c,v 6.4 2003/05/30 17:25:36 coulouri Exp $";
^~~~~
bandalg3.c: In function 'gband_linear_qgap':
bandalg3.c:314:16: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
else if(Y != rightd) _INS(rightd-Y)
^
bandalg3.c:185:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
bandalg3.c:313:21: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(X != M) _DEL(M - X)
^
bandalg3.c:185:25: note: 'X' was declared here
Int4 ib, best=MININT, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF bandalg4.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/bandalgn.h:73,
from bandalg4.c:37:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalg4.c: In function 'g_band4_align_small':
bandalg4.c:826:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (e == 1)
^
bandalg4.c:829:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (e == 2)
^
bandalg4.c:630:8: warning: variable 'band' set but not used [-Wunused-but-set-variable]
Int4 band, j;
^~~~
At top level:
bandalg4.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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:562:7: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
g_band4_align(A, B, r - 1, r + rmid, rmid + 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MIN(up, r + rmid), tb, 1, legA, legB, 1, 1, data);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bandalg4.c:824:27: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
k = (t=data->state[i][j]) %5;
^
bandalg4.c:640:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
bandalg4.c:824:24: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
k = (t=data->state[i][j]) %5;
^
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 -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:184:3: 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' [-Wdangling-else]
if (e == 1)
^
bandalg5.c:295:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
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 $";
^~~~~
bandalg5.c: In function 'gband_q3gap':
bandalg5.c:320:6: warning: 'Y' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (Y != rightd) _INS(rightd - Y);
^
bandalg5.c:146:28: note: 'Y' was declared here
Int4 ib, best=MININT, X, Y;
^
bandalg5.c:319:22: warning: 'X' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (X != M) _DEL(M - X);
^
bandalg5.c:146:25: note: 'X' was declared here
Int4 ib, best=MININT, X, Y;
^
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF bandalgn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from bandalgn.c:118:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
bandalgn.c: In function 'ExtendSeqAlign':
bandalgn.c:1113:22: warning: variable 'ddp' set but not used [-Wunused-but-set-variable]
DenseDiagPtr ddp;
^~~
bandalgn.c: In function 'CC_ExtendSeqAlign':
bandalgn.c:1188:22: warning: variable 'ddp' set but not used [-Wunused-but-set-variable]
DenseDiagPtr ddp;
^~~
At top level:
bandalgn.c:699:14: warning: 'HSblastna_to_ncbi4na' defined but not used [-Wunused-variable]
static Uint1 HSblastna_to_ncbi4na[] = { 1, /* A, 0 */
^~~~~~~~~~~~~~~~~~~~
bandalgn.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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:1055:10: warning: 'maxdi' may be used uninitialized in this function [-Wmaybe-uninitialized]
maxy = maxdi + width;
~~~~~^~~~~~~~~~~~~~~
bandalgn.c:1056:10: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 * 4)) + (sizetype)((unsigned int)a * 4))' 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 -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:184:3: 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 -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:2057:
/usr/include/features.h:184:3: 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:2503:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (**filenames == '"')
^
readdb.c: In function 's_GetBlastDirInfo':
readdb.c:2734:32: 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:3320:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (rdfp->cih)
^~
readdb.c:3326:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (rdbap->first_oid > 0) {
^~
readdb.c:3400:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (rdfp->cih && rdfp->aliasfilebit == 0)
^~
readdb.c:3406:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (rdbap->first_oid > 0) {
^~
readdb.c: In function 'FindBlastDBFileEx':
readdb.c:3480:33: warning: unused variable 'envp' [-Wunused-variable]
CharPtr buffer, buffer1, envp = NULL;
^~~~
readdb.c: In function 'readdb_new_internalEx':
readdb.c:3558:25: warning: unused variable 'envp' [-Wunused-variable]
CharPtr charptr, envp = NULL;
^~~~
readdb.c: In function 'readdb_get_link':
readdb.c:4752:12: warning: variable 'loaded_new' set but not used [-Wunused-but-set-variable]
Boolean loaded_new = FALSE;
^~~~~~~~~~
readdb.c:4751:24: 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:4896:38: 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:5236:22: warning: unused variable 'dummy_gi' [-Wunused-variable]
Int4 dummy_gi = 0; /* Not used, should have been handled above. */
^~~~~~~~
readdb.c:5180:13: warning: unused variable 'chptr' [-Wunused-variable]
CharPtr chptr = NULL;
^~~~~
readdb.c: In function 'FDBuildOldStyleDefline':
readdb.c:6366:33: 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 'PrintDbInformationWithRID':
readdb.c:7571:14: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (rdfp == FALSE)
^~
readdb.c:7571:9: note: did you mean to dereference the pointer?
if (rdfp == FALSE)
^
readdb.c: In function 'FDBLoadMembershipsTable':
readdb.c:8265:21: warning: variable 'fn_name' set but not used [-Wunused-but-set-variable]
const char* fn_name = NULL;
^~~~~~~
readdb.c: In function 'SeqIdE2Index':
readdb.c:8613:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ((tsip->version > 0) && (tsip->release == NULL))
^~
readdb.c:8615:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
break;
^~~~~
readdb.c:8618:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (tsip->version > 0)
^~
readdb.c:8620:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
break;
^~~~~
readdb.c:8577:13: warning: unused variable 'tmp' [-Wunused-variable]
CharPtr tmp, ptr=NULL;
^~~
readdb.c:8576:11: warning: unused variable 'tmptype' [-Wunused-variable]
Uint1 tmptype;
^~~~~~~
readdb.c: In function 'SeqIdSetE2Index':
readdb.c:8881:14: warning: variable 'oldanp' set but not used [-Wunused-but-set-variable]
SeqIdPtr oldanp;
^~~~~~
readdb.c: In function 'FindDBbyGI':
readdb.c:11397:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (gi > cih->maxgi)
^~
readdb.c:11400:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
cigi = cih->ci + gi;
^~~~
readdb.c: In function 'Fastacmd_Search_ex':
readdb.c:12080:22: warning: variable 'guess_gi' set but not used [-Wunused-but-set-variable]
Int4 guess_gi = -1;
^~~~~~~~
readdb.c: In function 'DumpOneSequence':
readdb.c:12407:20: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
fprintf(fp, "%d\n", gi->data.intvalue);
~^ ~~~~~~~~~~~~~~~~~
%lld
readdb.c:12417:14: 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:2067:
readdb.c: At top level:
../include/objentgene.h:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: warning: 'Method_methodAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~~
readdb.c:12829:1: 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:2060:0:
../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 6.549 2016/09/02 15:04:59 ucko Exp $";
^~~~~
readdb.c: In function 'ReadDBOpenMHdrAndSeqFiles':
readdb.c:2259:27: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%chr", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:2277:27: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:2296:27: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%chr", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:2252:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:2252:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c: In function 'readdb_get_taxonomy_names':
readdb.c:5679:28: 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:6668:44: 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 'readdb_new_internalEx':
readdb.c:3671:25: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%cin", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3811:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%cnd", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3812:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer1, "%s.%cni", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3825:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer, "%s.%csd", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3826:26: warning: '%c' directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=]
sprintf(buffer1, "%s.%csi", rdfp->full_filename, is_prot? 'p':'n');
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3845:29: warning: '.ppd' directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
sprintf(buffer, "%s.ppd", rdfp->full_filename);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:3846:29: warning: '.ppi' directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
sprintf(buffer1, "%s.ppi", rdfp->full_filename);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c: In function 'GetAccList':
readdb.c:11821:29: warning: 'AccListLast' may be used uninitialized in this function [-Wmaybe-uninitialized]
AccListLast->next = AccListTmp;
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
readdb.c: In function 'FD_ConstructMultivolumeDBList':
readdb.c:12688:31: warning: '%02ld' directive writing between 2 and 10 bytes into a region of size 9 [-Wformat-overflow=]
sprintf(numstr, ".%02ld ", (long) i);
^~~~~
readdb.c:12688:29: note: directive argument in the range [0, 2147483647]
sprintf(numstr, ".%02ld ", (long) i);
^~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readdb.c:12690:31: warning: '%03ld' directive writing between 3 and 10 bytes into a region of size 9 [-Wformat-overflow=]
sprintf(numstr, ".%03ld ", (long) i);
^~~~~
readdb.c:12690:29: note: directive argument in the range [0, 2147483647]
sprintf(numstr, ".%03ld ", (long) i);
^~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from readdb.c:2057:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 6 and 13 bytes into a destination of size 10
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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;
^~~~~~~~~~
ncbisam.c:1070:23: warning: 'KeyDataSamples' may be used uninitialized in this function [-Wmaybe-uninitialized]
KeyDataSamples[SampleCount].key = SwapUint4(UINT4_MAX);
^
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 -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:86:
/usr/include/features.h:184:3: 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:699:12: warning: type defaults to 'int' in declaration of 'tmpa' [-Wimplicit-int]
register tmpa = UCHAR(*a), tmpb = UCHAR(*b);
^~~~
ncbisort.c:699:30: warning: type defaults to 'int' in declaration of 'tmpb' [-Wimplicit-int]
register tmpa = UCHAR(*a), tmpb = UCHAR(*b);
^~~~
In file included from ncbisort.c:86:0:
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 6.9 2012/08/22 23:02:39 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF salign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/salign.h:10,
from salign.c:45:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
salign.c: In function 'BandAlignTwoSeqLocsFunc':
salign.c:173:13: warning: variable 'is_prot' set but not used [-Wunused-but-set-variable]
Boolean is_prot;
^~~~~~~
salign.c: In function 'SortBlastHits':
salign.c:391:15: warning: variable 'totalvalmax' set but not used [-Wunused-but-set-variable]
totalvalmax = INT4_MAX,
^~~~~~~~~~~
salign.c: In function 'link_solution':
salign.c:1188:15: warning: unused variable 'first' [-Wunused-variable]
Boolean first = TRUE;
^~~~~
At top level:
salign.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: salign.c,v 6.11 2009/01/21 17:09:18 bollin Exp $";
^~~~~
salign.c: In function 'SortBlastHits':
salign.c:455:6: warning: 'salpdup' may be used uninitialized in this function [-Wmaybe-uninitialized]
SeqAlignSetFree (salpdup);
^~~~~~~~~~~~~~~~~~~~~~~~~
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.5':
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 -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:184:3: 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 were 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 were 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 were 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 were 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF urkutil.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/accentr.h:125,
from urkutil.c:59:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkutil.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkutil.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF urkpcc.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkpcc.h:54,
from urkpcc.c:56:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkpcc.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkpcc.c,v 6.13 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF urkptpf.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objres.h:73,
from urkptpf.c:65:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkptpf.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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 $";
^~~~~
urkepi.c: In function 'FilterEpi':
urkepi.c:1053:21: warning: 'right' may be used uninitialized in this function [-Wmaybe-uninitialized]
cfap->right = right;
~~~~~~~~~~~~^~~~~~~
urkepi.c:936:56: note: 'right' was declared here
Int4 i, n, j, k, start, stop, loop, fact, left, right;
^~~~~
urkepi.c:1052:20: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized]
cfap->left = left;
~~~~~~~~~~~^~~~~~
urkepi.c:936:50: note: 'left' was declared here
Int4 i, n, j, k, start, stop, loop, fact, left, right;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF urkfltr.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkfltr.h:51,
from urkfltr.c:56:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkfltr.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkfltr.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF urkdust.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkdust.h:51,
from urkdust.c:56:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkdust.c: In function 'DustMe_h':
urkdust.c:196:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
(dcvp->curlevel <= newlevel) && dcvp->curend == loop+1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
urkdust.c: In function 'DustForGraph':
urkdust.c:776:17: warning: variable 'drphead' set but not used [-Wunused-but-set-variable]
DustRegionPtr drphead;
^~~~~~~
At top level:
urkdust.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkdust.c,v 6.10 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF urksigu.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urksigu.h:57,
from urksigu.c:59:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urksigu.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urksigu.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF seg.c
seg.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seg.c,v 6.19 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
seg.c: In function 'getprob':
seg.c:935:15: warning: 'ans2' may be used uninitialized in this function [-Wmaybe-uninitialized]
ans = ans1 + ans2 - totseq;
~~~~~^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF urkbias.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from urkbias.c:56:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkbias.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkbias.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF urkcnsrt.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urkcnsrt.h:60,
from urkcnsrt.c:80:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urkcnsrt.c:1203:13: warning: 'ScanFrame' defined but not used [-Wunused-function]
static void ScanFrame (BioseqPtr bsp, SeqLocPtr slp, Int4 frame,
^~~~~~~~~
urkcnsrt.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: urkcnsrt.c,v 6.21 2003/05/30 17:25:38 coulouri Exp $";
^~~~~
urkcnsrt.c: In function 'Scan3Frames':
urkcnsrt.c:1385:5: warning: 'length' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (i = n; i < length; i++)
^~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF urktree.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/urktree.h:51,
from urktree.c:53:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
urktree.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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:507:12: 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 -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:184:3: 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:534:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) {
^~~
pattern1.c:547:7: 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:750:11: 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' [-Wdangling-else]
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 were 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 $";
^~~~~
pattern1.c: In function 'get_patL':
pattern1.c:1348:42: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
*end = wordIndex*BITS_PACKED_PER_WORD+j;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
pattern1.c: In function 'align':
pattern1.c:1158:8: warning: 'CDrow' may be used uninitialized in this function [-Wmaybe-uninitialized]
score = (CDrow-1)->CC;
~~~~~~^~~~~~~~~~~~~~~
pattern1.c: In function 'get_patLL':
pattern1.c:1393:5: warning: 'pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (j = 0; j < pos; j+= wordIndex) {
^~~
pattern1.c: In function 'init_pattern':
pattern1.c:192:11: warning: 'tj' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 tj; /*temporary copy of j*/
^~
pattern1.c: In function 'align_of_pattern':
pattern1.c:1562:19: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized]
local_score += ALIGN_B(querySeq-1, dbSeq-1, queryMatchOffset, dbMatchOffset,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BAND_LOW, BAND_HIGH, matrix, gap_open, gap_extend, alignScript, data);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF impatool.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from impatool.c:73:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
impatool.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: impatool.c,v 6.16 2006/06/30 18:44:40 camacho Exp $";
^~~~~
impatool.c: In function 'IMPALAPrintHelp':
impatool.c:301:20: warning: 'ret_buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
ret_buffer = MemFree(ret_buffer);
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF posit2.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from posit2.c:78:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
posit2.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: posit2.c,v 6.12 2006/09/18 20:54:27 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF mbalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/mbalign.h:4,
from mbalign.c:176:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
mbalign.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: mbalign.c,v 6.43 2006/02/02 17:57:34 papadopo Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF vecscrn.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/vecscrn.h:74,
from vecscrn.c:103:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
vecscrn.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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 -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:184:3: 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 'SaveUntilChar':
rpsutil.c:2190:13: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (ptr != NULLB)
^~
rpsutil.c:2190:9: note: did you mean to dereference the pointer?
if (ptr != NULLB)
^
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 'RPSInitEx':
rpsutil.c:451:28: warning: '.rps' directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
sprintf(rps_matrix, "%s.rps", rpsinfo->rdfp->full_filename);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/rpsutil.h:128,
from rpsutil.c:281:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:452:28: warning: '.loo' directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
sprintf(rps_lookup, "%s.loo", rpsinfo->rdfp->full_filename);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/rpsutil.h:128,
from rpsutil.c:281:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rpsutil.c:453:25: warning: '.aux' directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
sprintf(rps_aux, "%s.aux", rpsinfo->rdfp->full_filename);
^~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/rpsutil.h:128,
from rpsutil.c:281:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 4100 bytes into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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;
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
In file included from ../include/ncbi.h:62:0,
from ../include/rpsutil.h:128,
from rpsutil.c:281:
rpsutil.c: In function 'RPSBgetCddHits':
../include/ncbistr.h:284:20: warning: 'dbname' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Nlm_StrCmp strcmp
^~~~~~
rpsutil.c:2212:21: note: 'dbname' was declared here
CharPtr dbname;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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;
^
At top level:
kappa.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: kappa.c,v 6.94 2013/11/04 15:42:10 boratyng Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF xmlblast.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/xmlblast.h:89,
from xmlblast.c:171:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
xmlblast.c: In function 'PSIXmlInit':
xmlblast.c:1239:13: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
Boolean retval = FALSE;
^~~~~~
At top level:
xmlblast.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:184:3: 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 -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:184:3: 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] = {
^
4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4,
{ }
-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4,
{ }
-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4,
{ }
-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4,
{ }
0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4,
{ }
-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4,
{ }
-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4,
{ }
0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4,
{ }
-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4,
{ }
-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4,
{ }
-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4,
{ }
-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4,
{ }
-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4,
{ }
-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4,
{ }
-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4,
{ }
1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4,
{ }
0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4,
{ }
-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4,
{ }
-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4,
{ }
0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4,
{ }
-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4,
{ }
-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4,
{ }
0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4,
{ }
-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1
{
};
}
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 -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:263:
/usr/include/features.h:184:3: 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:1740:21: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
Int4 offset;
^~~~~~
spidey.c: In function 'SPI_AlnSinglemRNAToPieces':
spidey.c:2854:19: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if (spot->from == spot->to == 0)
~~~~~~~~~~~^~~~~~~~~~~
spidey.c: In function 'SPI_FillInLastmRNAHoles':
spidey.c:6299:21: warning: variable 'internal' set but not used [-Wunused-but-set-variable]
Boolean internal;
^~~~~~~~
spidey.c: In function 'SPI_FindBestAlnByDotPlot':
spidey.c:6445:20: warning: variable 'strand' set but not used [-Wunused-but-set-variable]
Uint1 strand;
^~~~~~
spidey.c:6444:20: warning: variable 'start2' set but not used [-Wunused-but-set-variable]
Int4 start2;
^~~~~~
spidey.c:6443:20: warning: variable 'start1' set but not used [-Wunused-but-set-variable]
Int4 start1;
^~~~~~
spidey.c: In function 'SPI_ConnectAlnPieces':
spidey.c:7814:30: warning: variable 'tmparray' set but not used [-Wunused-but-set-variable]
SPI_FragPtr PNTR tmparray;
^~~~~~~~
spidey.c:7800:25: warning: variable 'sfpprev' set but not used [-Wunused-but-set-variable]
SPI_FragPtr sfpprev;
^~~~~~~
spidey.c: In function 'SPI_AdjustSplicesInPieces':
spidey.c:8448:23: warning: variable 'minus' set but not used [-Wunused-but-set-variable]
Boolean minus;
^~~~~
spidey.c: In function 'SPI_CheckMrnaOrder':
spidey.c:10296:35: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if ((ival->strand == Seq_strand_plus == ival2->strand
spidey.c:10300:38: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
|| (ival->strand == Seq_strand_minus == ival2->strand
spidey.c:10313:35: warning: suggest parentheses around comparison in operand of '==' [-Wparentheses]
if ((ival->strand == Seq_strand_plus == ival2->strand
spidey.c:10315:38: 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:263:
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 6.74 2016/09/02 14:57:38 ucko Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF motif.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/motif.h:45,
from motif.c:47:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
motif.c: In function 'MOT_FindPolyA':
motif.c:86:18: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
Uint1 buf[MOT_WINSIZE];
^~~
motif.c: In function 'MOT_FindKozak':
motif.c:216:18: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
Uint1 buf[MOT_WINSIZE];
^~~
In file included from ../include/samutil.h:234:0,
from ../include/alignmgr2.h:114,
from ../include/actutils.h:105,
from ../include/motif.h:48,
from motif.c:47:
motif.c: At top level:
../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr ));
^~~~~~~~~~~
../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static' but never defined [-Wunused-function]
static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~
../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static' but never defined [-Wunused-function]
static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~
motif.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: motif.c,v 6.7 2007/05/07 13:30:54 kans Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blfmtutl.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from blfmtutl.c:175:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blfmtutl.c: In function 'CBStatisticsGetReference':
blfmtutl.c:593:4: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
} else
^~~~
blfmtutl.c:595:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
add_string_to_bufferEx("Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,", &ret_buffer, &ret_buffer_length, TRUE);
^~~~~~~~~~~~~~~~~~~~~~
blfmtutl.c: In function 'BlastPrintTabularResults':
blfmtutl.c:1281:16: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for (index=1; ssp->next; index++)
^~~
blfmtutl.c:1283:20: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
num_gap_opens = index / 2;
^~~~~~~~~~~~~
At top level:
blfmtutl.c:1:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blfmtutl.c,v 1.44 2012/10/10 14:05:50 fongah2 Exp $";
^~~~~
blfmtutl.c: In function 'BlastPrintTabularResults':
blfmtutl.c:1117:13: warning: 'alignments_count' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (--alignments_count < 0)
^
blfmtutl.c:1353:19: warning: 's_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
s_end += s_shift;
~~~~~~^~~~~~~~~~
blfmtutl.c:1352:21: warning: 's_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
s_start += s_shift;
~~~~~~~~^~~~~~~~~~
blfmtutl.c:1351:19: warning: 'q_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
q_end += q_shift;
~~~~~~^~~~~~~~~~
blfmtutl.c:1350:21: warning: 'q_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
q_start += q_shift;
~~~~~~~~^~~~~~~~~~
blfmtutl.c:1081:24: 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:1413:26: 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 -D_PNG -I../include -DWIN_MOTIF matrix_frequency_data.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF compo_mode_condition.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF composition_adjustment.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF nlm_linear_algebra.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF optimize_target_freq.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF compo_heap.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF smith_waterman.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF redo_alignment.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF unified_pvalues.c
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 -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:61,
from ../include/gifgen.h:115,
from gdfontg.c:1:
/usr/include/features.h:184:3: 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 -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:61,
from ../include/gifgen.h:115,
from gdfontmb.c:1:
/usr/include/features.h:184:3: 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 -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:61,
from ../include/gifgen.h:115,
from gdfontt.c:1:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:61,
from ../include/gifgen.h:115,
from gdfontl.c:1:
/usr/include/features.h:184:3: 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 -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:61,
from ../include/gifgen.h:115,
from gdfonts.c:1:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:184:3: 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:3448:15: warning: 'fZCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fZCen += fZt / l;
~~~~~~^~~~~~~~~~
algorend.c:3447:15: warning: 'fYCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fYCen += fYt / l;
~~~~~~^~~~~~~~~~
algorend.c:3446:15: warning: 'fXCen' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXCen += fXt / l;
~~~~~~^~~~~~~~~~
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:3449:77: warning: 'fYTo' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fYCen - fYFrom) * (fZCen - fZTo) - (fZCen - fZFrom) * (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:3449:22: warning: 'fYFrom' may be used uninitialized in this function [-Wmaybe-uninitialized]
fXt = (fYCen - fYFrom) * (fZCen - fZTo) - (fZCen - fZFrom) * (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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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]
{
^
255, 255, 255, /* default 0 */
{ }
255, 20, 147, /* hotpink 1 */
{ }
255, 0, 255, /* magenta 2 */
{ }
155, 48, 255, /* purple 3 */
{ }
0, 0, 255, /* blue 4 */
{ }
30, 144, 255, /* sky 5 */
{ }
0, 255, 255, /* cyan 6 */
{ }
0, 255, 127, /* sea 7 */
{ }
0, 255, 0, /* green 8 */
{ }
255, 255, 0, /* yellow 9 */
{ }
255, 165, 0, /* gold 10 */
{ }
255, 69, 0, /* orange 11 */
{ }
255, 0, 0, /* red 12 */
{ }
255, 114, 86, /* pink 13 */
{ }
255, 174, 185, /* pinktint 14 */
{ }
255, 255, 255, /* white 15 */
{ }
0, 0, 0, /* black 16 */
{ }
176, 226, 255, /* bluetint 17 */
{ }
154, 255, 154, /* greentint 18 */
{ }
255, 236, 139, /* yellowtint 19 */
{ }
125, 125, 125, /* gray 20 */
{ }
139, 87, 66, /* brown 21 */
{ }
255, 0, 0, /* perm colors 22: red */
{ }
0, 255, 0, /* perm colors 23: green */
{ }
255, 0, 255, /* perm colors 24: magenta */
{ }
30, 144, 255, /* perm colors 25: sky */
{ }
155, 48, 255, /* perm colors 26: purple */
{ }
0, 255, 0, /* SS colors 27: helix, green */
{ }
255, 165, 0, /* SS colors 28: strand, gold */
{ }
255, 69, 0, /* SS colors 29: turn, orange */
{ }
0, 255, 255, /* SS colors 30: coil, cyan */
{ }
255, 255, 0, /* highlight colors 31: yellow */
{ }
0, 0, 0, /* background colors 32: black */
{ }
160, 82, 45, /* sienna 33 */
{ }
240, 230, 140, /* khaki 34 */
{ }
171, 130, 255, /* light purple 35 */
{ }
255, 200, 0, /* orange yellow 36 */
{ }
117, 128, 160, /* 37 */
{ }
5, 53, 239, /* 38 */
{ }
27, 62, 255, /* 39 */
{ }
84, 110, 203, /* 40 */
{ }
216, 77, 84, /* 41 */
{ }
125, 128, 135, /* 42 */
{ }
237, 29, 61, /* 43 */
{ }
184, 118, 120, /* 44 */
{ }
155, 9, 0, /* 45 */
{ }
155, 119, 107, /* 46 */
{ }
80, 110, 196, /* 47 */
{ }
122, 127, 157, /* 48 */
{ }
50, 85, 241, /* 49 */
{ }
201, 93, 91, /* 50 */
{ }
254, 0, 5, /* 51 */
{ }
155, 137, 133, /* 52 */
{ }
3, 53, 246 /* 53 */
{
};
}
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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));
^~~~~~~~~~~~~~~
cn3dmodl.c: In function 'Cn3D_ListDomainProc':
cn3dmodl.c:410:34: warning: ' ' directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=]
sprintf(MolName, "%4s %2s", domaindata[iCount]->pcPDBName,
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 9 and 24 bytes into a destination of size 20
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmodl.c:413:34: warning: ' ' directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=]
sprintf(MolName, "%4s %2s %2d",
^~
cn3dmodl.c:413:30: note: directive argument in the range [-32768, 32767]
sprintf(MolName, "%4s %2s %2d",
^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 13 and 32 bytes into a destination of size 20
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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:1295:29: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
pars->PBBRender = 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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]
{
^
255, 255, 255, /* default 0 */
{ }
255, 20, 147, /* hotpink 1 */
{ }
255, 0, 255, /* magenta 2 */
{ }
155, 48, 255, /* purple 3 */
{ }
0, 0, 255, /* blue 4 */
{ }
30, 144, 255, /* sky 5 */
{ }
0, 255, 255, /* cyan 6 */
{ }
0, 255, 127, /* sea 7 */
{ }
0, 255, 0, /* green 8 */
{ }
255, 255, 0, /* yellow 9 */
{ }
255, 165, 0, /* gold 10 */
{ }
255, 69, 0, /* orange 11 */
{ }
255, 0, 0, /* red 12 */
{ }
255, 114, 86, /* pink 13 */
{ }
255, 174, 185, /* pinktint 14 */
{ }
255, 255, 255, /* white 15 */
{ }
0, 0, 0, /* black 16 */
{ }
176, 226, 255, /* bluetint 17 */
{ }
154, 255, 154, /* greentint 18 */
{ }
255, 236, 139, /* yellowtint 19 */
{ }
125, 125, 125, /* gray 20 */
{ }
139, 87, 66, /* brown 21 */
{ }
255, 0, 0, /* perm colors 22: red */
{ }
0, 255, 0, /* perm colors 23: green */
{ }
255, 0, 255, /* perm colors 24: magenta */
{ }
30, 144, 255, /* perm colors 25: sky */
{ }
155, 48, 255, /* perm colors 26: purple */
{ }
0, 255, 0, /* SS colors 27: helix, green */
{ }
255, 165, 0, /* SS colors 28: strand, gold */
{ }
255, 69, 0, /* SS colors 29: turn, orange */
{ }
0, 255, 255, /* SS colors 30: coil, cyan */
{ }
255, 255, 0, /* highlight colors 31: yellow */
{ }
0, 0, 0, /* background colors 32: black */
{ }
160, 82, 45, /* sienna 33 */
{ }
240, 230, 140, /* khaki 34 */
{ }
171, 130, 255, /* light purple 35 */
{ }
255, 200, 0, /* orange yellow 36 */
{ }
117, 128, 160, /* 37 */
{ }
5, 53, 239, /* 38 */
{ }
27, 62, 255, /* 39 */
{ }
84, 110, 203, /* 40 */
{ }
216, 77, 84, /* 41 */
{ }
125, 128, 135, /* 42 */
{ }
237, 29, 61, /* 43 */
{ }
184, 118, 120, /* 44 */
{ }
155, 9, 0, /* 45 */
{ }
155, 119, 107, /* 46 */
{ }
80, 110, 196, /* 47 */
{ }
122, 127, 157, /* 48 */
{ }
50, 85, 241, /* 49 */
{ }
201, 93, 91, /* 50 */
{ }
254, 0, 5, /* 51 */
{ }
155, 137, 133, /* 52 */
{ }
3, 53, 246 /* 53 */
{
};
}
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'; did you mean 'Nlm_InitAppContext'? [-Wimplicit-function-declaration]
Nlm_SetOGLContext(NULL, NULL, NULL, NULL);
^~~~~~~~~~~~~~~~~
Nlm_InitAppContext
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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:184:3: 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 -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:184:3: 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));
^~~~~~~~~~~~~~~
cn3dmodl.c: In function 'Cn3D_ListDomainProc':
cn3dmodl.c:410:34: warning: ' ' directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=]
sprintf(MolName, "%4s %2s", domaindata[iCount]->pcPDBName,
^~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 9 and 24 bytes into a destination of size 20
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cn3dmodl.c:413:34: warning: ' ' directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=]
sprintf(MolName, "%4s %2s %2d",
^~
cn3dmodl.c:413:30: note: directive argument in the range [-32768, 32767]
sprintf(MolName, "%4s %2s %2d",
^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from cn3dmodl.c:302:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 13 and 32 bytes into a destination of size 20
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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:184:3: 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: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 */
^~~
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++) {
^~~
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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -D_PNG -I../include -DWIN_MOTIF aa_ungapped.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_diagnostics.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_engine.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_extend.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_filter.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_gapalign.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_hits.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_itree.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_lookup.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_message.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_options.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_seg.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_seqsrc.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_sw.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_setup.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_stat.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_traceback.c
blast_traceback.c: In function 'BLAST_ComputeTraceback_MT':
blast_traceback.c:1500:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for default(none) num_threads(actual_num_threads) schedule(guided) if (actual_num_threads > 1) \
blast_traceback.c:1524:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(retval)
blast_traceback.c:1530:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush(has_been_interrupted)
blast_traceback.c:1561:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(tback_gen_code)
blast_traceback.c:1591:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(retval)
blast_traceback.c:1631:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(tback_gen_code)
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_util.c
blast_util.c: In function 'BlastProgram2Number':
blast_util.c:306:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (strcasecmp("mapper", program) == 0)
^~
blast_util.c:309:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return 0;
^~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF gapinfo.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF greedy_align.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF link_hsps.c
link_hsps.c: In function 's_FwdCompareHSPs':
link_hsps.c:133:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
else if (h1->context > h2->context)
^~
link_hsps.c:136:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (h1->query.offset < h2->query.offset)
^~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF lookup_wrap.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF na_ungapped.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF ncbi_math.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF ncbi_std.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF pattern.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF phi_extend.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF phi_lookup.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF lookup_util.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_encoding.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_psi.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_psi_priv.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_kappa.c
blast_kappa.c: In function 'Blast_RedoAlignmentCore_MT':
blast_kappa.c:3407:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel \
blast_kappa.c:3426:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
#pragma omp for schedule(static)
blast_kappa.c:3428:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush(interrupt)
blast_kappa.c:3489:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(intrpt)
blast_kappa.c:3491:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush(interrupt)
blast_kappa.c:3504:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(intrpt)
blast_kappa.c:3506:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush(interrupt)
blast_kappa.c:3722:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(intrpt)
blast_kappa.c:3724:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush(interrupt)
blast_kappa.c:3730:0: warning: ignoring #pragma omp barrier [-Wunknown-pragmas]
#pragma omp barrier
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF matrix_freq_ratios.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_hspstream.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_parameters.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_posit.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF phi_gapalign.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_program.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_query_info.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_tune.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_aalookup.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_nalookup.c
blast_nalookup.c: In function 's_NaHashLookupScanSubjectForWordCounts':
blast_nalookup.c:1850:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for if (num_threads > 1) num_threads(num_threads) \
blast_nalookup.c:1858:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical (get_sequence_for_word_counts)
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_aascan.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_nascan.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_dynarray.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF split_query.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF gencode_singleton.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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 -D_PNG -I../include -DWIN_MOTIF hspfilter_collector.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_hspstream_mt_utils.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_traceback_mt_priv.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF boost_erf.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF jumper.c
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 blast_hspstream_mt_utils.o blast_traceback_mt_priv.o boost_erf.o jumper.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 -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:184:3: 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 -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:88,
from blast_input.c:34:
/usr/include/features.h:184:3: 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 $";
^~~~~
blast_input.c: In function 'BLAST_GetQuerySeqLoc':
blast_input.c:98:21: warning: '%ld' directive writing between 1 and 7 bytes into a region of size 4 [-Wformat-overflow=]
sprintf(prefix, "%ld", (long) (*ctr/MAX_NUM_QUERIES));
^~~
blast_input.c:98:20: note: directive argument in the range [-131080, 131080]
sprintf(prefix, "%ld", (long) (*ctr/MAX_NUM_QUERIES));
^~~~~
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:88,
from blast_input.c:34:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 8 bytes into a destination of size 4
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 1.120 2012/10/10 14:07:01 fongah2 Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_mtlock.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:61,
from ../include/ncbithr.h:87,
from blast_mtlock.c:39:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_mtlock.c:35:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] =
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_options_api.c
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_prelim.c
blast_prelim.c: In function 'Blast_PrelimSearchThreadRun':
blast_prelim.c:100:9: warning: variable 'status' set but not used [-Wunused-but-set-variable]
Int2 status = 0;
^~~~~~
At top level:
blast_prelim.c:34:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_prelim.c,v 1.8 2006/05/24 21:17:50 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_returns.c
blast_returns.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_returns.c,v 1.39 2010/06/10 13:44:46 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_seq.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/sequtil.h:43,
from ../include/seqport.h:47,
from blast_seq.c:34:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_seq.c: In function 's_SeqLocFillSequenceBuffer':
blast_seq.c:529:10: warning: variable 'seq_code' set but not used [-Wunused-but-set-variable]
Uint1 seq_code, strand;
^~~~~~~~
At top level:
blast_seq.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_seq.c,v 1.89 2008/06/09 17:29:14 madden Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_seqalign.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from ../include/algo/blast/api/blast_seqalign.h:42,
from blast_seqalign.c:35:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_seqalign.c: In function 's_HSPListToSeqAlignUngapped':
blast_seqalign.c:343:26: warning: variable 'hspset_cnt_old' set but not used [-Wunused-but-set-variable]
Int4 hsp_cnt, index2, hspset_cnt_old;
^~~~~~~~~~~~~~
At top level:
blast_seqalign.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_seqalign.c,v 1.64 2010/02/12 20:54:54 maning Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF blast_tabular.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/algo/blast/api/blast_tabular.h:42,
from blast_tabular.c:35:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
blast_tabular.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: blast_tabular.c,v 1.41 2009/06/01 14:33:38 maning Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF repeats_filter.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/asn.h:54,
from ../include/objloc.h:88,
from ../include/algo/blast/api/repeats_filter.h:41,
from repeats_filter.c:41:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
repeats_filter.c:2:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: repeats_filter.c,v 1.19 2007/12/19 21:56:48 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF seqsrc_multiseq.c
seqsrc_multiseq.c:33:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$Id: seqsrc_multiseq.c,v 1.28 2011/05/26 20:59:45 camacho Exp $";
^~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -D_PNG -I../include -DWIN_MOTIF seqsrc_readdb.c
In file included from /usr/include/arm-linux-gnueabihf/sys/types.h:25:0,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ../include/readdb.h:757,
from ../include/algo/blast/api/seqsrc_readdb.h:38,
from seqsrc_readdb.c:35:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
seqsrc_readdb.c: In function 's_ReaddbGetNextChunk':
seqsrc_readdb.c:375:11: warning: variable 'real_readdb_entries' set but not used [-Wunused-but-set-variable]
Uint4 real_readdb_entries;
^~~~~~~~~~~~~~~~~~~
At top level:
seqsrc_readdb.c:32:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
static char const rcsid[] = "$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 -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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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 -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:88,
from ../include/algo/blast/api/dust_filter.h:41,
from dust_filter.c:41:
/usr/include/features.h:184:3: 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 -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:184:3: 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 -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:61,
from ../include/ncbithr.h:87,
from hspfilter_queue.c:41:
/usr/include/features.h:184:3: 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;
^~~~~~
hspfilter_queue.c: In function 's_BlastHSPQueueNew':
hspfilter_queue.c:157:24: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
writer->InitFnPtr = &s_BlastHSPQueueInit;
^
hspfilter_queue.c:158:24: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
writer->FinalFnPtr = &s_BlastHSPQueueFinal;
^
hspfilter_queue.c: In function 'BlastHSPQueueInfoNew':
hspfilter_queue.c:189:26: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
writer_info->NewFnPtr = &s_BlastHSPQueueNew;
^
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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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:184:3: 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 'AsnCodeGenEnumDefines':
asncode.c:736:28: warning: format '%d' expects argument of type 'int', but argument 4 has type 'Nlm_Int8 {aka long long int}' [-Wformat=]
sprintf (iter->buf, "%s %d\n", AsnCodeCleanName (avtp->name, lclbuf,
~^
%lld
CLEAN_FOR_SLOT, iter -> acip -> maxDefineLength), avtp->intvalue);
~~~~~~~~~~~~~~
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' [-Wdangling-else]
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:4238:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (iter->atp != NULL)
^
asncode.c: In function 'AsnCode':
asncode.c:4317:48: 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:1211: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" GNUTLS_INCLUDE=-DHAVE_LIBGNUTLS 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" 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:157: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib makeset.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/all.h:9,
from makeset.c:9:
/usr/include/features.h:184:3: 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:7293:0: warning: "RNA_QUAL" redefined
#define RNA_QUAL &at[2254]
../include/all.h:5823:0: note: this is the location of the previous definition
#define RNA_QUAL &at[1025]
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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib getmesh.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/allpub.h:9,
from getmesh.c:8:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib indexpub.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/allpub.h:9,
from indexpub.c:7:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib getpub.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/allpub.h:9,
from getpub.c:7:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib asn2ff.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/accentr.h:125,
from asn2ff.c:7:
/usr/include/features.h:184:3: 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:50,
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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib checksub.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 checksub.c:8:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib asndhuff.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 ../include/asn.h:54,
from ../include/objsset.h:48,
from ../include/casn.h:96,
from asndhuff.c:47:
/usr/include/features.h:184:3: 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:182:16: 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:221:16: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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 'RunProgram':
entrcmd.c:1096:19: warning: 'lsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (! ProcessOutput(lsp, db, outputSpec, processingCount,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lsp != NULL ? lsp->num : processingCount,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
parseOnly))
~~~~~~~~~~
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:2235:9: warning: 'lsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
RunProgram(programStr, lsp, db, FALSE);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
entrcmd.c:2191:31: warning: 'lsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
temp = lsp->uids[k];
~~~^~~~~~
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:1620:15: warning: 'vector' may be used uninitialized in this function [-Wmaybe-uninitialized]
lsp->uids = vector;
~~~~~~~~~~^~~~~~~~
entrcmd.c:1582:13: note: 'vector' was declared here
Int4Ptr vector;
^~~~~~
entrcmd.c:2170:24: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib errhdr.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 errhdr.c:1:
/usr/include/features.h:184:3: 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 cdscan -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib findspl.c -lncbiacc -lncbicdr -lncbiobj -lncbi \
-lconnssl -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/accentr.h:125,
from findspl.c:62:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib fa2htgs.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 ../include/subutil.h:50,
from fa2htgs.c:30:
/usr/include/features.h:184:3: 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 testval -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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 vecscreen -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib vecscreen.c -lncbitool \
-lblastcompadj -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 vecscreen.c:57:
/usr/include/features.h:184:3: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib gil2bin.c -lncbitool -lblastcompadj \
-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 gil2bin.c:47:
/usr/include/features.h:184:3: 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 were guarded by the 'else'
return 0;
^~~~~~
gcc -o asn2xml -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib asn2xml.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 asn2xml.c:21:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib debruijn.c -lblast -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 debruijn.c:38:
/usr/include/features.h:184:3: 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:384:15: 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:632:12: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib asn2idx.c -lncbitool -lblastcompadj -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 asn2idx.c:47:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib sortbyquote.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 sortbyquote.c:45:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib subfuse.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 subfuse.c:45:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib pcretest.c -lpcre
gcc -o demo_regexp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib pcredemo.c -lpcre
gcc -o demo_regexp_grep -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib pcregrep.c -lpcre
pcregrep.c: In function 'main':
pcregrep.c:515:64: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
if (pattern_count == 1) s[0] = 0; else sprintf(s, " number %d", j);
^~
pcregrep.c:515:55: note: directive argument in the range [0, 2147483647]
if (pattern_count == 1) s[0] = 0; else sprintf(s, " number %d", j);
^~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from pcregrep.c:9:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 19 bytes into a destination of size 16
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" GNUTLS_INCLUDE=-DHAVE_LIBGNUTLS 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" THREAD_OBJ="ncbithr.o" \
THREAD_OTHERLIBS="-lpthread" \
NETENTREZVERSION="2.02c2ASN1SPEC6" BLIB31=libvibnet.a \
OGLLIBS= VIBLIBS= VIB="Psequin sbtedit udv ddv taxblast idfetch 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:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/taxonomy/client/*.c .
set: No match.
makenet.unx:475: 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:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/id0arch/client/*.c .
set: No match.
makenet.unx:475: 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:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/misc/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/misc/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ssparse/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/ssparse/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libparsn/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/libparsn/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/smart/smartnet/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/smart/smartnet/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/www/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/www/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/query/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../internal/query/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/ctlib/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/ctlib/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/oslib/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/oslib/*.h ../include
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/idloadlib/*.c .
set: No match.
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./ln-if-absent ../network/sybutils/idloadlib/*.h ../include
set: No match.
makenet.unx:475: 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/export_cmt.c .
./ln-if-absent ../internal/parser/flat2asn.c .
makenet.unx:475: recipe for target 'copy' failed
make[2]: [copy] Error 1 (ignored)
./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:475: 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 -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:184:3: 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 -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:184:3: 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 -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:125:
/usr/include/features.h:184:3: 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:201:19: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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 were 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 -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:184:3: 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] = {
^
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
9, 7, 4, 3,
{ }
9, 8, 5, 3,
{ }
10, 9, 5, 3,
{ }
10, 10, 5, 3,
{ }
11, 10, 5, 3,
{ }
11, 11, 5, 3,
{ }
12, 11, 5, 3,
{ }
12, 11, 5, 3,
{ }
12, 11, 5, 3
{
};
}
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 were 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 -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:184:3: 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] = {
^
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
8, 6, 3, 3,
{ }
9, 7, 4, 3,
{ }
9, 8, 5, 3,
{ }
10, 9, 5, 3,
{ }
10, 10, 5, 3,
{ }
11, 10, 5, 3,
{ }
11, 11, 5, 3,
{ }
12, 11, 5, 3,
{ }
12, 11, 5, 3,
{ }
12, 11, 5, 3
{
};
}
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 were 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
netcnfg.c: In function 'ShowNetConfigForm':
netcnfg.c:319:23: warning: variable 'ppt1' set but not used [-Wunused-but-set-variable]
PrompT ppt0, ppt1;
^~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 -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:184:3: 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:92:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1InfoAsnRead':
objtax1.c:502:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:501:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1ErrorAsnRead':
objtax1.c:1131:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1130:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1NameAsnRead':
objtax1.c:1296:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1295:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon1DataAsnRead':
objtax1.c:1482:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c:1481:12: warning: unused variable 'isError' [-Wunused-variable]
Boolean isError = FALSE;
^~~~~~~
objtax1.c: In function 'Taxon2DataAsnRead':
objtax1.c:1670:16: warning: variable 'func' set but not used [-Wunused-but-set-variable]
AsnReadFunc func;
^~~~
objtax1.c: In function 'Taxon1ReqAsnRead':
objtax1.c:284:16: warning: 'choice' may be used uninitialized in this function [-Wmaybe-uninitialized]
anp->choice = choice;
~~~~~~~~~~~~^~~~~~~~
objtax1.c: In function 'Taxon1RespAsnRead':
objtax1.c:920:16: 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 -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:184:3: 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 -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:1611:22: warning: 'lst' may be used uninitialized in this function [-Wmaybe-uninitialized]
lst->next= dst= OrgModNew();
~~~~~~~~~^~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:73,
from parttree.c:79:
/usr/include/features.h:184:3: 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 -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 -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:161:
/usr/include/features.h:184:3: 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:1359:37: warning: variable 'linlines' set but not used [-Wunused-but-set-variable]
Int2 numtaxa, numorgs, numhits, linlines, longname;
^~~~~~~~
taxblast.c: In function 'RDTaxLookupReset':
taxblast.c:2050:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
At top level:
taxblast.c:1967:13: 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 6.31 2015/07/06 19:25:47 madden Exp $";
^~~~~
taxblast.c: In function 'TXBGetTargetGi.isra.3':
taxblast.c:504:12: 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 -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:184:3: 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 -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:184:3: 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);
^
id1arch.c:558:65: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(repl_date,"%-20s",shp->replace_date->str);
^
In file included from /usr/include/stdio.h:862:0,
from ../include/ncbilcl.h:154,
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/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output 21 or more bytes into a destination of size 20
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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 -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:184:3: 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 'SubmitRequest':
netblap3.c:1763:18: warning: 'bllist' may be used uninitialized in this function [-Wmaybe-uninitialized]
bllist->next = blresp;
~~~~~~~~~~~~~^~~~~~~~
netblap3.c:1698:19: note: 'bllist' was declared here
BlastResponsePtr bllist, blresp, head;
^~~~~~
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 -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:184:3: 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 -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:184:3: 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:495:27: 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 -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:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
medutil.c: In function 'FixPubEquiv':
medutil.c:1134:16: warning: variable 'got' set but not used [-Wunused-but-set-variable]
Boolean got;
^~~
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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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 \
-lncbicn3d -lddvlib -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb \
-lncbitxc2 -lncbiid1 -lnetblast -lncbitool -lblastcompadj -lncbimla \
-lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbiobj -lconnssl -lncbi \
-lm
sequin1.c:46:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
static char *date_of_compilation = __DATE__;
^~~~~~~~
sequin1.c:47:36: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
static char *time_of_compilation = __TIME__;
^~~~~~~~
In file 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:82,
from sequin1.c:53:
/usr/include/features.h:184:3: 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:4884:76: 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:5196:16: warning: variable 'rsult' set but not used [-Wunused-but-set-variable]
Boolean rsult;
^~~~~
sequin1.c: In function 'BioseqViewFormMenus':
sequin1.c:8357:18: warning: variable 'mssgext' set but not used [-Wunused-but-set-variable]
Int2 mssgext;
^~~~~~~
sequin1.c: In function 'DeleteSelectedFeatureOrDescriptor':
sequin1.c:8894:19: warning: variable 'itemtype' set but not used [-Wunused-but-set-variable]
Uint2 itemtype;
^~~~~~~~
sequin1.c:8893:19: warning: variable 'itemID' set but not used [-Wunused-but-set-variable]
Uint4 itemID;
^~~~~~
sequin1.c:8891:19: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sequin1.c: In function 'IsolationSourceOk':
sequin1.c:14815:11: warning: unused variable 'specific_bad_fmt' [-Wunused-variable]
CharPtr specific_bad_fmt = "isolation-source should have a value like seawater, soil, etc. '%s' is not a valid isolation-source.";
^~~~~~~~~~~~~~~~
sequin1.c:14811:11: warning: unused variable 'is_ambiguous' [-Wunused-variable]
Boolean is_ambiguous = FALSE;
^~~~~~~~~~~~
sequin1.c: In function 'WizardTrackerFree':
sequin1.c:15809:20: warning: variable 'sep_next' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep, sep_next;
^~~~~~~~
sequin1.c: In function 'AddCodingRegionFromWizard':
sequin1.c:15881:33: warning: variable 'nsep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr old, psep, nsep;
^~~~
sequin1.c: In function 'SetWizardTrackerBaseSrcQuals':
sequin1.c:16157:7: warning: enumeration value 'eVirusClass_Unknown' not handled in switch [-Wswitch]
switch (wiz->virus_class) {
^~~~~~
sequin1.c:16204:7: warning: enumeration value 'eCulturedKingdom_Unknown' not handled in switch [-Wswitch]
switch (wiz->cultured_kingdom) {
^~~~~~
sequin1.c:16140:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c: In function 'SetWizardTrackerExtraSrcQuals':
sequin1.c:16328:7: warning: enumeration value 'eVirusClass_Unknown' not handled in switch [-Wswitch]
switch (wiz->virus_class) {
^~~~~~
sequin1.c:16354:7: warning: enumeration value 'eCulturedKingdom_Unknown' not handled in switch [-Wswitch]
switch (wiz->cultured_kingdom) {
^~~~~~
sequin1.c:16321:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c: In function 'AddWizardFeatureCallback':
sequin1.c:16687:3: warning: enumeration value 'eVirusFeat_None' not handled in switch [-Wswitch]
switch (wiz->virus_feat) {
^~~~~~
sequin1.c:16687:3: warning: enumeration value 'eVirusFeat_CDS' not handled in switch [-Wswitch]
sequin1.c: In function 'GetWGSNote':
sequin1.c:17010:11: warning: unused variable 'fmt' [-Wunused-variable]
CharPtr fmt = "[%s][WGS wizard]";
^~~
sequin1.c: In function 'FinishWizardAndLaunchSequin':
sequin1.c:17052:5: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c: In function 'HaveUniqueCombinationOfQuals':
sequin1.c:17401:15: warning: variable 'num_quals' set but not used [-Wunused-but-set-variable]
Int4 num_quals;
^~~~~~~~~
sequin1.c: In function 'GetWizardQualifierProblems':
sequin1.c:20626:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:20626:3: warning: enumeration value 'eWizardType_WGS' not handled in switch [-Wswitch]
sequin1.c: In function 'VirusQualsOk':
sequin1.c:20931:5: warning: enumeration value 'eVirusClass_Unknown' not handled in switch [-Wswitch]
switch (wiz->virus_class) {
^~~~~~
sequin1.c: In function 'CulturedSamplesOk':
sequin1.c:21036:5: warning: enumeration value 'eCulturedKingdom_Unknown' not handled in switch [-Wswitch]
switch (wiz->cultured_kingdom) {
^~~~~~
sequin1.c: In function 'WizardSrcQualsOk':
sequin1.c:21347:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c: In function 'CreateWizardSrcQualsForm':
sequin1.c:22401:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:22401:3: warning: enumeration value 'eWizardType_WGS' not handled in switch [-Wswitch]
sequin1.c: In function 'CheckFeatureQualsUniqueness':
sequin1.c:22719:8: warning: variable 'num_rows' set but not used [-Wunused-but-set-variable]
Int4 num_rows, row_num;
^~~~~~~~
sequin1.c: In function 'WizardFeatureQualsOk':
sequin1.c:22810:11: warning: variable 'num_features' set but not used [-Wunused-but-set-variable]
Int4 num_features;
^~~~~~~~~~~~
sequin1.c: In function 'TabTableToMultiModTabTable':
sequin1.c:23178:16: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp = NULL;
^~~
sequin1.c: In function 'MultiModTableToTabTable':
sequin1.c:23257:21: warning: variable 'fq' set but not used [-Wunused-but-set-variable]
WizardFeatQualPtr fq;
^~
sequin1.c: In function 'ShowAllFeatureQualSequences':
sequin1.c:23777:15: warning: variable 'show_all' set but not used [-Wunused-but-set-variable]
Boolean show_all = TRUE;
^~~~~~~~
sequin1.c: In function 'TabTableLineFromFeature':
sequin1.c:24725:14: warning: unused variable 'vals' [-Wunused-variable]
ValNodePtr vals = NULL, q_vnp;
^~~~
sequin1.c: In function 'PregenerateFeatures':
sequin1.c:24775:22: warning: unused variable 'problems' [-Wunused-variable]
CharPtr PNTR problems = NULL;
^~~~~~~~
sequin1.c: In function 'SetQualForSequencesFromWizardList':
sequin1.c:26026:20: warning: unused variable 'rval' [-Wunused-variable]
Boolean rval = FALSE;
^~~~
sequin1.c: In function 'CollectWizardSetType':
sequin1.c:27538:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:27538:3: warning: enumeration value 'eWizardType_Microsatellite' not handled in switch [-Wswitch]
sequin1.c:27538:3: warning: enumeration value 'eWizardType_WGS' not handled in switch [-Wswitch]
sequin1.c: In function 'SequencingMethodToDialog':
sequin1.c:28361:27: warning: variable 'info' set but not used [-Wunused-but-set-variable]
SequencingMethodInfoPtr info;
^~~~
sequin1.c: In function 'CollectWizardSourceType':
sequin1.c:28943:5: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:28943:5: warning: enumeration value 'eWizardType_Microsatellite' not handled in switch [-Wswitch]
sequin1.c:28943:5: warning: enumeration value 'eWizardType_DLoop' not handled in switch [-Wswitch]
sequin1.c:28943:5: warning: enumeration value 'eWizardType_WGS' not handled in switch [-Wswitch]
sequin1.c: In function 'HaveWizardSourceType':
sequin1.c:28976:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:28976:3: warning: enumeration value 'eWizardType_UnculturedSamples' not handled in switch [-Wswitch]
sequin1.c:28976:3: warning: enumeration value 'eWizardType_Microsatellite' not handled in switch [-Wswitch]
sequin1.c:28976:3: warning: enumeration value 'eWizardType_DLoop' not handled in switch [-Wswitch]
sequin1.c:28976:3: warning: enumeration value 'eWizardType_WGS' not handled in switch [-Wswitch]
sequin1.c: In function 'WizardSourceTypeForm':
sequin1.c:29038:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:29038:3: warning: enumeration value 'eWizardType_UnculturedSamples' not handled in switch [-Wswitch]
sequin1.c:29038:3: warning: enumeration value 'eWizardType_Microsatellite' not handled in switch [-Wswitch]
sequin1.c:29038:3: warning: enumeration value 'eWizardType_DLoop' not handled in switch [-Wswitch]
sequin1.c:29038:3: warning: enumeration value 'eWizardType_WGS' not handled in switch [-Wswitch]
sequin1.c: In function 'PopulateAAPopup':
sequin1.c:29856:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
sequin1.c: In function 'CountAmbiProc':
sequin1.c:31452:11: warning: unused variable 'normal' [-Wunused-variable]
Int4 normal = 0;
^~~~~~
sequin1.c: In function 'OkToTrimAmbiguous':
sequin1.c:31765:25: warning: variable 'p2' set but not used [-Wunused-but-set-variable]
GrouP p2 = NULL;
^~
sequin1.c:31764:25: warning: variable 'p1' set but not used [-Wunused-but-set-variable]
PrompT p1, title = NULL, pr = NULL, pt = NULL;
^~
sequin1.c: In function 'WGSVectorScreen':
sequin1.c:32753:15: warning: unused variable 'reasons' [-Wunused-variable]
CharPtr reasons[] = {"Low Quality", "Vector Contamination", "Low Quality and Vector Contamination"};
^~~~~~~
sequin1.c: In function 'WGSSequenceAdjustment':
sequin1.c:32916:31: warning: too many arguments for format [-Wformat-extra-args]
fprintf (lip->fp, "%s (too short)\n", a->id, "Low Quality");
^~~~~~~~~~~~~~~~~~
sequin1.c:32841:15: warning: unused variable 'quit_problems' [-Wunused-variable]
CharPtr quit_problems = NULL;
^~~~~~~~~~~~~
sequin1.c:32839:15: warning: unused variable 'max_dist' [-Wunused-variable]
Int4 max_dist = 20;
^~~~~~~~
sequin1.c: In function 'SetFastaText':
sequin1.c:33423:15: warning: unused variable 'intro' [-Wunused-variable]
CharPtr intro = NULL;
^~~~~
sequin1.c: In function 'ImportSeqCallback':
sequin1.c:33567:11: warning: variable 'x' set but not used [-Wunused-but-set-variable]
Int4 x = 0;
^
sequin1.c: In function 'ExportWizardFASTA':
sequin1.c:33590:17: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE;
^~~~
sequin1.c: In function 'ImportWizardFASTA':
sequin1.c:33624:15: warning: unused variable 'changed' [-Wunused-variable]
Boolean changed = FALSE;
^~~~~~~
sequin1.c: In function 'WizardFASTAFwd':
sequin1.c:33916:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (frm->wiz->wizard_type) {
^~~~~~
sequin1.c:33916:3: warning: enumeration value 'eWizardType_UnculturedSamples' not handled in switch [-Wswitch]
sequin1.c:33916:3: warning: enumeration value 'eWizardType_Viruses' not handled in switch [-Wswitch]
sequin1.c:33916:3: warning: enumeration value 'eWizardType_CulturedSamples' not handled in switch [-Wswitch]
sequin1.c:33916:3: warning: enumeration value 'eWizardType_IGS' not handled in switch [-Wswitch]
sequin1.c:33916:3: warning: enumeration value 'eWizardType_Microsatellite' not handled in switch [-Wswitch]
sequin1.c:33916:3: warning: enumeration value 'eWizardType_WGS' not handled in switch [-Wswitch]
sequin1.c: In function 'WizardFASTABack':
sequin1.c:34038:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (frm->wiz->wizard_type) {
^~~~~~
sequin1.c:34038:3: warning: enumeration value 'eWizardType_WGS' not handled in switch [-Wswitch]
sequin1.c: In function 'WizardFastaHelpBtn':
sequin1.c:34089:3: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^~~~~~
sequin1.c:34089:3: warning: enumeration value 'eWizardType_WGS' 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:78:
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: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/strimprt.h:73:0,
from ../include/mmdbapi1.h:234,
from ../include/accentr.h:143,
from ../include/accutils.h:119,
from sequin1.c:78:
../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:78:
../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: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));
^~~~~~~~~~~~~~~
In file included from ../include/netblap3.h:135:0,
from ../include/ingenwin.h:62,
from sequin1.c:89:
../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:92:
../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:117:0:
../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:1504:11: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
sequin1.c: In function 'Entrez2QueryProc':
sequin1.c:9715:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system ("entrez2 &");
^~~~~~~~~~~~~~~~~~~~
At top level:
sequin1.c:33848:16: warning: 'IsSequencingMethodOkForTSA' defined but not used [-Wunused-function]
static Boolean IsSequencingMethodOkForTSA (WizardTrackerPtr wiz)
^~~~~~~~~~~~~~~~~~~~~~~~~~
sequin1.c:33103:16: warning: 's_TSAFastaExample' defined but not used [-Wunused-variable]
static CharPtr s_TSAFastaExample[] = {
^~~~~~~~~~~~~~~~~
sequin1.c:32740:13: warning: 'WGSVectorScreen' defined but not used [-Wunused-function]
static void WGSVectorScreen (WizardTrackerPtr wiz, ValNodeBlockPtr block, Int4 min_length, Int4 max_dist)
^~~~~~~~~~~~~~~
sequin1.c:32059:13: warning: 'TrimTSABases' defined but not used [-Wunused-function]
static void TrimTSABases (SeqEntryPtr PNTR sequences)
^~~~~~~~~~~~
sequin1.c:29180:16: warning: 'WizardAssemblyDescriptionForm' defined but not used [-Wunused-function]
static Boolean WizardAssemblyDescriptionForm (WizardTrackerPtr wiz)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin1.c:29123:16: warning: 'WizardCommentForm' defined but not used [-Wunused-function]
static Boolean WizardCommentForm (WizardTrackerPtr wiz)
^~~~~~~~~~~~~~~~~
sequin1.c:21709:16: warning: 's_TSASrcTblHelpMsgs' defined but not used [-Wunused-variable]
static CharPtr s_TSASrcTblHelpMsgs[] = {
^~~~~~~~~~~~~~~~~~~
sequin1.c:21228:16: warning: 'TSASrcQualsOk' defined but not used [-Wunused-function]
static Boolean TSASrcQualsOk (WizardTrackerPtr wiz)
^~~~~~~~~~~~~
sequin1.c:20543:21: warning: 'GetTSAQualifiersProblems' defined but not used [-Wunused-function]
static CharPtr PNTR GetTSAQualifiersProblems (WizardTrackerPtr wiz)
^~~~~~~~~~~~~~~~~~~~~~~~
sequin1.c:10760:13: warning: 'ObjMgrReport' defined but not used [-Wunused-function]
static void ObjMgrReport (IteM i)
^~~~~~~~~~~~
In file included from ../include/netblap3.h:134:0,
from ../include/ingenwin.h:62,
from sequin1.c:89:
../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:2000:5: 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:82,
from sequin1.c:53:
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:8356:27: 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:82,
from sequin2.c:45:
/usr/include/features.h:184:3: 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:2847:16: warning: variable 'deleted_rows' set but not used [-Wunused-but-set-variable]
Int4 deleted_rows;
^~~~~~~~~~~~
sequin2.c: In function 'ImportFastaDialog':
sequin2.c:4587:17: 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:4859:15: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
Char buffer [EXPORT_PAGE_WIDTH + 1];
^~~~~~
sequin2.c: In function 'ExportOneDeltaBioseq':
sequin2.c:4958:15: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
Char buffer [EXPORT_PAGE_WIDTH + 1];
^~~~~~
sequin2.c: In function 'FindBioseqWithValue':
sequin2.c:7807:17: warning: variable 'bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr bsp = NULL;
^~~
sequin2.c: In function 'CollectNucleotideProteinAssociations':
sequin2.c:9174:73: 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 'AddCDSToSeqEntry':
sequin2.c:9713:37: warning: unused variable 'scope' [-Wunused-variable]
SeqEntryPtr setsep = NULL, scope, old_scope;
^~~~~
sequin2.c: In function 'GetModNameStartFromEqLoc':
sequin2.c:11770:11: warning: variable 'match_quote' set but not used [-Wunused-but-set-variable]
Char match_quote;
^~~~~~~~~~~
sequin2.c: In function 'GetValueFromTitle':
sequin2.c:12334:15: warning: variable 'is_nontext' set but not used [-Wunused-but-set-variable]
Boolean is_nontext;
^~~~~~~~~~
sequin2.c: In function 'PrepareSourceAssistantTableData':
sequin2.c:13585:36: 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:13787:30: warning: variable 'changed_val' set but not used [-Wunused-but-set-variable]
Boolean changed_val = FALSE;
^~~~~~~~~~~
sequin2.c: In function 'ApplyRowListToIDAndTitleEdit':
sequin2.c:15438:32: 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:16349:26: warning: variable 'row_list' set but not used [-Wunused-but-set-variable]
ValNodePtr row_list = NULL;
^~~~~~~~
sequin2.c: In function 'ApplyOrgModColumn':
sequin2.c:17198:11: warning: variable 'is_nontext' set but not used [-Wunused-but-set-variable]
Boolean is_nontext;
^~~~~~~~~~
sequin2.c: In function 'PrepareSequenceAssistantTableData':
sequin2.c:18172:36: 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:19591:50: 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:19741:74: 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:20911:19: warning: variable 'start_col' set but not used [-Wunused-but-set-variable]
Int4 start_row, start_col;
^~~~~~~~~
sequin2.c:20911:8: warning: variable 'start_row' set but not used [-Wunused-but-set-variable]
Int4 start_row, start_col;
^~~~~~~~~
sequin2.c: In function 'DownloadAndDisplay':
sequin2.c:26575:17: warning: variable 'dbname' set but not used [-Wunused-but-set-variable]
CharPtr dbname;
^~~~~~
sequin2.c: In function 'DownloadProc':
sequin2.c:26725:17: warning: variable 'dbname' set but not used [-Wunused-but-set-variable]
CharPtr dbname;
^~~~~~
sequin2.c: In function 'LoadSecondaryAccessionNumbersPlusHistFromFile':
sequin2.c:27908:17: warning: variable 'need_seqid' set but not used [-Wunused-but-set-variable]
Boolean need_seqid;
^~~~~~~~~~
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:26330:13: warning: 'GetRawBsps' defined but not used [-Wunused-function]
static void GetRawBsps (BioseqPtr bsp, Pointer userdata)
^~~~~~~~~~
sequin2.c:24919:1: warning: 'SequenceAssistantValidateSegments' defined but not used [-Wunused-function]
SequenceAssistantValidateSegments
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin2.c:10685:17: warning: 'GetSeqIdFromSeqEntryPtr' defined but not used [-Wunused-function]
static SeqIdPtr GetSeqIdFromSeqEntryPtr (SeqEntryPtr sep)
^~~~~~~~~~~~~~~~~~~~~~~
sequin2.c:8106:20: warning: 'FindSeqEntryWithTranscriptID' defined but not used [-Wunused-function]
static SeqEntryPtr FindSeqEntryWithTranscriptID (SeqEntryPtr sep, CharPtr transcript_id)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin2.c:6863:13: warning: 'ParseDeflineToBiop' defined but not used [-Wunused-function]
static void ParseDeflineToBiop(CharPtr defline, BioSourcePtr biop)
^~~~~~~~~~~~~~~~~~
sequin2.c:3922:1: warning: 'ReadOneSegSet' defined but not used [-Wunused-function]
ReadOneSegSet
^~~~~~~~~~~~~
sequin2.c: In function 'InsertMostUsedFeatureValNodes':
sequin2.c:28178:22: 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:82,
from sequin3.c:45:
/usr/include/features.h:184:3: 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:542:12: warning: variable 'olddelta' set but not used [-Wunused-but-set-variable]
Pointer olddelta;
^~~~~~~~
sequin3.c: In function 'FixLocus':
sequin3.c:1019:15: warning: variable 'embl_code' set but not used [-Wunused-but-set-variable]
CharPtr ptr, embl_code;
^~~~~~~~~
sequin3.c: In function 'RemoveGeneXrefsOnBioseqs':
sequin3.c:2237:22: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
sequin3.c: In function 'MakeCDS':
sequin3.c:7040:27: warning: variable 'nsep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr psep, nsep, old, topsep;
^~~~
sequin3.c: In function 'ConvertOneCDSToMiscFeat':
sequin3.c:9217:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| must_have_stops && !HasInternalStops (sfp))
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
sequin3.c: In function 'SuppressGenesOnFeatures':
sequin3.c:11108:20: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
sequin3.c: In function 'CheckForExistingMolInfo':
sequin3.c:12443:17: warning: variable 'bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr bsp;
^~~
sequin3.c: In function 'RemoveNthCDS':
sequin3.c:19694:17: warning: variable 'segCount' set but not used [-Wunused-but-set-variable]
Int4 segCount;
^~~~~~~~
sequin3.c: In function 'InstantiateGapFeatCallback':
sequin3.c:20956:15: warning: variable 'fuzz' set but not used [-Wunused-but-set-variable]
IntFuzzPtr fuzz;
^~~~
sequin3.c: In function 'GlobalDisableStrainForwarding':
sequin3.c:23530:14: warning: unused variable 'lip' [-Wunused-variable]
LogInfoPtr lip;
^~~
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:23279:16: warning: 'SummarizeFieldDiff' defined but not used [-Wunused-function]
static CharPtr SummarizeFieldDiff (FieldDiffPtr diff)
^~~~~~~~~~~~~~~~~~
sequin3.c:22333:13: warning: 'TestSegregateByList' defined but not used [-Wunused-function]
static void TestSegregateByList (IteM i)
^~~~~~~~~~~~~~~~~~~
sequin3.c:21921:13: warning: 'LabelFungalRNAs' defined but not used [-Wunused-function]
static void LabelFungalRNAs (IteM i)
^~~~~~~~~~~~~~~
sequin3.c:21906:13: warning: 'WriteAccessionsCallback' defined but not used [-Wunused-function]
static void WriteAccessionsCallback (BioseqPtr bsp, Pointer data)
^~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:21398:13: warning: 'ModernizeGenes' defined but not used [-Wunused-function]
static void ModernizeGenes (IteM i)
^~~~~~~~~~~~~~
sequin3.c:21371:13: warning: 'ModernizeRNAs' defined but not used [-Wunused-function]
static void ModernizeRNAs (IteM i)
^~~~~~~~~~~~~
sequin3.c:21344:13: warning: 'ModernizePCRs' defined but not used [-Wunused-function]
static void ModernizePCRs (IteM i)
^~~~~~~~~~~~~
sequin3.c:21234:13: warning: 'TestTax3B' defined but not used [-Wunused-function]
static void TestTax3B (IteM i)
^~~~~~~~~
sequin3.c:21228:13: warning: 'TestTax3A' defined but not used [-Wunused-function]
static void TestTax3A (IteM i)
^~~~~~~~~
sequin3.c:21095:13: warning: 'NewAligmentViewer' defined but not used [-Wunused-function]
static void NewAligmentViewer (IteM i)
^~~~~~~~~~~~~~~~~
sequin3.c:21064:13: warning: 'AddAllDbxrefsMenuItem' defined but not used [-Wunused-function]
static void AddAllDbxrefsMenuItem (IteM i)
^~~~~~~~~~~~~~~~~~~~~
sequin3.c:17134:16: warning: 's_NextQualifies' defined but not used [-Wunused-function]
static Boolean s_NextQualifies (SeqFeatPtr sfp,
^~~~~~~~~~~~~~~
sequin3.c:14836:25: warning: 'FsaStreamProc' defined but not used [-Wunused-function]
static void LIBCALLBACK FsaStreamProc (
^~~~~~~~~~~~~
sequin3.c:13705:13: warning: 'PrepareTaxListProc' defined but not used [-Wunused-function]
static void PrepareTaxListProc (IteM i)
^~~~~~~~~~~~~~~~~~
sequin3.c:11155:19: warning: 'CopyGeneRef' defined but not used [-Wunused-function]
static GeneRefPtr CopyGeneRef (GeneRefPtr srcGrp)
^~~~~~~~~~~
sequin3.c:5388:13: warning: 'InstantiateAssemblyGapFeats' defined but not used [-Wunused-function]
static void InstantiateAssemblyGapFeats (BioseqPtr bsp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:5310:16: warning: 'ValidateAssemblyGapFeat' defined but not used [-Wunused-function]
static Boolean ValidateAssemblyGapFeat (SeqFeatPtr sfp, BioseqPtr bsp)
^~~~~~~~~~~~~~~~~~~~~~~
sequin3.c:5268:13: warning: 'linkEvValues' defined but not used [-Wunused-variable]
static Int4 linkEvValues [] = {
^~~~~~~~~~~~
sequin3.c:5253:16: warning: 'linkEvStrings' defined but not used [-Wunused-variable]
static CharPtr linkEvStrings [] = {
^~~~~~~~~~~~~
sequin3.c:5237:13: warning: 'gapTypeValues' defined but not used [-Wunused-variable]
static Int4 gapTypeValues [] = {
^~~~~~~~~~~~~
sequin3.c:5220:16: warning: 'gapTypeStrings' defined but not used [-Wunused-variable]
static CharPtr gapTypeStrings [] = {
^~~~~~~~~~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from sequin.h:82,
from sequin3.c:45:
sequin3.c: In function 'AddMissingFieldsFromBioSample':
../include/vibdefns.h:318:18: warning: 'summ' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define CheckBox Nlm_CheckBox
^~~~~~~~~~~~
sequin3.c:23379:14: note: 'summ' was declared here
CharPtr summ, prev = NULL;
^~~~
sequin3.c: In function 'MakeBioSampleUpdateTable':
sequin3.c:22980:30: warning: 'diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
FieldDiffPtr sdiff, ddiff, diff;
^~~~
sequin3.c: In function 'CompareWithBioSampleEx':
sequin3.c:23104:30: warning: 'diff' may be used uninitialized in this function [-Wmaybe-uninitialized]
FieldDiffPtr sdiff, ddiff, diff;
^~~~
In file 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:82,
from sequin4.c:45:
/usr/include/features.h:184:3: 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:1621:20: warning: variable 'set_sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep, set_sep;
^~~~~~~
sequin4.c: In function 'RemoveOneSegSet':
sequin4.c:2295:30: 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:3142:20: warning: variable 'bssp' set but not used [-Wunused-but-set-variable]
BioseqSetPtr bssp;
^~~~
sequin4.c: In function 'LaunchOrfViewer':
sequin4.c:7256:9: warning: variable 'qu' set but not used [-Wunused-but-set-variable]
ButtoN qu, b1;
^~
sequin4.c: In function 'MRnaFromCdsCallback':
sequin4.c:7624:17: warning: variable 'entityID' set but not used [-Wunused-but-set-variable]
Uint2 entityID;
^~~~~~~~
sequin4.c: In function 'FindNonACGT':
sequin4.c:8773:21: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
sequin4.c: In function 'GetPubStatus':
sequin4.c:10801:14: 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:14157:13: warning: 'CleanupTruncateByProtAlignForm' defined but not used [-Wunused-function]
static void CleanupTruncateByProtAlignForm (GraphiC g, VoidPtr data)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin4.c:13699:25: warning: 'FeatToDeltaSeq' defined but not used [-Wunused-function]
static Int2 LIBCALLBACK FeatToDeltaSeq (Pointer data)
^~~~~~~~~~~~~~
sequin4.c:13659:16: warning: 'ListRawSequencesInAlignments' defined but not used [-Wunused-function]
static Boolean ListRawSequencesInAlignments (GatherContextPtr gcp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin4.c:9889:13: warning: 'PubConstraintClearText' defined but not used [-Wunused-function]
static void PubConstraintClearText (PubConstraintPtr pcp)
^~~~~~~~~~~~~~~~~~~~~~
sequin4.c:8853:18: warning: 'RevStringUpper' defined but not used [-Wunused-function]
static void NEAR RevStringUpper (CharPtr str)
^~~~~~~~~~~~~~
sequin4.c:8504:13: warning: 'MakeGeneXref' defined but not used [-Wunused-function]
static void MakeGeneXref (SeqFeatPtr sfpr, SeqFeatPtr sfpg)
^~~~~~~~~~~~
sequin4.c:6747:13: warning: 'AddOrfListToDoc' defined but not used [-Wunused-function]
static void AddOrfListToDoc(DoC doc, ValNodePtr list)
^~~~~~~~~~~~~~~
sequin4.c:3264:17: warning: 'CorrectIDsForSeqHistAlign' defined but not used [-Wunused-function]
static SeqIdPtr CorrectIDsForSeqHistAlign (TAlignmentFilePtr afp, SeqEntryPtr sep)
^~~~~~~~~~~~~~~~~~~~~~~~~
sequin4.c:3237:18: 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:50,
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 'ExplodeGroup.isra.99':
sequin4.c:5521:9: warning: 'nucbsp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SetExplodedProtein (orig_prot, nucprot_bssp, nucbsp, sfp, prot_id_str_prefix, cum_offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin4.c: In function 'MakeExonsFromFeatureIntervalsVisitFunc':
sequin4.c:5910:14: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
intron = AddIntronForInterval (bsp->length, stop, last, strand, bsp, fuzz_from, fuzz_to, part_number);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin4.c:5801:15: note: 'strand' was declared here
Uint1 strand;
^~~~~~
sequin4.c:5910:14: warning: 'stop' may be used uninitialized in this function [-Wmaybe-uninitialized]
intron = AddIntronForInterval (bsp->length, stop, last, strand, bsp, fuzz_from, fuzz_to, part_number);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin4.c:5800:15: note: 'stop' was declared here
Int4 stop;
^~~~
sequin4.c:5908:14: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
intron = AddIntronForInterval (start, -1, last, strand, bsp, fuzz_from, fuzz_to, part_number);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin4.c:5799:15: note: 'start' was declared here
Int4 start;
^~~~~
In file 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:82,
from sequin5.c:47:
/usr/include/features.h:184:3: 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:247:18: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
sequin5.c: In function 'RemoveGBIDsProc':
sequin5.c:1372:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
sequin5.c: In function 'RemoveGBProtIDsProc':
sequin5.c:1422:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
sequin5.c: In function 'RemoveGIProc':
sequin5.c:1473:18: warning: variable 'nextid' set but not used [-Wunused-but-set-variable]
SeqIdPtr nextid, sip;
^~~~~~
sequin5.c: In function 'SetmRNAFieldString':
sequin5.c:6548:17: warning: variable 'field_choice' set but not used [-Wunused-but-set-variable]
Int4 field_choice;
^~~~~~~~~~~~
sequin5.c: In function 'GetCDSGeneProtField':
sequin5.c:7233:11: warning: variable 'field_choice' set but not used [-Wunused-but-set-variable]
Int4 field_choice;
^~~~~~~~~~~~
sequin5.c: In function 'GetRNAFieldString':
sequin5.c:7628:21: warning: variable 'field_choice' set but not used [-Wunused-but-set-variable]
Int4 field_choice;
^~~~~~~~~~~~
sequin5.c:7622:14: warning: variable 'rrp' set but not used [-Wunused-but-set-variable]
RnaRefPtr rrp;
^~~
sequin5.c: In function 'SetRNAFieldString':
sequin5.c:7863:17: warning: variable 'rrp' set but not used [-Wunused-but-set-variable]
RnaRefPtr rrp;
^~~
sequin5.c: In function 'BioseqConstrainedFeaturesCallback':
sequin5.c:11293:21: warning: variable 'cop' set but not used [-Wunused-but-set-variable]
ConstraintOpPtr cop;
^~~
sequin5.c: In function 'SampleDialogCopy':
sequin5.c:13545:53: 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:13545:42: 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:14066:31: warning: variable 'dlg' set but not used [-Wunused-but-set-variable]
FeatureFieldChoiceDialogPtr dlg;
^~~
sequin5.c: In function 'CreateClickableListForSourceFeats':
sequin5.c:14854:27: warning: variable 'insertion_seq_txt' set but not used [-Wunused-but-set-variable]
CharPtr transposon_txt, insertion_seq_txt, note_txt;
^~~~~~~~~~~~~~~~~
sequin5.c:14854:11: 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:15014:24: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Boolean rval = FALSE;
^~~~
sequin5.c: In function 'GetRegionOpts':
sequin5.c:15152:25: warning: unused variable 'rval' [-Wunused-variable]
Boolean rval = FALSE;
^~~~
sequin5.c: In function 'NewConvertFeaturesByList':
sequin5.c:15322:14: warning: unused variable 'only_pseudo' [-Wunused-variable]
Boolean only_pseudo = FALSE;
^~~~~~~~~~~
sequin5.c: In function 'FeatureRemoveOrConvertAction':
sequin5.c:15588:25: warning: variable 'sfp' set but not used [-Wunused-but-set-variable]
SeqFeatPtr sfp;
^~~
sequin5.c: In function 'CDSGeneProtAECRDialog':
sequin5.c:18564:25: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin5.c: In function 'CDSGeneProtConvert':
sequin5.c:18931:18: warning: unused variable 'str_dst' [-Wunused-variable]
CharPtr str_dst = NULL;
^~~~~~~
sequin5.c: In function 'CDSGeneProtParse':
sequin5.c:19141:18: warning: variable 'avd' set but not used [-Wunused-but-set-variable]
ApplyValueData avd;
^~~
sequin5.c: In function 'RNAQualListDialog':
sequin5.c:21603:22: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin5.c: In function 'GetRNAFeatureList':
sequin5.c:21792:14: warning: variable 'matches' set but not used [-Wunused-but-set-variable]
Boolean matches;
^~~~~~~
sequin5.c: In function 'RNAQualConvertSwapParseList':
sequin5.c:21924:26: warning: variable 'avd' set but not used [-Wunused-but-set-variable]
ApplyValueData avd;
^~~
sequin5.c: In function 'RNAQualEditRemoveList':
sequin5.c:22021:20: warning: unused variable 'rval' [-Wunused-variable]
Boolean rval = TRUE;
^~~~
sequin5.c: In function 'GetGBQualSampleName':
sequin5.c:22729:14: warning: variable 'num_feature_choices' set but not used [-Wunused-but-set-variable]
Int4 num_feature_choices;
^~~~~~~~~~~~~~~~~~~
sequin5.c: In function 'ConvertGeneLocusTagToOldLocusTagCallback':
sequin5.c:22964:28: warning: variable 'mp' set but not used [-Wunused-but-set-variable]
LocusTagToOldLocusTagPtr mp;
^~
sequin5.c: In function 'NewSegregateBioseqSet':
sequin5.c:26425:22: warning: variable 'p' set but not used [-Wunused-but-set-variable]
PrompT p, p2;
^
sequin5.c: In function 'CompareBulkRows':
sequin5.c:27910:8: warning: variable 'col' set but not used [-Wunused-but-set-variable]
Int4 col;
^~~
sequin5.c: In function 'ResortBulkEditorRows':
sequin5.c:28177:20: warning: unused variable 'matches' [-Wunused-variable]
ValNodePtr matches = NULL, vnp;
^~~~~~~
sequin5.c:28174:26: warning: unused variable 'last_inserted' [-Wunused-variable]
Int4 row_num, sub_num, last_inserted = 0, comp, col;
^~~~~~~~~~~~~
sequin5.c: In function 'UpdateBulkEdDisplay':
sequin5.c:29258:17: warning: unused variable 'text_len' [-Wunused-variable]
Int4 i, text_len = 0, sub_num;
^~~~~~~~
sequin5.c: In function 'AddColumnToRowList':
sequin5.c:29993:11: warning: unused variable 'm' [-Wunused-variable]
Int4 i, m = 0, f = 0, num_columns = 1;
^
sequin5.c: In function 'ApplyBulkEditCommon':
sequin5.c:30418:23: warning: unused variable 'need_redraw' [-Wunused-variable]
Boolean need_redraw = FALSE;
^~~~~~~~~~~
sequin5.c: In function 'CopyAllFieldsFromList':
sequin5.c:30773:8: warning: unused variable 'num_full' [-Wunused-variable]
Int4 num_full = 0;
^~~~~~~~
sequin5.c: In function 'BulkEditorObjectList':
sequin5.c:32741:22: warning: unused variable 'subtype' [-Wunused-variable]
Uint1 subtype = 0;
^~~~~~~
sequin5.c: In function 'BulkEditorBaseForm':
sequin5.c:32798:22: warning: variable 'field_list' set but not used [-Wunused-but-set-variable]
BulkEdFieldPtr field_list = NULL;
^~~~~~~~~~
sequin5.c: In function 'GetSpecificHostCorrectionCategory':
sequin5.c:33567:22: 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:32057:13: warning: 'BulkSrcSetOrgModDescTF' defined but not used [-Wunused-function]
static void BulkSrcSetOrgModDescTF (Pointer target, Pointer data, Uint2 mod_type)
^~~~~~~~~~~~~~~~~~~~~~
sequin5.c:32036:16: warning: 'BulkSrcGetOrgModDescTF' defined but not used [-Wunused-function]
static Pointer BulkSrcGetOrgModDescTF (Uint1 data_choice, Pointer data, Uint2 mod_type)
^~~~~~~~~~~~~~~~~~~~~~
sequin5.c:31734:23: warning: 'GetBulkEditorFieldListForFeature' defined but not used [-Wunused-function]
static BulkEdFieldPtr GetBulkEditorFieldListForFeature (SeqFeatPtr sfp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin5.c:31268:16: warning: 'BulkGetPseudo' defined but not used [-Wunused-function]
static Pointer BulkGetPseudo (Pointer data)
^~~~~~~~~~~~~
sequin5.c:31257:13: warning: 'BulkSetPseudo' defined but not used [-Wunused-function]
static void BulkSetPseudo (Pointer target, Pointer val)
^~~~~~~~~~~~~
sequin5.c:31246:16: warning: 'BulkReleaseTrueFalse' defined but not used [-Wunused-function]
static Pointer BulkReleaseTrueFalse (Pointer p)
^~~~~~~~~~~~~~~~~~~~
sequin5.c:31080:15: warning: 'BulkNucLocationDialog' defined but not used [-Wunused-function]
static DialoG BulkNucLocationDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
^~~~~~~~~~~~~~~~~~~~~
sequin5.c:28858:28: warning: 'TwoFieldBulkEditNew' defined but not used [-Wunused-function]
static TwoFieldBulkEditPtr TwoFieldBulkEditNew (void)
^~~~~~~~~~~~~~~~~~~
sequin5.c:28605:28: warning: 'OneFieldBulkEditNew' defined but not used [-Wunused-function]
static OneFieldBulkEditPtr OneFieldBulkEditNew (void)
^~~~~~~~~~~~~~~~~~~
sequin5.c:28101:13: warning: 'FlatCopyRows' defined but not used [-Wunused-function]
static Int4 FlatCopyRows (BulkEditorRowPtr new_rows, BulkEditorRowPtr orig_rows, BulkEdFieldPtr field_list)
^~~~~~~~~~~~
sequin5.c:27569:13: warning: 'FreeBulkEditorValuesList' defined but not used [-Wunused-function]
static void FreeBulkEditorValuesList (ValNodePtr PNTR values_list, Int4 num_rows, BulkEdFieldPtr field_list)
^~~~~~~~~~~~~~~~~~~~~~~~
sequin5.c:21287:23: warning: 'AECRRNAQualFree' defined but not used [-Wunused-function]
static AECRRNAQualPtr AECRRNAQualFree (AECRRNAQualPtr ap)
^~~~~~~~~~~~~~~
sequin5.c:12796:25: warning: 'ParseFieldSrcFree' defined but not used [-Wunused-function]
static ParseFieldSrcPtr ParseFieldSrcFree (ParseFieldSrcPtr pfsp)
^~~~~~~~~~~~~~~~~
sequin5.c:438:13: warning: 'ProcessOligo' defined but not used [-Wunused-function]
static void ProcessOligo (SeqEntryPtr sep, CharPtr sequence, CharPtr title)
^~~~~~~~~~~~
sequin5.c:171:16: warning: 'GetSequenceString' defined but not used [-Wunused-function]
static CharPtr GetSequenceString (BioseqPtr bsp)
^~~~~~~~~~~~~~~~~
sequin5.c:88:13: warning: 'CommonLaunchBioseqViewer' defined but not used [-Wunused-function]
static void CommonLaunchBioseqViewer (SeqEntryPtr sep, CharPtr path, Boolean directToEditor)
^~~~~~~~~~~~~~~~~~~~~~~~
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 'ConvertDescriptorFieldCallback':
sequin5.c:5784:18: 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:82,
from sequin5.c:47:
sequin5.c: In function 'ApplyEditConvertRemoveCombo.constprop':
../include/vibdefns.h:535:22: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AlignObjects Nlm_AlignObjects
^~~~~~~~~~~~~~~~
sequin5.c:17563:42: 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:82,
from sequin6.c:45:
/usr/include/features.h:184:3: 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 'RemoveOrgModText':
sequin6.c:3069:35: warning: variable 'next_mod' set but not used [-Wunused-but-set-variable]
OrgModPtr mod, prev_mod = NULL, next_mod;
^~~~~~~~
sequin6.c: In function 'TrimCodingRegionsFoNsCallback':
sequin6.c:4576:31: warning: unused variable 'cut' [-Wunused-variable]
SeqLocPtr slp, sp, cut;
^~~
sequin6.c:4576:22: warning: unused variable 'slp' [-Wunused-variable]
SeqLocPtr slp, sp, cut;
^~~
sequin6.c: In function 'GapLocationsFromNs':
sequin6.c:4750:15: warning: variable 'seq_ext' set but not used [-Wunused-but-set-variable]
ValNodePtr seq_ext;
^~~~~~~
sequin6.c:4749:15: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len;
^~~
sequin6.c: In function 'ApplyBioFeatToList':
sequin6.c:6400:23: warning: variable 'oldscope' set but not used [-Wunused-but-set-variable]
SeqEntryPtr nsep, oldscope;
^~~~~~~~
sequin6.c: In function 'RNAWordsFromString':
sequin6.c:13298:32: warning: variable 'last_pos' set but not used [-Wunused-but-set-variable]
CharPtr last_hit = NULL, last_pos = NULL;
^~~~~~~~
sequin6.c:13298:15: 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:14382:15: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin6.c: In function 'DoPartialFeatureProc':
sequin6.c:14631:16: warning: variable 'dash_at_end' set but not used [-Wunused-but-set-variable]
Boolean dash_at_end = FALSE;
^~~~~~~~~~~
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:9215:13: warning: 'LongestMatch' defined but not used [-Wunused-function]
static Int2 LongestMatch (
^~~~~~~~~~~~
sequin6.c:9121:13: warning: 'RevcompString' defined but not used [-Wunused-function]
static void RevcompString (
^~~~~~~~~~~~~
sequin6.c:9093:13: warning: 'ExtractString' defined but not used [-Wunused-function]
static void ExtractString (
^~~~~~~~~~~~~
sequin6.c:5459:1: warning: 'RemoveTerminalNsFromLocation' defined but not used [-Wunused-function]
RemoveTerminalNsFromLocation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin6.c:5046:13: warning: 'AppendFirstToFeat' defined but not used [-Wunused-function]
static void AppendFirstToFeat (SeqFeatPtr sfp, Pointer userdata)
^~~~~~~~~~~~~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from sequin.h:82,
from sequin6.c:45:
sequin6.c: In function 'CreateFieldSubfieldDlg.constprop':
../include/vibdefns.h:535:22: warning: 'g2' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define AlignObjects Nlm_AlignObjects
^~~~~~~~~~~~~~~~
sequin6.c:430:29: note: 'g2' was declared here
GrouP p, g, g2;
^~
sequin7.c:46:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
static char *date_of_compilation = __DATE__;
^~~~~~~~
sequin7.c:47:36: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
static char *time_of_compilation = __TIME__;
^~~~~~~~
In file 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:82,
from sequin7.c:53:
/usr/include/features.h:184:3: 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:959:18: warning: variable 'grp' set but not used [-Wunused-but-set-variable]
GeneRefPtr grp;
^~~
sequin7.c: In function 'FinishConvertingToCDS':
sequin7.c:2771:17: warning: variable 'nsep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr nsep;
^~~~
sequin7.c: In function 'SetBestFrame':
sequin7.c:5218:26: warning: variable 'seq_str2' set but not used [-Wunused-but-set-variable]
CharPtr seq_str1, seq_str2;
^~~~~~~~
sequin7.c:5218:16: warning: variable 'seq_str1' set but not used [-Wunused-but-set-variable]
CharPtr seq_str1, seq_str2;
^~~~~~~~
sequin7.c: In function 'RemoveProteinsAndOptionallyRenormalize':
sequin7.c:5679:18: warning: unused variable 'tmp' [-Wunused-variable]
ValNodePtr tmp;
^~~
sequin7.c:5675:18: warning: unused variable 'ompc' [-Wunused-variable]
OMProcControl ompc;
^~~~
sequin7.c:5672:18: warning: unused variable 'itemID' [-Wunused-variable]
Uint4 itemID;
^~~~~~
sequin7.c:5671:18: warning: unused variable 'bsp' [-Wunused-variable]
BioseqPtr bsp;
^~~
sequin7.c: In function 'RNABlastOptionNew':
sequin7.c:7045:17: warning: variable 'rval' set but not used [-Wunused-but-set-variable]
Int2 rval;
^~~~
sequin7.c: In function 'GetSubListForRNAStrandCorrection':
sequin7.c:7325:27: warning: variable 'found_id' set but not used [-Wunused-but-set-variable]
Boolean found_id;
^~~~~~~~
sequin7.c: In function 'ShowClickableItemListEx':
sequin7.c:9473:28: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin7.c: In function 'ChooseFeaturesForConversion':
sequin7.c:9614:28: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin7.c: In function 'GetTableOptions':
sequin7.c:13793:30: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin7.c: In function 'RemoveCDSandmRNAForGene':
sequin7.c:14076:27: 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:14159:48: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
|| best_left == fcontext.left && best_right < fcontext.right) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin7.c: In function 'TrimTaxFix':
sequin7.c:15679:46: 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:16522:21: warning: unused variable 'trim_list' [-Wunused-variable]
ValNodePtr trim_list = NULL;
^~~~~~~~~
sequin7.c: In function 'BarcodeBlastOptionNew':
sequin7.c:16791:17: 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:74:
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:77:
../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:7390:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
sequin7.c:14322:13: warning: 'FindBadLatLonSourceFeat' defined but not used [-Wunused-function]
static void FindBadLatLonSourceFeat (SeqFeatPtr sfp, Pointer userdata)
^~~~~~~~~~~~~~~~~~~~~~~
sequin7.c:12208:13: warning: 'RemoveBarcodeKeywordsFromLowTrace' defined but not used [-Wunused-function]
static void RemoveBarcodeKeywordsFromLowTrace (ButtoN b)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin7.c:6629:16: warning: 'DoesBioseqMatchStringConstraint' defined but not used [-Wunused-function]
static Boolean DoesBioseqMatchStringConstraint (BioseqPtr bsp, StringConstraintXPtr scp)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin7.c:4781:13: 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 = __TIME__;
^~~~~~~~~~~~~~~~~~~
sequin7.c: In function 'CombineToCreatePseudoGene':
sequin7.c:14273:27: 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:14159:48: warning: 'best_right' may be used uninitialized in this function [-Wmaybe-uninitialized]
|| best_left == fcontext.left && best_right < fcontext.right) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin7.c:14159:18: 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:82,
from sequin8.c:45:
/usr/include/features.h:184:3: 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:1198:20: warning: variable 'first' set but not used [-Wunused-but-set-variable]
Uint1 first;
^~~~~
sequin8.c: In function 'SelectBestRepeatsFromList':
sequin8.c:7867:18: warning: variable 'best_len' set but not used [-Wunused-but-set-variable]
Int4 best_len;
^~~~~~~~
sequin8.c:7862:18: warning: variable 'strand2' set but not used [-Wunused-but-set-variable]
Uint1 strand1, strand2;
^~~~~~~
sequin8.c:7862:9: warning: variable 'strand1' set but not used [-Wunused-but-set-variable]
Uint1 strand1, strand2;
^~~~~~~
sequin8.c: In function 'ExamineAln':
sequin8.c:8328:8: warning: variable 'len' set but not used [-Wunused-but-set-variable]
Int4 len, num_aln = 0;
^~~
sequin8.c: In function 'FindIntervalConflict':
sequin8.c:10165:39: warning: self-comparison always evaluates to true [-Wtautological-compare]
} else if (left2 <= left1 && right2 >= right2) {
^~
sequin8.c: In function 'BuildConflictLists':
sequin8.c:10507:69: warning: self-comparison always evaluates to false [-Wtautological-compare]
if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) {
^~
sequin8.c:10513:69: warning: self-comparison always evaluates to false [-Wtautological-compare]
if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) {
^~
sequin8.c: In function 'ScrollToDiscrepancyItem':
sequin8.c:14861:17: warning: variable 'special_flag' set but not used [-Wunused-but-set-variable]
Boolean special_flag = FALSE;
^~~~~~~~~~~~
sequin8.c: In function 'SortVnpByLinkStatus':
sequin8.c:17767:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (fcontext2.itemID < fcontext2.itemID) {
^
sequin8.c: In function 'SortVnpBymRNAPos':
sequin8.c:17784:22: warning: variable 'mrna2' set but not used [-Wunused-but-set-variable]
SeqFeatPtr mrna1, mrna2;
^~~~~
sequin8.c:17784:15: 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:18941:19: warning: 'DivideClickableItemListByEntityID' defined but not used [-Wunused-function]
static ValNodePtr DivideClickableItemListByEntityID (ValNodePtr clickable_list)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:14351:13: warning: 'VisitFeaturesInViewedBioseqs' defined but not used [-Wunused-function]
static void VisitFeaturesInViewedBioseqs (Pointer userdata, VisitFeaturesFunc callback)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:12559:13: warning: 'MakeProteinTitlesInSequinStyle' defined but not used [-Wunused-function]
static void MakeProteinTitlesInSequinStyle (Uint2 entityID, SeqEntryPtr sep)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:12367:13: warning: 'ShowAssemblyAlignment' defined but not used [-Wunused-function]
static void ShowAssemblyAlignment (SeqAlignPtr salp)
^~~~~~~~~~~~~~~~~~~~~
sequin8.c:8326:13: warning: 'ExamineAln' defined but not used [-Wunused-function]
static void ExamineAln (SeqAlignPtr sap)
^~~~~~~~~~
sequin8.c:7262:16: warning: 'DoesFirstRepeatContainAllOtherRepeats' defined but not used [-Wunused-function]
static Boolean DoesFirstRepeatContainAllOtherRepeats (ValNodePtr start, ValNodePtr stop)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:6810:16: warning: 'DoesRowContainPoint' defined but not used [-Wunused-function]
static Boolean DoesRowContainPoint (SeqAlignRowPtr row, Int4 point)
^~~~~~~~~~~~~~~~~~~
sequin8.c:6475:13: warning: 'CKA_ShowAln' defined but not used [-Wunused-function]
static void CKA_ShowAln(SeqAlignPtr sap, CKA_AccPtr acc_head)
^~~~~~~~~~~
sequin8.c:6269:16: 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:1538:18: warning: 'SqnGetBioseqGivenSeqLoc' defined but not used [-Wunused-function]
static BioseqPtr SqnGetBioseqGivenSeqLoc (SeqLocPtr slp, Uint2 entityID)
^~~~~~~~~~~~~~~~~~~~~~~
sequin8.c:536:13: warning: 'FixReadingFrame' defined but not used [-Wunused-function]
static void FixReadingFrame (
^~~~~~~~~~~~~~~
sequin8.c:309:13: 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:184:3: 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:629:19: warning: variable 'hits' set but not used [-Wunused-but-set-variable]
Int2 hits;
^~~~
sequin9.c: In function 'AcceptArgumentFormProc':
sequin9.c:1529:18: warning: variable 'choice' set but not used [-Wunused-but-set-variable]
Int2 choice;
^~~~~~
sequin9.c: In function 'ExtendBothEnds':
sequin9.c:4838:17: warning: variable 'oldbsp' set but not used [-Wunused-but-set-variable]
BioseqPtr oldbsp;
^~~~~~
sequin9.c: In function 'Extend5Prime':
sequin9.c:4906:17: warning: variable 'oldbsp' set but not used [-Wunused-but-set-variable]
BioseqPtr oldbsp;
^~~~~~
sequin9.c: In function 'Extend3Prime':
sequin9.c:4966:17: warning: variable 'oldbsp' set but not used [-Wunused-but-set-variable]
BioseqPtr oldbsp;
^~~~~~
sequin9.c: In function 'FixProteinString':
sequin9.c:5177:16: 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:5254:13: warning: variable 'start' set but not used [-Wunused-but-set-variable]
Int4 start, stop, new_stop;
^~~~~
sequin9.c: In function 'ExtendProtein5':
sequin9.c:5447:23: warning: variable 'new_stop' set but not used [-Wunused-but-set-variable]
Int4 stop, new_stop;
^~~~~~~~
sequin9.c: In function 'PrepareUpdateAlignmentForProtein':
sequin9.c:5975:17: warning: variable 'changed_frame' set but not used [-Wunused-but-set-variable]
Boolean changed_frame;
^~~~~~~~~~~~~
sequin9.c: In function 'DrawAlignDiffs':
sequin9.c:7468:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, i;
^~~~
sequin9.c:7468:14: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, i;
^~~~
sequin9.c: In function 'MakeAlignDetails':
sequin9.c:7603:12: warning: variable 'aln_length' set but not used [-Wunused-but-set-variable]
Int4 aln_length;
^~~~~~~~~~
sequin9.c: In function 'MakeAlignSequence':
sequin9.c:7652:56: warning: variable 'to' set but not used [-Wunused-but-set-variable]
Int4 aln_length, len, lens, start, stop, from, to, i, j;
^~
sequin9.c:7652:50: 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:12920:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, i;
^~~~
sequin9.c:12920:14: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
Int4 len1, len2, i;
^~~~
sequin9.c: In function 'MakeAlignmentDetailsPicture':
sequin9.c:13005:12: warning: variable 'aln_length' set but not used [-Wunused-but-set-variable]
Int4 aln_length;
^~~~~~~~~~
sequin9.c: In function 'MakeUpdateAlignmentSequenceString':
sequin9.c:13087:44: warning: variable 'to' set but not used [-Wunused-but-set-variable]
Int4 len, lens, start, stop, from, to, i, j;
^~
sequin9.c:13087:38: 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:15261:46: 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:16366:30: warning: variable 'update_bsp' set but not used [-Wunused-but-set-variable]
BioseqPtr update_bsp = NULL;
^~~~~~~~~~
sequin9.c:16365:30: warning: variable 'update_entityID' set but not used [-Wunused-but-set-variable]
Uint2 update_entityID = 0;
^~~~~~~~~~~~~~~
sequin9.c: In function 'UpdateAllSequences':
sequin9.c:16656:30: warning: unused variable 'update_entityID' [-Wunused-variable]
Uint2 update_entityID = 0;
^~~~~~~~~~~~~~~
sequin9.c:16655:30: warning: unused variable 'update_bsp' [-Wunused-variable]
BioseqPtr update_bsp = NULL;
^~~~~~~~~~
sequin9.c: In function 'CleanupUpdateMultiSequence':
sequin9.c:16976:30: warning: unused variable 'entityIDList' [-Wunused-variable]
ValNodePtr entityIDList = NULL;
^~~~~~~~~~~~
sequin9.c: In function 'RemoveIdenticalUpdates':
sequin9.c:17219:30: warning: unused variable 'update_entityID' [-Wunused-variable]
Uint2 update_entityID = 0;
^~~~~~~~~~~~~~~
sequin9.c: In function 'UpdateSequenceViaDownload':
sequin9.c:18323:15: 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:177:33: warning: 'Method_methodFree' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr ));
^~~~~~~~~~~~~~~~~
../include/objentgene.h:178:33: warning: 'Method_methodAsnRead' declared 'static' but never defined [-Wunused-function]
static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
^~~~~~~~~~~~~~~~~~~~
../include/objentgene.h:179:24: 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:16618:29: warning: 'FeatureUpdateNew' defined but not used [-Wunused-function]
static FeatureUpdateInfoPtr FeatureUpdateNew (BioseqPtr orig_bsp, BioseqPtr update_bsp)
^~~~~~~~~~~~~~~~
sequin9.c:1466:16: warning: 'StrSaveNoNullEncodeSpaces' defined but not used [-Wunused-function]
static CharPtr StrSaveNoNullEncodeSpaces (CharPtr from)
^~~~~~~~~~~~~~~~~~~~~~~~~
sequin9.c: In function 'ListIds':
sequin9.c:16197:14: warning: 'bssp' may be used uninitialized in this function [-Wmaybe-uninitialized]
for (s = bssp->seq_set; s != NULL; s = s->next) {
~~^~~~~~~~~~~~~~~
sequin9.c: In function 'TruncateSeqGraphValues':
sequin9.c:3192:14: warning: 'fmax' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (((FloatHiPtr)new_values)[newpos] > fmax) {
^
sequin9.c:3195:14: warning: 'fmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (((FloatHiPtr)new_values)[newpos] < fmin) {
^
sequin9.c: In function 'PrepareUpdateAlignmentForProtein':
sequin9.c:5884:41: warning: 'gene_sfp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (fp == NULL || gene == NULL || gene->location == NULL) return;
~~~~^~~~~~~~~~
sequin9.c:5981:17: 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:82,
from sequin10.c:45:
/usr/include/features.h:184:3: 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 'DoAutoDefLine':
sequin10.c:198:17: warning: unused variable 'uop' [-Wunused-variable]
UserObjectPtr uop;
^~~
sequin10.c: In function 'ApplyTableQuals':
sequin10.c:4576:26: warning: variable 'fqtd' set but not used [-Wunused-but-set-variable]
FeatureQualTableData fqtd;
^~~~
sequin10.c: In function 'OkCancelTellMeMore':
sequin10.c:4937:10: warning: variable 'p1' set but not used [-Wunused-but-set-variable]
PrompT p1;
^~
sequin10.c: In function 'LookupJournalTitlesInObjectTable':
sequin10.c:5094:11: warning: unused variable 'rval' [-Wunused-variable]
Boolean rval = TRUE;
^~~~
sequin10.c: In function 'EraseAllFieldsWhenBlank':
sequin10.c:5874:19: warning: unused variable 'columns' [-Wunused-variable]
ValNodePtr columns = NULL;
^~~~~~~
sequin10.c: In function 'ExternalSourceQualifierTableReader':
sequin10.c:6812:22: warning: variable 'any_valid' set but not used [-Wunused-but-set-variable]
Boolean any_valid = FALSE;
^~~~~~~~~
sequin10.c: In function 'LoadFeatureFieldTable':
sequin10.c:9115:24: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
sequin10.c: In function 'OrgModListsMatch':
sequin10.c:10856:14: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
sequin10.c: In function 'SubtypeListsMatch':
sequin10.c:11049:14: warning: variable 'found' set but not used [-Wunused-but-set-variable]
Boolean found;
^~~~~
sequin10.c: In function 'TrimSequencesByAlignment':
sequin10.c:12402:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
ButtoN b;
^
sequin10.c: In function 'AddOneFeatureBetween':
sequin10.c:12809:14: 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:14399:13: warning: 'PrintTPAHistErrors' defined but not used [-Wunused-function]
static void PrintTPAHistErrors (LogInfoPtr lip, ValNodePtr errors)
^~~~~~~~~~~~~~~~~~
sequin10.c:12050:19: warning: 'FindGeneInSeqEntryByLocusTag' defined but not used [-Wunused-function]
static SeqFeatPtr FindGeneInSeqEntryByLocusTag (SeqEntryPtr sep, CharPtr locus_tag)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequin10.c:9201:16: warning: 'GetRevSectionInterval' defined but not used [-Wunused-function]
static Pointer GetRevSectionInterval (Uint1 data_choice, Pointer data, Pointer metadata)
^~~~~~~~~~~~~~~~~~~~~
sequin10.c:9183:16: warning: 'GetRevSectionSequence' defined but not used [-Wunused-function]
static Pointer GetRevSectionSequence (Uint1 data_choice, Pointer data, Pointer metadata)
^~~~~~~~~~~~~~~~~~~~~
sequin10.c:3058:19: warning: 'FreeTableData' defined but not used [-Wunused-function]
static ValNodePtr FreeTableData (ValNodePtr lines)
^~~~~~~~~~~~~
sequin10.c:1495:19: warning: 'OrgModTableColumnListFree' defined but not used [-Wunused-function]
static ValNodePtr OrgModTableColumnListFree (ValNodePtr vnp)
^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/vibrant.h:130:0,
from ../include/dlogutil.h:48,
from sequin.h:82,
from sequin10.c:45:
sequin10.c: In function 'AutoDefBaseFormCommon':
../include/vibdefns.h:318:18: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define CheckBox Nlm_CheckBox
^~~~~~~~~~~~
sequin10.c:726:24: 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:82,
from sequinx.c:46:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF -UINTERNAL_NCBI_SEQUIN sbtedit.c \
-lncbicn3d -lddvlib -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb \
-lncbitxc2 -lncbiid1 -lnetblast -lncbitool -lblastcompadj -lncbimla \
-lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbiobj -lncbi -lm
sbtedit.c:48:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
static char *date_of_compilation = __DATE__;
^~~~~~~~
sbtedit.c:49:36: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
static char *time_of_compilation = __TIME__;
^~~~~~~~
In file 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:82,
from sbtedit.c:55:
/usr/include/features.h:184:3: 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:604:15: 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 = __TIME__;
^~~~~~~~~~~~~~~~~~~
sbtedit.c:48:14: warning: 'date_of_compilation' defined but not used [-Wunused-variable]
static char *date_of_compilation = __DATE__;
^~~~~~~~~~~~~~~~~~~
: sbtedit
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF udvmain.o -lncbiid1 -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lddvlib \
-lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant \
-lncbitool -lblastcompadj -lncbiobj \
-lncbi -lm
gcc -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF ddvmain.o -lncbiid1 -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lddvlib \
-lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbitool \
-lblastcompadj -lncbiobj -lncbi \
-lm
gcc -g -o taxblast -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF taxblast_main.c \
-lblastapi -lblast -lnetblast -lncbiid1 -lncbitxc2 -lncbitool -lblastcompadj \
-lnetcli -lncbiobj -lconnssl -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF idfetch.c -lncbiid1 -lnetcli -lncbiobj -lconnssl -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 idfetch.c:30:
/usr/include/features.h:184:3: 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:358:46: warning: variable 'any_type' set but not used [-Wunused-but-set-variable]
found_colon = FALSE, dna_type = FALSE, any_type = FALSE;
^~~~~~~~
idfetch.c:358:28: 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 'ProcessOneDocSum':
idfetch.c:803:25: warning: unused variable 'e2ry' [-Wunused-variable]
Entrez2ReplyPtr e2ry;
^~~~
idfetch.c:802:25: warning: unused variable 'e2rq' [-Wunused-variable]
Entrez2RequestPtr e2rq;
^~~~
idfetch.c: In function 'IdFetch_func':
idfetch.c:852:13: warning: missing braces around initializer [-Wmissing-braces]
SeqId si={SEQID_GI,0,0};
^
{}
idfetch.c:859:10: warning: variable 'group_segs' set but not used [-Wunused-but-set-variable]
Uint1 group_segs;
^~~~~~~~~~
idfetch.c: In function 'BEGetUidsFromQuery':
idfetch.c:1113:14: warning: unused variable 'e2rp' [-Wunused-variable]
E2ReplyPtr e2rp;
^~~~
idfetch.c: In function 'IdFetch_func':
idfetch.c:961:5: 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:501:13: warning: 'type_int' may be used uninitialized in this function [-Wmaybe-uninitialized]
Int4 tgi = TryGetGi( type_int, tacc, NULL, 0);
^~~
gcc -g -o asn2gb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF asn2gb.c -lncbiid1 -lnetcli \
-lncbitool -lblastcompadj -lncbiobj -lconnssl -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 asn2gb.c:41:
/usr/include/features.h:184:3: 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:1748:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c: In function 'CompareFlatFiles':
asn2gb.c:1185:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1192:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1217:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1243:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1246:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1251:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1254:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c: In function 'ReportDiffs':
asn2gb.c:1072:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1075:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1078:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1081:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1084:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
asn2gb.c:1097:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
asn2gb.c:1291:13: warning: 'CheckOrder' defined but not used [-Wunused-function]
static void CheckOrder (
^~~~~~~~~~
asn2gb.c:968:13: warning: 'FreeUnpubAffil' defined but not used [-Wunused-function]
static void FreeUnpubAffil (
^~~~~~~~~~~~~~
asn2gb.c: In function 'HandleMultipleRecords.constprop':
asn2gb.c:1626:24: warning: '%s' directive argument is null [-Wformat-overflow=]
sprintf (buf, "%s.before", accn);
^~
asn2gb.c:1628:24: warning: '%s' directive argument is null [-Wformat-overflow=]
sprintf (buf, "%s.gbff.before", accn);
^~
gcc -o tbl2asn -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF tbl2asn.c -lncbitool -lblastcompadj \
-lncbiobj -lnetcli -lconnssl -lncbi -lm
tbl2asn.c:45:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
static char *date_of_compilation = __DATE__;
^~~~~~~~
In 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:47:
/usr/include/features.h:184:3: 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 'HasTaxon':
tbl2asn.c:872:11: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (orp == FALSE) return FALSE;
^~
tbl2asn.c:872:7: note: did you mean to dereference the pointer?
if (orp == FALSE) return FALSE;
^
tbl2asn.c: In function 'ProcessOneAnnot':
tbl2asn.c:2566:15: warning: variable 'sep' set but not used [-Wunused-but-set-variable]
SeqEntryPtr sep;
^~~
tbl2asn.c: In function 'WarnAboutIncompleteFileRead':
tbl2asn.c:4297:16: warning: variable 'str' set but not used [-Wunused-but-set-variable]
CharPtr str;
^~~
tbl2asn.c: In function 'MakeOneRnaTitle':
tbl2asn.c:5536:22: warning: variable 'cds' set but not used [-Wunused-but-set-variable]
SeqFeatPtr cds;
^~~
tbl2asn.c: In function 'FindSingleNucleotideOrNucProtSetInBioseqInSet':
tbl2asn.c:6986:30: 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:66:
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:69:
../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:6580:16: warning: 'ValidateAssemblyGapFeat' defined but not used [-Wunused-function]
static Boolean ValidateAssemblyGapFeat (SeqFeatPtr sfp, BioseqPtr bsp)
^~~~~~~~~~~~~~~~~~~~~~~
tbl2asn.c:6005:20: warning: 'GetDescriptorTypeAlreadyInList' defined but not used [-Wunused-function]
static SeqDescrPtr GetDescriptorTypeAlreadyInList (
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tbl2asn.c:5901:13: warning: 'ParseOneOrgLabel' defined but not used [-Wunused-function]
static void ParseOneOrgLabel (
^~~~~~~~~~~~~~~~
tbl2asn.c:2654:16: warning: 'ExceptionExplainsMismatch' defined but not used [-Wunused-function]
static Boolean ExceptionExplainsMismatch (CharPtr except_text)
^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -o gene2xml -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF gene2xml.c -lnetcli -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 gene2xml.c:41:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF entrez2.c -lncbiid1 -lnetcli -lncbidesk \
-lblastapi -lblast -lncbimmdb -lncbitool -lblastcompadj \
-lncbiobj -lvibrant -lconnssl -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/vibtypes.h:94,
from ../include/vibrant.h:124,
from entrez2.c:49:
/usr/include/features.h:184:3: 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:868:12: warning: variable 'server' set but not used [-Wunused-but-set-variable]
CharPtr server = "www.ncbi.nlm.nih.gov";
^~~~~~
entrez2.c:866:12: warning: variable 'port' set but not used [-Wunused-but-set-variable]
Uint2 port = 2441;
^~~~
entrez2.c:865:12: warning: variable 'path' set but not used [-Wunused-but-set-variable]
CharPtr path = "/entrez/utils/entrez2server.fcgi";
^~~~
At top level:
entrez2.c:726:13: warning: 'AboutProc' defined but not used [-Wunused-function]
static void AboutProc (IteM i)
^~~~~~~~~
: entrez2
gcc -g -o gbseqget -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF gbseqget.c -lncbiid1 -lnetcli \
-lncbitool -lblastcompadj -lncbiobj -lconnssl -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 gbseqget.c:41:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF asn2all.c ncbithr.o -lncbiid1 \
-lnetcli -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \
-lm -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:184:3: 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:68:27: warning: variable 'stop_time' set but not used [-Wunused-but-set-variable]
time_t start_time, stop_time;
^~~~~~~~~
asn2all.c:68:15: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF asn2asn.c -lncbiid1 -lnetcli -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 asn2asn.c:17:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF asn2fsa.c ncbithr.o -lncbiid1 \
-lnetcli -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \
-lm -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:184:3: 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:217:15: warning: variable 'vnp' set but not used [-Wunused-but-set-variable]
ValNodePtr vnp;
^~~
asn2fsa.c: In function 'DoLockFarComponents':
asn2fsa.c:408:27: warning: variable 'stop_time' set but not used [-Wunused-but-set-variable]
time_t start_time, stop_time;
^~~~~~~~~
asn2fsa.c:408:15: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF asndisc.c ncbithr.o -lncbiid1 \
-lnetcli -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \
-lm -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:184:3: 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:735:19: warning: variable 'memory_usage' set but not used [-Wunused-but-set-variable]
Boolean memory_usage = FALSE;
^~~~~~~~~~~~
asndisc.c:733:19: warning: variable 'detailed_report' set but not used [-Wunused-but-set-variable]
Boolean detailed_report = FALSE;
^~~~~~~~~~~~~~~
asndisc.c:729:19: warning: variable 'subcit' set but not used [-Wunused-but-set-variable]
SeqDescrPtr subcit = NULL;
^~~~~~
gcc -o asnmacro -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF asnmacro.c -lblastapi -lblast -lncbitool -lblastcompadj \
-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 asnmacro.c:45:
/usr/include/features.h:184:3: 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:1376:21: warning: 'amp' defined but not used [-Wunused-variable]
static AsnModulePtr amp = ampx;
^~~
../include/asnmacro.h:1375:19: warning: 'at' defined but not used [-Wunused-variable]
static AsnTypePtr at = atx;
^~
../include/asnmacro.h:1374:23: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF asnval.c ncbithr.o -lncbiid1 \
-lnetcli -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \
-lm -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:184:3: 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:558:27: warning: variable 'stop_time' set but not used [-Wunused-but-set-variable]
time_t start_time, stop_time;
^~~~~~~~~
asnval.c:558:15: warning: variable 'start_time' set but not used [-Wunused-but-set-variable]
time_t start_time, stop_time;
^~~~~~~~~~
gcc -o cleanasn -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF cleanasn.c -lblastapi -lblast -lncbiid1 \
-lncbitool -lblastcompadj -lnetcli -lncbiobj -lconnssl -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 cleanasn.c:45:
/usr/include/features.h:184:3: 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 'FindISOJTA':
cleanasn.c:2186:17: warning: variable 'is_issn' set but not used [-Wunused-but-set-variable]
Boolean is_issn = FALSE;
^~~~~~~
cleanasn.c: In function 'JournalIsPresent':
cleanasn.c:10641:14: warning: variable 'is_issn' set but not used [-Wunused-but-set-variable]
Boolean is_issn = FALSE;
^~~~~~~
cleanasn.c: In function 'RemoveGIProc':
cleanasn.c:10946:18: 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 ../include/actutils.h:105,
from cleanasn.c:66:
cleanasn.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));
^~~~~~~~~~~~~~~
cleanasn.c: In function 'ReportAsnDiffs':
cleanasn.c:3907:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c: In function 'DoGBFFReport':
cleanasn.c:8330:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8333:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8359:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8388:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8446:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8449:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c: In function 'DoValidatorReport':
cleanasn.c:8505:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8508:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:8536:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c: In function 'CppBasicCleanup':
cleanasn.c:11556:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:11560:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:11586:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:11588:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:11590:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:11592:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:11594:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
cleanasn.c:11604:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result]
system (cmmd);
^~~~~~~~~~~~~
At top level:
cleanasn.c:14106:13: warning: 'AccessionToGi' defined but not used [-Wunused-function]
static Int4 AccessionToGi (CharPtr string)
^~~~~~~~~~~~~
cleanasn.c:14065:16: warning: 'PvtStrToLong' defined but not used [-Wunused-function]
static Boolean PvtStrToLong (CharPtr str, Int4Ptr longval)
^~~~~~~~~~~~
cleanasn.c:12099:20: warning: 'MakeVirtualProtein' defined but not used [-Wunused-function]
static SeqEntryPtr MakeVirtualProtein (void)
^~~~~~~~~~~~~~~~~~
cleanasn.c:10401:13: warning: 'CheckPubmedSI' defined but not used [-Wunused-function]
static void CheckPubmedSI (
^~~~~~~~~~~~~
cleanasn.c:10219:13: warning: 'DoUnpublishedReport' defined but not used [-Wunused-function]
static void DoUnpublishedReport (
^~~~~~~~~~~~~~~~~~~
cleanasn.c:9089:19: warning: 'DuplicateStringList' defined but not used [-Wunused-function]
static ValNodePtr DuplicateStringList (
^~~~~~~~~~~~~~~~~~~
cleanasn.c:6073:16: warning: 'IsStopWord' defined but not used [-Wunused-function]
static Boolean IsStopWord (
^~~~~~~~~~
cleanasn.c:5235:13: warning: 'FindOneCds' defined but not used [-Wunused-function]
static void FindOneCds (
^~~~~~~~~~
cleanasn.c:5214:13: warning: 'PrintSegSeqTitleAfter' defined but not used [-Wunused-function]
static void PrintSegSeqTitleAfter (
^~~~~~~~~~~~~~~~~~~~~
cleanasn.c:5193:13: warning: 'PrintSegSeqTitleBefore' defined but not used [-Wunused-function]
static void PrintSegSeqTitleBefore (
^~~~~~~~~~~~~~~~~~~~~~
cleanasn.c:5178:13: warning: 'PrintPartsTitle' defined but not used [-Wunused-function]
static void PrintPartsTitle (
^~~~~~~~~~~~~~~
cleanasn.c:4899:13: warning: 'CountParts' defined but not used [-Wunused-function]
static void CountParts (
^~~~~~~~~~
cleanasn.c:4848:13: warning: 'NormalizeSegSetTitle' defined but not used [-Wunused-function]
static void NormalizeSegSetTitle (
^~~~~~~~~~~~~~~~~~~~
cleanasn.c:1910:13: warning: 'FindSegSeq' defined but not used [-Wunused-function]
static void FindSegSeq (
^~~~~~~~~~
gcc -g -o insdseqget -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF insdseqget.c -lncbiid1 -lnetcli \
-lncbitool -lblastcompadj -lncbiobj -lconnssl -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 insdseqget.c:41:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF nps2gps.c -lncbitool -lblastcompadj \
-lncbiobj -lconnssl -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 nps2gps.c:41:
/usr/include/features.h:184:3: 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:422:22: warning: variable 'cds' set but not used [-Wunused-but-set-variable]
SeqFeatPtr cds;
^~~
nps2gps.c: In function 'MakeIdFromLocation':
nps2gps.c:706:16: warning: variable 'altid' set but not used [-Wunused-but-set-variable]
ValNodePtr altid;
^~~~~
nps2gps.c: In function 'LoopThroughCDSs':
nps2gps.c:1221:22: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Int2 count;
^~~~~
nps2gps.c: In function 'NPStoGPS':
nps2gps.c:1891:39: warning: variable 'lastmrna' set but not used [-Wunused-but-set-variable]
SeqFeatPtr cds, gene, mrna, lastmrna, sfp, lastsfp;
^~~~~~~~
At top level:
nps2gps.c:589:17: warning: 'MakeIdFromLocusTag' defined but not used [-Wunused-function]
static SeqIdPtr MakeIdFromLocusTag (
^~~~~~~~~~~~~~~~~~
gcc -o spidey -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF spideymain.c -lncbiid1 -lncbitool \
-lblastcompadj -lnetcli -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 spideymain.c:79:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF trna2sap.c -lncbitool -lblastcompadj \
-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 trna2sap.c:41:
/usr/include/features.h:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -I../include -L../shlib -DWIN_MOTIF trna2tbl.c -lncbitool -lblastcompadj \
-lncbiobj -lncbi -lm
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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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:184:3: 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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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>>'
create-stamp debian/debhelper-build-stamp
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.6.1.20170106 debian/tmp/usr/lib/arm-linux-gnueabihf
for x in ncbiacc ncbiCacc netentr; do \
rm -f debian/tmp/usr/lib/arm-linux-gnueabihf/lib$x.so.6.1.20170106 && \
ln -s libncbiNacc.so.6 \
debian/tmp/usr/lib/arm-linux-gnueabihf/lib$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.6.1.20170106 && \
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.6.1.20170106; do \
base=`basename $f .so.6.1.20170106` && \
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
mv debian/tmp/usr/bin/Cn3D debian/tmp/usr/bin/Cn3D-3.0
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 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
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
dh_missing -a
dh_strip -a
debian/rules override_dh_makeshlibs-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_makeshlibs -V
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ncbi-tools-bin/usr/bin/errhdr debian/ncbi-tools-bin/usr/bin/findspl debian/ncbi-tools-bin/usr/bin/idfetch debian/ncbi-tools-bin/usr/bin/fa2htgs debian/ncbi-tools-bin/usr/bin/asnval debian/ncbi-tools-bin/usr/bin/makeset debian/ncbi-tools-bin/usr/bin/asndisc debian/ncbi-tools-bin/usr/bin/taxblast debian/ncbi-tools-bin/usr/bin/gbseqget debian/ncbi-tools-bin/usr/bin/vecscreen debian/ncbi-tools-bin/usr/bin/asn2xml debian/ncbi-tools-bin/usr/bin/insdseqget debian/ncbi-tools-bin/usr/bin/asn2idx debian/ncbi-tools-bin/usr/bin/cleanasn debian/ncbi-tools-bin/usr/bin/nps2gps debian/ncbi-tools-bin/usr/bin/trna2sap debian/ncbi-tools-bin/usr/bin/asn2gb debian/ncbi-tools-bin/usr/bin/asntool debian/ncbi-tools-bin/usr/bin/indexpub debian/ncbi-tools-bin/usr/bin/asn2ff debian/ncbi-tools-bin/usr/bin/asn2fsa debian/ncbi-tools-bin/usr/bin/asnmacro debian/ncbi-tools-bin/usr/bin/subfuse debian/ncbi-tools-bin/usr/bin/getmesh debian/ncbi-tools-bin/usr/bin/asn2all debian/ncbi-tools-bin/usr/bin/spidey debian/ncbi-tools-bin/usr/bin/asndhuff debian/ncbi-tools-bin/usr/bin/sortbyquote debian/ncbi-tools-bin/usr/bin/getpub debian/ncbi-tools-bin/usr/bin/gene2xml debian/ncbi-tools-bin/usr/bin/tbl2asn debian/ncbi-tools-bin/usr/bin/asn2asn debian/ncbi-tools-bin/usr/bin/trna2tbl debian/ncbi-tools-bin/usr/bin/gil2bin were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ncbi-tools-x11/usr/bin/Psequin debian/ncbi-tools-x11/usr/bin/ddv debian/ncbi-tools-x11/usr/bin/Cn3D-3.0 debian/ncbi-tools-x11/usr/bin/udv debian/ncbi-tools-x11/usr/bin/sbtedit debian/ncbi-tools-x11/usr/bin/entrez2 were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
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. Architecture mismatch: armhf, want: all any
dh_builddeb -Nncbi-rrna-data
dpkg-deb: building package 'libncbi6' in '../libncbi6_6.1.20170106-4_armhf.deb'.
dpkg-deb: building package 'ncbi-tools-bin' in '../ncbi-tools-bin_6.1.20170106-4_armhf.deb'.
dpkg-deb: building package 'ncbi-tools-x11-dbgsym' in '../ncbi-tools-x11-dbgsym_6.1.20170106-4_armhf.deb'.
dpkg-deb: building package 'libvibrant6-dev' in '../libvibrant6-dev_6.1.20170106-4_armhf.deb'.
dpkg-deb: building package 'libvibrant6b' in '../libvibrant6b_6.1.20170106-4_armhf.deb'.
dpkg-deb: building package 'ncbi-tools-bin-dbgsym' in '../ncbi-tools-bin-dbgsym_6.1.20170106-4_armhf.deb'.
dpkg-deb: building package 'ncbi-tools-x11' in '../ncbi-tools-x11_6.1.20170106-4_armhf.deb'.
dpkg-deb: building package 'libvibrant6b-dbgsym' in '../libvibrant6b-dbgsym_6.1.20170106-4_armhf.deb'.
dpkg-deb: building package 'libncbi6-dbgsym' in '../libncbi6-dbgsym_6.1.20170106-4_armhf.deb'.
dpkg-deb: building package 'libncbi6-dev' in '../libncbi6-dev_6.1.20170106-4_armhf.deb'.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../ncbi-tools6_6.1.20170106-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build ncbi-tools6-6.1.20170106
dpkg-source: info: using options from ncbi-tools6-6.1.20170106/debian/source/options: --single-debian-patch
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-06-28T06:48:16Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
ncbi-tools6_6.1.20170106-4_armhf.changes:
-----------------------------------------
Format: 1.8
Date: Mon, 25 Jun 2018 21:36:10 -0400
Source: ncbi-tools6
Binary: libncbi6 libncbi6-dev ncbi-data ncbi-rrna-data ncbi-tools-bin ncbi-tools-x11 libvibrant6b libvibrant6-dev
Architecture: armhf
Version: 6.1.20170106-4
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Aaron M. Ucko <ucko@debian.org>
Description:
libncbi6 - NCBI libraries for biology applications
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
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)
Closes: 902364
Changes:
ncbi-tools6 (6.1.20170106-4) unstable; urgency=medium
.
* debian/compat: Advance to Debhelper 11.
* debian/control:
- Mark *-data reshuffling with Breaks, not just Replaces. (Closes: #902364.)
- Build-Depends: Advance to debhelper (>= 11~).
* debian/copyright: Fix years (packaging through 2018, upstream through 2017).
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libncbi6-dbgsym_6.1.20170106-4_armhf.deb
----------------------------------------
new Debian package, version 2.0.
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Package: libncbi6-dbgsym
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Installed-Size: 9174
Depends: libncbi6 (= 6.1.20170106-4)
Section: debug
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lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/share/doc/libncbi6-dbgsym -> libncbi6
libncbi6-dev_6.1.20170106-4_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 4524288 bytes: control archive=12736 bytes.
585 bytes, 16 lines control
34592 bytes, 512 lines md5sums
Package: libncbi6-dev
Source: ncbi-tools6
Version: 6.1.20170106-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 18296
Depends: libncbi6 (= 6.1.20170106-4)
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 2018-06-26 01:36 ./
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/include/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/include/ncbi/
-rw-r--r-- root/root 6100 2001-05-25 01:42 ./usr/include/ncbi/PubStructAsn.h
-rw-r--r-- root/root 2122 2000-01-18 19:42 ./usr/include/ncbi/a2ferr.h
-rw-r--r-- root/root 894 1997-08-25 18:04 ./usr/include/ncbi/a2ferrdf.h
-rw-r--r-- root/root 7162 1997-08-25 18:04 ./usr/include/ncbi/a2fstruc.h
-rw-r--r-- root/root 17078 2000-01-12 20:17 ./usr/include/ncbi/accentr.h
-rw-r--r-- root/root 1560 1999-03-16 22:47 ./usr/include/ncbi/accid1.h
-rw-r--r-- root/root 6923 1999-04-01 13:56 ./usr/include/ncbi/accutils.h
-rw-r--r-- root/root 3913 2008-12-02 16:16 ./usr/include/ncbi/acerdapi.h
-rw-r--r-- root/root 11450 2010-08-30 12:39 ./usr/include/ncbi/aceread.h
-rw-r--r-- root/root 9154 2008-05-02 18:02 ./usr/include/ncbi/actutils.h
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/include/ncbi/algo/
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drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/include/ncbi/algo/blast/api/
-rw-r--r-- root/root 7098 2016-06-21 13:53 ./usr/include/ncbi/algo/blast/api/blast_api.h
-rw-r--r-- root/root 11493 2006-10-06 12:22 ./usr/include/ncbi/algo/blast/api/blast_format.h
-rw-r--r-- root/root 6228 2007-03-12 16:12 ./usr/include/ncbi/algo/blast/api/blast_input.h
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-rw-r--r-- root/root 1757 2005-03-31 16:18 ./usr/include/ncbi/algo/blast/api/blast_mtlock.h
-rw-r--r-- root/root 8274 2007-03-08 14:57 ./usr/include/ncbi/algo/blast/api/blast_options_api.h
-rw-r--r-- root/root 5490 2005-04-06 23:27 ./usr/include/ncbi/algo/blast/api/blast_prelim.h
-rw-r--r-- root/root 8867 2007-07-10 15:28 ./usr/include/ncbi/algo/blast/api/blast_returns.h
-rw-r--r-- root/root 4784 2006-11-21 17:21 ./usr/include/ncbi/algo/blast/api/blast_seq.h
-rw-r--r-- root/root 6271 2010-02-12 20:36 ./usr/include/ncbi/algo/blast/api/blast_seqalign.h
-rw-r--r-- root/root 7223 2006-06-09 17:43 ./usr/include/ncbi/algo/blast/api/blast_tabular.h
-rw-r--r-- root/root 2455 2005-07-19 14:16 ./usr/include/ncbi/algo/blast/api/dust_filter.h
-rw-r--r-- root/root 3454 2009-06-01 13:54 ./usr/include/ncbi/algo/blast/api/hspfilter_queue.h
-rw-r--r-- root/root 2717 2006-04-26 12:46 ./usr/include/ncbi/algo/blast/api/repeats_filter.h
-rw-r--r-- root/root 2058 2006-11-21 17:22 ./usr/include/ncbi/algo/blast/api/seqsrc_multiseq.h
-rw-r--r-- root/root 2595 2005-04-21 15:00 ./usr/include/ncbi/algo/blast/api/seqsrc_readdb.h
-rw-r--r-- root/root 11556 2009-05-27 19:29 ./usr/include/ncbi/algo/blast/api/twoseq_api.h
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/include/ncbi/algo/blast/composition_adjustment/
-rw-r--r-- root/root 7185 2005-12-19 15:38 ./usr/include/ncbi/algo/blast/composition_adjustment/compo_heap.h
-rw-r--r-- root/root 2645 2010-03-26 14:54 ./usr/include/ncbi/algo/blast/composition_adjustment/compo_mode_condition.h
-rw-r--r-- root/root 21137 2016-05-02 18:04 ./usr/include/ncbi/algo/blast/composition_adjustment/composition_adjustment.h
-rw-r--r-- root/root 3353 2010-03-26 14:54 ./usr/include/ncbi/algo/blast/composition_adjustment/composition_constants.h
-rw-r--r-- root/root 2586 2006-04-03 17:43 ./usr/include/ncbi/algo/blast/composition_adjustment/matrix_frequency_data.h
-rw-r--r-- root/root 5063 2008-08-21 19:55 ./usr/include/ncbi/algo/blast/composition_adjustment/nlm_linear_algebra.h
-rw-r--r-- root/root 4287 2005-12-19 15:38 ./usr/include/ncbi/algo/blast/composition_adjustment/optimize_target_freq.h
-rw-r--r-- root/root 23519 2016-06-23 13:19 ./usr/include/ncbi/algo/blast/composition_adjustment/redo_alignment.h
-rw-r--r-- root/root 7526 2005-12-19 15:38 ./usr/include/ncbi/algo/blast/composition_adjustment/smith_waterman.h
-rw-r--r-- root/root 2710 2006-07-17 17:18 ./usr/include/ncbi/algo/blast/composition_adjustment/unified_pvalues.h
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/include/ncbi/algo/blast/core/
-rw-r--r-- root/root 4512 2007-03-01 22:25 ./usr/include/ncbi/algo/blast/core/aa_ungapped.h
-rw-r--r-- root/root 18882 2011-10-21 13:29 ./usr/include/ncbi/algo/blast/core/blast_aalookup.h
-rw-r--r-- root/root 3097 2010-07-23 14:36 ./usr/include/ncbi/algo/blast/core/blast_aascan.h
-rw-r--r-- root/root 15533 2012-06-06 16:04 ./usr/include/ncbi/algo/blast/core/blast_def.h
-rw-r--r-- root/root 5405 2011-06-13 18:24 ./usr/include/ncbi/algo/blast/core/blast_diagnostics.h
-rw-r--r-- root/root 7534 2007-03-20 14:55 ./usr/include/ncbi/algo/blast/core/blast_dynarray.h
-rw-r--r-- root/root 4102 2008-01-24 21:25 ./usr/include/ncbi/algo/blast/core/blast_encoding.h
-rw-r--r-- root/root 11636 2016-06-20 15:49 ./usr/include/ncbi/algo/blast/core/blast_engine.h
-rw-r--r-- root/root 1987 2004-08-10 16:40 ./usr/include/ncbi/algo/blast/core/blast_export.h
-rw-r--r-- root/root 9962 2012-05-16 17:09 ./usr/include/ncbi/algo/blast/core/blast_extend.h
-rw-r--r-- root/root 14025 2010-05-12 12:54 ./usr/include/ncbi/algo/blast/core/blast_filter.h
-rw-r--r-- root/root 12714 2016-06-20 15:49 ./usr/include/ncbi/algo/blast/core/blast_gapalign.h
-rw-r--r-- root/root 6483 2012-11-28 17:05 ./usr/include/ncbi/algo/blast/core/blast_gapalign_priv.h
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-rw-r--r-- root/root 3266 2016-03-18 14:29 ./usr/include/ncbi/algo/blast/core/blast_hspstream_mt_utils.h
-rw-r--r-- root/root 7769 2011-02-09 14:39 ./usr/include/ncbi/algo/blast/core/blast_itree.h
-rw-r--r-- root/root 6835 2016-03-18 14:29 ./usr/include/ncbi/algo/blast/core/blast_kappa.h
-rw-r--r-- root/root 7207 2017-01-04 16:59 ./usr/include/ncbi/algo/blast/core/blast_lookup.h
-rw-r--r-- root/root 6558 2014-08-07 19:29 ./usr/include/ncbi/algo/blast/core/blast_message.h
-rw-r--r-- root/root 30024 2016-12-06 15:29 ./usr/include/ncbi/algo/blast/core/blast_nalookup.h
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-rw-r--r-- root/root 48874 2016-07-01 15:49 ./usr/include/ncbi/algo/blast/core/blast_options.h
-rw-r--r-- root/root 20677 2013-10-17 13:44 ./usr/include/ncbi/algo/blast/core/blast_parameters.h
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lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbitool.so -> libncbitool.so.6.1.20170106
-rw-r--r-- root/root 110248 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbitxc2.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbitxc2.so -> libncbitxc2.so.6.1.20170106
-rw-r--r-- root/root 90718 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetblast.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetblast.so -> libnetblast.so.6.1.20170106
-rw-r--r-- root/root 19224 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetcli.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetcli.so -> libnetcli.so.6.1.20170106
-rw-r--r-- root/root 129396 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetentr.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetentr.so -> libncbiNacc.so
-rw-r--r-- root/root 51308 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/ncbithr.o
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/libncbi6-dev/
-rw-r--r-- root/root 178 2016-10-11 03:31 ./usr/share/doc/libncbi6-dev/README.Debian
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/share/doc/libncbi6-dev/README.gz -> changelog.gz
-rw-r--r-- root/root 1313 2006-08-28 23:12 ./usr/share/doc/libncbi6-dev/README.sdk
-rw-r--r-- root/root 2512 2004-10-05 20:15 ./usr/share/doc/libncbi6-dev/access.txt.gz
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-rw-r--r-- root/root 4598 2003-02-28 16:22 ./usr/share/doc/libncbi6-dev/asn2gph.txt.gz
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-rw-r--r-- root/root 18160 2008-06-16 15:51 ./usr/share/doc/libncbi6-dev/changelog.gz
-rw-r--r-- root/root 2881 2018-06-26 01:33 ./usr/share/doc/libncbi6-dev/copyright
-rw-r--r-- root/root 367300 2009-02-23 19:30 ./usr/share/doc/libncbi6-dev/sdk.doc.gz
libncbi6_6.1.20170106-4_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 3279236 bytes: control archive=65144 bytes.
650 bytes, 15 lines control
2561 bytes, 32 lines md5sums
644 bytes, 16 lines shlibs
442869 bytes, 11649 lines symbols
67 bytes, 2 lines triggers
Package: libncbi6
Source: ncbi-tools6
Version: 6.1.20170106-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10422
Depends: ncbi-data (= 6.1.20170106-4), libc6 (>= 2.15), libgnutls30 (>= 3.5.6)
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 2018-06-26 01:36 ./
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libblast.so.6 -> libblast.so.6.1.20170106
-rw-r--r-- root/root 627520 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libblast.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libblastapi.so.6 -> libblastapi.so.6.1.20170106
-rw-r--r-- root/root 99640 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libblastapi.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libblastcompadj.so.6 -> libblastcompadj.so.6.1.20170106
-rw-r--r-- root/root 71064 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libblastcompadj.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libconnssl.so.6 -> libconnssl.so.6.1.20170106
-rw-r--r-- root/root 13624 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libconnssl.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbi.so.6 -> libncbi.so.6.1.20170106
-rw-r--r-- root/root 704008 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbi.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbiCacc.so.6 -> libncbiNacc.so.6
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbiNacc.so.6 -> libncbiNacc.so.6.1.20170106
-rw-r--r-- root/root 135216 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbiNacc.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbiacc.so.6 -> libncbiNacc.so.6
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbicdr.so.6 -> libncbicdr.so.6.1.20170106
-rw-r--r-- root/root 105604 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbicdr.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbiid1.so.6 -> libncbiid1.so.6.1.20170106
-rw-r--r-- root/root 33040 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbiid1.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbimla.so.6 -> libncbimla.so.6.1.20170106
-rw-r--r-- root/root 49904 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbimla.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbimmdb.so.6 -> libncbimmdb.so.6.1.20170106
-rw-r--r-- root/root 565032 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbimmdb.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbiobj.so.6 -> libncbiobj.so.6.1.20170106
-rw-r--r-- root/root 5960532 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbiobj.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbitool.so.6 -> libncbitool.so.6.1.20170106
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lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbitxc2.so.6 -> libncbitxc2.so.6.1.20170106
-rw-r--r-- root/root 92324 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbitxc2.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetblast.so.6 -> libnetblast.so.6.1.20170106
-rw-r--r-- root/root 84672 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetblast.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetcli.so.6 -> libnetcli.so.6.1.20170106
-rw-r--r-- root/root 18140 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetcli.so.6.1.20170106
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libnetentr.so.6 -> libncbiNacc.so.6
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libvibgif.so.6 -> libvibgif.so.6.1.20170106
-rw-r--r-- root/root 124916 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libvibgif.so.6.1.20170106
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc-base/
-rw-r--r-- root/root 580 2016-10-11 03:31 ./usr/share/doc-base/ncbi-tools-dispatcher
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./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 2018-06-26 01:36 ./usr/share/doc/libncbi6/README.config.gz
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./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 2018-06-26 01:36 ./usr/share/doc/libncbi6/README.net-cfg
-rw-r--r-- root/root 94 2016-10-11 03:31 ./usr/share/doc/libncbi6/TODO.Debian
-rw-r--r-- root/root 1140 2018-06-24 16:12 ./usr/share/doc/libncbi6/bkgd.gif
-rw-r--r-- root/root 16990 2018-06-26 01:36 ./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 2881 2018-06-26 01:33 ./usr/share/doc/libncbi6/copyright
-rw-r--r-- root/root 22653 2018-06-26 01:36 ./usr/share/doc/libncbi6/dispatcher.html
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/libncbi6/examples/
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-rw-r--r-- root/root 3418 2018-06-24 16:12 ./usr/share/doc/libncbi6/ncbi2.css
-rw-r--r-- root/root 5529 2001-12-12 20:36 ./usr/share/doc/libncbi6/ncbixml.txt.gz
-rw-r--r-- root/root 50 2018-06-24 16:12 ./usr/share/doc/libncbi6/spacer10.gif
libvibrant6-dev_6.1.20170106-4_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 1292488 bytes: control archive=3876 bytes.
614 bytes, 14 lines control
7633 bytes, 122 lines md5sums
337 bytes, 13 lines * postinst #!/bin/sh
Package: libvibrant6-dev
Source: ncbi-tools6
Version: 6.1.20170106-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5622
Depends: libglu1-mesa-dev | libglu-dev, libmotif-dev, libncbi6-dev (= 6.1.20170106-4), libvibrant6b (= 6.1.20170106-4), 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 2018-06-26 01:36 ./
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/include/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/include/ncbi/
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-rw-r--r-- root/root 4028 1997-08-25 18:21 ./usr/include/ncbi/apparam.h
-rw-r--r-- root/root 5272 2014-02-24 19:08 ./usr/include/ncbi/biosrc.h
-rw-r--r-- root/root 15773 2012-09-27 14:49 ./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 2017-01-06 18:52 ./usr/include/ncbi/cn3d.h
-rw-r--r-- root/root 2819 1999-10-29 14:15 ./usr/include/ncbi/cn3dentr.h
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-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
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-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 4763 2012-10-10 21:06 ./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 6760 2012-12-20 22:10 ./usr/include/ncbi/vsmutil.h
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/
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-rw-r--r-- root/root 104292 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libddvlib.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libddvlib.so -> libddvlib.so.6.1.20170106
-rw-r--r-- root/root 186550 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbicn3d.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbicn3d.so -> libncbicn3dOGL.so
-rw-r--r-- root/root 192526 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbicn3dOGL.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbicn3dOGL.so -> libncbicn3dOGL.so.6.1.20170106
-rw-r--r-- root/root 2584278 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbidesk.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libncbidesk.so -> libncbidesk.so.6.1.20170106
-rw-r--r-- root/root 145440 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libvibgif.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libvibgif.so -> libvibgif.so.6.1.20170106
-rw-r--r-- root/root 112982 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libvibnet.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libvibnet.so -> libvibnet.so.6.1.20170106
-rw-r--r-- root/root 726474 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libvibrant.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libvibrant.so -> libvibrantOGL.so
-rw-r--r-- root/root 768726 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libvibrantOGL.a
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/lib/arm-linux-gnueabihf/libvibrantOGL.so -> libvibrantOGL.so.6.1.20170106
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/
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lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/share/doc/libvibrant6-dev/README.gz -> changelog.gz
-rw-r--r-- root/root 16990 2018-06-26 01:36 ./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 2881 2018-06-26 01:33 ./usr/share/doc/libvibrant6-dev/copyright
libvibrant6b-dbgsym_6.1.20170106-4_armhf.deb
--------------------------------------------
new Debian package, version 2.0.
size 3366240 bytes: control archive=788 bytes.
585 bytes, 13 lines control
530 bytes, 5 lines md5sums
Package: libvibrant6b-dbgsym
Source: ncbi-tools6
Version: 6.1.20170106-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3686
Depends: libvibrant6b (= 6.1.20170106-4)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libvibrant6b
Build-Ids: 3fa5bcce3b08ef8743b63a3c280743d6cdc2b2d0 4b787310d8b387a91d8166b2df11c1a227452a95 8bec1124e44c28cc887f13555ad2c83b19e164c5 9bed2a8e30568760d7650d18efcd2e85c6ba6541 e8f466aadfd4da72ec83686495b82b02a299098d
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lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/share/doc/libvibrant6b-dbgsym -> libvibrant6b
libvibrant6b_6.1.20170106-4_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 1053584 bytes: control archive=15952 bytes.
802 bytes, 17 lines control
752 bytes, 9 lines md5sums
226 bytes, 5 lines shlibs
91711 bytes, 2469 lines symbols
67 bytes, 2 lines triggers
Package: libvibrant6b
Source: ncbi-tools6
Version: 6.1.20170106-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2814
Depends: libncbi6 (<< 6.1.20170106.1), libncbi6 (>= 6.1.20170106), libc6 (>= 2.11), 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.
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-rw-r--r-- root/root 18160 2008-06-16 15:51 ./usr/share/doc/libvibrant6b/changelog.gz
-rw-r--r-- root/root 2881 2018-06-26 01:33 ./usr/share/doc/libvibrant6b/copyright
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-rw-r--r-- root/root 48 2016-10-11 03:31 ./usr/share/lintian/overrides/libvibrant6b
ncbi-tools-bin-dbgsym_6.1.20170106-4_armhf.deb
----------------------------------------------
new Debian package, version 2.0.
size 1134352 bytes: control archive=2184 bytes.
1845 bytes, 12 lines control
3816 bytes, 36 lines md5sums
Package: ncbi-tools-bin-dbgsym
Source: ncbi-tools6
Version: 6.1.20170106-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1448
Depends: ncbi-tools-bin (= 6.1.20170106-4)
Section: debug
Priority: optional
Description: debug symbols for ncbi-tools-bin
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-rw-r--r-- root/root 8648 2018-06-26 01:36 ./usr/lib/debug/.build-id/ca/fdda643125c3b2deee31e9e0a05a1234beb3aa.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/d6/
-rw-r--r-- root/root 25344 2018-06-26 01:36 ./usr/lib/debug/.build-id/d6/104fc65f226183feb3e336ff73994a1ef108a8.debug
-rw-r--r-- root/root 14040 2018-06-26 01:36 ./usr/lib/debug/.build-id/d6/437ef0c75a20571bb1fded29af0add3dc2e758.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/e2/
-rw-r--r-- root/root 52484 2018-06-26 01:36 ./usr/lib/debug/.build-id/e2/e9b2a04c917c9221519a9821df1099fd140a7b.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/e3/
-rw-r--r-- root/root 8624 2018-06-26 01:36 ./usr/lib/debug/.build-id/e3/a858d4e7e4479efd19ee242c324d6923af489d.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/fe/
-rw-r--r-- root/root 14832 2018-06-26 01:36 ./usr/lib/debug/.build-id/fe/c344223af344037e0a983705f9c0ffa58f672c.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin-dbgsym -> ncbi-tools-bin
ncbi-tools-bin_6.1.20170106-4_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 1832400 bytes: control archive=3440 bytes.
1061 bytes, 21 lines control
6564 bytes, 100 lines md5sums
Package: ncbi-tools-bin
Source: ncbi-tools6
Version: 6.1.20170106-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2788
Depends: libncbi6 (<< 6.1.20170106.1), libncbi6 (>= 6.1.20170106), libc6 (>= 2.7)
Suggests: libvibrant6b, ncbi-blast+, ncbi-tools-x11
Breaks: blast2 (<< 1:2.2.26.20160908), libncbi6-dev (<< 6.1.20110713-3~)
Replaces: blast2 (<< 1:2.2.26.20160908), 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 now come from a separate source base, corresponding to the
ncbi-blast+ and ncbi-blast+-legacy packages.
drwxr-xr-x root/root 0 2018-06-26 01:36 ./
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/bin/
-rwxr-xr-x root/root 43420 2018-06-26 01:36 ./usr/bin/asn2all
-rwxr-xr-x root/root 9964 2018-06-26 01:36 ./usr/bin/asn2asn
-rwxr-xr-x root/root 14940 2018-06-26 01:36 ./usr/bin/asn2ff
-rwxr-xr-x root/root 35388 2018-06-26 01:36 ./usr/bin/asn2fsa
-rwxr-xr-x root/root 31092 2018-06-26 01:36 ./usr/bin/asn2gb
-rwxr-xr-x root/root 9972 2018-06-26 01:36 ./usr/bin/asn2idx
-rwxr-xr-x root/root 9924 2018-06-26 01:36 ./usr/bin/asn2xml
-rwxr-xr-x root/root 9764 2018-06-26 01:36 ./usr/bin/asndhuff
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-rwxr-xr-x root/root 238488 2018-06-26 01:36 ./usr/bin/asntool
-rwxr-xr-x root/root 44060 2018-06-26 01:36 ./usr/bin/asnval
-rwxr-xr-x root/root 5656 2018-06-26 01:36 ./usr/bin/checksub
-rwxr-xr-x root/root 117588 2018-06-26 01:36 ./usr/bin/cleanasn
-rwxr-xr-x root/root 5656 2018-06-26 01:36 ./usr/bin/debruijn
-rwxr-xr-x root/root 9684 2018-06-26 01:36 ./usr/bin/errhdr
-rwxr-xr-x root/root 23452 2018-06-26 01:36 ./usr/bin/fa2htgs
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-rwxr-xr-x root/root 14020 2018-06-26 01:36 ./usr/bin/gbseqget
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-rwxr-xr-x root/root 27772 2018-06-26 01:36 ./usr/bin/getpub
-rwxr-xr-x root/root 5708 2018-06-26 01:36 ./usr/bin/gil2bin
-rwxr-xr-x root/root 26672 2018-06-26 01:36 ./usr/bin/idfetch
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-rwxr-xr-x root/root 228196 2018-06-26 01:36 ./usr/bin/makeset
-rwxr-xr-x root/root 30892 2018-06-26 01:36 ./usr/bin/nps2gps
-rwxr-xr-x root/root 9804 2018-06-26 01:36 ./usr/bin/sortbyquote
-rwxr-xr-x root/root 18996 2018-06-26 01:36 ./usr/bin/spidey
-rwxr-xr-x root/root 9804 2018-06-26 01:36 ./usr/bin/subfuse
-rwxr-xr-x root/root 5748 2018-06-26 01:36 ./usr/bin/taxblast
-rwxr-xr-x root/root 105852 2018-06-26 01:36 ./usr/bin/tbl2asn
-rwxr-xr-x root/root 14348 2018-06-26 01:36 ./usr/bin/trna2sap
-rwxr-xr-x root/root 5588 2018-06-26 01:36 ./usr/bin/trna2tbl
-rwxr-xr-x root/root 9844 2018-06-26 01:36 ./usr/bin/vecscreen
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin/
-rw-r--r-- root/root 2740 2002-08-29 03:24 ./usr/share/doc/ncbi-tools-bin/README.asn2xml
-rw-r--r-- root/root 5839 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin/README.fa2htgs.gz
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin/README.gz -> changelog.gz
-rw-r--r-- root/root 179 2018-04-12 20:49 ./usr/share/doc/ncbi-tools-bin/README.test
-rw-r--r-- root/root 6289 2017-01-06 18:52 ./usr/share/doc/ncbi-tools-bin/asnpub.all.gz
-rw-r--r-- root/root 16990 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin/changelog.Debian.gz
-rw-r--r-- root/root 18160 2008-06-16 15:51 ./usr/share/doc/ncbi-tools-bin/changelog.gz
-rw-r--r-- root/root 2881 2018-06-26 01:33 ./usr/share/doc/ncbi-tools-bin/copyright
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin/examples/
-rw-r--r-- root/root 4923 2014-07-09 22:00 ./usr/share/doc/ncbi-tools-bin/examples/gbf2tbl.pl.gz
-rwxr-xr-x root/root 1784 2012-02-13 15:20 ./usr/share/doc/ncbi-tools-bin/examples/patric2tbl.pl
-rwxr-xr-x root/root 606 2012-06-09 01:22 ./usr/share/doc/ncbi-tools-bin/examples/rast2sqn.sh
-rwxr-xr-x root/root 195 2012-02-13 15:20 ./usr/share/doc/ncbi-tools-bin/examples/rastbatch.sh
-rw-r--r-- root/root 3078 2014-07-22 21:00 ./usr/share/doc/ncbi-tools-bin/examples/tblfix.pl.gz
-rwxr-xr-x root/root 2051 2012-02-13 19:28 ./usr/share/doc/ncbi-tools-bin/examples/trna2tbl.rb
-rw-r--r-- root/root 3821 2015-04-20 22:27 ./usr/share/doc/ncbi-tools-bin/gene2xml.txt.gz
-rw-r--r-- root/root 11172 1997-08-25 18:20 ./usr/share/doc/ncbi-tools-bin/medline.prt.gz
-rw-r--r-- root/root 1861 2018-06-24 14:58 ./usr/share/doc/ncbi-tools-bin/run-unit-test.gz
-rw-r--r-- root/root 6454 2011-08-23 14:36 ./usr/share/doc/ncbi-tools-bin/tbl2asn.txt.gz
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin/test-data/
-rw-r--r-- root/root 599 2018-04-03 23:34 ./usr/share/doc/ncbi-tools-bin/test-data/Sc_16.fsa
-rw-r--r-- root/root 2885 2018-06-24 14:58 ./usr/share/doc/ncbi-tools-bin/test-data/Sc_16.sbt
-rw-r--r-- root/root 187 2018-04-03 23:34 ./usr/share/doc/ncbi-tools-bin/test-data/Sc_16.tbl
-rw-r--r-- root/root 625726 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin/test-data/dsRNA_viruses.ags.gz
-rw-r--r-- root/root 28072 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin/test-data/dsRNA_viruses.gene_info.gz
-rw-r--r-- root/root 2373 2018-04-17 17:49 ./usr/share/doc/ncbi-tools-bin/test-data/idfetch_g1234.npset.gz
-rw-r--r-- root/root 411571 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin/test-data/nc0225.aso.gz
-rw-r--r-- root/root 324732 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-bin/test-data/spidey_genome.fasta.gz
-rw-r--r-- root/root 2060 2018-06-24 14:58 ./usr/share/doc/ncbi-tools-bin/test-data/spidey_mRNA.fasta.gz
-rw-r--r-- root/root 3050 2018-04-12 20:49 ./usr/share/doc/ncbi-tools-bin/test-data/trnascan-se_sample.output
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/lintian/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 129 2016-10-11 03:31 ./usr/share/lintian/overrides/ncbi-tools-bin
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/man/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/man/man1/
-rw-r--r-- root/root 1838 2018-06-26 01:36 ./usr/share/man/man1/asn2all.1.gz
-rw-r--r-- root/root 505 2018-06-26 01:36 ./usr/share/man/man1/asn2asn.1.gz
-rw-r--r-- root/root 1167 2018-06-26 01:36 ./usr/share/man/man1/asn2ff.1.gz
-rw-r--r-- root/root 1020 2018-06-26 01:36 ./usr/share/man/man1/asn2fsa.1.gz
-rw-r--r-- root/root 1570 2018-06-26 01:36 ./usr/share/man/man1/asn2gb.1.gz
-rw-r--r-- root/root 597 2018-06-26 01:36 ./usr/share/man/man1/asn2idx.1.gz
-rw-r--r-- root/root 613 2018-06-26 01:36 ./usr/share/man/man1/asn2xml.1.gz
-rw-r--r-- root/root 376 2018-06-26 01:36 ./usr/share/man/man1/asndhuff.1.gz
-rw-r--r-- root/root 2956 2018-06-26 01:36 ./usr/share/man/man1/asndisc.1.gz
-rw-r--r-- root/root 600 2018-06-26 01:36 ./usr/share/man/man1/asnmacro.1.gz
-rw-r--r-- root/root 1294 2018-06-26 01:36 ./usr/share/man/man1/asntool.1.gz
-rw-r--r-- root/root 1391 2018-06-26 01:36 ./usr/share/man/man1/asnval.1.gz
-rw-r--r-- root/root 462 2018-06-26 01:36 ./usr/share/man/man1/checksub.1.gz
-rw-r--r-- root/root 2713 2018-06-26 01:36 ./usr/share/man/man1/cleanasn.1.gz
-rw-r--r-- root/root 485 2018-06-26 01:36 ./usr/share/man/man1/debruijn.1.gz
-rw-r--r-- root/root 661 2018-06-26 01:36 ./usr/share/man/man1/errhdr.1.gz
-rw-r--r-- root/root 3498 2018-06-26 01:36 ./usr/share/man/man1/fa2htgs.1.gz
-rw-r--r-- root/root 361 2018-06-26 01:36 ./usr/share/man/man1/findspl.1.gz
-rw-r--r-- root/root 715 2018-06-26 01:36 ./usr/share/man/man1/gbseqget.1.gz
-rw-r--r-- root/root 911 2018-06-26 01:36 ./usr/share/man/man1/gene2xml.1.gz
-rw-r--r-- root/root 382 2018-06-26 01:36 ./usr/share/man/man1/getmesh.1.gz
-rw-r--r-- root/root 509 2018-06-26 01:36 ./usr/share/man/man1/getpub.1.gz
-rw-r--r-- root/root 382 2018-06-26 01:36 ./usr/share/man/man1/gil2bin.1.gz
-rw-r--r-- root/root 1294 2018-06-26 01:36 ./usr/share/man/man1/idfetch.1.gz
-rw-r--r-- root/root 410 2018-06-26 01:36 ./usr/share/man/man1/indexpub.1.gz
-rw-r--r-- root/root 651 2018-06-26 01:36 ./usr/share/man/man1/insdseqget.1.gz
-rw-r--r-- root/root 462 2018-06-26 01:36 ./usr/share/man/man1/makeset.1.gz
-rw-r--r-- root/root 785 2018-06-26 01:36 ./usr/share/man/man1/nps2gps.1.gz
-rw-r--r-- root/root 492 2018-06-26 01:36 ./usr/share/man/man1/sortbyquote.1.gz
-rw-r--r-- root/root 3957 2018-06-26 01:36 ./usr/share/man/man1/spidey.1.gz
-rw-r--r-- root/root 411 2018-06-26 01:36 ./usr/share/man/man1/subfuse.1.gz
-rw-r--r-- root/root 403 2018-06-26 01:36 ./usr/share/man/man1/taxblast.1.gz
-rw-r--r-- root/root 2486 2018-06-26 01:36 ./usr/share/man/man1/tbl2asn.1.gz
-rw-r--r-- root/root 706 2018-06-26 01:36 ./usr/share/man/man1/trna2sap.1.gz
-rw-r--r-- root/root 361 2018-06-26 01:36 ./usr/share/man/man1/trna2tbl.1.gz
-rw-r--r-- root/root 1026 2018-06-26 01:36 ./usr/share/man/man1/vecscreen.1.gz
ncbi-tools-x11-dbgsym_6.1.20170106-4_armhf.deb
----------------------------------------------
new Debian package, version 2.0.
size 2222384 bytes: control archive=820 bytes.
615 bytes, 12 lines control
636 bytes, 6 lines md5sums
Package: ncbi-tools-x11-dbgsym
Source: ncbi-tools6
Version: 6.1.20170106-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2477
Depends: ncbi-tools-x11 (= 6.1.20170106-4)
Section: debug
Priority: optional
Description: debug symbols for ncbi-tools-x11
Build-Ids: 18d36e5d33586344af075195354db5a156898c8a 345164f52af271d484c47ac7bd759b416af4da72 4bcc80b14b2a6d91378a90daefb1d27e9fe71722 56169e225358ac21d8ae0c10d7c28eef30b00d1a 6586982d281ef404582ba834733626bbe18c5416 aa654df6295e30fff49dba952ba4c87e7641cdd7
drwxr-xr-x root/root 0 2018-06-26 01:36 ./
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/18/
-rw-r--r-- root/root 36400 2018-06-26 01:36 ./usr/lib/debug/.build-id/18/d36e5d33586344af075195354db5a156898c8a.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/34/
-rw-r--r-- root/root 24980 2018-06-26 01:36 ./usr/lib/debug/.build-id/34/5164f52af271d484c47ac7bd759b416af4da72.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/4b/
-rw-r--r-- root/root 26096 2018-06-26 01:36 ./usr/lib/debug/.build-id/4b/cc80b14b2a6d91378a90daefb1d27e9fe71722.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/56/
-rw-r--r-- root/root 26456 2018-06-26 01:36 ./usr/lib/debug/.build-id/56/169e225358ac21d8ae0c10d7c28eef30b00d1a.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/65/
-rw-r--r-- root/root 2379512 2018-06-26 01:36 ./usr/lib/debug/.build-id/65/86982d281ef404582ba834733626bbe18c5416.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/debug/.build-id/aa/
-rw-r--r-- root/root 24636 2018-06-26 01:36 ./usr/lib/debug/.build-id/aa/654df6295e30fff49dba952ba4c87e7641cdd7.debug
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-x11-dbgsym -> ncbi-tools-x11
ncbi-tools-x11_6.1.20170106-4_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 939132 bytes: control archive=2440 bytes.
780 bytes, 17 lines control
4362 bytes, 59 lines md5sums
194 bytes, 8 lines * postinst #!/bin/sh
68 bytes, 5 lines * prerm #!/bin/sh
Package: ncbi-tools-x11
Source: ncbi-tools6
Version: 6.1.20170106-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2217
Depends: libncbi6 (<< 6.1.20170106.1), libncbi6 (>= 6.1.20170106), libvibrant6b (<< 6.1.20170106.1), libvibrant6b (>= 6.1.20170106), libc6 (>= 2.4)
Suggests: 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
NCBI C SDK: Cn3D, Network Entrez, Sequin, ddv, and udv. These
programs are not part of ncbi-tools-bin because they depend on
several additional library packages.
drwxr-xr-x root/root 0 2018-06-26 01:36 ./
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/bin/
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-rwxr-xr-x root/root 9764 2018-06-26 01:36 ./usr/bin/ddv
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/bin/entrez -> entrez2
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-rwxr-xr-x root/root 34264 2018-06-26 01:36 ./usr/bin/sbtedit
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/bin/sequin -> Psequin
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drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/mime/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/lib/mime/packages/
-rw-r--r-- root/root 158 2016-10-11 03:31 ./usr/lib/mime/packages/ncbi-tools-x11
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/applications/
-rw-r--r-- root/root 204 2018-06-26 01:36 ./usr/share/applications/Cn3D-3.0.desktop
-rw-r--r-- root/root 258 2018-06-26 01:36 ./usr/share/applications/Psequin.desktop
-rw-r--r-- root/root 232 2018-06-26 01:36 ./usr/share/applications/ddv.desktop
-rw-r--r-- root/root 237 2018-06-26 01:36 ./usr/share/applications/entrez2.desktop
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-rw-r--r-- root/root 212 2018-06-26 01:36 ./usr/share/applications/udv.desktop
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc-base/
-rw-r--r-- root/root 470 2016-10-11 03:31 ./usr/share/doc-base/ncbi-tools-firewall
-rw-r--r-- root/root 547 2016-10-11 03:31 ./usr/share/doc-base/sequin
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-x11/
lrwxrwxrwx root/root 0 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-x11/README.gz -> changelog.gz
-rw-r--r-- root/root 2123 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-x11/README.sequin.gz
-rw-r--r-- root/root 1140 2018-06-24 16:12 ./usr/share/doc/ncbi-tools-x11/bkgd.gif
-rw-r--r-- root/root 16990 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-x11/changelog.Debian.gz
-rw-r--r-- root/root 18160 2008-06-16 15:51 ./usr/share/doc/ncbi-tools-x11/changelog.gz
-rw-r--r-- root/root 2881 2018-06-26 01:33 ./usr/share/doc/ncbi-tools-x11/copyright
-rw-r--r-- root/root 3658 1999-11-01 22:01 ./usr/share/doc/ncbi-tools-x11/firedialog.gif
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drwxr-xr-x root/root 0 2018-06-26 01:36 ./usr/share/doc/ncbi-tools-x11/images/
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| Summary |
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Build Architecture: armhf
Build-Space: 918520
Build-Time: 2482
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 339
Job: ncbi-tools6_6.1.20170106-4
Machine Architecture: armhf
Package: ncbi-tools6
Package-Time: 2899
Source-Version: 6.1.20170106-4
Space: 918520
Status: successful
Version: 6.1.20170106-4
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Finished at 2018-06-28T06:48:16Z
Build needed 00:48:19, 918520k disk space