clustalo →
1.2.3-1 →
armhf → 2016-09-17 11:32:08
sbuild (Debian sbuild) 0.68.0 (15 Jan 2016) on bm-wb-01
+==============================================================================+
| clustalo 1.2.3-1 (armhf) 17 Sep 2016 11:06 |
+==============================================================================+
Package: clustalo
Version: 1.2.3-1
Source Version: 1.2.3-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/clustalo-IIl8_F/clustalo-1.2.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clustalo-IIl8_F' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/stretch-staging-armhf-sbuild-e77ac333-ed7c-4187-b448-c8b8bc3fb5f0' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9286 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.2 MB]
Fetched 20.5 MB in 23s (858 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'clustalo' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/clustalo.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/clustalo.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1179 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main clustalo 1.2.3-1 (dsc) [2178 B]
Get:2 http://172.17.0.1/private stretch-staging/main clustalo 1.2.3-1 (tar) [1171 kB]
Get:3 http://172.17.0.1/private stretch-staging/main clustalo 1.2.3-1 (diff) [6628 B]
Fetched 1179 kB in 0s (6468 kB/s)
Download complete and in download only mode
+------------------------------------------------------------------------------+
| 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-z2BunC/apt_archive/sbuild-build-depends-core-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ Packages [526 B]
Ign:4 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ Sources
Ign:5 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ Packages
Get:4 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ Sources [276 B]
Get:5 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ Packages [759 B]
Reading package lists...
W: file:///<<BUILDDIR>>/resolver-z2BunC/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
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:
fuse2fs libfuse2 manpages
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 33 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-z2BunC/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 12775 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), dh-autoreconf, dh-linktree, libargtable2-dev, doxygen, graphviz, sphinx-common
Filtered Build-Depends: debhelper (>= 9), dh-autoreconf, dh-linktree, libargtable2-dev, doxygen, graphviz, sphinx-common
dpkg-deb: building package 'sbuild-build-depends-clustalo-dummy' in '/<<BUILDDIR>>/resolver-rSdgdp/apt_archive/sbuild-build-depends-clustalo-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ Sources [261 B]
Get:5 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ Packages [582 B]
Ign:4 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ Sources
Ign:5 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ Packages
Get:4 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ Sources [341 B]
Get:5 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ Packages [838 B]
Reading package lists...
W: file:///<<BUILDDIR>>/resolver-rSdgdp/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
Install clustalo 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:
fuse2fs libfuse2 manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-linktree dh-strip-nondeterminism doxygen file fontconfig
fontconfig-config fonts-dejavu-core gcc-5-base gettext gettext-base graphviz
groff-base intltool-debian libarchive-zip-perl libargtable2-0
libargtable2-dev libargtable2-docs libasan2 libbsd0 libcairo2 libcdt5
libcgraph6 libclang1-3.6 libcroco3 libdatrie1 libedit2 libexpat1 libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-5-dev
libgd3 libglib2.0-0 libgraphite2-3 libgts-0.7-5 libgvc6 libgvpr2
libharfbuzz0b libice6 libicu57 libjbig0 libjpeg62-turbo libjs-jquery
libjs-sphinxdoc libjs-underscore libllvm3.6v5 libltdl7 libmagic-mgc
libmagic1 libobjc-5-dev libobjc4 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16
libsigsegv2 libsm6 libstdc++-5-dev libthai-data libthai0 libtiff5
libtimedate-perl libtool libunistring0 libwebp6 libx11-6 libx11-data libxau6
libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6
libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf
sphinx-common ucf x11-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make doxygen-latex doxygen-doc doxygen-gui gettext-doc
libasprintf-dev libgettextpo-dev gsfonts graphviz-doc groff libgd-tools
libstdc++-5-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur fonts-liberation libglib2.0-data shared-mime-info
xdg-user-dirs libgts-bin javascript-common libltdl-dev xml-core
libmail-sendmail-perl python-sphinx | python3-sphinx
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-linktree dh-strip-nondeterminism doxygen file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base
intltool-debian libarchive-zip-perl libargtable2-0 libargtable2-dev
libargtable2-docs libasan2 libbsd0 libcairo2 libcdt5 libcgraph6
libclang1-3.6 libcroco3 libdatrie1 libedit2 libexpat1 libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-5-dev
libgd3 libglib2.0-0 libgraphite2-3 libgts-0.7-5 libgvc6 libgvpr2
libharfbuzz0b libice6 libicu57 libjbig0 libjpeg62-turbo libjs-jquery
libjs-sphinxdoc libjs-underscore libllvm3.6v5 libltdl7 libmagic-mgc
libmagic1 libobjc-5-dev libobjc4 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16
libsigsegv2 libsm6 libstdc++-5-dev libthai-data libthai0 libtiff5
libtimedate-perl libtool libunistring0 libwebp6 libx11-6 libx11-data libxau6
libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6
libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf
sbuild-build-depends-clustalo-dummy sphinx-common ucf x11-common
The following packages will be upgraded:
gcc-5-base
1 upgraded, 97 newly installed, 0 to remove and 32 not upgraded.
Need to get 48.5 MB/48.5 MB of archives.
After this operation, 175 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-rSdgdp/apt_archive ./ sbuild-build-depends-clustalo-dummy 0.invalid.0 [818 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libedit2 armhf 3.1-20150325-1 [70.7 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.24-2 [262 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.7 [271 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.7 [313 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf fontconfig armhf 2.11.0-6.7 [402 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.49.6-1 [2518 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libgts-0.7-5 armhf 0.7.6+darcs121130-1.2 [129 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1.1 [41.3 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf gcc-5-base armhf 5.4.1-1 [173 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-1+b1 [803 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.023-2 [13.4 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.023-2 [8202 B]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10 [823 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf dh-linktree all 0.4 [10.3 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libllvm3.6v5 armhf 1:3.6.2-3 [6970 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libasan2 armhf 5.4.1-1 [223 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libgcc-5-dev armhf 5.4.1-1 [445 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libstdc++-5-dev armhf 5.4.1-1 [1434 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libobjc4 armhf 6.1.1-11+rpi1 [90.8 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libobjc-5-dev armhf 5.4.1-1 [335 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libclang1-3.6 armhf 1:3.6.2-3 [2945 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf doxygen armhf 1.8.11-3 [3231 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libcdt5 armhf 2.38.0-15 [56.7 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libcgraph6 armhf 2.38.0-15 [75.5 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.0-1 [109 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.6-2 [203 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libwebp6 armhf 0.5.1-2 [200 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libxpm4 armhf 1:3.5.11-1+b1 [42.4 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libgd3 armhf 2.2.3-3+b1 [117 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-0 armhf 0.33.6-1 [454 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0 armhf 1.11.1-1.1 [17.1 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0 armhf 1.11.1-1.1 [11.6 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libcairo2 armhf 1.14.6-1+b1 [686 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libltdl7 armhf 2.4.6-2 [386 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libthai-data all 0.1.25-1 [165 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libdatrie1 armhf 0.2.10-2 [32.5 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libthai0 armhf 0.1.25-1 [48.5 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libpango-1.0-0 armhf 1.40.2-1 [299 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libgraphite2-3 armhf 1.3.8-1 [62.5 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz0b armhf 1.2.7-1+b1 [589 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libpangoft2-1.0-0 armhf 1.40.2-1 [236 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libpangocairo-1.0-0 armhf 1.40.2-1 [225 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libpathplan4 armhf 2.38.0-15 [60.0 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libxdot4 armhf 2.38.0-15 [54.2 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libgvc6 armhf 2.38.0-15 [537 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf libgvpr2 armhf 2.38.0-15 [185 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+16 [251 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf libxaw7 armhf 2:1.0.13-1 [164 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf graphviz armhf 2.38.0-15 [670 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf libargtable2-0 armhf 13-1 [15.9 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf libargtable2-docs all 13-1 [2621 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf libargtable2-dev armhf 13-1 [55.7 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf libjs-jquery all 1.12.4-1 [167 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf libjs-underscore all 1.8.3~dfsg-1 [63.8 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf libjs-sphinxdoc all 1.4.6-1 [66.7 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf sphinx-common all 1.4.6-1 [348 kB]
debconf: delaying package configuration, since apt-utils is not installed
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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
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Setting up libtool (2.4.6-2) ...
Setting up libgts-0.7-5:armhf (0.7.6+darcs121130-1.2) ...
Setting up libfontconfig1:armhf (2.11.0-6.7) ...
Setting up libsm6:armhf (2:1.2.2-1+b1) ...
Setting up libxcb-render0:armhf (1.11.1-1.1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libclang1-3.6:armhf (1:3.6.2-3) ...
Setting up libxcb-shm0:armhf (1.11.1-1.1) ...
Setting up libxpm4:armhf (1:3.5.11-1+b1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.9-2) ...
Setting up fontconfig (2.11.0-6.7) ...
Regenerating fonts cache... done.
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up po-debconf (1.0.19) ...
Setting up doxygen (1.8.11-3) ...
Setting up libgd3:armhf (2.2.3-3+b1) ...
Setting up libxmu6:armhf (2:1.1.2-2) ...
Setting up libpango-1.0-0:armhf (1.40.2-1) ...
Setting up libxaw7:armhf (2:1.0.13-1) ...
Setting up libcairo2:armhf (1.14.6-1+b1) ...
Setting up libpangoft2-1.0-0:armhf (1.40.2-1) ...
Setting up libpangocairo-1.0-0:armhf (1.40.2-1) ...
Setting up libgvc6 (2.38.0-15) ...
Setting up graphviz (2.38.0-15) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (10) ...
Setting up dh-linktree (0.4) ...
Setting up dh-strip-nondeterminism (0.023-2) ...
Setting up sbuild-build-depends-clustalo-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.23-4) ...
Processing triggers for systemd (230-7+b1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.6.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.23-4 libstdc++-5-dev_5.4.1-1 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3~pre3 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-15 binutils_2.26.1-1 bsdmainutils_9.0.10 bsdutils_1:2.28-6 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10 debianutils_4.8 dh-autoreconf_12 dh-linktree_0.4 dh-strip-nondeterminism_0.023-2 diffutils_1:3.3-3 dmsetup_2:1.02.130-1 doxygen_1.8.11-3 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fontconfig_2.11.0-6.7 fontconfig-config_2.11.0-6.7 fonts-dejavu-core_2.37-1 fuse2fs_1.43.1-1 g++_4:6.1.1-1 g++-6_6.1.1-11+rpi1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-1 gcc-6_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_1.4.20-6 gpgv_1.4.20-6 graphviz_2.38.0-15 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 init_1.42 init-system-helpers_1.42 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg5.0_1.3~pre3 libarchive-zip-perl_1.59-1 libargtable2-0_13-1 libargtable2-dev_13-1 libargtable2-docs_13-1 libasan2_5.4.1-1 libasan3_6.1.1-11+rpi1 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.5-1 libaudit1_1:2.6.5-1 libblkid1_2.28-6 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-4 libc-dev-bin_2.23-4 libc6_2.23-4 libc6-dev_2.23-4 libcairo2_1.14.6-1+b1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcdt5_2.38.0-15 libcgraph6_2.38.0-15 libclang1-3.6_1:3.6.2-3 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdatrie1_0.2.10-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.8-1 libdebconfclient0_0.215 libdevmapper1.02.1_2:1.02.130-1 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 libedit2_3.1-20150325-1 libexpat1_2.2.0-1 libfakeroot_1.21-1 libfdisk1_2.28-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.023-2 libfontconfig1_2.11.0-6.7 libfreetype6_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-5-dev_5.4.1-1 libgcc-6-dev_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.2-2 libgd3_2.2.3-3+b1 libgdbm3_1.8.3-14 libglib2.0-0_2.49.6-1 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libgraphite2-3_1.3.8-1 libgts-0.7-5_0.7.6+darcs121130-1.2 libgvc6_2.38.0-15 libgvpr2_2.38.0-15 libharfbuzz0b_1.2.7-1+b1 libice6_2:1.0.9-1+b1 libicu57_57.1-4 libidn11_1.33-1 libisl15_0.17.1-1 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.5.0-1 libjs-jquery_1.12.4-1 libjs-sphinxdoc_1.4.6-1 libjs-underscore_1.8.3~dfsg-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libllvm3.6v5_1:3.6.2-3 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libobjc-5-dev_5.4.1-1 libobjc4_6.1.1-11+rpi1 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpango-1.0-0_1.40.2-1 libpangocairo-1.0-0_1.40.2-1 libpangoft2-1.0-0_1.40.2-1 libpathplan4_2.38.0-15 libpcre3_2:8.39-1 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libpixman-1-0_0.33.6-1 libpng12-0_1.2.54-6 libpng16-16_1.6.24-2 libprocps6_2:3.3.12-2 libreadline6_6.3-8+b3 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsm6_2:1.2.2-1+b1 libsmartcols1_2.28-6 libss2_1.43.1-1 libstdc++-5-dev_5.4.1-1 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_230-7+b1 libthai-data_0.1.25-1 libthai0_0.1.25-1 libtiff5_4.0.6-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1 libtool_2.4.6-2 libubsan0_6.1.1-11+rpi1 libudev1_230-7+b1 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-6 libwebp6_0.5.1-2 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-render0_1.11.1-1.1 libxcb-shm0_1.11.1-1.1 libxcb1_1.11.1-1.1 libxdmcp6_1:1.1.2-1.1 libxdot4_2.38.0-15 libxext6_2:1.3.3-1 libxml2_2.9.4+dfsg1-1+b1 libxmu6_2:1.1.2-2 libxpm4_1:3.5.11-1+b1 libxrender1_1:0.9.9-2 libxt6_1:1.1.5-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.07-1 mawk_1.3.3-17 mount_2.28-6 multiarch-support_2.23-4 nano_2.6.2-1 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 po-debconf_1.0.19 procps_2:3.3.12-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-clustalo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 sphinx-common_1.4.6-1 startpar_0.59-3.1 systemd_230-7+b1 systemd-sysv_230-7+b1 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016f-1 ucf_3.0036 udev_230-7+b1 util-linux_2.28-6 x11-common_1:7.7+16 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Aug 30 07:50:48 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./clustalo_1.2.3-1.dsc
dpkg-source: info: extracting clustalo in clustalo-1.2.3
dpkg-source: info: unpacking clustalo_1.2.3.orig.tar.gz
dpkg-source: info: unpacking clustalo_1.2.3-1.debian.tar.xz
dpkg-source: info: applying log2.patch
Check disc 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=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-e77ac333-ed7c-4187-b448-c8b8bc3fb5f0
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package clustalo
dpkg-buildpackage: info: source version 1.2.3-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build clustalo-1.2.3
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf --with linktree
dh_testdir
dh_auto_clean
dh_autoreconf_clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f _configs.sed
rm -rf doc
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules build-arch
dh build-arch --with autoreconf --with linktree
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:147: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:147: the top level
configure.ac:147: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:147: the top level
configure.ac:169: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from...
m4/libtool.m4:785: _LT_LANG is expanded from...
m4/libtool.m4:768: LT_LANG is expanded from...
configure.ac:169: the top level
configure.ac:147: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:147: the top level
configure.ac:147: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:147: the top level
configure.ac:169: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from...
m4/libtool.m4:785: _LT_LANG is expanded from...
m4/libtool.m4:768: LT_LANG is expanded from...
configure.ac:169: the top level
configure.ac:147: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:147: the top level
configure.ac:147: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:147: the top level
configure.ac:169: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from...
m4/libtool.m4:785: _LT_LANG is expanded from...
m4/libtool.m4:768: LT_LANG is expanded from...
configure.ac:169: the top level
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:130: installing './compile'
configure.ac:112: installing './missing'
src/Makefile.am: installing './depcomp'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking
configure: WARNING: unrecognized options: --disable-maintainer-mode
configure:
Welcome to Clustal Omega - version 1.2.3 (AndreaGiacomo)
+NMMMMMMMMMS=
MMMMM? :MMMMM8
IMMMMS MMMMM,
~MMMMN ,MMMMM
=MMMMM MMMMM
?MMMMM +MMMMM
MMMMMS MMMMM
MMMMM MMMMM:
MMMMM MMMMM+
MMMMM MMMMM~
MMMMM MMMMM
MMMMMZ MMMMM
MMMMM ,MMMMZ
MMMM8 MMMM+
MMMMS MMMM,
MMMMO MMMM
,N SMMM MMM8 +8
,M7 M+ M+ :M8
,MMMMMMMMMMMMI MMMMMMMMMMMM8
,MMMMMMMMMMMM8 MMMMMMMMMMMM8
,MMMMMMMMMMMMN MMMMMMMMMMMM8
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking whether make sets $(MAKE)... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
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configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make all-recursive
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
Making all in hhalign
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/hhalign'
/bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o hhalign.lo hhalign.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o
In file included from hhalign.cpp:62:0:
hhutil-C.h: In function 'void ReadDefaultsFile(int&, char**)':
hhutil-C.h:516:53: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
^
hhutil-C.h:521:56: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
^
In file included from hhalign.cpp:70:0:
hhhmm-C.h: In member function 'HMM& HMM::operator=(HMM&)':
hhhmm-C.h:189:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k]=new(char[strlen(q.sname[k])+1]);
^
hhhmm-C.h:194:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[strlen(q.seq[k])+1]);
^
hhhmm-C.h: In member function 'int HMM::Read(FILE*, char*)':
hhhmm-C.h:330:48: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char *cur_seq = new(char[par.maxColCnt]); //Sequence currently read in
^
hhhmm-C.h:361:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k-1]=new(char[strlen(cur_seq)+1]);
^
hhhmm-C.h:368:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0'
^
hhhmm-C.h:464:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[strlen(cur_seq)+1]);
^
hhhmm-C.h: In member function 'int HMM::ReadHMMer(FILE*, char*)':
hhhmm-C.h:736:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:757:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:778:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:860:55: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1036:46: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k+1]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1038:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h:1041:29: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k+1]=new(char[L+2]);
^
hhhmm-C.h:1059:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1063:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
hhhmm-C.h:1238:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1259:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1280:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1350:69: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1530:49: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k+1]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1532:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h:1535:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k+1]=new(char[L+2]);
^
hhhmm-C.h:1553:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1555:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h: In member function 'void HMM::InsertCalibration(char*)':
hhhmm-C.h:2110:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char** lines = new(char*[3*L+100000]);
^
hhhmm-C.h:2139:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
lines[nline]=new(char[strlen(line)+1]);
^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In constructor 'Alignment::Alignment(int, int)':
hhalignment-C.h:85:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname = new(char*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:86:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq = new(char*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:87:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
l = new(int[maxres]);
^
hhalignment-C.h:88:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X = new(char*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:89:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
I = new(short unsigned int*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:90:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
keep = new(char[maxseq+2]); /* MR1 */
^
hhalignment-C.h:91:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
display = new(char[maxseq+2]); /* MR1 */
^
hhalignment-C.h:92:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
wg = new(float[maxseq+2]); /* MR1 */
^
hhalignment-C.h:93:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
nseqs = new(int[maxres+2]); /* MR1 */
^
hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)':
hhalignment-C.h:146:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char *cur_seq=new(char[par.maxColCnt]);
^
hhalignment-C.h:188:61: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:190:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:192:73: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
I[k]=new(short unsigned int[strlen(cur_seq)+2]);
^
In file included from hhalign.cpp:71:0:
hhalignment-C.h:241:58: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k] = new(char[strlen(cur_name)+1]);
^
hhalignment-C.h:356:45: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:358:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:360:57: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
I[k]=new(short unsigned int[strlen(cur_seq)+2]);
^
hhalignment-C.h: In member function 'void Alignment::Compress(const char*)':
hhalignment-C.h:428:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */
^
hhalignment-C.h:560:52: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
percent_gaps = new(float[par.maxColCnt]);
^
hhalignment-C.h:566:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
if (nres==NULL) nres=new(int[N_in]);
^
hhalignment-C.h:804:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
match_state = new(char[par.maxColCnt]);
^
hhalignment-C.h: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)':
hhalignment-C.h:966:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char *dummy = new(char[N_in+1]);
^
hhalignment-C.h: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)':
hhalignment-C.h:1029:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid
^
hhalignment-C.h:1030:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0;
^
hhalignment-C.h:1031:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering /* MR1, used to be called idmax*/
^
hhalignment-C.h:1032:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL]
^
hhalignment-C.h:1033:36: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid)
^
hhalignment-C.h:1034:24: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i
^
hhalignment-C.h:1062:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
first=new(int[N_in]);// first non-gap position in sequence k
^
hhalignment-C.h:1063:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
last =new(int[N_in]);// last non-gap position in sequence k
^
hhalignment-C.h:1078:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
nres=new(int[N_in]);
^
hhalignment-C.h:1092:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences
^
hhalignment-C.h: In member function 'int Alignment::HomologyFilter(int, float, float)':
hhalignment-C.h:1358:33: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char* coreseq=new(char[N_in]); // coreseq[k]=1 if sequence belongs to core of alignment (i.e. it is very similar to query)
^
hhalignment-C.h: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM&)':
hhalignment-C.h:1409:36: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore
^
hhalignment-C.h:1418:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
first=new(int[N_in]);// first non-gap position in sequence k
^
hhalignment-C.h:1419:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
last =new(int[N_in]);// last non-gap position in sequence k
^
hhalignment-C.h:1432:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
nres=new(int[N_in]);
^
hhalignment-C.h: In member function 'void Alignment::FrequenciesAndTransitions(HMM&, char*)':
hhalignment-C.h:1715:49: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
q.seq[q.ncons]=new(char[L+2]);
^
hhalignment-C.h:1722:64: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
q.sname[q.nfirst]=new(char[strlen(name)+11]);
^
hhalignment-C.h:1726:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
q.seq[q.nfirst]=new(char[L+2]);
^
hhalignment-C.h:1784:61: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
q.sname[nn]=new(char[strlen(sname[k])+1]);
^
hhalignment-C.h:1787:57: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
q.seq[nn]=new(char[strlen(seq[k])+1]);
^
hhalignment-C.h: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)':
hhalignment-C.h:1874:41: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
^
hhalignment-C.h:1881:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
wi = new(float[N_in+2]);
^
hhalignment-C.h:1891:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
n = new(int*[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::Transitions_from_I_state(HMM&, char*)':
hhalignment-C.h:2166:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
^
hhalignment-C.h:2174:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
wi = new(float[N_in+2]);
^
hhalignment-C.h:2185:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
n = new(int*[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::Transitions_from_D_state(HMM&, char*)':
hhalignment-C.h:2368:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
^
hhalignment-C.h:2377:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
wi = new(float[N_in+2]); /* FIXME: FS */
^
hhalignment-C.h:2388:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
n = new(int*[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::MergeMasterSlave(Hit&, char*)':
hhalignment-C.h:2699:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
int* imatch=new(int[hit.j2+1]);
^
hhalignment-C.h:2831:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char* new_seq=new(char[2*maxcol]);
^
hhalignment-C.h:2844:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[N_in]=new(char[h]);
^
hhalignment-C.h:2847:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X[N_in]=new(char[h]);
^
hhalignment-C.h:2849:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
I[N_in]=new(short unsigned int[h]);
^
hhalignment-C.h:2851:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[N_in]=new(char[strlen(Tali.sname[k])+1]);
^
hhalignment-C.h: In member function 'void Alignment::AddSequence(char*, int*)':
hhalignment-C.h:2882:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X[N_in]=new(char[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::GetPositionSpecificWeights(float**)':
hhalignment-C.h:2932:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
n = new(int*[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::Transfer(char**, int)':
hhalignment-C.h:3049:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
I[k] = new(short unsigned int[iLen+2+GOOD_MEASURE]);
^
hhalignment-C.h:3050:45: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X[k] = new(char[iLen+2+GOOD_MEASURE]);
^
hhalignment-C.h:3051:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k] = new(char[iLen+2+GOOD_MEASURE]);
^
In file included from hhalign.cpp:72:0:
hhhit-C.h: In member function 'void Hit::AllocateBacktraceMatrix(int, int)':
hhhit-C.h:180:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bMM=new(char*[Nq]);
^
hhhit-C.h:181:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bMI=new(char*[Nq]);
^
hhhit-C.h:182:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bIM=new(char*[Nq]);
^
hhhit-C.h:183:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bDG=new(char*[Nq]);
^
hhhit-C.h:184:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bGD=new(char*[Nq]);
^
hhhit-C.h:185:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
cell_off=new(char*[Nq]);
^
hhhit-C.h:188:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bMM[i]=new(char[Nt]);
^
hhhit-C.h:189:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bMI[i]=new(char[Nt]);
^
hhhit-C.h:190:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bIM[i]=new(char[Nt]);
^
hhhit-C.h:191:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bGD[i]=new(char[Nt]);
^
hhhit-C.h:192:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bDG[i]=new(char[Nt]);
^
hhhit-C.h:193:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
cell_off[i]=new(char[Nt]);
^
hhhit-C.h: In member function 'void Hit::AllocateForwardMatrix(int, int)':
hhhit-C.h:240:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_MM=new(double*[Nq]);
^
hhhit-C.h:241:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_MI=new(double*[Nq]);
^
hhhit-C.h:242:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_DG=new(double*[Nq]);
^
hhhit-C.h:243:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_IM=new(double*[Nq]);
^
hhhit-C.h:244:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_GD=new(double*[Nq]);
^
hhhit-C.h:245:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
scale=new(double[Nq+1]); // need Nq+3?
^
hhhit-C.h:248:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_MM[i] = new(double[Nt]);
^
hhhit-C.h:249:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_MI[i] = new(double[Nt]);
^
hhhit-C.h:250:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_DG[i] = new(double[Nt]);
^
hhhit-C.h:251:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_IM[i] = new(double[Nt]);
^
hhhit-C.h:252:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_GD[i] = new(double[Nt]);
^
hhhit-C.h: In member function 'void Hit::AllocateBackwardMatrix(int, int)':
hhhit-C.h:297:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
B_MM=new(double*[Nq]);
^
hhhit-C.h:304:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
B_MM[i] = new(double[Nt]);
^
hhhit-C.h: In member function 'void Hit::Viterbi(HMM&, HMM&, float**)':
hhhit-C.h:377:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *sMM = new(float[par.maxResLen]); // sMM[i][j] = score of best alignment up to indices (i,j) ending in (Match,Match)
^
hhhit-C.h:378:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *sGD = new(float[par.maxResLen]); // sGD[i][j] = score of best alignment up to indices (i,j) ending in (Gap,Delete)
^
hhhit-C.h:379:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *sDG = new(float[par.maxResLen]); // sDG[i][j] = score of best alignment up to indices (i,j) ending in (Delete,Gap)
^
hhhit-C.h:380:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *sIM = new(float[par.maxResLen]); // sIM[i][j] = score of best alignment up to indices (i,j) ending in (Ins,Match)
^
hhhit-C.h:381:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *sMI = new(float[par.maxResLen]); // sMI[i][j] = score of best alignment up to indices (i,j) ending in (Match,Ins)
^
hhhit-C.h: In member function 'void Hit::Backtrace(HMM&, HMM&)':
hhhit-C.h:1127:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
^
hhhit-C.h:1128:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S = new( float[nsteps+1]);
^
hhhit-C.h:1129:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S_ss = new( float[nsteps+1]);
^
hhhit-C.h: In member function 'void Hit::StochasticBacktrace(HMM&, HMM&, char)':
hhhit-C.h:1229:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double* scale_cum = new(double[q.L+2]);
^
hhhit-C.h:1248:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double* sumF=new(double[q.L+t.L]);
^
hhhit-C.h:1372:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
^
hhhit-C.h:1373:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S = new( float[nsteps+1]);
^
hhhit-C.h:1374:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S_ss = new( float[nsteps+1]);
^
hhhit-C.h: In member function 'void Hit::BacktraceMAC(HMM&, HMM&)':
hhhit-C.h:1476:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
^
hhhit-C.h:1477:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S = new( float[nsteps+1]);
^
hhhit-C.h:1478:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S_ss = new( float[nsteps+1]);
^
hhhit-C.h:1479:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
P_posterior = new( float[nsteps+1]);
^
hhhit-C.h: In member function 'void Hit::InitializeBacktrace(HMM&, HMM&)':
hhhit-C.h:1684:54: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
longname=new(char[strlen(t.longname)+1])();
^
hhhit-C.h:1685:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
name =new(char[strlen(t.name)+1])();
^
hhhit-C.h:1686:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
file =new(char[strlen(t.file)+1])();
^
hhhit-C.h:1697:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname=new(char*[t.n_display])(); // Call Compare only once with irep=1
^
hhhit-C.h:1698:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq =new(char*[t.n_display])(); // Call Compare only once with irep=1
^
hhhit-C.h:1731:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
this->i = new( int[i2+j2+2])();
^
hhhit-C.h:1732:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
this->j = new( int[i2+j2+2])();
^
hhhit-C.h:1733:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
states = new( char[i2+j2+2])();
^
In file included from hhalign.cpp:73:0:
hhhalfalignment-C.h: In constructor 'HalfAlignment::HalfAlignment(int)':
hhhalfalignment-C.h:67:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written
^
hhhalfalignment-C.h:68:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment
^
hhhalfalignment-C.h:69:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k
^
hhhalfalignment-C.h:70:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k]
^
In file included from hhalign.cpp:74:0:
hhfullalignment-C.h: In member function 'void FullAlignment::PrintHHR(FILE*, Hit&)':
hhfullalignment-C.h:360:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
lq = new(short unsigned int[qa->n+2]);
^
hhfullalignment-C.h:361:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
lt = new(short unsigned int[ta->n+2]);
^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()':
hhhitlist-C.h:1286:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:1289:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:1294:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:1297:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:1304:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:1305:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:1306:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:1307:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:1308:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:1309:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:1310:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:1311:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:1374:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1375:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1378:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1379:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:1454:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1457:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1471:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1472:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
for (m=0; m<M; m++) Cinv[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring2()':
hhhitlist-C.h:1651:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:1654:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:1659:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:1662:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:1669:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:1670:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:1671:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:1672:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:1673:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:1674:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:1675:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:1676:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:1740:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1741:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1744:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1745:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:1822:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1825:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1839:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1840:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
for (m=0; m<M; m++) Cinv[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring3()':
hhhitlist-C.h:2021:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:2024:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:2029:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:2032:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:2039:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:2040:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:2041:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:2042:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:2043:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:2044:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:2045:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:2046:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:2115:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2116:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:2119:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2120:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:2187:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2190:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2204:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:2205:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
for (m=0; m<M; m++) Cinv[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring4()':
hhhitlist-C.h:2386:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:2389:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:2394:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:2397:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:2404:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:2405:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:2406:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:2407:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:2408:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:2409:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:2410:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:2411:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:2473:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2476:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2539:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2542:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::InvertMatrix(double**, double**, int)':
hhhitlist-C.h:2841:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** V = new(double*[N]);
^
hhhitlist-C.h:2842:29: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double* s = new(double[N]);
^
hhhitlist-C.h:2843:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
for (k=0; k<N; k++) V[k] = new(double[N]);
^
hhhitlist-C.h: In member function 'void HitList::SVD(double**, int, double*, double**)':
hhhitlist-C.h:2926:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
rv1=new(double[n]);
^
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libtool: link: ar cru .libs/libhhalign.a .libs/hhalign.o
ar: `u' modifier ignored since `D' is the default (see `U')
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make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/hhalign'
Making all in squid
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/squid'
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c alignio.c -fPIE -o alignio.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c cluster.c -fPIE -o cluster.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c eps.c -fPIC -DPIC -o .libs/eps.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c eps.c -fPIE -o eps.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c file.c -fPIC -DPIC -o .libs/file.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c file.c -fPIE -o file.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c getopt.c -fPIE -o getopt.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gki.c -fPIC -DPIC -o .libs/gki.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gki.c -fPIE -o gki.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gsi.c -fPIC -DPIC -o .libs/gsi.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gsi.c -fPIE -o gsi.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gsi64.c -fPIC -DPIC -o .libs/gsi64.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gsi64.c -fPIE -o gsi64.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c hsregex.c -fPIC -DPIC -o .libs/hsregex.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c hsregex.c -fPIE -o hsregex.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c log.c -fPIE -o log.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o muscle_upgma.lo muscle_upgma.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_upgma.c -fPIC -DPIC -o .libs/muscle_upgma.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_upgma.c -fPIE -o muscle_upgma.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o muscle_tree.lo muscle_tree.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_tree.c -fPIC -DPIC -o .libs/muscle_tree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_tree.c -fPIE -o muscle_tree.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o mbed.lo mbed.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c mbed.c -fPIC -DPIC -o .libs/mbed.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c mbed.c -fPIE -o mbed.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_dist.lo pair_dist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c pair_dist.c -fPIC -DPIC -o .libs/pair_dist.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c pair_dist.c -fPIE -o pair_dist.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o progress.lo progress.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c -fPIC -DPIC -o .libs/progress.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c -fPIE -o progress.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o seq.lo seq.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c seq.c -fPIC -DPIC -o .libs/seq.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c seq.c -fPIE -o seq.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o symmatrix.lo symmatrix.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c symmatrix.c -fPIC -DPIC -o .libs/symmatrix.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c symmatrix.c -fPIE -o symmatrix.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o tree.lo tree.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c tree.c -fPIC -DPIC -o .libs/tree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c tree.c -fPIE -o tree.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.c -fPIC -DPIC -o .libs/util.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.c -fPIE -o util.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o weights.lo weights.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c weights.c -fPIC -DPIC -o .libs/weights.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c weights.c -fPIE -o weights.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now -o libclustal.la hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo -largtable2 -lm
libtool: link: ar cru .libs/libclustal.a .libs/hhalign_wrapper.o .libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libclustal.a
libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" )
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/clustal'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o clustal-omega.lo clustal-omega.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c -fPIC -DPIC -o .libs/clustal-omega.o
clustal-omega.c: In function 'PrintLongVersion':
clustal-omega.c:152:49: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__);
^~~~~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c -fPIE -o clustal-omega.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -static -fPIE -pie -Wl,-z,relro -Wl,-z,now -o libclustalo.la -rpath /usr/lib/arm-linux-gnueabihf clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la -largtable2 -lm
libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/<<PKGBUILDDIR>>/src/clustal/.libs/libclustal.a")
libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/<<PKGBUILDDIR>>/src/hhalign/.libs/libhhalign.a")
libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/<<PKGBUILDDIR>>/src/squid/.libs/libsquid.a")
libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/<<PKGBUILDDIR>>/src/kmpp/.libs/libkmpp.a")
libtool: link: ar cru .libs/libclustalo.a clustal-omega.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KmUtils.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libclustalo.a
libtool: link: rm -fr .libs/libclustalo.lax
libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" )
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.cpp
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o mymain.o mymain.c
/bin/bash ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm
libtool: link: g++ -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o clustalo main.o mymain.o ./.libs/libclustalo.a /usr/lib/arm-linux-gnueabihf/libargtable2.so -lm -fopenmp
./.libs/libclustalo.a(clustal-omega.o): In function `AlnToHHMFile':
./src/clustal-omega.c:393: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j1 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
Making check in hhalign
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/hhalign'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/hhalign'
Making check in squid
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/squid'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/squid'
Making check in kmpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/kmpp'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/kmpp'
Making check in clustal
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/clustal'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/clustal'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf --with linktree
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install -a
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making install in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
Making install in hhalign
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/hhalign'
make[5]: Entering directory '/<<PKGBUILDDIR>>/src/hhalign'
make[5]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/clustalo/hhalign'
/usr/bin/install -c -m 644 general.h hhfunc.h '/<<PKGBUILDDIR>>/debian/tmp/usr/include/clustalo/hhalign'
make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/hhalign'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/hhalign'
Making install in squid
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/squid'
make[5]: Entering directory '/<<PKGBUILDDIR>>/src/squid'
make[5]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/clustalo/squid'
/usr/bin/install -c -m 644 gki.h gsi64.h msa.h rk.h squid.h stopwatch.h sqfuncs.h sre_random.h ssi.h stockholm.h vectorops.h version.h '/<<PKGBUILDDIR>>/debian/tmp/usr/include/clustalo/squid'
make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/squid'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/squid'
Making install in kmpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/kmpp'
make[5]: Entering directory '/<<PKGBUILDDIR>>/src/kmpp'
make[5]: Nothing to be done for 'install-exec-am'.
make[5]: Nothing to be done for 'install-data-am'.
make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/kmpp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/kmpp'
Making install in clustal
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/clustal'
make[5]: Entering directory '/<<PKGBUILDDIR>>/src/clustal'
make[5]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/clustalo/clustal'
/usr/bin/install -c -m 644 hhalign_wrapper.h ktuple_pair.h log.h mbed.h muscle_tree.h pair_dist.h progress.h seq.h symmatrix.h tree.h util.h weights.h '/<<PKGBUILDDIR>>/debian/tmp/usr/include/clustalo/clustal'
make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/clustal'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/clustal'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
make[5]: Entering directory '/<<PKGBUILDDIR>>/src'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ../libtool --mode=install /usr/bin/install -c libclustalo.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libclustalo.lai /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.la
libtool: install: /usr/bin/install -c .libs/libclustalo.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c clustalo '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
libtool: install: /usr/bin/install -c clustalo /<<PKGBUILDDIR>>/debian/tmp/usr/bin/clustalo
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/clustalo/'
/usr/bin/install -c -m 644 clustal-omega-config.h clustal-omega.h '/<<PKGBUILDDIR>>/debian/tmp/usr/include/clustalo/'
make[5]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/clustal-omega'
/usr/bin/install -c -m 644 README '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/clustal-omega'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 clustalo.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -rf debian/tmp/usr/lib/pkgconfig
rm -f debian/tmp/usr/lib/*/libclustalo.la
mv debian/tmp/usr/include debian/libclustalo-dev/usr
mv debian/tmp/usr/lib debian/libclustalo-dev/usr
mv debian/tmp/usr/bin debian/clustalo/usr
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_linktree -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package libclustalo-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.3-1_armhf.deb'.
dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.3-1_armhf.deb'.
dpkg-deb: building package 'clustalo' in '../clustalo_1.2.3-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../clustalo_1.2.3-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build clustalo-1.2.3
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160917-1129
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clustalo_1.2.3-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Tue, 30 Aug 2016 09:46:54 +0200
Source: clustalo
Binary: clustalo libclustalo-dev libclustalo-doc
Architecture: armhf
Version: 1.2.3-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
clustalo - General purpose multiple sequence alignment program for proteins
libclustalo-dev - library to embed Clustal Omega
libclustalo-doc - API documentation for library to embed Clustal Omega
Closes: 835074 835740
Changes:
clustalo (1.2.3-1) unstable; urgency=medium
.
* New upstream version
* Remove duplicated definitions of log2
Closes: #835074, #835740
Checksums-Sha1:
ea8f65900382b85516afb43c18d6e5167cdaeb1b 593566 clustalo-dbgsym_1.2.3-1_armhf.deb
4b8f2070427c65bd048bb8aff4c28ca6023509bf 226732 clustalo_1.2.3-1_armhf.deb
c866371020749328805fc0240efafd2e0824003b 281562 libclustalo-dev_1.2.3-1_armhf.deb
Checksums-Sha256:
0514b36072c6d671d5e53fed3c823669e8d2e2166b3dbca1fcd07fb30717d093 593566 clustalo-dbgsym_1.2.3-1_armhf.deb
d62bb1968e26da55b98460fbbfada4d285297768a3b18c360ed28e2171df6a42 226732 clustalo_1.2.3-1_armhf.deb
f440a921e9a9148082d4eaf4ea4b889360e95d586fbb1c10ab129236369e3355 281562 libclustalo-dev_1.2.3-1_armhf.deb
Files:
f7f983701fd0ee586310a60be7f77ab0 593566 debug extra clustalo-dbgsym_1.2.3-1_armhf.deb
c6905aefc868f4830b1ef84b3dba9e4e 226732 science optional clustalo_1.2.3-1_armhf.deb
413f0ffd3355bbb97aa9b718a8c7a137 281562 libdevel optional libclustalo-dev_1.2.3-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clustalo-dbgsym_1.2.3-1_armhf.deb
---------------------------------
new debian package, version 2.0.
size 593566 bytes: control archive=481 bytes.
411 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: clustalo-dbgsym
Source: clustalo
Version: 1.2.3-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 637
Depends: clustalo (= 1.2.3-1)
Section: debug
Priority: extra
Homepage: http://www.clustal.org/omega/
Description: Debug symbols for clustalo
Auto-Built-Package: debug-symbols
Build-Ids: 69df2eeccf4c6d55292c294ee6b5efb402dceacc
drwxr-xr-x root/root 0 2016-08-30 07:46 ./
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/lib/debug/.build-id/69/
-rw-r--r-- root/root 642044 2016-08-30 07:46 ./usr/lib/debug/.build-id/69/df2eeccf4c6d55292c294ee6b5efb402dceacc.debug
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-08-30 07:46 ./usr/share/doc/clustalo-dbgsym -> clustalo
clustalo_1.2.3-1_armhf.deb
--------------------------
new debian package, version 2.0.
size 226732 bytes: control archive=796 bytes.
649 bytes, 14 lines control
476 bytes, 7 lines md5sums
Package: clustalo
Version: 1.2.3-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 562
Depends: libargtable2-0 (>= 7), libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: http://www.clustal.org/omega/
Description: General purpose multiple sequence alignment program for proteins
Clustal-Omega is a general purpose multiple sequence alignment (MSA)
program for dna/rna/proteins. It produces high quality MSAs and is capable of
handling data-sets of hundreds of thousands of sequences in reasonable
time.
drwxr-xr-x root/root 0 2016-08-30 07:46 ./
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/bin/
-rwxr-xr-x root/root 543440 2016-08-30 07:46 ./usr/bin/clustalo
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/doc/clustalo/
-rw-r--r-- root/root 10994 2013-08-27 12:07 ./usr/share/doc/clustalo/README.gz
-rw-r--r-- root/root 792 2016-08-30 07:46 ./usr/share/doc/clustalo/changelog.Debian.gz
-rw-r--r-- root/root 1706 2016-07-20 13:31 ./usr/share/doc/clustalo/changelog.gz
-rw-r--r-- root/root 1174 2016-08-30 07:46 ./usr/share/doc/clustalo/copyright
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/doc/clustalo/examples/
-rw-r--r-- root/root 2269 2016-08-30 07:46 ./usr/share/doc/clustalo/examples/example.fa
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/man/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/man/man1/
-rw-r--r-- root/root 1083 2016-08-30 07:46 ./usr/share/man/man1/clustalo.1.gz
libclustalo-dev_1.2.3-1_armhf.deb
---------------------------------
new debian package, version 2.0.
size 281562 bytes: control archive=1474 bytes.
504 bytes, 15 lines control
2409 bytes, 33 lines md5sums
Package: libclustalo-dev
Source: clustalo
Version: 1.2.3-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 942
Depends: libargtable2-dev, clustalo (= 1.2.3-1)
Suggests: libclustalo-doc
Section: libdevel
Priority: optional
Homepage: http://www.clustal.org/omega/
Description: library to embed Clustal Omega
This package contains headers and libraries to include
Clustal Omega in a program. It provides clustal usage
with an API.
drwxr-xr-x root/root 0 2016-08-30 07:46 ./
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/include/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/include/clustalo/
-rw-r--r-- root/root 9523 2016-08-30 07:46 ./usr/include/clustalo/clustal-omega-config.h
-rw-r--r-- root/root 4740 2016-08-30 07:46 ./usr/include/clustalo/clustal-omega.h
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/include/clustalo/clustal/
-rw-r--r-- root/root 1159 2016-08-30 07:46 ./usr/include/clustalo/clustal/hhalign_wrapper.h
-rw-r--r-- root/root 1251 2016-08-30 07:46 ./usr/include/clustalo/clustal/ktuple_pair.h
-rw-r--r-- root/root 1787 2016-08-30 07:46 ./usr/include/clustalo/clustal/log.h
-rw-r--r-- root/root 866 2016-08-30 07:46 ./usr/include/clustalo/clustal/mbed.h
-rw-r--r-- root/root 4112 2016-08-30 07:46 ./usr/include/clustalo/clustal/muscle_tree.h
-rw-r--r-- root/root 1303 2016-08-30 07:46 ./usr/include/clustalo/clustal/pair_dist.h
-rw-r--r-- root/root 1257 2016-08-30 07:46 ./usr/include/clustalo/clustal/progress.h
-rw-r--r-- root/root 4032 2016-08-30 07:46 ./usr/include/clustalo/clustal/seq.h
-rw-r--r-- root/root 2310 2016-08-30 07:46 ./usr/include/clustalo/clustal/symmatrix.h
-rw-r--r-- root/root 1066 2016-08-30 07:46 ./usr/include/clustalo/clustal/tree.h
-rw-r--r-- root/root 2308 2016-08-30 07:46 ./usr/include/clustalo/clustal/util.h
-rw-r--r-- root/root 741 2016-08-30 07:46 ./usr/include/clustalo/clustal/weights.h
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/include/clustalo/hhalign/
-rw-r--r-- root/root 2961 2016-08-30 07:46 ./usr/include/clustalo/hhalign/general.h
-rw-r--r-- root/root 859 2016-08-30 07:46 ./usr/include/clustalo/hhalign/hhfunc.h
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/include/clustalo/squid/
-rw-r--r-- root/root 1381 2016-08-30 07:46 ./usr/include/clustalo/squid/gki.h
-rw-r--r-- root/root 3473 2016-08-30 07:46 ./usr/include/clustalo/squid/gsi64.h
-rw-r--r-- root/root 13442 2016-08-30 07:46 ./usr/include/clustalo/squid/msa.h
-rw-r--r-- root/root 1264 2016-08-30 07:46 ./usr/include/clustalo/squid/rk.h
-rw-r--r-- root/root 10390 2016-08-30 07:46 ./usr/include/clustalo/squid/sqfuncs.h
-rw-r--r-- root/root 19594 2016-08-30 07:46 ./usr/include/clustalo/squid/squid.h
-rw-r--r-- root/root 489 2016-08-30 07:46 ./usr/include/clustalo/squid/sre_random.h
-rw-r--r-- root/root 7610 2016-08-30 07:46 ./usr/include/clustalo/squid/ssi.h
-rw-r--r-- root/root 1868 2016-08-30 07:46 ./usr/include/clustalo/squid/stockholm.h
-rw-r--r-- root/root 1937 2016-08-30 07:46 ./usr/include/clustalo/squid/stopwatch.h
-rw-r--r-- root/root 1434 2016-08-30 07:46 ./usr/include/clustalo/squid/vectorops.h
-rw-r--r-- root/root 333 2016-08-30 07:46 ./usr/include/clustalo/squid/version.h
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 824044 2016-08-30 07:46 ./usr/lib/arm-linux-gnueabihf/libclustalo.a
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 250 2016-08-30 07:46 ./usr/lib/arm-linux-gnueabihf/pkgconfig/clustalo.pc
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-30 07:46 ./usr/share/doc/libclustalo-dev/
-rw-r--r-- root/root 792 2016-08-30 07:46 ./usr/share/doc/libclustalo-dev/changelog.Debian.gz
-rw-r--r-- root/root 1706 2016-07-20 13:31 ./usr/share/doc/libclustalo-dev/changelog.gz
-rw-r--r-- root/root 1174 2016-08-30 07:46 ./usr/share/doc/libclustalo-dev/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 26256
Build-Time: 659
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 657
Job: clustalo_1.2.3-1
Machine Architecture: armhf
Package: clustalo
Package-Time: 1369
Source-Version: 1.2.3-1
Space: 26256
Status: successful
Version: 1.2.3-1
--------------------------------------------------------------------------------
Finished at 20160917-1129
Build needed 00:22:49, 26256k disc space