clustalo →
1.2.4-8 →
armhf → 2023-12-09 06:31:59
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| clustalo 1.2.4-8 (armhf) Sat, 09 Dec 2023 06:29:59 +0000 |
+==============================================================================+
Package: clustalo
Version: 1.2.4-8
Source Version: 1.2.4-8
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-85339b84-f010-4ca3-884f-956096afc4fb' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/clustalo-dFejT2/resolver-qJUMmT' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.3 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.3 MB in 5s (5486 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| 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://salsa.debian.org/med-team/clustalo.git
Please use:
git clone https://salsa.debian.org/med-team/clustalo.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1184 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main clustalo 1.2.4-8 (dsc) [2178 B]
Get:2 http://172.17.4.1/private trixie-staging/main clustalo 1.2.4-8 (tar) [1171 kB]
Get:3 http://172.17.4.1/private trixie-staging/main clustalo 1.2.4-8 (diff) [11.0 kB]
Fetched 1184 kB in 0s (5701 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clustalo-dFejT2/clustalo-1.2.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clustalo-dFejT2' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libargtable2-dev, doxygen, graphviz, sphinx-common, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libargtable2-dev, doxygen, graphviz, sphinx-common, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [669 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [701 B]
Fetched 1979 B in 0s (0 B/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils bsdutils debhelper
dh-autoreconf dh-strip-nondeterminism doxygen dpkg-dev dwz file fontconfig
fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base
graphviz groff-base intltool-debian libabsl20220623 libaom3
libarchive-zip-perl libargtable2-0 libargtable2-dev libargtable2-docs
libavif16 libblkid1 libbrotli1 libbsd0 libcairo2 libcdt5 libcgraph6
libclang-cpp14 libclang1-14 libdatrie1 libdav1d7 libde265-0
libdebhelper-perl libdeflate0 libdpkg-perl libedit2 libelf1 libexpat1
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgav1-1 libgd3 libglib2.0-0 libgraphite2-3 libgts-0.7-5 libgvc6 libgvpr2
libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libice6
libicu72 libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc
libjs-underscore libjson-perl liblab-gamut1 liblerc4 libllvm14 libltdl7
libmagic-mgc libmagic1 libmount1 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16
librav1e0 libsharpyuv0 libsm6 libsmartcols1 libsub-override-perl
libsvtav1enc1d1 libthai-data libthai0 libtiff6 libtool libuchardet0 libuuid1
libwebp7 libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1
libxt6 libyuv0 libz3-4 m4 man-db mount po-debconf sensible-utils
sphinx-common util-linux x11-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make doxygen-latex
doxygen-doc doxygen-gui debian-keyring gettext-doc libasprintf-dev
libgettextpo-dev gsfonts graphviz-doc groff git bzr libgd-tools
low-memory-monitor libheif-plugin-ffmpegdec libheif-plugin-jpegdec
libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc
libheif-plugin-rav1e libheif-plugin-svtenc cryptsetup-bin libtool-doc
gfortran | fortran95-compiler gcj-jdk xapian-tools m4-doc apparmor less
www-browser nfs-common libmail-box-perl dosfstools kbd util-linux-extra
util-linux-locales
Recommended packages:
libalgorithm-merge-perl curl | wget | lynx fonts-liberation2
libfile-fcntllock-perl libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgts-bin libheif-plugin-aomenc libheif-plugin-x265
javascript-common libjson-xs-perl libltdl-dev uuid-runtime
libmail-sendmail-perl python3-sphinx
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism doxygen dwz file fontconfig
fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base
graphviz groff-base intltool-debian libabsl20220623 libaom3
libarchive-zip-perl libargtable2-0 libargtable2-dev libargtable2-docs
libavif16 libbrotli1 libbsd0 libcairo2 libcdt5 libcgraph6 libclang-cpp14
libclang1-14 libdatrie1 libdav1d7 libde265-0 libdebhelper-perl libdeflate0
libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1
libfreetype6 libfribidi0 libgav1-1 libgd3 libglib2.0-0 libgraphite2-3
libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libheif-plugin-dav1d
libheif-plugin-libde265 libheif1 libice6 libicu72 libjbig0 libjpeg62-turbo
libjs-jquery libjs-sphinxdoc libjs-underscore libjson-perl liblab-gamut1
liblerc4 libllvm14 libltdl7 libmagic-mgc libmagic1 libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1
libpixman-1-0 libpng16-16 librav1e0 libsharpyuv0 libsm6 libsub-override-perl
libsvtav1enc1d1 libthai-data libthai0 libtiff6 libtool libuchardet0 libwebp7
libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0
libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6
libyuv0 libz3-4 m4 man-db po-debconf sbuild-build-depends-main-dummy
sensible-utils sphinx-common x11-common
The following packages will be upgraded:
bsdutils dpkg-dev libblkid1 libdpkg-perl libmount1 libsmartcols1 libuuid1
mount util-linux
9 upgraded, 113 newly installed, 0 to remove and 57 not upgraded.
1 not fully installed or removed.
Need to get 87.1 MB/89.1 MB of archives.
After this operation, 337 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [912 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.2-6 [134 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.2-6 [86.5 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.2-6 [1110 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.2-6 [145 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.2-6 [167 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.2-6 [102 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.2-6 [28.1 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-6 [81.2 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.8 [82.1 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.8 [956 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.7-4 [111 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libedit2 armhf 3.1-20230828-1 [76.0 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libz3-4 armhf 4.8.12-3.1 [5797 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libllvm14 armhf 1:14.0.6-16+rpi1 [19.5 MB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libclang-cpp14 armhf 1:14.0.6-16+rpi1 [9466 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libclang1-14 armhf 1:14.0.6-16+rpi1 [5212 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libxapian30 armhf 1.4.22-1 [968 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf doxygen armhf 1.9.4-4 [3840 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libpng16-16 armhf 1.6.40-2 [258 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libfreetype6 armhf 2.13.2+dfsg-1 [366 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-mono all 2.37-8 [489 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-core all 2.37-8 [840 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf fontconfig-config armhf 2.14.2-6 [316 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libfontconfig1 armhf 2.14.2-6 [367 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf fontconfig armhf 2.14.2-6 [461 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libcdt5 armhf 2.42.2-7+b2 [37.3 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libcgraph6 armhf 2.42.2-7+b2 [56.0 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libaom3 armhf 3.7.1-1 [1393 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libdav1d7 armhf 1.3.0-2+rpi1 [214 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libabsl20220623 armhf 20220623.1-3 [356 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libgav1-1 armhf 0.18.0-1+rpi1+b1 [285 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf librav1e0 armhf 0.6.6-3+rpi1 [548 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libsharpyuv0 armhf 1.3.2-0.3 [106 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libsvtav1enc1d1 armhf 1.7.0+dfsg-2 [884 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf libyuv0 armhf 0.0~git20231118.e6d5adb-1 [82.8 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf libavif16 armhf 1.0.1-2+b1 [93.8 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libheif-plugin-dav1d armhf 1.17.1-1+b1 [9480 B]
Get:69 http://172.17.4.1/private trixie-staging/main armhf libde265-0 armhf 1.0.13-1+rpi1 [139 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libheif-plugin-libde265 armhf 1.17.1-1+b1 [12.4 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libheif1 armhf 1.17.1-1+b1 [235 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf libjbig0 armhf 2.1-6.1 [27.0 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf liblerc4 armhf 4.0.0+ds-4 [132 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libwebp7 armhf 1.3.2-0.3 [261 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libtiff6 armhf 4.5.1+git230720-1 [298 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libx11-data all 2:1.8.7-1 [328 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libx11-6 armhf 2:1.8.7-1 [729 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libxpm4 armhf 1:3.5.17-1 [49.3 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libgd3 armhf 2.3.3-9+b1 [102 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libglib2.0-0 armhf 2.78.1-4 [1257 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf libgts-0.7-5 armhf 0.7.6+darcs121130-5 [134 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf libpixman-1-0 armhf 0.42.2-1 [461 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libcairo2 armhf 1.18.0-1 [425 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf libltdl7 armhf 2.4.7-7 [390 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf libfribidi0 armhf 1.0.13-3 [69.9 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libharfbuzz0b armhf 8.0.1-1 [2098 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf libthai-data all 0.1.29-1 [176 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libdatrie1 armhf 0.2.13-2+b2 [39.9 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libthai0 armhf 0.1.29-1 [54.5 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libpango-1.0-0 armhf 1.51.0+ds-3 [188 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libpangoft2-1.0-0 armhf 1.51.0+ds-3 [40.3 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf libpangocairo-1.0-0 armhf 1.51.0+ds-3 [30.5 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libpathplan4 armhf 2.42.2-7+b2 [39.5 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf libgvc6 armhf 2.42.2-7+b2 [566 kB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf libgvpr2 armhf 2.42.2-7+b2 [162 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf liblab-gamut1 armhf 2.42.2-7+b2 [197 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf libxt6 armhf 1:1.2.1-1.1 [155 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf libxmu6 armhf 2:1.1.3-3 [52.0 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libxaw7 armhf 2:1.0.14-1 [165 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf graphviz armhf 2.42.2-7+b2 [479 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf libargtable2-0 armhf 13-1.1 [15.9 kB]
Get:114 http://172.17.4.1/private trixie-staging/main armhf libargtable2-docs all 13-1.1 [2622 kB]
Get:115 http://172.17.4.1/private trixie-staging/main armhf libargtable2-dev armhf 13-1.1 [55.5 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:117 http://172.17.4.1/private trixie-staging/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf libjs-sphinxdoc all 7.2.6-2 [149 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf libjson-perl all 4.10000-1 [87.5 kB]
Get:120 http://172.17.4.1/private trixie-staging/main armhf sphinx-common all 7.2.6-2 [703 kB]
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Setting up fontconfig (2.14.2-6) ...
Regenerating fonts cache... done.
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Setting up libxrender1:armhf (1:0.9.10-1.1) ...
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Not building database; man-db/auto-update is not 'true'.
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Setting up libxmu6:armhf (2:1.1.3-3) ...
Setting up debhelper (13.11.8) ...
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Setting up doxygen (1.9.4-4) ...
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Setting up libheif-plugin-libde265:armhf (1.17.1-1+b1) ...
Setting up libheif1:armhf (1.17.1-1+b1) ...
Setting up libgd3:armhf (2.3.3-9+b1) ...
Setting up libgvc6 (2.42.2-7+b2) ...
Setting up graphviz (2.42.2-7+b2) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc-12_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.2 bash_5.2.15-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.2-6 bsdutils_1:2.39.2-6 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-10+rpi1 cpp-13_13.2.0-5+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.8 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 doxygen_1.9.4-4 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 fontconfig_2.14.2-6 fontconfig-config_2.14.2-6 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-10+rpi1 gcc-12-base_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 gcc-13-base_13.2.0-5+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 graphviz_2.42.2-7+b2 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libabsl20220623_20220623.1-3 libacl1_2.3.1-3 libaom3_3.7.1-1 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libargtable2-0_13-1.1 libargtable2-dev_13-1.1 libargtable2-docs_13-1.1 libasan8_13.2.0-5+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-5+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libavif16_1.0.1-2+b1 libbinutils_2.41-6+rpi1 libblkid1_2.39.2-6 libbrotli1_1.1.0-2 libbsd0_0.11.7-4 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcairo2_1.18.0-1 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcc1-0_13.2.0-5+rpi1 libcdt5_2.42.2-7+b2 libcgraph6_2.42.2-7+b2 libclang-cpp14_1:14.0.6-16+rpi1 libclang1-14_1:14.0.6-16+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libdatrie1_0.2.13-2+b2 libdav1d7_1.3.0-2+rpi1 libdb5.3_5.3.28+dfsg2-2 libde265-0_1.0.13-1+rpi1 libdebconfclient0_0.271 libdebhelper-perl_13.11.8 libdeflate0_1.18-1 libdpkg-perl_1.22.1+rpi1 libedit2_3.1-20230828-1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libfontconfig1_2.14.2-6 libfreetype6_2.13.2+dfsg-1 libfribidi0_1.0.13-3 libgav1-1_0.18.0-1+rpi1+b1 libgcc-12-dev_12.3.0-10+rpi1 libgcc-13-dev_13.2.0-5+rpi1 libgcc-s1_13.2.0-5+rpi1 libgcrypt20_1.10.2-3 libgd3_2.3.3-9+b1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libglib2.0-0_2.78.1-4 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4 libgomp1_13.2.0-5+rpi1 libgpg-error0_1.47-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20.1-4 libgts-0.7-5_0.7.6+darcs121130-5 libgvc6_2.42.2-7+b2 libgvpr2_2.42.2-7+b2 libharfbuzz0b_8.0.1-1 libheif-plugin-dav1d_1.17.1-1+b1 libheif-plugin-libde265_1.17.1-1+b1 libheif1_1.17.1-1+b1 libhogweed6_3.9.1-2 libice6_2:1.0.10-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjbig0_2.1-6.1 libjpeg62-turbo_1:2.1.5-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_7.2.6-2 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjson-perl_4.10000-1 libk5crypto3_1.20.1-4 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-4 libkrb5support0_1.20.1-4 libksba8_1.6.4-2 liblab-gamut1_2.42.2-7+b2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblerc4_4.0.0+ds-4 libllvm14_1:14.0.6-16+rpi1 liblocale-gettext-perl_1.07-6 libltdl7_2.4.7-7 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231016-1 libnettle8_3.9.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.25.0-5 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpango-1.0-0_1.51.0+ds-3 libpangocairo-1.0-0_1.51.0+ds-3 libpangoft2-1.0-0_1.51.0+ds-3 libpathplan4_2.42.2-7+b2 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-9 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpng16-16_1.6.40-2 librav1e0_0.6.6-3+rpi1 libreadline8_8.2-1.3 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-6+rpi1 libsharpyuv0_1.3.2-0.3 libsm6_2:1.2.3-1 libsmartcols1_2.39.2-6 libsqlite3-0_3.43.2-1 libss2_1.47.0-2 libssl3_3.0.11-1 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 libsub-override-perl_0.09-4 libsvtav1enc1d1_1.7.0+dfsg-2 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libthai-data_0.1.29-1 libthai0_0.1.29-1 libtiff6_4.5.1+git230720-1 libtinfo6_6.4+20231016-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-5+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring5_1.1-2 libuuid1_2.39.2-6 libwebp7_1.3.2-0.3 libx11-6_2:1.8.7-1 libx11-data_2:1.8.7-1 libxapian30_1.4.22-1 libxau6_1:1.0.9-1 libxaw7_2:1.0.14-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.14+dfsg-1.3 libxmu6_2:1.1.3-3 libxpm4_1:3.5.17-1 libxrender1_1:0.9.10-1.1 libxt6_1:1.2.1-1.1 libxxhash0_0.8.2-2 libyuv0_0.0~git20231118.e6d5adb-1 libz3-4_4.8.12-3.1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20230808-1 mount_2.39.2-6 ncurses-base_6.4+20231016-1 ncurses-bin_6.4+20231016-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sphinx-common_7.2.6-2 sysvinit-utils_3.08-3 tar_1.34+dfsg-1.2 tzdata_2023c-10 usr-is-merged_37 util-linux_2.39.2-6 x11-common_1:7.7+23 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: clustalo
Binary: clustalo, libclustalo-dev, libclustalo-doc
Architecture: any all
Version: 1.2.4-8
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Olivier Sallou <osallou@debian.org>, Andreas Tille <tille@debian.org>
Homepage: http://www.clustal.org/omega/
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/clustalo
Vcs-Git: https://salsa.debian.org/med-team/clustalo.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libargtable2-dev, doxygen, graphviz, sphinx-common
Package-List:
clustalo deb science optional arch=any
libclustalo-dev deb libdevel optional arch=any
libclustalo-doc deb doc optional arch=all
Checksums-Sha1:
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fe001e75d9b2f417cd476689a9c746ee79bc0c7d 10980 clustalo_1.2.4-8.debian.tar.xz
Checksums-Sha256:
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Files:
6c0459f4c463a30e942ce7e0efc91422 1170516 clustalo_1.2.4.orig.tar.gz
7b89249d2195ce9ef2f3c295548d33fd 10980 clustalo_1.2.4-8.debian.tar.xz
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gpgv: Signature made Wed Dec 6 21:28:55 2023 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./clustalo_1.2.4-8.dsc: no acceptable signature found
dpkg-source: info: extracting clustalo in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking clustalo_1.2.4.orig.tar.gz
dpkg-source: info: unpacking clustalo_1.2.4-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying clustalo-log-format-calls.patch
dpkg-source: info: applying array_out_of_bounds.patch
dpkg-source: info: applying memory_leak.patch
dpkg-source: info: applying fix_syntax.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-85339b84-f010-4ca3-884f-956096afc4fb
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package clustalo
dpkg-buildpackage: info: source version 1.2.4-8
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if [ -e src/clustal-omega-config.h~ ] ; then \
mv src/clustal-omega-config.h~ src/clustal-omega-config.h ; \
fi
dh_clean
rm -f _configs.sed
rm -rf doc
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
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:287: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:287: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:287: the top level
configure.ac:133: installing './compile'
configure.ac:115: installing './missing'
src/Makefile.am: installing './depcomp'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp -a src/clustal-omega-config.h src/clustal-omega-config.h~
dh_auto_configure
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
configure:
Welcome to Clustal Omega - version 1.2.4 (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 race-free 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 whether make supports the include directive... yes (GNU style)
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
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checking for unistd.h... yes
checking for wchar.h... yes
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether _XOPEN_SOURCE should be defined... no
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 grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
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 file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking how to run the C++ preprocessor... g++ -E
checking for egrep... (cached) /bin/grep -E
checking for assert.h... yes
checking for ctype.h... yes
checking for float.h... yes
checking for limits.h... yes
checking for math.h... yes
checking for memory.h... yes
checking for stdarg.h... yes
checking for stdio.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for inline... inline
checking for log in -lm... yes
checking for log2 in -lm... yes
checking for argtable2.h... yes
checking for arg_parse in -largtable2... yes
checking for OpenMP flag of C compiler... -fopenmp
checking whether byte ordering is bigendian... no
checking for ntohs... yes
checking for ntohl... yes
checking for ntons... no
checking for ntonl... no
checking size of unsigned short... 2
checking size of unsigned int... 4
checking size of unsigned long... 4
checking size of unsigned long long... 8
checking for stroul... no
checking for strtoull... yes
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checking for fseeko64... yes
checking for ftell64... no
checking for fseek64... no
checking for off_t... yes
checking size of fpos_t... 12
checking if malloc debugging is wanted... no
checking whether to build with debug information... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating clustalo.pc
config.status: creating Doxyfile
config.status: creating src/clustal/Makefile
config.status: creating src/hhalign/Makefile
config.status: creating src/kmpp/Makefile
config.status: creating src/squid/Makefile
config.status: creating src/config.h
config.status: executing src/clustal-omega-config.h commands
config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines
config.status: executing depfiles commands
config.status: executing libtool commands
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j4
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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o
In file included from hhalign.cpp:70:
hhhmm-C.h: In member function ‘void HMM::UseSecStrucDependentGapPenalties()’:
hhhmm-C.h:1748:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
1748 | iis[0]=iis[L]=0;
| ~~~~~~^~
hhhmm-C.h:1734:17: note: at offset [-2147483648, -1] into destination object ‘iis’ of size [0, 2147483647]
1734 | unsigned char iis[par.maxResLen]; // inside-integer array
| ^~~
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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hhalign.cpp -o hhalign.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o libhhalign.la hhalign.lo -largtable2 -lm
libtool: link: ar cr .libs/libhhalign.a .libs/hhalign.o
libtool: link: ranlib .libs/libhhalign.a
libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" )
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/hhalign'
Making all in squid
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/squid'
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o a2m.lo a2m.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o aligneval.lo aligneval.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o alignio.lo alignio.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o clustal.lo clustal.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c a2m.c -fPIC -DPIC -o .libs/a2m.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c alignio.c -fPIC -DPIC -o .libs/alignio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal.c -fPIC -DPIC -o .libs/clustal.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c aligneval.c -fPIC -DPIC -o .libs/aligneval.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c a2m.c -o a2m.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o cluster.lo cluster.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal.c -o clustal.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c aligneval.c -o aligneval.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c cluster.c -fPIC -DPIC -o .libs/cluster.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c alignio.c -o alignio.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o dayhoff.lo dayhoff.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o eps.lo eps.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c cluster.c -o cluster.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c dayhoff.c -fPIC -DPIC -o .libs/dayhoff.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c eps.c -o eps.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c dayhoff.c -o dayhoff.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o file.lo file.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o getopt.lo getopt.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gki.lo gki.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c file.c -fPIC -DPIC -o .libs/file.o
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gsi.lo gsi.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c getopt.c -fPIC -DPIC -o .libs/getopt.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gsi.c -fPIC -DPIC -o .libs/gsi.o
file.c: In function ‘EnvFileOpen’:
file.c:243:26: warning: ‘%s’ directive writing up to 1022 bytes into a region of size between 1 and 1023 [-Wformat-overflow=]
243 | sprintf(full, "%s%c%s", s, DIRSLASH, fname);
| ^~
In file included from /usr/include/stdio.h:906,
from file.c:24:
In function ‘sprintf’,
inlined from ‘EnvFileOpen’ at file.c:243:7:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 2046 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c file.c -o file.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c getopt.c -o getopt.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gki.c -o gki.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gsi64.lo gsi64.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gsi.c -o gsi.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o hsregex.lo hsregex.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gsi64.c -o gsi64.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o iupac.lo iupac.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hsregex.c -fPIC -DPIC -o .libs/hsregex.o
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o msa.lo msa.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c iupac.c -fPIC -DPIC -o .libs/iupac.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c msa.c -fPIC -DPIC -o .libs/msa.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c iupac.c -o iupac.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o msf.lo msf.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o phylip.lo phylip.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c msf.c -fPIC -DPIC -o .libs/msf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c phylip.c -fPIC -DPIC -o .libs/phylip.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c phylip.c -o phylip.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c msf.c -o msf.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o revcomp.lo revcomp.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hsregex.c -o hsregex.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c revcomp.c -fPIC -DPIC -o .libs/revcomp.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c revcomp.c -o revcomp.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c msa.c -o msa.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o rk.lo rk.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o selex.lo selex.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c rk.c -fPIC -DPIC -o .libs/rk.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c selex.c -fPIC -DPIC -o .libs/selex.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c rk.c -o rk.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o seqencode.lo seqencode.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c seqencode.c -fPIC -DPIC -o .libs/seqencode.o
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o shuffle.lo shuffle.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c shuffle.c -fPIC -DPIC -o .libs/shuffle.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c seqencode.c -o seqencode.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c selex.c -o selex.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sqerror.lo sqerror.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sqio.lo sqio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sqerror.c -fPIC -DPIC -o .libs/sqerror.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sqio.c -fPIC -DPIC -o .libs/sqio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sqerror.c -o sqerror.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c shuffle.c -o shuffle.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o squidcore.lo squidcore.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c squidcore.c -fPIC -DPIC -o .libs/squidcore.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c squidcore.c -o squidcore.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sre_ctype.lo sre_ctype.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_ctype.c -fPIC -DPIC -o .libs/sre_ctype.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_ctype.c -o sre_ctype.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sre_math.lo sre_math.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sre_random.lo sre_random.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sre_string.lo sre_string.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_math.c -fPIC -DPIC -o .libs/sre_math.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_random.c -fPIC -DPIC -o .libs/sre_random.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_string.c -fPIC -DPIC -o .libs/sre_string.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_random.c -o sre_random.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_math.c -o sre_math.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_string.c -o sre_string.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 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o ssi.lo ssi.c
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c ssi.c -fPIC -DPIC -o .libs/ssi.o
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/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c symmatrix.c -fPIC -DPIC -o .libs/symmatrix.o
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c symmatrix.c -o symmatrix.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c tree.c -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c util.c -fPIC -DPIC -o .libs/util.o
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c seq.c -o seq.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c util.c -o util.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c weights.c -o weights.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 cr .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
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'
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mymain.o mymain.c
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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]
152 | PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__);
| ^~~~~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -static -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 cr .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
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" )
/bin/bash ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm
libtool: link: g++ -O3 -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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
/usr/bin/ld: ./.libs/libclustalo.a(clustal-omega.o): in function `AlnToHHMFile':
./src/clustal-omega.c:393:(.text+0x628): 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>>'
debian/rules override_dh_auto_test-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
Making check in hhalign
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/hhalign'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/hhalign'
Making check in squid
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/squid'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/squid'
Making check in kmpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/kmpp'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/kmpp'
Making check in clustal
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/clustal'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/clustal'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# Run additional test from python-biopython package to verify that
# this will work as well
src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force
rm temp_test.aln temp_test.dnd
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
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_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/clustalo/usr/bin/clustalo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/clustalo/usr/bin/clustalo was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package libclustalo-dev: substitution variable ${shlibs:Depends} used, but is not defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-8_armhf.deb'.
dpkg-deb: building package 'clustalo' in '../clustalo_1.2.4-8_armhf.deb'.
dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.4-8_armhf.deb'.
dpkg-genbuildinfo --build=any -O../clustalo_1.2.4-8_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../clustalo_1.2.4-8_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-12-09T06:31:55Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clustalo_1.2.4-8_armhf.changes:
-------------------------------
Format: 1.8
Date: Wed, 06 Dec 2023 22:09:24 +0100
Source: clustalo
Binary: clustalo clustalo-dbgsym libclustalo-dev
Architecture: armhf
Version: 1.2.4-8
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi5 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
Closes: 1043849
Changes:
clustalo (1.2.4-8) unstable; urgency=medium
.
* Fix clean target
Closes: #1043849
* Standards-Version: 4.6.2 (routine-update)
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+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: clustalo
Binary: clustalo clustalo-dbgsym libclustalo-dev
Architecture: armhf
Version: 1.2.4-8
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sat, 09 Dec 2023 06:31:55 +0000
Build-Path: /<<PKGBUILDDIR>>
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automake (= 1:1.16.5-1.3),
autopoint (= 0.21-14),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
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bash (= 5.2.15-2),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.2-6),
bsdutils (= 1:2.39.2-6),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-10+rpi1),
cpp-13 (= 13.2.0-5+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.8),
debianutils (= 5.14),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
doxygen (= 1.9.4-4),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
fontconfig (= 2.14.2-6),
fontconfig-config (= 2.14.2-6),
fonts-dejavu-core (= 2.37-8),
fonts-dejavu-mono (= 2.37-8),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-5+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-10+rpi1),
gcc-12-base (= 12.3.0-10+rpi1),
gcc-13 (= 13.2.0-5+rpi1),
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libc-bin (= 2.37-12+rpi2),
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libuchardet0 (= 0.0.8-1),
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m4 (= 1.4.19-4),
make (= 4.3-4.1),
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mawk (= 1.3.4.20230808-1),
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patch (= 2.7.6-7),
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po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
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sysvinit-utils (= 3.08-3),
tar (= 1.34+dfsg-1.2),
usr-is-merged (= 37),
util-linux (= 2.39.2-6),
x11-common (= 1:7.7+23),
xz-utils (= 5.4.4-0.1),
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Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1701896964"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clustalo-dbgsym_1.2.4-8_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 704564 bytes: control archive=536 bytes.
374 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clustalo-dbgsym
Source: clustalo
Version: 1.2.4-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 741
Depends: clustalo (= 1.2.4-8)
Section: debug
Priority: optional
Description: debug symbols for clustalo
Build-Ids: 0eeacadcc57e2c77630431a074bf9e4a4b57d967
drwxr-xr-x root/root 0 2023-12-06 21:09 ./
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/
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drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/lib/debug/.build-id/0e/
-rw-r--r-- root/root 748272 2023-12-06 21:09 ./usr/lib/debug/.build-id/0e/eacadcc57e2c77630431a074bf9e4a4b57d967.debug
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/share/
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-12-06 21:09 ./usr/share/doc/clustalo-dbgsym -> clustalo
clustalo_1.2.4-8_armhf.deb
--------------------------
new Debian package, version 2.0.
size 224620 bytes: control archive=936 bytes.
707 bytes, 14 lines control
547 bytes, 8 lines md5sums
Package: clustalo
Version: 1.2.4-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 557
Depends: libargtable2-0 (>= 7), libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libstdc++6 (>= 13.1)
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, primarily for amino-acid sequences. It produces high quality MSAs
and is capable of handling data sets of hundreds of thousands of sequences
in reasonable time, using multiple processors where available.
drwxr-xr-x root/root 0 2023-12-06 21:09 ./
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/bin/
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drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/share/
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/share/doc/
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-rw-r--r-- root/root 10994 2023-12-06 21:09 ./usr/share/doc/clustalo/README.gz
-rw-r--r-- root/root 1057 2023-12-06 21:09 ./usr/share/doc/clustalo/changelog.Debian.gz
-rw-r--r-- root/root 1730 2016-12-21 15:00 ./usr/share/doc/clustalo/changelog.gz
-rw-r--r-- root/root 1230 2023-12-06 21:09 ./usr/share/doc/clustalo/copyright
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/share/doc/clustalo/examples/
-rw-r--r-- root/root 2269 2023-12-06 21:09 ./usr/share/doc/clustalo/examples/example.fa
-rw-r--r-- root/root 1742 2023-12-06 21:09 ./usr/share/doc/clustalo/examples/f002
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/share/man/
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/share/man/man1/
-rw-r--r-- root/root 1083 2023-12-06 21:09 ./usr/share/man/man1/clustalo.1.gz
libclustalo-dev_1.2.4-8_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 277560 bytes: control archive=1524 bytes.
509 bytes, 14 lines control
2409 bytes, 33 lines md5sums
Package: libclustalo-dev
Source: clustalo
Version: 1.2.4-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 931
Depends: libargtable2-dev, clustalo (= 1.2.4-8)
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 Omega usage with an API.
drwxr-xr-x root/root 0 2023-12-06 21:09 ./
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/
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drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/include/clustalo/clustal/
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-rw-r--r-- root/root 1251 2023-12-06 21:09 ./usr/include/clustalo/clustal/ktuple_pair.h
-rw-r--r-- root/root 1787 2023-12-06 21:09 ./usr/include/clustalo/clustal/log.h
-rw-r--r-- root/root 866 2023-12-06 21:09 ./usr/include/clustalo/clustal/mbed.h
-rw-r--r-- root/root 4112 2023-12-06 21:09 ./usr/include/clustalo/clustal/muscle_tree.h
-rw-r--r-- root/root 1303 2023-12-06 21:09 ./usr/include/clustalo/clustal/pair_dist.h
-rw-r--r-- root/root 1257 2023-12-06 21:09 ./usr/include/clustalo/clustal/progress.h
-rw-r--r-- root/root 4032 2023-12-06 21:09 ./usr/include/clustalo/clustal/seq.h
-rw-r--r-- root/root 2310 2023-12-06 21:09 ./usr/include/clustalo/clustal/symmatrix.h
-rw-r--r-- root/root 1066 2023-12-06 21:09 ./usr/include/clustalo/clustal/tree.h
-rw-r--r-- root/root 2308 2023-12-06 21:09 ./usr/include/clustalo/clustal/util.h
-rw-r--r-- root/root 741 2023-12-06 21:09 ./usr/include/clustalo/clustal/weights.h
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-rw-r--r-- root/root 2961 2023-12-06 21:09 ./usr/include/clustalo/hhalign/general.h
-rw-r--r-- root/root 859 2023-12-06 21:09 ./usr/include/clustalo/hhalign/hhfunc.h
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/include/clustalo/squid/
-rw-r--r-- root/root 1381 2023-12-06 21:09 ./usr/include/clustalo/squid/gki.h
-rw-r--r-- root/root 3473 2023-12-06 21:09 ./usr/include/clustalo/squid/gsi64.h
-rw-r--r-- root/root 13442 2023-12-06 21:09 ./usr/include/clustalo/squid/msa.h
-rw-r--r-- root/root 1264 2023-12-06 21:09 ./usr/include/clustalo/squid/rk.h
-rw-r--r-- root/root 10390 2023-12-06 21:09 ./usr/include/clustalo/squid/sqfuncs.h
-rw-r--r-- root/root 19594 2023-12-06 21:09 ./usr/include/clustalo/squid/squid.h
-rw-r--r-- root/root 489 2023-12-06 21:09 ./usr/include/clustalo/squid/sre_random.h
-rw-r--r-- root/root 7610 2023-12-06 21:09 ./usr/include/clustalo/squid/ssi.h
-rw-r--r-- root/root 1868 2023-12-06 21:09 ./usr/include/clustalo/squid/stockholm.h
-rw-r--r-- root/root 1937 2023-12-06 21:09 ./usr/include/clustalo/squid/stopwatch.h
-rw-r--r-- root/root 1434 2023-12-06 21:09 ./usr/include/clustalo/squid/vectorops.h
-rw-r--r-- root/root 333 2023-12-06 21:09 ./usr/include/clustalo/squid/version.h
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/lib/
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 808998 2023-12-06 21:09 ./usr/lib/arm-linux-gnueabihf/libclustalo.a
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 250 2023-12-06 21:09 ./usr/lib/arm-linux-gnueabihf/pkgconfig/clustalo.pc
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/share/
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-12-06 21:09 ./usr/share/doc/libclustalo-dev/
-rw-r--r-- root/root 1059 2023-12-06 21:09 ./usr/share/doc/libclustalo-dev/changelog.Debian.gz
-rw-r--r-- root/root 1730 2016-12-21 15:00 ./usr/share/doc/libclustalo-dev/changelog.gz
-rw-r--r-- root/root 1230 2023-12-06 21:09 ./usr/share/doc/libclustalo-dev/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 28868
Build-Time: 65
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 43
Job: clustalo_1.2.4-8
Machine Architecture: arm64
Package: clustalo
Package-Time: 116
Source-Version: 1.2.4-8
Space: 28868
Status: successful
Version: 1.2.4-8
--------------------------------------------------------------------------------
Finished at 2023-12-09T06:31:55Z
Build needed 00:01:56, 28868k disk space