Thu Apr 11 17:34:31 UTC 2024 I: starting to build clustalo/trixie/armhf on jenkins on '2024-04-11 17:34' Thu Apr 11 17:34:31 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_28/2929/console.log Thu Apr 11 17:34:31 UTC 2024 I: Downloading source for trixie/clustalo=1.2.4-8 --2024-04-11 17:34:31-- http://deb.debian.org/debian/pool/main/c/clustalo/clustalo_1.2.4-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2178 (2.1K) [text/prs.lines.tag] Saving to: ‘clustalo_1.2.4-8.dsc’ 0K .. 100% 230M=0s 2024-04-11 17:34:31 (230 MB/s) - ‘clustalo_1.2.4-8.dsc’ saved [2178/2178] Thu Apr 11 17:34:31 UTC 2024 I: clustalo_1.2.4-8.dsc -----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 Uploaders: Olivier Sallou , Andreas Tille 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: 9ff2c88df0f488de61f80d997198700407ac6c04 1170516 clustalo_1.2.4.orig.tar.gz fe001e75d9b2f417cd476689a9c746ee79bc0c7d 10980 clustalo_1.2.4-8.debian.tar.xz Checksums-Sha256: 8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee 1170516 clustalo_1.2.4.orig.tar.gz a1f6b4f0989b0e028f7866cd20f41634ebd56309a0c15936f5380245b65baf38 10980 clustalo_1.2.4-8.debian.tar.xz Files: 6c0459f4c463a30e942ce7e0efc91422 1170516 clustalo_1.2.4.orig.tar.gz 7b89249d2195ce9ef2f3c295548d33fd 10980 clustalo_1.2.4-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVw55cRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGp7hAAktY572iL7FE7y+fhKBfO10eiDcemP8DC 4bER2AkxOMIMdQ/W0cET2j2xpW4Q+nIn8XqHBTL7kuQDXNjih7XLbb88ve/Pgt1x +sYQzza3pLwmlz39dsQQYqrgvHD0+8NabV/aHZtOnSJUNn9RAU6JZP8veycflTNO pHVWZB4nArZjZPappavIpwQhuWzGeJDAzJlOXg1dRyZxXmhiiZoY2dlqSIevZMpV +4ky3WIuThbfKSmhTWAPTeM07EIA2qg6MOWndo2r34D6nbDMrThV6HxVXpyg0Lmm pMN6AUstPmGI/kRvfSR1mSDYzCGk50ZPiMnSEOXZ4L0ntLsO5+YFi6xQmS8E2qyv NmN5eJNTDnRsgEVFabH80I3Mk216MHcGQkoOBtqvN9HLLfscDqcBeeGTLxiwLY1s DJQK0L5oTp2utK1IWGaDp1LtAhwt8cnwmKHA9lSauwv0M82NvBJnAwDrSe1fJoUk WXJ7inzT1pLseU3oUfUgxMBnvjLyaTxzKTp4Cirl4j/nH2KmGYxg6AcL6ZZsDFzm a8ivzqrj5nBHoR2ND56Atoc909j/yalZ8QTfB12JWex/yME/E6gfWPDD9fgH26Uq 30HIPGBV4xYtadF5F+lfXwk2Qbq/8MtpEi08jjVgljRV49wj3aCczAl9EFD4ITMd FN2FHv47zeA= =H2N2 -----END PGP SIGNATURE----- Thu Apr 11 17:34:31 UTC 2024 I: Checking whether the package is not for us Thu Apr 11 17:34:31 UTC 2024 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net. Thu Apr 11 17:34:31 UTC 2024 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net. Thu Apr 11 17:42:35 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Apr 11 05:34:37 -12 2024 I: pbuilder-time-stamp: 1712856877 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [clustalo_1.2.4-8.dsc] I: copying [./clustalo_1.2.4.orig.tar.gz] I: copying [./clustalo_1.2.4-8.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Dec 6 21:28:55 2023 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 clustalo-1.2.4 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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/21681/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='226c44d9db0c4656bf58b9e027a90b85' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='21681' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0kXMf4DF/pbuilderrc_gYxc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0kXMf4DF/b1 --logfile b1/build.log clustalo_1.2.4-8.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64a 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 11 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/21681/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libargtable2-dev, doxygen, graphviz, sphinx-common dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19635 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libargtable2-dev; however: Package libargtable2-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on sphinx-common; however: Package sphinx-common is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} intltool-debian{a} libabsl20220623{a} libaom3{a} libarchive-zip-perl{a} libargtable2-0{a} libargtable2-dev{a} libargtable2-docs{a} libavif16{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libclang-cpp16{a} libclang1-16{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfmt9{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0{a} libgraphite2-3{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblab-gamut1{a} liblerc4{a} libllvm16{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} librav1e0{a} libsharpyuv0{a} libsm6{a} libsub-override-perl{a} libsvtav1enc1d1{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libyuv0{a} libz3-4{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} sphinx-common{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-liberation2 javascript-common libarchive-cpio-perl libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libltdl-dev libmail-sendmail-perl lynx python3-sphinx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 112 newly installed, 0 to remove and 0 not upgraded. Need to get 88.0 MB of archives. After unpacking 336 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libbsd0 armhf 0.12.2-1 [127 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libedit2 armhf 3.1-20230828-1 [76.8 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libz3-4 armhf 4.8.12-3.1+b2 [6324 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libllvm16 armhf 1:16.0.6-20 [20.6 MB] Get: 35 http://deb.debian.org/debian trixie/main armhf libclang-cpp16 armhf 1:16.0.6-20 [9875 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libclang1-16 armhf 1:16.0.6-20 [5545 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libfmt9 armhf 9.1.0+ds1-2 [105 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf doxygen armhf 1.9.8+ds-2 [4458 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.5.0-2+b2 [80.2 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libpng16-16 armhf 1.6.43-1 [262 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libfreetype6 armhf 2.13.2+dfsg-1+b1 [371 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf fontconfig-config armhf 2.15.0-1.1 [317 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libfontconfig1 armhf 2.15.0-1.1 [370 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf fontconfig armhf 2.15.0-1.1 [461 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libcdt5 armhf 2.42.2-8 [37.0 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libcgraph6 armhf 2.42.2-8 [56.0 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libaom3 armhf 3.8.2-2 [1526 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libdav1d7 armhf 1.4.1-1 [262 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libabsl20220623 armhf 20220623.1-3 [361 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libgav1-1 armhf 0.18.0-1+b1 [284 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf librav1e0 armhf 0.7.1-2 [546 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libsharpyuv0 armhf 1.3.2-0.4 [105 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libsvtav1enc1d1 armhf 1.7.0+dfsg-2+b1 [936 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-2+b2 [143 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libyuv0 armhf 0.0~git202401110.af6ac82-1 [85.1 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libavif16 armhf 1.0.4-1 [95.0 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libheif-plugin-dav1d armhf 1.17.6-1 [9252 B] Get: 61 http://deb.debian.org/debian trixie/main armhf libde265-0 armhf 1.0.15-1 [145 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libheif-plugin-libde265 armhf 1.17.6-1 [12.0 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libheif1 armhf 1.17.6-1 [242 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libjbig0 armhf 2.1-6.1+b1 [27.3 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf liblerc4 armhf 4.0.0+ds-4+b1 [137 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libwebp7 armhf 1.3.2-0.4 [261 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libtiff6 armhf 4.5.1+git230720-4 [301 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.7-1 [328 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.7-1 [735 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libxpm4 armhf 1:3.5.17-1 [49.5 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libgd3 armhf 2.3.3-9+b1 [103 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libglib2.0-0 armhf 2.78.4-1 [1281 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libgts-0.7-5 armhf 0.7.6+darcs121130-5+b1 [137 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libpixman-1-0 armhf 0.42.2-1+b1 [476 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libxcb-render0 armhf 1.15-1 [114 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libxcb-shm0 armhf 1.15-1 [106 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libcairo2 armhf 1.18.0-1+b1 [441 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libltdl7 armhf 2.4.7-7 [390 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libfribidi0 armhf 1.0.13-3+b1 [69.4 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libgraphite2-3 armhf 1.3.14-2 [63.2 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libharfbuzz0b armhf 8.3.0-2 [2155 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libthai-data all 0.1.29-2 [168 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libdatrie1 armhf 0.2.13-3 [34.4 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libthai0 armhf 0.1.29-2 [45.8 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libpango-1.0-0 armhf 1.52.0+ds-1 [192 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libpangoft2-1.0-0 armhf 1.52.0+ds-1 [41.8 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libpangocairo-1.0-0 armhf 1.52.0+ds-1 [31.2 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libpathplan4 armhf 2.42.2-8 [39.3 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libgvc6 armhf 2.42.2-8 [578 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libgvpr2 armhf 2.42.2-8 [164 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf liblab-gamut1 armhf 2.42.2-8 [198 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf x11-common all 1:7.7+23 [252 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libice6 armhf 2:1.0.10-1 [51.9 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libxt6 armhf 1:1.2.1-1.1 [157 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libxmu6 armhf 2:1.1.3-3 [52.6 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf libxaw7 armhf 2:1.0.14-1 [167 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf graphviz armhf 2.42.2-8 [497 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf libargtable2-0 armhf 13-1.1 [15.8 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf libargtable2-docs all 13-1.1 [2622 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf libargtable2-dev armhf 13-1.1 [56.4 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libjson-perl all 4.10000-1 [87.5 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf sphinx-common all 7.2.6-6 [702 kB] Fetched 88.0 MB in 2s (40.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19635 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. 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Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../027-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../028-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../029-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../030-libbsd0_0.12.2-1_armhf.deb ... Unpacking libbsd0:armhf (0.12.2-1) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../031-libedit2_3.1-20230828-1_armhf.deb ... Unpacking libedit2:armhf (3.1-20230828-1) ... Selecting previously unselected package libz3-4:armhf. Preparing to unpack .../032-libz3-4_4.8.12-3.1+b2_armhf.deb ... Unpacking libz3-4:armhf (4.8.12-3.1+b2) ... 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Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../039-libbrotli1_1.1.0-2+b3_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../040-libpng16-16_1.6.43-1_armhf.deb ... Unpacking libpng16-16:armhf (1.6.43-1) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../041-libfreetype6_2.13.2+dfsg-1+b1_armhf.deb ... Unpacking libfreetype6:armhf (2.13.2+dfsg-1+b1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../042-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../043-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../044-fontconfig-config_2.15.0-1.1_armhf.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../045-libfontconfig1_2.15.0-1.1_armhf.deb ... Unpacking libfontconfig1:armhf (2.15.0-1.1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../046-fontconfig_2.15.0-1.1_armhf.deb ... Unpacking fontconfig (2.15.0-1.1) ... Selecting previously unselected package libcdt5:armhf. Preparing to unpack .../047-libcdt5_2.42.2-8_armhf.deb ... Unpacking libcdt5:armhf (2.42.2-8) ... Selecting previously unselected package libcgraph6:armhf. Preparing to unpack .../048-libcgraph6_2.42.2-8_armhf.deb ... Unpacking libcgraph6:armhf (2.42.2-8) ... Selecting previously unselected package libaom3:armhf. Preparing to unpack .../049-libaom3_3.8.2-2_armhf.deb ... Unpacking libaom3:armhf (3.8.2-2) ... Selecting previously unselected package libdav1d7:armhf. Preparing to unpack .../050-libdav1d7_1.4.1-1_armhf.deb ... Unpacking libdav1d7:armhf (1.4.1-1) ... Selecting previously unselected package libabsl20220623:armhf. Preparing to unpack .../051-libabsl20220623_20220623.1-3_armhf.deb ... Unpacking libabsl20220623:armhf (20220623.1-3) ... Selecting previously unselected package libgav1-1:armhf. Preparing to unpack .../052-libgav1-1_0.18.0-1+b1_armhf.deb ... Unpacking libgav1-1:armhf (0.18.0-1+b1) ... Selecting previously unselected package librav1e0:armhf. Preparing to unpack .../053-librav1e0_0.7.1-2_armhf.deb ... Unpacking librav1e0:armhf (0.7.1-2) ... Selecting previously unselected package libsharpyuv0:armhf. Preparing to unpack .../054-libsharpyuv0_1.3.2-0.4_armhf.deb ... Unpacking libsharpyuv0:armhf (1.3.2-0.4) ... Selecting previously unselected package libsvtav1enc1d1:armhf. Preparing to unpack .../055-libsvtav1enc1d1_1.7.0+dfsg-2+b1_armhf.deb ... Unpacking libsvtav1enc1d1:armhf (1.7.0+dfsg-2+b1) ... Selecting previously unselected package libjpeg62-turbo:armhf. 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Unpacking libtiff6:armhf (4.5.1+git230720-4) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../068-libxau6_1%3a1.0.9-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../069-libxdmcp6_1%3a1.1.2-3_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-3) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../070-libxcb1_1.15-1_armhf.deb ... Unpacking libxcb1:armhf (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../071-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../072-libx11-6_2%3a1.8.7-1_armhf.deb ... Unpacking libx11-6:armhf (2:1.8.7-1) ... Selecting previously unselected package libxpm4:armhf. Preparing to unpack .../073-libxpm4_1%3a3.5.17-1_armhf.deb ... Unpacking libxpm4:armhf (1:3.5.17-1) ... Selecting previously unselected package libgd3:armhf. Preparing to unpack .../074-libgd3_2.3.3-9+b1_armhf.deb ... Unpacking libgd3:armhf (2.3.3-9+b1) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../075-libglib2.0-0_2.78.4-1_armhf.deb ... Unpacking libglib2.0-0:armhf (2.78.4-1) ... Selecting previously unselected package libgts-0.7-5:armhf. Preparing to unpack .../076-libgts-0.7-5_0.7.6+darcs121130-5+b1_armhf.deb ... Unpacking libgts-0.7-5:armhf (0.7.6+darcs121130-5+b1) ... Selecting previously unselected package libpixman-1-0:armhf. Preparing to unpack .../077-libpixman-1-0_0.42.2-1+b1_armhf.deb ... Unpacking libpixman-1-0:armhf (0.42.2-1+b1) ... Selecting previously unselected package libxcb-render0:armhf. Preparing to unpack .../078-libxcb-render0_1.15-1_armhf.deb ... Unpacking libxcb-render0:armhf (1.15-1) ... Selecting previously unselected package libxcb-shm0:armhf. Preparing to unpack .../079-libxcb-shm0_1.15-1_armhf.deb ... Unpacking libxcb-shm0:armhf (1.15-1) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../080-libxext6_2%3a1.3.4-1+b1_armhf.deb ... Unpacking libxext6:armhf (2:1.3.4-1+b1) ... Selecting previously unselected package libxrender1:armhf. Preparing to unpack .../081-libxrender1_1%3a0.9.10-1.1_armhf.deb ... Unpacking libxrender1:armhf (1:0.9.10-1.1) ... Selecting previously unselected package libcairo2:armhf. Preparing to unpack .../082-libcairo2_1.18.0-1+b1_armhf.deb ... Unpacking libcairo2:armhf (1.18.0-1+b1) ... Selecting previously unselected package libltdl7:armhf. Preparing to unpack .../083-libltdl7_2.4.7-7_armhf.deb ... Unpacking libltdl7:armhf (2.4.7-7) ... Selecting previously unselected package libfribidi0:armhf. Preparing to unpack .../084-libfribidi0_1.0.13-3+b1_armhf.deb ... Unpacking libfribidi0:armhf (1.0.13-3+b1) ... Selecting previously unselected package libgraphite2-3:armhf. Preparing to unpack .../085-libgraphite2-3_1.3.14-2_armhf.deb ... 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Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:armhf (1.18.0-1+b1) ... Setting up sphinx-common (7.2.6-6) ... Setting up libxt6:armhf (1:1.2.1-1.1) ... Setting up libclang-cpp16 (1:16.0.6-20) ... Setting up libpangoft2-1.0-0:armhf (1.52.0+ds-1) ... Setting up libpangocairo-1.0-0:armhf (1.52.0+ds-1) ... Setting up libxmu6:armhf (2:1.1.3-3) ... Setting up debhelper (13.15.3) ... Setting up libxaw7:armhf (2:1.0.14-1) ... Setting up doxygen (1.9.8+ds-2) ... Setting up libheif-plugin-dav1d:armhf (1.17.6-1) ... Setting up libheif-plugin-libde265:armhf (1.17.6-1) ... Setting up libheif1:armhf (1.17.6-1) ... Setting up libgd3:armhf (2.3.3-9+b1) ... Setting up libgvc6 (2.42.2-8) ... Setting up graphviz (2.42.2-8) ... Processing triggers for libc-bin (2.37-15) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/clustalo-1.2.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../clustalo_1.2.4-8_source.changes dpkg-buildpackage: info: source package clustalo dpkg-buildpackage: info: source version 1.2.4-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4' 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 '/build/reproducible-path/clustalo-1.2.4' debian/rules binary dh binary dh_update_autotools_config cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead dh_autoreconf 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 '/build/reproducible-path/clustalo-1.2.4' 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... /usr/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 checking for sys/types.h... yes 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... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/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... /usr/bin/dd checking how to truncate binary pipes... /usr/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) /usr/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 checking for ftello... yes checking for fseeko... yes checking for ftello64... yes 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 '/build/reproducible-path/clustalo-1.2.4' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4' # nothing to do here make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' dh_auto_build -Nlibclustalo-doc make -j3 make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4' Making all in src make[2]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' make all-recursive make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' Making all in hhalign make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/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=/build/reproducible-path/clustalo-1.2.4=. -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=/build/reproducible-path/clustalo-1.2.4=. -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=/build/reproducible-path/clustalo-1.2.4=. -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 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compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c file.c -fPIC -DPIC -o .libs/file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c eps.c -o eps.o >/dev/null 2>&1 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 ()); | ~~~~~~~~~~~~~~~~~ /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=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o getopt.lo getopt.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c file.c -o file.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time 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-O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -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=/build/reproducible-path/clustalo-1.2.4=. -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=/build/reproducible-path/clustalo-1.2.4=. -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 '/build/reproducible-path/clustalo-1.2.4/src/clustal' make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -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=/build/reproducible-path/clustalo-1.2.4=. -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=/build/reproducible-path/clustalo-1.2.4=. -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=/build/reproducible-path/clustalo-1.2.4=. -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=/build/reproducible-path/clustalo-1.2.4=. -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=/build/reproducible-path/clustalo-1.2.4=. -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 "/build/reproducible-path/clustalo-1.2.4/src/clustal/.libs/libclustal.a") libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/build/reproducible-path/clustalo-1.2.4/src/hhalign/.libs/libhhalign.a") libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/build/reproducible-path/clustalo-1.2.4/src/squid/.libs/libsquid.a") libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/build/reproducible-path/clustalo-1.2.4/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=/build/reproducible-path/clustalo-1.2.4=. -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=/build/reproducible-path/clustalo-1.2.4=. -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+0x4e0): warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src' make[3]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src' make[2]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src' make[2]: Entering directory '/build/reproducible-path/clustalo-1.2.4' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4' dh_auto_test -a make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/clustalo-1.2.4' Making check in src make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' Making check in hhalign make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign' Making check in squid make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/squid' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/squid' Making check in kmpp make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/kmpp' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/kmpp' Making check in clustal make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/clustal' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/clustal' make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src' make[3]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src' make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' make[2]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' # 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 '/build/reproducible-path/clustalo-1.2.4' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4' echo "Do not run build time test" Do not run build time test make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4' dh_auto_install -a make -j1 install DESTDIR=/build/reproducible-path/clustalo-1.2.4/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/clustalo-1.2.4' Making install in src make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' Making install in hhalign make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign' make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/hhalign' /usr/bin/install -c -m 644 general.h hhfunc.h '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/hhalign' make[5]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign' make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign' Making install in squid make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/squid' make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/squid' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/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 '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/squid' make[5]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/squid' make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/squid' Making install in kmpp make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/kmpp' make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/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 '/build/reproducible-path/clustalo-1.2.4/src/kmpp' make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/kmpp' Making install in clustal make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/clustal' make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/clustal' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/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 '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/clustal' make[5]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/clustal' make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/clustal' make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf' /bin/bash ../libtool --mode=install /usr/bin/install -c libclustalo.la '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libclustalo.lai /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.la libtool: install: /usr/bin/install -c .libs/libclustalo.a /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a libtool: install: chmod 644 /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a libtool: install: ranlib /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c clustalo '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c clustalo /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/bin/clustalo /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/' /usr/bin/install -c -m 644 clustal-omega-config.h clustal-omega.h '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/' make[5]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src' make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src' make[3]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src' make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4' make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/share/doc/clustal-omega' /usr/bin/install -c -m 644 README '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/share/doc/clustal-omega' /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 clustalo.pc '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' make[3]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' make[2]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' 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 '/build/reproducible-path/clustalo-1.2.4' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4' # Generate doxygen doc mkdir -p doc doxygen Doxyfile warning: Tag 'SYMBOL_CACHE_SIZE' at line 289 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SHOW_DIRECTORIES' at line 473 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 744 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_ALIGN_MEMBERS' at line 799 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_SCHEMA' at line 1136 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_DTD' at line 1142 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1307 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 1320 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1329 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTNAME' at line 1353 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTSIZE' at line 1358 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_TRANSPARENT' at line 1482 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: argument 'a4wide' for option PAPER_TYPE is not a valid enum value Using the default: a4! warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. /build/reproducible-path/clustalo-1.2.4/src/clustal-omega.c:726: warning: argument 'pdSeqWeights_p' from the argument list of AlignmentOrder has multiple @param documentation sections /build/reproducible-path/clustalo-1.2.4/src/clustal-omega.c:726: warning: The following parameters of AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMbed, bool bPercID) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' parameter 'bPercID' /build/reproducible-path/clustalo-1.2.4/src/clustal-omega.c:726: warning: argument 'pdSeqWeights_p' from the argument list of AlignmentOrder has multiple @param documentation sections /build/reproducible-path/clustalo-1.2.4/src/clustal-omega.c:726: warning: The following parameters of AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMbed, bool bPercID) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' parameter 'bPercID' /build/reproducible-path/clustalo-1.2.4/src/clustal/mbed.c:646: warning: The following parameter of BisectingKmeans(bisecting_kmeans_result_t **prKMeansResult_p, const int iNObjs, const int iDim, double **ppdVectors, const int iMinRequiredObjsPerCluster, const int iMaxAllowedObjsPerCluster, char ***ppcClusterSplits_p) is not documented: parameter 'ppcClusterSplits_p' /build/reproducible-path/clustalo-1.2.4/src/clustal/mbed.c:1133: warning: The following parameters of Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' /build/reproducible-path/clustalo-1.2.4/src/clustal/mbed.c:1133: warning: The following parameters of Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' /build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:264: warning: Unsupported xml/html tag found /build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:270: warning: Unsupported xml/html tag found /build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:249: warning: The following parameter of PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID, int istart, const unsigned long int iend, int jstart, const unsigned long int jend, char *fdist_in, char *fdist_out) is not documented: parameter 'bPercID' /build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:264: warning: Unsupported xml/html tag found /build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:270: warning: Unsupported xml/html tag found /build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:249: warning: The following parameter of PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID, int istart, const unsigned long int iend, int jstart, const unsigned long int jend, char *fdist_in, char *fdist_out) is not documented: parameter 'bPercID' /build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:399: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch) are not documented: parameter 'iSeqFmt' parameter 'bIsProfile' parameter 'bDealignInputSeqs' parameter 'pcHMMBatch' /build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:1104: warning: The following parameters of SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs) are not documented: parameter 'bIsProfile' parameter 'bDealignInputSeqs' /build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:867: warning: The following parameter of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) is not documented: parameter 'bResno' /build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:399: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch) are not documented: parameter 'iSeqFmt' parameter 'bIsProfile' parameter 'bDealignInputSeqs' parameter 'pcHMMBatch' /build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:1104: warning: The following parameters of SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs) are not documented: parameter 'bIsProfile' parameter 'bDealignInputSeqs' /build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:867: warning: The following parameter of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) is not documented: parameter 'bResno' /build/reproducible-path/clustalo-1.2.4/src/clustal/symmatrix.c:231: warning: found documented return type for SymMatrixGetValueP that does not return anything /build/reproducible-path/clustalo-1.2.4/src/clustal/symmatrix.c:307: warning: The following parameter of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) is not documented: parameter 'bPercID' /build/reproducible-path/clustalo-1.2.4/src/clustal/symmatrix.c:231: warning: found documented return type for SymMatrixGetValueP that does not return anything /build/reproducible-path/clustalo-1.2.4/src/clustal/symmatrix.c:307: warning: The following parameter of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) is not documented: parameter 'bPercID' find doc -name "*.md5" -delete make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing 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 dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libclustalo-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libclustalo-doc: substitution variable ${js:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'clustalo' in '../clustalo_1.2.4-8_armhf.deb'. dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-8_armhf.deb'. dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.4-8_armhf.deb'. dpkg-deb: building package 'libclustalo-doc' in '../libclustalo-doc_1.2.4-8_all.deb'. dpkg-genbuildinfo --build=binary -O../clustalo_1.2.4-8_armhf.buildinfo dpkg-genchanges --build=binary -O../clustalo_1.2.4-8_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/21681 and its subdirectories I: Current time: Thu Apr 11 05:42:12 -12 2024 I: pbuilder-time-stamp: 1712857332 Thu Apr 11 17:42:38 UTC 2024 I: 1st build successful. Starting 2nd build on remote node cbxi4pro0-armhf-rb.debian.net. Thu Apr 11 17:42:38 UTC 2024 I: Preparing to do remote build '2' on cbxi4pro0-armhf-rb.debian.net. Thu Apr 11 17:55:09 UTC 2024 I: Deleting $TMPDIR on cbxi4pro0-armhf-rb.debian.net. Thu Apr 11 17:55:12 UTC 2024 I: 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 libclustalo-doc Architecture: armhf all Version: 1.2.4-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: clustalo - General-purpose multiple sequence alignment program for proteins libclustalo-dev - Library to embed Clustal Omega libclustalo-doc - API documentation for library to embed Clustal Omega Closes: 1043849 Changes: clustalo (1.2.4-8) unstable; urgency=medium . * Fix clean target Closes: #1043849 * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 93febcf600c74bb4b4aeddfe4e4f1fb1d688779c 718188 clustalo-dbgsym_1.2.4-8_armhf.deb facb8d1214e0ae886ac0fb32063950eafa016761 8282 clustalo_1.2.4-8_armhf.buildinfo 05ca8758064b034b3db568d61fd174b5ca33dba2 229032 clustalo_1.2.4-8_armhf.deb de73d0dc907ecd4fd0d455420381c76b6b0eb520 280904 libclustalo-dev_1.2.4-8_armhf.deb 9f5541e59a79ffdeb7cdc1b42482d5216ab29606 1756460 libclustalo-doc_1.2.4-8_all.deb Checksums-Sha256: 87ca6c53b5469defbe6d4a7146e2340a6cf1dbef5194240516d5f9f94a1c1d98 718188 clustalo-dbgsym_1.2.4-8_armhf.deb c087c6b23519342b91d6630fbf2ac253157a733632f51d9e1be942569015ace3 8282 clustalo_1.2.4-8_armhf.buildinfo 6a92138893ea1931442ec39edab288cdc7fc08a7469bc3be4c6a9fc240c01878 229032 clustalo_1.2.4-8_armhf.deb 41109bc64707da00039596da83a35234cd89cdc4709687f9e262ffd994c2477b 280904 libclustalo-dev_1.2.4-8_armhf.deb 143fcffd0fd13521ca7ccfe7dc09654ee88943746bb2891342983086869bef59 1756460 libclustalo-doc_1.2.4-8_all.deb Files: 5ed1d790a24e1033864f0e2b1c8c9b9f 718188 debug optional clustalo-dbgsym_1.2.4-8_armhf.deb fb4d7069e11d74b981e4c16ded7128fe 8282 science optional clustalo_1.2.4-8_armhf.buildinfo 59b9920467e4a3316bb36734164a3776 229032 science optional clustalo_1.2.4-8_armhf.deb aa1834f2cd5ae685033363eb859b3bf5 280904 libdevel optional libclustalo-dev_1.2.4-8_armhf.deb 93b8529cdd7cad6fba47944fac7ca32a 1756460 doc optional libclustalo-doc_1.2.4-8_all.deb Thu Apr 11 17:55:13 UTC 2024 I: diffoscope 263 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_28-2929.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.0kXMf4DF/clustalo_1.2.4-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.0kXMf4DF/clustalo_1.2.4-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.0kXMf4DF/clustalo_1.2.4-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.0kXMf4DF/b1/clustalo_1.2.4-8_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.0kXMf4DF/b2/clustalo_1.2.4-8_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.394s) 0.394s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.051s) 0.051s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 743ms CPU time consumed: 744ms Thu Apr 11 17:55:15 UTC 2024 I: diffoscope 263 found no differences in the changes files, and a .buildinfo file also exists. Thu Apr 11 17:55:15 UTC 2024 I: clustalo from trixie built successfully and reproducibly on armhf. Thu Apr 11 17:55:16 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Apr 11 17:55:16 UTC 2024 I: Submitting 12K b1/clustalo_1.2.4-8_armhf.buildinfo.asc Thu Apr 11 17:55:18 UTC 2024 I: Submitting 12K b2/clustalo_1.2.4-8_armhf.buildinfo.asc Thu Apr 11 17:55:19 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Apr 11 17:55:19 UTC 2024 I: Done submitting .buildinfo files. Thu Apr 11 17:55:19 UTC 2024 I: Removing signed clustalo_1.2.4-8_armhf.buildinfo.asc files: removed './b1/clustalo_1.2.4-8_armhf.buildinfo.asc' removed './b2/clustalo_1.2.4-8_armhf.buildinfo.asc'