Fri Jan 10 01:02:24 UTC 2025 I: starting to build clustalo/trixie/armhf on jenkins on '2025-01-10 01:02' Fri Jan 10 01:02:24 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_34/15240/console.log Fri Jan 10 01:02:24 UTC 2025 I: Downloading source for trixie/clustalo=1.2.4-8 --2025-01-10 01:02:24-- http://deb.debian.org/debian/pool/main/c/clustalo/clustalo_1.2.4-8.dsc Connecting to 46.16.76.132:3128... 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% 258M=0s 2025-01-10 01:02:24 (258 MB/s) - ‘clustalo_1.2.4-8.dsc’ saved [2178/2178] Fri Jan 10 01:02:24 UTC 2025 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----- Fri Jan 10 01:02:24 UTC 2025 I: Checking whether the package is not for us Fri Jan 10 01:02:24 UTC 2025 I: Starting 1st build on remote node virt32z-armhf-rb.debian.net. Fri Jan 10 01:02:24 UTC 2025 I: Preparing to do remote build '1' on virt32z-armhf-rb.debian.net. Fri Jan 10 01:10:00 UTC 2025 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 9 13:02:31 -12 2025 I: pbuilder-time-stamp: 1736470951 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 dpkg-source: warning: cannot verify inline signature for ./clustalo_1.2.4-8.dsc: unsupported subcommand 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/26834/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='bf598abdecd749d99469fe882785e6bb' 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='26834' 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.hG5FSh1G/pbuilderrc_SIjt --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.hG5FSh1G/b1 --logfile b1/build.log clustalo_1.2.4-8.dsc' SUDO_GID='110' SUDO_UID='103' 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 virt32z 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/26834/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 ... 19567 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} libabsl20230802{a} libaom3{a} libarchive-zip-perl{a} libargtable2-0{a} libargtable2-dev{a} libavif16{a} libbrotli1{a} libcairo2{a} libcdt5{a} libcgraph6{a} libclang-cpp19{a} libclang1-19{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfmt10{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{a} libgraphite2-3{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblab-gamut1{a} liblerc4{a} libllvm19{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libraqm0{a} librav1e0.7{a} libsharpyuv0{a} libsm6{a} libsvtav1enc2{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{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} libxt6t64{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-liberation 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, 113 newly installed, 0 to remove and 0 not upgraded. Need to get 91.8 MB of archives. After unpacking 360 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-3 [195 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-13 [84.7 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 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 0.22.5-3 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.23 [90.6 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-8 [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 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-3 [1488 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 13.23 [919 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libedit2 armhf 3.1-20240808-1 [77.9 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libffi8 armhf 3.4.6-1 [20.0 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libz3-4 armhf 4.13.3-1 [7252 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libllvm19 armhf 1:19.1.6-1+b1 [23.8 MB] Get: 35 http://deb.debian.org/debian trixie/main armhf libclang-cpp19 armhf 1:19.1.6-1+b1 [11.6 MB] Get: 36 http://deb.debian.org/debian trixie/main armhf libclang1-19 armhf 1:19.1.6-1+b1 [6611 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libfmt10 armhf 10.1.1+ds1-4 [118 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf doxygen armhf 1.9.8+ds-2+b3 [4499 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libpng16-16t64 armhf 1.6.44-3 [263 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [385 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+b1 [318 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libfontconfig1 armhf 2.15.0-1.1+b1 [371 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf fontconfig armhf 2.15.0-1.1+b1 [461 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libcdt5 armhf 2.42.4-2+b1 [37.9 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libcgraph6 armhf 2.42.4-2+b1 [56.8 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libaom3 armhf 3.11.0-1 [1599 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libdav1d7 armhf 1.5.0-1+b1 [250 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libabsl20230802 armhf 20230802.1-4 [432 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libgav1-1 armhf 0.19.0-3 [297 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf librav1e0.7 armhf 0.7.1-9 [585 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libsvtav1enc2 armhf 2.3.0+dfsg-1 [970 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libyuv0 armhf 0.0.1898.20241219-1 [86.6 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libavif16 armhf 1.1.1-1 [103 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libsharpyuv0 armhf 1.4.0-0.1+b1 [111 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libheif-plugin-dav1d armhf 1.19.5-1 [10.9 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libde265-0 armhf 1.0.15-1+b2 [145 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libheif-plugin-libde265 armhf 1.19.5-1 [14.3 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libheif1 armhf 1.19.5-1 [432 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libimagequant0 armhf 2.18.0-1+b2 [30.5 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libfribidi0 armhf 1.0.16-1 [24.6 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libglib2.0-0t64 armhf 2.82.4-1 [1327 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libgraphite2-3 armhf 1.3.14-2+b1 [63.1 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libharfbuzz0b armhf 10.1.0-2 [420 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libraqm0 armhf 0.10.2-1 [11.6 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libjbig0 armhf 2.1-6.1+b2 [27.3 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf liblerc4 armhf 4.0.0+ds-5 [146 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libwebp7 armhf 1.4.0-0.1+b1 [266 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libtiff6 armhf 4.5.1+git230720-5 [302 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.11-1 [19.7 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.5-1 [26.4 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.17.0-2+b1 [140 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.10-2 [337 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.10-2 [750 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libxpm4 armhf 1:3.5.17-1+b3 [50.3 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libgd3 armhf 2.3.3-12+b1 [105 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libgts-0.7-5t64 armhf 0.7.6+darcs121130-5.2+b1 [133 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libpixman-1-0 armhf 0.44.0-3 [164 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libxcb-render0 armhf 1.17.0-2+b1 [114 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libxcb-shm0 armhf 1.17.0-2+b1 [105 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b3 [45.2 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libxrender1 armhf 1:0.9.10-1.1+b3 [25.0 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libcairo2 armhf 1.18.2-2 [443 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libltdl7 armhf 2.4.7-8 [390 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libthai-data all 0.1.29-2 [168 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libdatrie1 armhf 0.2.13-3+b1 [34.7 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libthai0 armhf 0.1.29-2+b1 [46.0 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libpango-1.0-0 armhf 1.55.0+ds-3 [200 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libpangoft2-1.0-0 armhf 1.55.0+ds-3 [47.7 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libpangocairo-1.0-0 armhf 1.55.0+ds-3 [31.3 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libpathplan4 armhf 2.42.4-2+b1 [39.9 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libgvc6 armhf 2.42.4-2+b1 [581 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libgvpr2 armhf 2.42.4-2+b1 [168 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf liblab-gamut1 armhf 2.42.4-2+b1 [198 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf x11-common all 1:7.7+23.1 [216 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libice6 armhf 2:1.1.1-1 [58.5 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libsm6 armhf 2:1.2.4-1 [33.5 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf libxt6t64 armhf 1:1.2.1-1.2+b2 [160 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf libxmu6 armhf 2:1.1.3-3+b4 [51.2 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf libxaw7 armhf 2:1.0.16-1 [177 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf graphviz armhf 2.42.4-2+b1 [500 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf libargtable2-0 armhf 13-3 [15.8 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf libargtable2-dev armhf 13-3 [39.7 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libjs-sphinxdoc all 8.1.3-3 [30.4 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf libjson-perl all 4.10000-1 [87.5 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf sphinx-common all 8.1.3-3 [617 kB] Fetched 91.8 MB in 17s (5313 kB/s) Preconfiguring packages ... 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 ... 19567 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. 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Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libllvm19:armhf (1:19.1.6-1+b1) ... Setting up libice6:armhf (2:1.1.1-1) ... Setting up gettext (0.22.5-3) ... Setting up libclang1-19 (1:19.1.6-1+b1) ... Setting up libxpm4:armhf (1:3.5.17-1+b3) ... Setting up libxrender1:armhf (1:0.9.10-1.1+b3) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libxext6:armhf (2:1.3.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:armhf (0.1.29-2+b1) ... Setting up libglib2.0-0t64:armhf (2.82.4-1) ... No schema files found: doing nothing. Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... Setting up libargtable2-dev (13-3) ... Setting up libgav1-1:armhf (0.19.0-3) ... Setting up libjs-sphinxdoc (8.1.3-3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libgvpr2:armhf (2.42.4-2+b1) ... Setting up groff-base (1.23.0-7) ... Setting up libharfbuzz0b:armhf (10.1.0-2) ... Setting up libgts-0.7-5t64:armhf (0.7.6+darcs121130-5.2+b1) ... Setting up libfontconfig1:armhf (2.15.0-1.1+b1) ... Setting up libsm6:armhf (2:1.2.4-1) ... Setting up libclang-cpp19 (1:19.1.6-1+b1) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libavif16:armhf (1.1.1-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:armhf (1.55.0+ds-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:armhf (1.18.2-2) ... Setting up doxygen (1.9.8+ds-2+b3) ... Setting up libraqm0:armhf (0.10.2-1) ... Setting up sphinx-common (8.1.3-3) ... Setting up libxt6t64:armhf (1:1.2.1-1.2+b2) ... Setting up libpangoft2-1.0-0:armhf (1.55.0+ds-3) ... Setting up libpangocairo-1.0-0:armhf (1.55.0+ds-3) ... Setting up libxmu6:armhf (2:1.1.3-3+b4) ... Setting up debhelper (13.23) ... Setting up libxaw7:armhf (2:1.0.16-1) ... Setting up libheif-plugin-dav1d:armhf (1.19.5-1) ... Setting up libheif-plugin-libde265:armhf (1.19.5-1) ... Setting up libheif1:armhf (1.19.5-1) ... Setting up libgd3:armhf (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b1) ... Setting up graphviz (2.42.4-2+b1) ... Processing triggers for libc-bin (2.40-4) ... 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 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.m4:663: 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... 16 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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'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:970, 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. 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compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c mbed.c -fPIC -DPIC -o .libs/mbed.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o pair_dist.lo pair_dist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration 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-DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c progress.c -fPIC -DPIC -o .libs/progress.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c progress.c -o progress.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration 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--mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o symmatrix.lo symmatrix.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c symmatrix.c -fPIC -DPIC -o .libs/symmatrix.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c tree.c -o tree.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c seq.c -o seq.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration 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-I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -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 -Werror=implicit-function-declaration -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. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -Werror=implicit-function-declaration -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. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -Werror=implicit-function-declaration -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. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -Werror=implicit-function-declaration -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. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -Werror=implicit-function-declaration -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 -Werror=implicit-function-declaration -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: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged 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 '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-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/26834 and its subdirectories I: Current time: Thu Jan 9 13:09:51 -12 2025 I: pbuilder-time-stamp: 1736471391 Fri Jan 10 01:10:02 UTC 2025 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net. Fri Jan 10 01:10:02 UTC 2025 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net. Fri Jan 10 01:16:08 UTC 2025 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. Fri Jan 10 01:16:11 UTC 2025 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: 4dc284bd6c131843729df0fc86acff8a62c074c1 721824 clustalo-dbgsym_1.2.4-8_armhf.deb 00428497d362ed724f65ad134da22d26fa6b0e1c 7944 clustalo_1.2.4-8_armhf.buildinfo b10ede8a2b66e8b7fdd93d8c701c816c43adbc4e 231384 clustalo_1.2.4-8_armhf.deb 4d2d3e452a68c2cedca5e3c2cb5dda12d334c47d 283276 libclustalo-dev_1.2.4-8_armhf.deb 9f5541e59a79ffdeb7cdc1b42482d5216ab29606 1756460 libclustalo-doc_1.2.4-8_all.deb Checksums-Sha256: c028babb1def5e790f4f8187b9d80039183d9486451717bffce1624b5e4befaf 721824 clustalo-dbgsym_1.2.4-8_armhf.deb dbfb52ec043ac78d34bfef10bed4a71d8e8f5ef90335109ab0e768b0f59cdf0d 7944 clustalo_1.2.4-8_armhf.buildinfo a69bd7ae99b4cb798a181c515ed5fd9cd6d89c211e8b19b9c8146de3a3c7543d 231384 clustalo_1.2.4-8_armhf.deb 57f5400a4b8f242c441f1cbef93c9cdbf84c70e6e6a68ea2cbcad3c189a92a04 283276 libclustalo-dev_1.2.4-8_armhf.deb 143fcffd0fd13521ca7ccfe7dc09654ee88943746bb2891342983086869bef59 1756460 libclustalo-doc_1.2.4-8_all.deb Files: d424901f4cd5510d386673009cdcb9b1 721824 debug optional clustalo-dbgsym_1.2.4-8_armhf.deb 9b8571a046526783399051129172b245 7944 science optional clustalo_1.2.4-8_armhf.buildinfo f6b6019bc74dca03d58dc436687a02a2 231384 science optional clustalo_1.2.4-8_armhf.deb 209528aa843bf14ff63cdec2fd7b2411 283276 libdevel optional libclustalo-dev_1.2.4-8_armhf.deb 93b8529cdd7cad6fba47944fac7ca32a 1756460 doc optional libclustalo-doc_1.2.4-8_all.deb Fri Jan 10 01:16:12 UTC 2025 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_34-15240.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.hG5FSh1G/clustalo_1.2.4-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.hG5FSh1G/clustalo_1.2.4-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.hG5FSh1G/clustalo_1.2.4-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.hG5FSh1G/b1/clustalo_1.2.4-8_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.hG5FSh1G/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: 0.352s) 0.352s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.041s) 0.041s 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: 640ms CPU time consumed: 640ms Fri Jan 10 01:16:12 UTC 2025 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Fri Jan 10 01:16:12 UTC 2025 I: clustalo from trixie built successfully and reproducibly on armhf. Fri Jan 10 01:16:14 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Jan 10 01:16:14 UTC 2025 I: Submitting 12K b1/clustalo_1.2.4-8_armhf.buildinfo.asc Fri Jan 10 01:16:15 UTC 2025 I: Submitting 12K b2/clustalo_1.2.4-8_armhf.buildinfo.asc Fri Jan 10 01:16:16 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Jan 10 01:16:16 UTC 2025 I: Done submitting .buildinfo files. Fri Jan 10 01:16:16 UTC 2025 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'