Mon May 13 17:24:41 UTC 2024 I: starting to build clustalo/unstable/arm64 on jenkins on '2024-05-13 17:24' Mon May 13 17:24:41 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_17/35954/console.log Mon May 13 17:24:41 UTC 2024 I: Downloading source for unstable/clustalo=1.2.4-8 --2024-05-13 17:24:41-- 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% 238M=0s 2024-05-13 17:24:41 (238 MB/s) - ‘clustalo_1.2.4-8.dsc’ saved [2178/2178] Mon May 13 17:24:41 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----- Mon May 13 17:24:41 UTC 2024 I: Checking whether the package is not for us Mon May 13 17:24:41 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Mon May 13 17:24:41 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Mon May 13 17:26:28 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 15 11:47:43 -12 2025 I: pbuilder-time-stamp: 1750031263 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/2679671/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='8ab62b8a16ab443f99f331e576513915' 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='2679671' 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.KMbaaW7l/pbuilderrc_gdso --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KMbaaW7l/b1 --logfile b1/build.log clustalo_1.2.4-8.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 15 14:06 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2679671/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: arm64 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 ... 19744 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} libann0{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-cpp16t64{a} libclang1-16t64{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfmt9{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} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblab-gamut1{a} liblerc4{a} libllvm16t64{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} 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} 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-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, 113 newly installed, 0 to remove and 0 not upgraded. Need to get 90.9 MB of archives. After unpacking 406 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libllvm16t64 arm64 1:16.0.6-27 [20.7 MB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libclang-cpp16t64 arm64 1:16.0.6-27 [10.5 MB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libclang1-16t64 arm64 1:16.0.6-27 [5932 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libfmt9 arm64 9.1.0+ds1-2 [107 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 doxygen arm64 1.9.8+ds-2+b1 [4484 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libann0 arm64 1.1.2+doc-9+b1 [23.6 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libcdt5 arm64 2.42.2-9+b1 [38.7 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libcgraph6 arm64 2.42.2-9+b1 [60.6 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.8.2-2 [1528 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.4.1-1 [251 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-2+b1 [481 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 librav1e0 arm64 0.7.1-2 [630 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc1d1 arm64 1.7.0+dfsg-2+b1 [1083 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0~git202401110.af6ac82-1 [123 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.0.4-3 [99.4 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.17.6-1+b2 [9888 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b1 [151 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.17.6-1+b2 [13.0 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.17.6-1+b2 [247 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-1 [143 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b1 [52.9 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-9+b3 [114 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.80.2-1 [1393 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2 [141 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-1 [114 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-1 [105 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.0-3+b1 [478 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-7+b1 [393 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.52.2+ds-1 [206 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.52.2+ds-1 [45.5 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.52.2+ds-1 [33.0 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libpathplan4 arm64 2.42.2-9+b1 [40.6 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libgvc6 arm64 2.42.2-9+b1 [619 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libgvpr2 arm64 2.42.2-9+b1 [180 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 liblab-gamut1 arm64 2.42.2-9+b1 [198 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b2 [55.5 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.14-1+b2 [182 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 graphviz arm64 2.42.2-9+b1 [569 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libargtable2-0 arm64 13-2 [17.1 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libargtable2-docs all 13-2 [2621 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libargtable2-dev arm64 13-2 [41.2 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.2.6-7 [150 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 7.2.6-7 [702 kB] Fetched 90.9 MB in 1s (154 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 ... 19744 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%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../002-libmagic1t64_1%3a5.45-3_arm64.deb ... 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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:arm64. Preparing to unpack .../030-libbsd0_0.12.2-1_arm64.deb ... Unpacking libbsd0:arm64 (0.12.2-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../031-libedit2_3.1-20230828-1+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20230828-1+b1) ... Selecting previously unselected package libz3-4:arm64. Preparing to unpack .../032-libz3-4_4.8.12-3.1+b2_arm64.deb ... Unpacking libz3-4:arm64 (4.8.12-3.1+b2) ... Selecting previously unselected package libllvm16t64:arm64. 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Unpacking libsvtav1enc1d1:arm64 (1.7.0+dfsg-2+b1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../057-libjpeg62-turbo_1%3a2.1.5-3_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3) ... Selecting previously unselected package libyuv0:arm64. Preparing to unpack .../058-libyuv0_0.0~git202401110.af6ac82-1_arm64.deb ... Unpacking libyuv0:arm64 (0.0~git202401110.af6ac82-1) ... Selecting previously unselected package libavif16:arm64. Preparing to unpack .../059-libavif16_1.0.4-3_arm64.deb ... Unpacking libavif16:arm64 (1.0.4-3) ... Selecting previously unselected package libheif-plugin-dav1d:arm64. Preparing to unpack .../060-libheif-plugin-dav1d_1.17.6-1+b2_arm64.deb ... Unpacking libheif-plugin-dav1d:arm64 (1.17.6-1+b2) ... Selecting previously unselected package libde265-0:arm64. Preparing to unpack .../061-libde265-0_1.0.15-1+b1_arm64.deb ... Unpacking libde265-0:arm64 (1.0.15-1+b1) ... 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Unpacking libwebp7:arm64 (1.4.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../068-libtiff6_4.5.1+git230720-4_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-4) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../069-libxau6_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../070-libxdmcp6_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../071-libxcb1_1.17.0-1_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../072-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../073-libx11-6_2%3a1.8.7-1+b1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxpm4:arm64. Preparing to unpack .../074-libxpm4_1%3a3.5.17-1+b1_arm64.deb ... Unpacking libxpm4:arm64 (1:3.5.17-1+b1) ... Selecting previously unselected package libgd3:arm64. Preparing to unpack .../075-libgd3_2.3.3-9+b3_arm64.deb ... Unpacking libgd3:arm64 (2.3.3-9+b3) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../076-libglib2.0-0t64_2.80.2-1_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.80.2-1) ... Selecting previously unselected package libgts-0.7-5t64:arm64. Preparing to unpack .../077-libgts-0.7-5t64_0.7.6+darcs121130-5.2_arm64.deb ... Unpacking libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../078-libpixman-1-0_0.42.2-1+b1_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.42.2-1+b1) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../079-libxcb-render0_1.17.0-1_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-1) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../080-libxcb-shm0_1.17.0-1_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../081-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../082-libxrender1_1%3a0.9.10-1.1+b1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1+b1) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../083-libcairo2_1.18.0-3+b1_arm64.deb ... Unpacking libcairo2:arm64 (1.18.0-3+b1) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../084-libltdl7_2.4.7-7+b1_arm64.deb ... Unpacking libltdl7:arm64 (2.4.7-7+b1) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../085-libfribidi0_1.0.13-3+b1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.13-3+b1) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../086-libgraphite2-3_1.3.14-2_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../087-libharfbuzz0b_8.3.0-2+b1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (8.3.0-2+b1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../088-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../089-libdatrie1_0.2.13-3_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.13-3) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../090-libthai0_0.1.29-2_arm64.deb ... Unpacking libthai0:arm64 (0.1.29-2) ... 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Setting up libsm6:arm64 (2:1.2.3-1+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libavif16:arm64 (1.0.4-3) ... Setting up libxpm4:arm64 (1:3.5.17-1+b1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libclang1-16t64 (1:16.0.6-27) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libclang-cpp16t64 (1:16.0.6-27) ... Setting up libcairo2:arm64 (1.18.0-3+b1) ... Setting up doxygen (1.9.8+ds-2+b1) ... Setting up sphinx-common (7.2.6-7) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... Setting up libpangoft2-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libpangocairo-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libxmu6:arm64 (2:1.1.3-3+b2) ... Setting up debhelper (13.15.3) ... Setting up libxaw7:arm64 (2:1.0.14-1+b2) ... 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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 arm64 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=aarch64-linux-gnu --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/aarch64-linux-gnu --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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu 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... 8 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 -j12 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -c hhalign.cpp 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-I../../src -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 -mbranch-protection=standard -c tree.c -o tree.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o util.lo util.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c pair_dist.c -o pair_dist.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -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 -mbranch-protection=standard -c muscle_upgma.c -o muscle_upgma.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o weights.lo weights.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c symmatrix.c -o symmatrix.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c util.c -fPIC -DPIC -o .libs/util.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c ktuple_pair.c -o ktuple_pair.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -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 -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c util.c -o util.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c mbed.c -o mbed.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -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 -mbranch-protection=standard -c weights.c -o weights.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -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 -mbranch-protection=standard -c seq.c -o seq.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c muscle_tree.c -o muscle_tree.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -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 -mbranch-protection=standard -c hhalign_wrapper.c -o hhalign_wrapper.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 -mbranch-protection=standard -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 -mbranch-protection=standard -c -o main.o main.cpp gcc -DHAVE_CONFIG_H -I. -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 -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -static -Wl,-z,relro -Wl,-z,now -o libclustalo.la -rpath /usr/lib/aarch64-linux-gnu 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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -o clustalo main.o mymain.o ./.libs/libclustalo.a /usr/lib/aarch64-linux-gnu/libargtable2.so -lm -fopenmp /usr/bin/ld: ./.libs/libclustalo.a(clustal-omega.o): in function `AlnToHHMFile': ./src/./src/clustal-omega.c:393:(.text+0x624): 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 -j12 check "TESTSUITEFLAGS=-j12 --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/aarch64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libclustalo.la '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libclustalo.lai /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/aarch64-linux-gnu/libclustalo.la libtool: install: /usr/bin/install -c .libs/libclustalo.a /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/aarch64-linux-gnu/libclustalo.a libtool: install: chmod 644 /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/aarch64-linux-gnu/libclustalo.a libtool: install: ranlib /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/aarch64-linux-gnu/libclustalo.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /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/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 clustalo.pc '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/aarch64-linux-gnu/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 dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libclustalo-doc: substitution variable ${js:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libclustalo-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'clustalo' in '../clustalo_1.2.4-8_arm64.deb'. dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.4-8_arm64.deb'. dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-8_arm64.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_arm64.buildinfo dpkg-genchanges --build=binary -O../clustalo_1.2.4-8_arm64.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/2679671 and its subdirectories I: Current time: Sun Jun 15 11:49:25 -12 2025 I: pbuilder-time-stamp: 1750031365 Mon May 13 17:26:28 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Mon May 13 17:26:28 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Mon May 13 17:28:18 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Mon May 13 17:28:19 UTC 2024 I: clustalo_1.2.4-8_arm64.changes: Format: 1.8 Date: Wed, 06 Dec 2023 22:09:24 +0100 Source: clustalo Binary: clustalo clustalo-dbgsym libclustalo-dev libclustalo-doc Architecture: arm64 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: 950a8a6844b831326a119a87657503c015540965 729432 clustalo-dbgsym_1.2.4-8_arm64.deb 01c0ad145d205e2bde2a9503d871cbd2a6ba4083 8194 clustalo_1.2.4-8_arm64.buildinfo 4db58c2628abc481bad4735167322794eb508d4e 232536 clustalo_1.2.4-8_arm64.deb e1653a993f84e66ee5acc3bb73c63a9a2e9501e7 291236 libclustalo-dev_1.2.4-8_arm64.deb 9f5541e59a79ffdeb7cdc1b42482d5216ab29606 1756460 libclustalo-doc_1.2.4-8_all.deb Checksums-Sha256: 3ebdde344d6e8a34fa98ebd0b89036a53e1a83165d058aa9f6df70a01f4008bd 729432 clustalo-dbgsym_1.2.4-8_arm64.deb 8b091d6633a29108441d65ecd8d02384da99667a1b2f1df3ab83cb1ea7ee4c81 8194 clustalo_1.2.4-8_arm64.buildinfo 2bdafa74101b639a7b881ce38d6b2b70ca578af49dde511b95f7f0f81fa378b1 232536 clustalo_1.2.4-8_arm64.deb edd720f0926d7e046a919f187dc1528f2678a7d64f81cb607429ee167c1285c1 291236 libclustalo-dev_1.2.4-8_arm64.deb 143fcffd0fd13521ca7ccfe7dc09654ee88943746bb2891342983086869bef59 1756460 libclustalo-doc_1.2.4-8_all.deb Files: 4ead39115cf27f813fa5567941bfc90c 729432 debug optional clustalo-dbgsym_1.2.4-8_arm64.deb 27ec36a950d6d5db01515a0030ee1786 8194 science optional clustalo_1.2.4-8_arm64.buildinfo 1949fb85268c9ec8f6149179d1b23bc7 232536 science optional clustalo_1.2.4-8_arm64.deb f6409043e1e6282ab1aea891425a3ab6 291236 libdevel optional libclustalo-dev_1.2.4-8_arm64.deb 93b8529cdd7cad6fba47944fac7ca32a 1756460 doc optional libclustalo-doc_1.2.4-8_all.deb Mon May 13 17:28:20 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_17-35954.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.KMbaaW7l/clustalo_1.2.4-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.KMbaaW7l/clustalo_1.2.4-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.KMbaaW7l/clustalo_1.2.4-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.KMbaaW7l/b1/clustalo_1.2.4-8_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.KMbaaW7l/b2/clustalo_1.2.4-8_arm64.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: 0.049s) 0.049s 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: 729ms CPU time consumed: 730ms Mon May 13 17:28:21 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Mon May 13 17:28:21 UTC 2024 I: clustalo from unstable built successfully and reproducibly on arm64. Mon May 13 17:28:23 UTC 2024 I: Submitting .buildinfo files to external archives: Mon May 13 17:28:23 UTC 2024 I: Submitting 12K b1/clustalo_1.2.4-8_arm64.buildinfo.asc Mon May 13 17:28:24 UTC 2024 I: Submitting 12K b2/clustalo_1.2.4-8_arm64.buildinfo.asc Mon May 13 17:28:25 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 13 17:28:25 UTC 2024 I: Done submitting .buildinfo files. Mon May 13 17:28:25 UTC 2024 I: Removing signed clustalo_1.2.4-8_arm64.buildinfo.asc files: removed './b1/clustalo_1.2.4-8_arm64.buildinfo.asc' removed './b2/clustalo_1.2.4-8_arm64.buildinfo.asc'