Running as unit: rb-build-amd64_37-82929.service ==================================================================================== Wed Sep 17 07:22:46 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_37) on jenkins, called using "infom01-amd64 infom02-amd64" as arguments. Wed Sep 17 07:22:46 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-NZpOHyYw" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Sep 17 07:22:46 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Wed Sep 17 07:22:46 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-3e6c8o' Wed Sep 17 07:22:46 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Wed Sep 17 07:22:46 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-NJ844g' ok, let's check if proteinortho is building anywhere yet… ok, proteinortho is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of proteinortho in forky on amd64 on jenkins now. 1st build will be done on infom01-amd64.debian.net. 2nd build will be done on infom02-amd64.debian.net. ============================================================================= Wed Sep 17 07:23:05 UTC 2025 I: starting to build proteinortho/forky/amd64 on jenkins on '2025-09-17 07:22' Wed Sep 17 07:23:05 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_37/82929/console.log 1758093785 amd64 forky proteinortho Wed Sep 17 07:23:05 UTC 2025 I: Downloading source for forky/proteinortho=6.3.1+dfsg-1 --2025-09-17 07:23:05-- http://deb.debian.org/debian/pool/main/p/proteinortho/proteinortho_6.3.1%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2161 (2.1K) [text/prs.lines.tag] Saving to: ‘proteinortho_6.3.1+dfsg-1.dsc’ 0K .. 100% 236M=0s 2025-09-17 07:23:05 (236 MB/s) - ‘proteinortho_6.3.1+dfsg-1.dsc’ saved [2161/2161] --2025-09-17 07:23:05-- http://deb.debian.org/debian/pool/main/p/proteinortho/proteinortho_6.3.1%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2161 (2.1K) [text/prs.lines.tag] Saving to: ‘proteinortho_6.3.1+dfsg-1.dsc’ 0K .. 100% 236M=0s 2025-09-17 07:23:05 (236 MB/s) - ‘proteinortho_6.3.1+dfsg-1.dsc’ saved [2161/2161] Wed Sep 17 07:23:05 UTC 2025 I: proteinortho_6.3.1+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: proteinortho Binary: proteinortho Architecture: any Version: 6.3.1+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://gitlab.com/paulklemm_PHD/proteinortho Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/proteinortho Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner (>= 2.0.10~), procps, debhelper Package-List: proteinortho deb science optional arch=any Checksums-Sha1: 36ddff1bcbf8dde0a19795f74e154e74aadc1705 375988 proteinortho_6.3.1+dfsg.orig.tar.xz d2526cacd7835c2f294f0219e9514a1644f13e78 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz Checksums-Sha256: 7ce978cf6d33a6f67a3138d7f4cafe3ed5c1dcfbdd70224f1514385df9531679 375988 proteinortho_6.3.1+dfsg.orig.tar.xz ab190de700fdc10752e33b2e0c263f6166a2dfb8d8a119d987a7265b99df61fe 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz Files: 286e6fd86b91807e92db7e8bd7a3c87c 375988 proteinortho_6.3.1+dfsg.orig.tar.xz ee4d531727d1dc02b1af12b004ed1c99 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWg1C8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHolg/8CJZu3mudXnpM0z+TV/H6OgBg+eGm/mkU opYsSgqwFb4k6PwHTa9VA3Zq+liUKDRLBvRyz0olnOff5RhE5t+xys2LMHLj+n4g Maij/jnhq+XbAefm4Z0MFg4LsVH/rrKCn+fWlCV7H4YoKL/QEkbsIebdD4l+7jhV qe1cMgEHjmG+6XccBmpii+dLyIQGGuRGIIdmaOzmxPw8EzFQkE7uOdhWG42PtPgo YVM/JZyLXe7gtY73UM8MFOTIuJ/RVOwx/BUOjuC6P9zu0TimNhwBnNvwQW+PECu5 nJWgm1mixkpGvsQSNsu7ITUPMbbr/LE9Vu7yt/1V28SbCQxgsNwuONG1+Qyao3lt vv9nhH9YUOktpfyr2dCJinpqEQ5uv1eYeSXpyNIJzwWSPeWQW+zxuPDSa0u750br C3/8UjoMWTrVDbTc0Y9CN9coUHkghXPvLsxxpqpj4gBIWgjFM3SMNP56p1Rv5uRx QZUk5F81PteMIwgkp0z3bY0ZezA2o7eLFjGmrwLwl4l0hdWrjHyhumtJuTldFZt9 HJ6rlvfDuj+Kml2uC41CMoHV5thvnQC2MjBVQjG38IYf2AAyd6oafGFA8hHqF4qu eL69T0QQeXHICNXvCE4xyjVM8xIWfeYNCbkZULbOq7bdEzueDZEP/GzLCUkM+d2d YXWwk5h9Tsw= =8nLU -----END PGP SIGNATURE----- Wed Sep 17 07:23:05 UTC 2025 I: Checking whether the package is not for us Wed Sep 17 07:23:05 UTC 2025 I: Starting 1st build on remote node infom01-amd64.debian.net. Wed Sep 17 07:23:05 UTC 2025 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Wed Sep 17 07:23:05 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Wed Sep 17 07:23:05 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-mVFWWZ' ==================================================================================== Wed Sep 17 07:23:06 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "1 proteinortho forky /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM 6.3.1+dfsg-1" as arguments. Wed Sep 17 07:23:06 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-llYpKp88" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Sep 17 07:23:06 UTC 2025 I: Downloading source for forky/proteinortho=6.3.1+dfsg-1 Reading package lists... NOTICE: 'proteinortho' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/proteinortho.git Please use: git clone https://salsa.debian.org/med-team/proteinortho.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 385 kB of source archives. Get:1 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] Get:2 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (tar) [376 kB] Get:3 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (diff) [7248 B] Fetched 385 kB in 0s (1055 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'proteinortho' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/proteinortho.git Please use: git clone https://salsa.debian.org/med-team/proteinortho.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 385 kB of source archives. Get:1 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] Get:2 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (tar) [376 kB] Get:3 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (diff) [7248 B] Fetched 385 kB in 0s (1055 kB/s) Download complete and in download only mode ============================================================================= Building proteinortho in forky on amd64 on infom01-amd64 now. Date: Wed Sep 17 07:23:07 UTC 2025 Date UTC: Wed Sep 17 07:23:07 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 16 19:23:07 -12 2025 I: pbuilder-time-stamp: 1758093787 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 [proteinortho_6.3.1+dfsg-1.dsc] I: copying [./proteinortho_6.3.1+dfsg.orig.tar.xz] I: copying [./proteinortho_6.3.1+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting proteinortho in proteinortho-6.3.1+dfsg dpkg-source: info: unpacking proteinortho_6.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking proteinortho_6.3.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying deb_diamond I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3205547/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='7d7f6e7c6f2a47d2af1dc55b1fb3670c' 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='3205547' 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.OYY6awEM/pbuilderrc_3mMg --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b1 --logfile b1/build.log proteinortho_6.3.1+dfsg-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3205547/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: amd64 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), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner (>= 2.0.10~), procps, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev | libatlas-base-dev | liblapack.so; however: Package liblapack-dev is not installed. Package libatlas-base-dev is not installed. Package liblapack.so is not installed. pbuilder-satisfydepends-dummy depends on diamond-aligner (>= 2.0.10~); however: Package diamond-aligner is not installed. pbuilder-satisfydepends-dummy depends on procps; however: Package procps is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} diamond-aligner{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} liblapack-dev{a} liblapack3{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libncbi-vdb3{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2-16{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} ncbi-vdb-data{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl linux-sysctl-defaults lynx med-config psmisc wget 0 packages upgraded, 61 newly installed, 0 to remove and 0 not upgraded. Need to get 53.2 MB of archives. After unpacking 229 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 38 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 diamond-aligner amd64 2.1.11-2 [2648 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-3 [894 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Fetched 53.2 MB in 6s (8378 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... 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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/proteinortho-6.3.1+dfsg/ && 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 > ../proteinortho_6.3.1+dfsg-1_source.changes dpkg-buildpackage: info: source package proteinortho dpkg-buildpackage: info: source version 6.3.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' rm -rf src/BUILD test/C*.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.* rm -rf src/lapack-3.8.0/ make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' CC = cc CCFLAGS = CXX = g++ Creating build directory ... CXXFLAGS = -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection MTUNEARCHFLAGS = LDFLAGS = -Wl,-z,relro -Wl,-z,now LDLIBS = STATIC = FALSE [ 10%] Prepare proteinortho_clustering ... [ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking) g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -o src/BUILD/Linux_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive [ 25%] Building **graphMinusRemovegraph** g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph src/graphMinusRemovegraph.cpp -Wl,-z,relro -Wl,-z,now [ 50%] Building **cleanupblastgraph** g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph src/cleanupblastgraph.cpp -Wl,-z,relro -Wl,-z,now - test max_of_diag() : OK - test generate_random_vector() : OK - test get_new_x() : OK - test makeOrthogonal() : OK - test normalize() : OK - test getY() : OK - test lapack() : OK - test power() : OK - test smirnov-grubb() : OK All test passed. ......OK dynamic linking was successful for proteinortho_clustering! [100%] Everything is compiled with no errors. make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_auto_test --no-parallel make -j1 test make[2]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' [TEST] Clean up all test files... [TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped) [1/12] -p=blastp test: passed [2/12] -p=blastp+ synteny (PoFF) test: tput: unknown terminal "unknown" tput: unknown terminal "unknown" tput: unknown terminal "unknown" tput: unknown terminal "unknown" passed [3/12] -p=diamond test: passed [4/12] -p=diamond (--moresensitive) test (subparaBlast): passed [5/12] -p=lastp (lastal) test: lastal missing, skipping... [6/12] -p=topaz test: topaz missing, skipping... [7/12] -p=usearch test: usearch missing, skipping... [8/12] -p=ublast test: usearch missing, skipping... [9/12] -p=rapsearch test: rapsearch missing, skipping... [10/12] -p=blatp (blat) test: blat missing, skipping... [11/12] -p=mmseqsp (mmseqs) test: mmseqs missing, skipping... [12/12] -p=autoblast (automatically detect blastp,blastn,...) test: passed [TEST] Clean up all test files... ./proteinortho6.pl -silent -force -project=test_blastp -p=blastp test/*.faa; [TEST] 2. -step=3 tests (proteinortho_clustering) [1/6] various test functions of proteinortho_clustering (if this fails, try make clean first): passed [2/6] Test proteinortho_clustering using lapack: passed [3/6] Test proteinortho_clustering using power: passed [4/6] Test proteinortho_clustering using lapack and no weights: passed [5/6] Test proteinortho_clustering using maxnodes/flooding: passed [6/6] Test proteinortho_clustering using no clustering at all: passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 0 test/ring4_K5.blast-graph >test_power_ring4_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_power_ring4_K5.proteinortho.tsv "ring4_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/ring4_K5.blast-graph >test_lapack_ring4_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_ring4_K5.proteinortho.tsv "ring4_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/P3_K5.blast-graph >test_lapack_P3_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_P3_K5.proteinortho.tsv "P3_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/P4.blast-graph >test_lapack_P4.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_P4.proteinortho.tsv "P4"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/K5.blast-graph >test_lapack_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_K5.proteinortho.tsv "K5"; passed ./proteinortho6.pl -silent -force -project=test_diamond -p=diamond test/*.faa 2>/dev/null; testing if there is a protein that occurs twice in the output: passed ./proteinortho6.pl -silent -force -singles -project=test_singles_diamond -p=diamond test/*.faa 2>/dev/null; testing if all proteins are in the output (using -singles): set -e ; diff test_singles_diamond.true test_singles_diamond.test; passed [TEST] All tests passed make[2]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' rm test_* remove.* test/C_clean.faa make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' mkdir -p /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin dh_auto_install -- install PREFIX=/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin make -j12 install DESTDIR=/build/reproducible-path/proteinortho-6.3.1\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/build/reproducible-path/proteinortho-6.3.1\+dfsg/debian/proteinortho/usr/bin make[2]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' INSTALLING everything to /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin 'proteinortho6.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl' 'proteinortho' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho' 'src/BUILD/Linux_x86_64/proteinortho_extract_from_graph.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl' 'src/BUILD/Linux_x86_64/proteinortho_formatUsearch.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl' 'src/BUILD/Linux_x86_64/proteinortho_compareProteinorthoGraphs.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl' 'src/BUILD/Linux_x86_64/proteinortho_do_mcl.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl' 'src/BUILD/Linux_x86_64/proteinortho2html.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl' 'src/BUILD/Linux_x86_64/proteinortho2xml.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl' 'src/BUILD/Linux_x86_64/proteinortho_clustering' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering' 'src/BUILD/Linux_x86_64/proteinortho_singletons.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl' 'src/BUILD/Linux_x86_64/proteinortho_ffadj_mcs.py' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py' 'src/BUILD/Linux_x86_64/proteinortho2tree.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl' 'src/BUILD/Linux_x86_64/proteinortho_history.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl' 'src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph' 'src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph' 'src/BUILD/Linux_x86_64/proteinortho_grab_proteins.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl' 'src/BUILD/Linux_x86_64/proteinortho_summary.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_summary.pl' Everything installed successfully to /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin. If needed you can add /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin'. make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_fixperms find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'proteinortho' in '../proteinortho_6.3.1+dfsg-1_amd64.deb'. dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../proteinortho_6.3.1+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../proteinortho_6.3.1+dfsg-1_amd64.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: including full 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/3205547 and its subdirectories I: Current time: Tue Sep 16 19:26:13 -12 2025 I: pbuilder-time-stamp: 1758093973 Wed Sep 17 07:26:13 UTC 2025 I: Signing ./b1/proteinortho_6.3.1+dfsg-1_amd64.buildinfo as proteinortho_6.3.1+dfsg-1_amd64.buildinfo.asc Wed Sep 17 07:26:13 UTC 2025 I: Signed ./b1/proteinortho_6.3.1+dfsg-1_amd64.buildinfo as ./b1/proteinortho_6.3.1+dfsg-1_amd64.buildinfo.asc Wed Sep 17 07:26:13 UTC 2025 - build #1 for proteinortho/forky/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Wed Sep 17 07:26:13 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-llYpKp88, removing. /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 17 07:26 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 17 07:23 b2 -rw-rw-r-- 1 jenkins jenkins 2161 Jan 12 2024 proteinortho_6.3.1+dfsg-1.dsc -rw------- 1 jenkins jenkins 3319 Sep 17 07:23 rbuildlog.p6PlcBP /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b1: total 2820 -rw-r--r-- 1 jenkins jenkins 41220 Sep 17 07:26 build.log -rw-r--r-- 1 jenkins jenkins 2037324 Sep 17 07:26 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 7248 Sep 17 07:26 proteinortho_6.3.1+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2161 Sep 17 07:26 proteinortho_6.3.1+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5887 Sep 17 07:26 proteinortho_6.3.1+dfsg-1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 6769 Sep 17 07:26 proteinortho_6.3.1+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1509 Sep 17 07:26 proteinortho_6.3.1+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 374728 Sep 17 07:26 proteinortho_6.3.1+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1628 Sep 17 07:26 proteinortho_6.3.1+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 375988 Sep 17 07:26 proteinortho_6.3.1+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b2: total 0 Wed Sep 17 07:26:13 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 16 19:23:07 -12 2025 I: pbuilder-time-stamp: 1758093787 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 [proteinortho_6.3.1+dfsg-1.dsc] I: copying [./proteinortho_6.3.1+dfsg.orig.tar.xz] I: copying [./proteinortho_6.3.1+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting proteinortho in proteinortho-6.3.1+dfsg dpkg-source: info: unpacking proteinortho_6.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking proteinortho_6.3.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying deb_diamond I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3205547/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='7d7f6e7c6f2a47d2af1dc55b1fb3670c' 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='3205547' 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.OYY6awEM/pbuilderrc_3mMg --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b1 --logfile b1/build.log proteinortho_6.3.1+dfsg-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3205547/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: amd64 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), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner (>= 2.0.10~), procps, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev | libatlas-base-dev | liblapack.so; however: Package liblapack-dev is not installed. Package libatlas-base-dev is not installed. Package liblapack.so is not installed. pbuilder-satisfydepends-dummy depends on diamond-aligner (>= 2.0.10~); however: Package diamond-aligner is not installed. pbuilder-satisfydepends-dummy depends on procps; however: Package procps is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} diamond-aligner{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} liblapack-dev{a} liblapack3{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libncbi-vdb3{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2-16{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} ncbi-vdb-data{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl linux-sysctl-defaults lynx med-config psmisc wget 0 packages upgraded, 61 newly installed, 0 to remove and 0 not upgraded. Need to get 53.2 MB of archives. After unpacking 229 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 38 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 diamond-aligner amd64 2.1.11-2 [2648 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-3 [894 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Fetched 53.2 MB in 6s (8378 kB/s) Preconfiguring packages ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../45-libuv1t64_1.51.0-2_amd64.deb ... Unpacking libuv1t64:amd64 (1.51.0-2) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../46-ncbi-data_6.1.20170106+dfsg2-6_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-6) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../47-ncbi-blast+_2.16.0+ds-7_amd64.deb ... Unpacking ncbi-blast+ (2.16.0+ds-7) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up liblmdb0:amd64 (0.9.31-1+b2) ... Setting up ncbi-data (6.1.20170106+dfsg2-6) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libuv1t64:amd64 (1.51.0-2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up diamond-aligner (2.1.11-2) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Sep 17 07:24:26 UTC 2025. Universal Time is now: Wed Sep 17 07:24:26 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libgfortran5:amd64 (15.2.0-3) ... Setting up autoconf (2.72-3.1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up procps (2:4.0.4-9) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Setting up libmbedcrypto16:amd64 (3.6.4-2) ... Setting up readline-common (8.3-3) ... Setting up libblas-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libmbedx509-7:amd64 (3.6.4-2) ... Setting up liblapack-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libmbedtls21:amd64 (3.6.4-2) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up python3 (3.13.7-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up ncbi-blast+ (2.16.0+ds-7) ... Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... 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/proteinortho-6.3.1+dfsg/ && 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 > ../proteinortho_6.3.1+dfsg-1_source.changes dpkg-buildpackage: info: source package proteinortho dpkg-buildpackage: info: source version 6.3.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' rm -rf src/BUILD test/C*.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.* rm -rf src/lapack-3.8.0/ make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' CC = cc CCFLAGS = CXX = g++ Creating build directory ... CXXFLAGS = -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection MTUNEARCHFLAGS = LDFLAGS = -Wl,-z,relro -Wl,-z,now LDLIBS = STATIC = FALSE [ 10%] Prepare proteinortho_clustering ... [ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking) g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -o src/BUILD/Linux_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive [ 25%] Building **graphMinusRemovegraph** g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph src/graphMinusRemovegraph.cpp -Wl,-z,relro -Wl,-z,now [ 50%] Building **cleanupblastgraph** g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph src/cleanupblastgraph.cpp -Wl,-z,relro -Wl,-z,now - test max_of_diag() : OK - test generate_random_vector() : OK - test get_new_x() : OK - test makeOrthogonal() : OK - test normalize() : OK - test getY() : OK - test lapack() : OK - test power() : OK - test smirnov-grubb() : OK All test passed. ......OK dynamic linking was successful for proteinortho_clustering! [100%] Everything is compiled with no errors. make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_auto_test --no-parallel make -j1 test make[2]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' [TEST] Clean up all test files... [TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped) [1/12] -p=blastp test: passed [2/12] -p=blastp+ synteny (PoFF) test: tput: unknown terminal "unknown" tput: unknown terminal "unknown" tput: unknown terminal "unknown" tput: unknown terminal "unknown" passed [3/12] -p=diamond test: passed [4/12] -p=diamond (--moresensitive) test (subparaBlast): passed [5/12] -p=lastp (lastal) test: lastal missing, skipping... [6/12] -p=topaz test: topaz missing, skipping... [7/12] -p=usearch test: usearch missing, skipping... [8/12] -p=ublast test: usearch missing, skipping... [9/12] -p=rapsearch test: rapsearch missing, skipping... [10/12] -p=blatp (blat) test: blat missing, skipping... [11/12] -p=mmseqsp (mmseqs) test: mmseqs missing, skipping... [12/12] -p=autoblast (automatically detect blastp,blastn,...) test: passed [TEST] Clean up all test files... ./proteinortho6.pl -silent -force -project=test_blastp -p=blastp test/*.faa; [TEST] 2. -step=3 tests (proteinortho_clustering) [1/6] various test functions of proteinortho_clustering (if this fails, try make clean first): passed [2/6] Test proteinortho_clustering using lapack: passed [3/6] Test proteinortho_clustering using power: passed [4/6] Test proteinortho_clustering using lapack and no weights: passed [5/6] Test proteinortho_clustering using maxnodes/flooding: passed [6/6] Test proteinortho_clustering using no clustering at all: passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 0 test/ring4_K5.blast-graph >test_power_ring4_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_power_ring4_K5.proteinortho.tsv "ring4_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/ring4_K5.blast-graph >test_lapack_ring4_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_ring4_K5.proteinortho.tsv "ring4_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/P3_K5.blast-graph >test_lapack_P3_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_P3_K5.proteinortho.tsv "P3_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/P4.blast-graph >test_lapack_P4.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_P4.proteinortho.tsv "P4"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/K5.blast-graph >test_lapack_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_K5.proteinortho.tsv "K5"; passed ./proteinortho6.pl -silent -force -project=test_diamond -p=diamond test/*.faa 2>/dev/null; testing if there is a protein that occurs twice in the output: passed ./proteinortho6.pl -silent -force -singles -project=test_singles_diamond -p=diamond test/*.faa 2>/dev/null; testing if all proteins are in the output (using -singles): set -e ; diff test_singles_diamond.true test_singles_diamond.test; passed [TEST] All tests passed make[2]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' rm test_* remove.* test/C_clean.faa make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' mkdir -p /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin dh_auto_install -- install PREFIX=/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin make -j12 install DESTDIR=/build/reproducible-path/proteinortho-6.3.1\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/build/reproducible-path/proteinortho-6.3.1\+dfsg/debian/proteinortho/usr/bin make[2]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' INSTALLING everything to /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin 'proteinortho6.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl' 'proteinortho' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho' 'src/BUILD/Linux_x86_64/proteinortho_extract_from_graph.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl' 'src/BUILD/Linux_x86_64/proteinortho_formatUsearch.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl' 'src/BUILD/Linux_x86_64/proteinortho_compareProteinorthoGraphs.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl' 'src/BUILD/Linux_x86_64/proteinortho_do_mcl.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl' 'src/BUILD/Linux_x86_64/proteinortho2html.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl' 'src/BUILD/Linux_x86_64/proteinortho2xml.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl' 'src/BUILD/Linux_x86_64/proteinortho_clustering' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering' 'src/BUILD/Linux_x86_64/proteinortho_singletons.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl' 'src/BUILD/Linux_x86_64/proteinortho_ffadj_mcs.py' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py' 'src/BUILD/Linux_x86_64/proteinortho2tree.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl' 'src/BUILD/Linux_x86_64/proteinortho_history.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl' 'src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph' 'src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph' 'src/BUILD/Linux_x86_64/proteinortho_grab_proteins.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl' 'src/BUILD/Linux_x86_64/proteinortho_summary.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_summary.pl' Everything installed successfully to /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin. If needed you can add /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin'. make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_fixperms find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'proteinortho' in '../proteinortho_6.3.1+dfsg-1_amd64.deb'. dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../proteinortho_6.3.1+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../proteinortho_6.3.1+dfsg-1_amd64.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: including full 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/3205547 and its subdirectories I: Current time: Tue Sep 16 19:26:13 -12 2025 I: pbuilder-time-stamp: 1758093973 Wed Sep 17 07:26:14 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Wed Sep 17 07:26:14 UTC 2025 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Wed Sep 17 07:26:14 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Wed Sep 17 07:26:14 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-TmE4vN' ==================================================================================== Tue Oct 20 13:49:15 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "2 proteinortho forky /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM 6.3.1+dfsg-1" as arguments. Tue Oct 20 13:49:15 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-G7aJ4Xei" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Oct 20 13:49:15 UTC 2026 I: Downloading source for forky/proteinortho=6.3.1+dfsg-1 Reading package lists... NOTICE: 'proteinortho' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/proteinortho.git Please use: git clone https://salsa.debian.org/med-team/proteinortho.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 385 kB of source archives. Get:1 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] Get:2 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (tar) [376 kB] Get:3 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (diff) [7248 B] Fetched 385 kB in 0s (2709 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'proteinortho' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/proteinortho.git Please use: git clone https://salsa.debian.org/med-team/proteinortho.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 385 kB of source archives. Get:1 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] Get:2 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (tar) [376 kB] Get:3 http://deb.debian.org/debian forky/main proteinortho 6.3.1+dfsg-1 (diff) [7248 B] Fetched 385 kB in 0s (2709 kB/s) Download complete and in download only mode ============================================================================= Re-Building proteinortho in forky on amd64 on infom02-amd64 now. Date: Tue Oct 20 13:49:15 UTC 2026 Date UTC: Tue Oct 20 13:49:15 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/pbuilderrc_uKhP + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' proteinortho = debian-installer -o proteinortho = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' proteinortho = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/pbuilderrc_uKhP --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b2 --logfile b2/build.log proteinortho_6.3.1+dfsg-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 21 03:49:15 +14 2026 I: pbuilder-time-stamp: 1792504155 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 [proteinortho_6.3.1+dfsg-1.dsc] I: copying [./proteinortho_6.3.1+dfsg.orig.tar.xz] I: copying [./proteinortho_6.3.1+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting proteinortho in proteinortho-6.3.1+dfsg dpkg-source: info: unpacking proteinortho_6.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking proteinortho_6.3.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying deb_diamond I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/D01_modify_environment starting debug: Running on infom02-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 20 13:49 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DIRSTACK=() DISTRIBUTION=forky EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=1560d509fbe94481a7bc6cf5f12425dd LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2928926 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/pbuilderrc_uKhP --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b2 --logfile b2/build.log proteinortho_6.3.1+dfsg-1.dsc' SUDO_GID=109 SUDO_HOME=/var/lib/jenkins SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2928926/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: amd64 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), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner (>= 2.0.10~), procps, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev | libatlas-base-dev | liblapack.so; however: Package liblapack-dev is not installed. Package libatlas-base-dev is not installed. Package liblapack.so is not installed. pbuilder-satisfydepends-dummy depends on diamond-aligner (>= 2.0.10~); however: Package diamond-aligner is not installed. pbuilder-satisfydepends-dummy depends on procps; however: Package procps is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} diamond-aligner{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} liblapack-dev{a} liblapack3{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libncbi-vdb3{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2-16{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} ncbi-vdb-data{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl linux-sysctl-defaults lynx med-config psmisc wget 0 packages upgraded, 61 newly installed, 0 to remove and 0 not upgraded. Need to get 53.2 MB of archives. After unpacking 229 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 38 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 diamond-aligner amd64 2.1.11-2 [2648 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-3 [894 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Fetched 53.2 MB in 1s (46.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (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 ... 20251 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (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 ... 21266 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-9_amd64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.23.1-2+b1_amd64.deb ... 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Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../27-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-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 .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package diamond-aligner. Preparing to unpack .../32-diamond-aligner_2.1.11-2_amd64.deb ... Unpacking diamond-aligner (2.1.11-2) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../33-libblas3_3.12.1-7_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-7) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../34-libblas-dev_3.12.1-7_amd64.deb ... Unpacking libblas-dev:amd64 (3.12.1-7) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../35-libgfortran5_15.2.0-3_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-3) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../36-liblapack3_3.12.1-7_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-7) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../37-liblapack-dev_3.12.1-7_amd64.deb ... Unpacking liblapack-dev:amd64 (3.12.1-7) ... Selecting previously unselected package liblmdb0:amd64. Preparing to unpack .../38-liblmdb0_0.9.31-1+b2_amd64.deb ... Unpacking liblmdb0:amd64 (0.9.31-1+b2) ... Selecting previously unselected package libmbedcrypto16:amd64. Preparing to unpack .../39-libmbedcrypto16_3.6.4-2_amd64.deb ... Unpacking libmbedcrypto16:amd64 (3.6.4-2) ... Selecting previously unselected package libmbedx509-7:amd64. Preparing to unpack .../40-libmbedx509-7_3.6.4-2_amd64.deb ... Unpacking libmbedx509-7:amd64 (3.6.4-2) ... Selecting previously unselected package libmbedtls21:amd64. Preparing to unpack .../41-libmbedtls21_3.6.4-2_amd64.deb ... Unpacking libmbedtls21:amd64 (3.6.4-2) ... Selecting previously unselected package ncbi-vdb-data. Preparing to unpack .../42-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... Selecting previously unselected package libncbi-vdb3:amd64. Preparing to unpack .../43-libncbi-vdb3_3.2.1+dfsg-2_amd64.deb ... Unpacking libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../44-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../45-libuv1t64_1.51.0-2_amd64.deb ... Unpacking libuv1t64:amd64 (1.51.0-2) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../46-ncbi-data_6.1.20170106+dfsg2-6_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-6) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../47-ncbi-blast+_2.16.0+ds-7_amd64.deb ... Unpacking ncbi-blast+ (2.16.0+ds-7) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up liblmdb0:amd64 (0.9.31-1+b2) ... Setting up ncbi-data (6.1.20170106+dfsg2-6) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libuv1t64:amd64 (1.51.0-2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up diamond-aligner (2.1.11-2) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 20 13:49:57 UTC 2026. Universal Time is now: Tue Oct 20 13:49:57 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libgfortran5:amd64 (15.2.0-3) ... Setting up autoconf (2.72-3.1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up procps (2:4.0.4-9) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Setting up libmbedcrypto16:amd64 (3.6.4-2) ... Setting up readline-common (8.3-3) ... Setting up libblas-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libmbedx509-7:amd64 (3.6.4-2) ... Setting up liblapack-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libmbedtls21:amd64 (3.6.4-2) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up python3 (3.13.7-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up ncbi-blast+ (2.16.0+ds-7) ... Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... 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: user script /srv/workspace/pbuilder/2928926/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for forky I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/proteinortho-6.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../proteinortho_6.3.1+dfsg-1_source.changes dpkg-buildpackage: info: source package proteinortho dpkg-buildpackage: info: source version 6.3.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j16 clean make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' rm -rf src/BUILD test/C*.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.* rm -rf src/lapack-3.8.0/ make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j16 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' CC = cc CCFLAGS = Creating build directory ... CXX = g++ CXXFLAGS = -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection MTUNEARCHFLAGS = LDFLAGS = -Wl,-z,relro -Wl,-z,now LDLIBS = STATIC = FALSE [ 10%] Prepare proteinortho_clustering ... [ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking) g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -o src/BUILD/Linux_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive [ 25%] Building **graphMinusRemovegraph** g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph src/graphMinusRemovegraph.cpp -Wl,-z,relro -Wl,-z,now [ 50%] Building **cleanupblastgraph** g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph src/cleanupblastgraph.cpp -Wl,-z,relro -Wl,-z,now - test max_of_diag() : OK - test generate_random_vector() : OK - test get_new_x() : OK - test makeOrthogonal() : OK - test normalize() : OK - test getY() : OK - test lapack() : OK - test power() : OK - test smirnov-grubb() : OK All test passed. ......OK dynamic linking was successful for proteinortho_clustering! [100%] Everything is compiled with no errors. make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_auto_test --no-parallel make -j1 test make[2]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' [TEST] Clean up all test files... [TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped) [1/12] -p=blastp test: passed [2/12] -p=blastp+ synteny (PoFF) test: tput: unknown terminal "unknown" tput: unknown terminal "unknown" tput: unknown terminal "unknown" tput: unknown terminal "unknown" passed [3/12] -p=diamond test: passed [4/12] -p=diamond (--moresensitive) test (subparaBlast): passed [5/12] -p=lastp (lastal) test: lastal missing, skipping... [6/12] -p=topaz test: topaz missing, skipping... [7/12] -p=usearch test: usearch missing, skipping... [8/12] -p=ublast test: usearch missing, skipping... [9/12] -p=rapsearch test: rapsearch missing, skipping... [10/12] -p=blatp (blat) test: blat missing, skipping... [11/12] -p=mmseqsp (mmseqs) test: mmseqs missing, skipping... [12/12] -p=autoblast (automatically detect blastp,blastn,...) test: passed [TEST] Clean up all test files... ./proteinortho6.pl -silent -force -project=test_blastp -p=blastp test/*.faa; [TEST] 2. -step=3 tests (proteinortho_clustering) [1/6] various test functions of proteinortho_clustering (if this fails, try make clean first): passed [2/6] Test proteinortho_clustering using lapack: passed [3/6] Test proteinortho_clustering using power: passed [4/6] Test proteinortho_clustering using lapack and no weights: passed [5/6] Test proteinortho_clustering using maxnodes/flooding: passed [6/6] Test proteinortho_clustering using no clustering at all: passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 0 test/ring4_K5.blast-graph >test_power_ring4_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_power_ring4_K5.proteinortho.tsv "ring4_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/ring4_K5.blast-graph >test_lapack_ring4_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_ring4_K5.proteinortho.tsv "ring4_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/P3_K5.blast-graph >test_lapack_P3_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_P3_K5.proteinortho.tsv "P3_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/P4.blast-graph >test_lapack_P4.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_P4.proteinortho.tsv "P4"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/K5.blast-graph >test_lapack_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_K5.proteinortho.tsv "K5"; passed ./proteinortho6.pl -silent -force -project=test_diamond -p=diamond test/*.faa 2>/dev/null; testing if there is a protein that occurs twice in the output: passed ./proteinortho6.pl -silent -force -singles -project=test_singles_diamond -p=diamond test/*.faa 2>/dev/null; testing if all proteins are in the output (using -singles): set -e ; diff test_singles_diamond.true test_singles_diamond.test; passed [TEST] All tests passed make[2]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' rm test_* remove.* test/C_clean.faa make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' mkdir -p /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin dh_auto_install -- install PREFIX=/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin make -j16 install DESTDIR=/build/reproducible-path/proteinortho-6.3.1\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/build/reproducible-path/proteinortho-6.3.1\+dfsg/debian/proteinortho/usr/bin make[2]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' INSTALLING everything to /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin 'proteinortho6.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl' 'proteinortho' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho' 'src/BUILD/Linux_x86_64/proteinortho_extract_from_graph.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl' 'src/BUILD/Linux_x86_64/proteinortho_formatUsearch.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl' 'src/BUILD/Linux_x86_64/proteinortho_compareProteinorthoGraphs.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl' 'src/BUILD/Linux_x86_64/proteinortho_do_mcl.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl' 'src/BUILD/Linux_x86_64/proteinortho2html.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl' 'src/BUILD/Linux_x86_64/proteinortho2xml.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl' 'src/BUILD/Linux_x86_64/proteinortho_clustering' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering' 'src/BUILD/Linux_x86_64/proteinortho_singletons.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl' 'src/BUILD/Linux_x86_64/proteinortho_ffadj_mcs.py' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py' 'src/BUILD/Linux_x86_64/proteinortho2tree.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl' 'src/BUILD/Linux_x86_64/proteinortho_history.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl' 'src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph' 'src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph' 'src/BUILD/Linux_x86_64/proteinortho_grab_proteins.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl' 'src/BUILD/Linux_x86_64/proteinortho_summary.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_summary.pl' Everything installed successfully to /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin. If needed you can add /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin'. make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_fixperms find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'proteinortho' in '../proteinortho_6.3.1+dfsg-1_amd64.deb'. dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../proteinortho_6.3.1+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../proteinortho_6.3.1+dfsg-1_amd64.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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/B01_cleanup finished 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/2928926 and its subdirectories I: Current time: Wed Oct 21 03:51:31 +14 2026 I: pbuilder-time-stamp: 1792504291 + false + set +x Tue Oct 20 13:51:31 UTC 2026 I: Signing ./b2/proteinortho_6.3.1+dfsg-1_amd64.buildinfo as proteinortho_6.3.1+dfsg-1_amd64.buildinfo.asc Tue Oct 20 13:51:31 UTC 2026 I: Signed ./b2/proteinortho_6.3.1+dfsg-1_amd64.buildinfo as ./b2/proteinortho_6.3.1+dfsg-1_amd64.buildinfo.asc Tue Oct 20 13:51:31 UTC 2026 - build #2 for proteinortho/forky/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Tue Oct 20 13:51:31 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-G7aJ4Xei, removing. /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM: total 56 drwxrwxr-x 2 jenkins jenkins 4096 Sep 17 07:26 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 17 07:28 b2 -rw-rw-r-- 1 jenkins jenkins 2161 Jan 12 2024 proteinortho_6.3.1+dfsg-1.dsc -rw------- 1 jenkins jenkins 44828 Sep 17 07:26 rbuildlog.p6PlcBP /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b1: total 2820 -rw-r--r-- 1 jenkins jenkins 41220 Sep 17 07:26 build.log -rw-r--r-- 1 jenkins jenkins 2037324 Sep 17 07:26 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 7248 Sep 17 07:26 proteinortho_6.3.1+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2161 Sep 17 07:26 proteinortho_6.3.1+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5887 Sep 17 07:26 proteinortho_6.3.1+dfsg-1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 6769 Sep 17 07:26 proteinortho_6.3.1+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1509 Sep 17 07:26 proteinortho_6.3.1+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 374728 Sep 17 07:26 proteinortho_6.3.1+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1628 Sep 17 07:26 proteinortho_6.3.1+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 375988 Sep 17 07:26 proteinortho_6.3.1+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b2: total 2820 -rw-rw-r-- 1 jenkins jenkins 43141 Sep 17 07:28 build.log -rw-r--r-- 1 jenkins jenkins 2037324 Sep 17 07:28 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 7248 Sep 17 07:28 proteinortho_6.3.1+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2161 Sep 17 07:28 proteinortho_6.3.1+dfsg-1.dsc -rw-rw-r-- 1 jenkins jenkins 5881 Sep 17 07:28 proteinortho_6.3.1+dfsg-1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 6763 Sep 17 07:28 proteinortho_6.3.1+dfsg-1_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1509 Sep 17 07:28 proteinortho_6.3.1+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 374728 Sep 17 07:28 proteinortho_6.3.1+dfsg-1_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1628 Sep 17 07:28 proteinortho_6.3.1+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 375988 Sep 17 07:28 proteinortho_6.3.1+dfsg.orig.tar.xz Wed Sep 17 07:28:32 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. Wed Sep 17 07:28:32 UTC 2025 I: proteinortho_6.3.1+dfsg-1_amd64.changes: Format: 1.8 Date: Fri, 12 Jan 2024 06:50:22 +0100 Source: proteinortho Binary: proteinortho proteinortho-dbgsym Architecture: amd64 Version: 6.3.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: proteinortho - Detection of (Co-)orthologs in large-scale protein analysis Closes: 1046514 Changes: proteinortho (6.3.1+dfsg-1) unstable; urgency=medium . * New upstream version * Clean up after testing Closes: #1046514 Checksums-Sha1: c1e9e5b14aedbe055745dd3647c8678b65d7f3c2 2037324 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb c1792a870fbe25a5b57f3393a4668c6a42f5b2f0 5887 proteinortho_6.3.1+dfsg-1_amd64.buildinfo 50a43ff24133614c42c179af0321f8e8871d969b 374728 proteinortho_6.3.1+dfsg-1_amd64.deb Checksums-Sha256: 8e1710f1c028ea7f5dff9c2a2e92e5761da5ef8b1c77dcdf01c0270fb784384a 2037324 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb d9eef8222bcf66065f2cbbd56b1d9ba294452533db60f99ede15ef863e5fec65 5887 proteinortho_6.3.1+dfsg-1_amd64.buildinfo 6302393a653736e819fd3c00e71e09376299546c0d2728f790101a35444de1a7 374728 proteinortho_6.3.1+dfsg-1_amd64.deb Files: 90ad8457293e15f9458da5f5f8881d32 2037324 debug optional proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb ce20ab5035b50c7811d51783fcfdf0a6 5887 science optional proteinortho_6.3.1+dfsg-1_amd64.buildinfo b595ae1430c373367c1fce35e0ab262a 374728 science optional proteinortho_6.3.1+dfsg-1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/proteinortho_6.3.1+dfsg-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/proteinortho_6.3.1+dfsg-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/proteinortho_6.3.1+dfsg-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/proteinortho_6.3.1+dfsg-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/forky/amd64/proteinortho_6.3.1+dfsg-1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/proteinortho_6.3.1+dfsg-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-17 07:26:13.767634066 +0000 +++ b2/build.log 2025-09-17 07:28:32.407811604 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 16 19:23:07 -12 2025 -I: pbuilder-time-stamp: 1758093787 +I: Current time: Wed Oct 21 03:49:15 +14 2026 +I: pbuilder-time-stamp: 1792504155 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -24,52 +24,84 @@ dpkg-source: info: applying deb_diamond I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3205547/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 20 13:49 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2928926/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='7d7f6e7c6f2a47d2af1dc55b1fb3670c' - 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='3205547' - PS1='# ' - PS2='> ' + INVOCATION_ID=1560d509fbe94481a7bc6cf5f12425dd + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2928926 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.OYY6awEM/pbuilderrc_3mMg --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b1 --logfile b1/build.log proteinortho_6.3.1+dfsg-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/pbuilderrc_uKhP --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b2 --logfile b2/build.log proteinortho_6.3.1+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3205547/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -178,7 +210,7 @@ Get: 59 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] -Fetched 53.2 MB in 6s (8378 kB/s) +Fetched 53.2 MB in 1s (46.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) @@ -394,8 +426,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Sep 17 07:24:26 UTC 2025. -Universal Time is now: Wed Sep 17 07:24:26 UTC 2025. +Local time is now: Tue Oct 20 13:49:57 UTC 2026. +Universal Time is now: Tue Oct 20 13:49:57 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -453,7 +485,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/proteinortho-6.3.1+dfsg/ && 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 > ../proteinortho_6.3.1+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/proteinortho-6.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../proteinortho_6.3.1+dfsg-1_source.changes dpkg-buildpackage: info: source package proteinortho dpkg-buildpackage: info: source version 6.3.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -463,7 +499,7 @@ debian/rules clean dh clean dh_auto_clean - make -j12 clean + make -j16 clean make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' rm -rf src/BUILD test/C*.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.* rm -rf src/lapack-3.8.0/ @@ -475,12 +511,12 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j12 "INSTALL=install --strip-program=true" + make -j16 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' CC = cc CCFLAGS = -CXX = g++ Creating build directory ... +CXX = g++ CXXFLAGS = -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection MTUNEARCHFLAGS = LDFLAGS = -Wl,-z,relro -Wl,-z,now @@ -569,7 +605,7 @@ make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' mkdir -p /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin dh_auto_install -- install PREFIX=/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin - make -j12 install DESTDIR=/build/reproducible-path/proteinortho-6.3.1\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/build/reproducible-path/proteinortho-6.3.1\+dfsg/debian/proteinortho/usr/bin + make -j16 install DESTDIR=/build/reproducible-path/proteinortho-6.3.1\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/build/reproducible-path/proteinortho-6.3.1\+dfsg/debian/proteinortho/usr/bin make[2]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' INSTALLING everything to /build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin 'proteinortho6.pl' -> '/build/reproducible-path/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl' @@ -633,12 +669,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2928926/tmp/hooks/B01_cleanup finished 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/3205547 and its subdirectories -I: Current time: Tue Sep 16 19:26:13 -12 2025 -I: pbuilder-time-stamp: 1758093973 +I: removing directory /srv/workspace/pbuilder/2928926 and its subdirectories +I: Current time: Wed Oct 21 03:51:31 +14 2026 +I: pbuilder-time-stamp: 1792504291 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/proteinortho_6.3.1+dfsg-1.diff: 68.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/proteinortho_6.3.1+dfsg-1.diff.gz b2/build.log: 79.2% -- replaced with stdout Compressing the 1st log... b1/build.log: 79.7% -- replaced with stdout Wed Sep 17 07:28:33 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_proteinortho_forky_amd64_1758094113 + touch /var/log/reproducible-builds/diffoscope_stamp_proteinortho_forky_amd64_1758094113 + RESULT=0 + systemd-run '--description=diffoscope on proteinortho/6.3.1+dfsg-1 in forky/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_37-82929 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM --run-session -c jenkins-reproducible-forky-diffoscope-7897f295-6928-43bd-9497-408e135984d3 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/dbd-tmp-JpaS7uI ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/proteinortho_6.3.1+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/proteinortho_6.3.1+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/proteinortho_6.3.1+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b1/proteinortho_6.3.1+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b2/proteinortho_6.3.1+dfsg-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_37-82929.service; invocation ID: 823addc36cf94e50b3fcbe9958b487d0 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/proteinortho_6.3.1+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/proteinortho_6.3.1+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/proteinortho_6.3.1+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b1/proteinortho_6.3.1+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.OYY6awEM/b2/proteinortho_6.3.1+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.002s) 0.002s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 206ms CPU time consumed: 172ms Memory peak: 18.6M (swap: 0B) _ _ _ _ _ __ _ __ ___ | |_ ___(_)_ __ ___ _ __| |_| |__ ___ | '_ \| '__/ _ \| __/ _ \ | '_ \ / _ \| '__| __| '_ \ / _ \ | |_) | | | (_) | || __/ | | | | (_) | | | |_| | | | (_) | | .__/|_| \___/ \__\___|_|_| |_|\___/|_| \__|_| |_|\___/ |_| Wed Sep 17 07:36:50 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Wed Sep 17 07:36:50 UTC 2025 I: proteinortho from forky built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-17 07:36:51] INFO: Starting at 2025-09-17 07:36:51.311131 [2025-09-17 07:36:51] INFO: Generating the pages of 1 package(s) [2025-09-17 07:36:52] CRITICAL: https://tests.reproducible-builds.org/debian/forky/amd64/proteinortho didn't produce a buildlog, even though it has been built. [2025-09-17 07:36:52] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/proteinortho didn't produce a buildlog, even though it has been built. [2025-09-17 07:36:52] INFO: Finished at 2025-09-17 07:36:52.110343, took: 0:00:00.799216 Wed Sep 17 07:36:52 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/forky/amd64/proteinortho.html Wed Sep 17 07:36:52 UTC 2025 I: Removing signed proteinortho_6.3.1+dfsg-1_amd64.buildinfo.asc files: removed './b1/proteinortho_6.3.1+dfsg-1_amd64.buildinfo.asc' removed './b2/proteinortho_6.3.1+dfsg-1_amd64.buildinfo.asc' 1758094612 amd64 forky proteinortho Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/proteinortho_6.3.1+dfsg-1.rbuild.log: 76.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/proteinortho_6.3.1+dfsg-1.rbuild.log.gz [2025-09-17 07:36:52] INFO: Starting at 2025-09-17 07:36:52.712782 [2025-09-17 07:36:53] INFO: Generating the pages of 1 package(s) [2025-09-17 07:36:53] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/proteinortho didn't produce a buildlog, even though it has been built. [2025-09-17 07:36:53] INFO: Finished at 2025-09-17 07:36:53.406640, took: 0:00:00.693864 All cleanup done. Wed Sep 17 07:36:53 UTC 2025 - total duration: 0h 14m 4s. Wed Sep 17 07:36:53 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-NZpOHyYw, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 14min 7.303s CPU time consumed: 4.397s Memory peak: 51.3M (swap: 0B)