Tue Jan 9 01:11:19 UTC 2024 I: starting to build proteinortho/bookworm/amd64 on jenkins on '2024-01-09 01:11' Tue Jan 9 01:11:19 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_22/12144/console.log Tue Jan 9 01:11:19 UTC 2024 I: Downloading source for bookworm/proteinortho=6.1.7+dfsg-1 --2024-01-09 01:11:20-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/proteinortho/proteinortho_6.1.7%2bdfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2161 (2.1K) [text/prs.lines.tag] Saving to: ‘proteinortho_6.1.7+dfsg-1.dsc’ 0K .. 100% 289M=0s 2024-01-09 01:11:20 (289 MB/s) - ‘proteinortho_6.1.7+dfsg-1.dsc’ saved [2161/2161] Tue Jan 9 01:11:20 UTC 2024 I: proteinortho_6.1.7+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: proteinortho Binary: proteinortho Architecture: any Version: 6.1.7+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: 29811b2acf3417951bb5d028320c29aa3412425f 361184 proteinortho_6.1.7+dfsg.orig.tar.xz 55358cf9e5a4c831b806e57840d50f495242603b 7532 proteinortho_6.1.7+dfsg-1.debian.tar.xz Checksums-Sha256: 14edfb3dd8dff76bc2f6ce544c8885a0babf59f63a5098e3e35d25e62b88b392 361184 proteinortho_6.1.7+dfsg.orig.tar.xz bef72174cd12b03b3961f1fbf33e4b4fd99f774a1189deeaf5588f9726604435 7532 proteinortho_6.1.7+dfsg-1.debian.tar.xz Files: 6c9a51302f1b8d4d6f7d77176af5e918 361184 proteinortho_6.1.7+dfsg.orig.tar.xz 2963ebab45b9cb2ac2e1fe392483d653 7532 proteinortho_6.1.7+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPGvpcRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEMjw//aZZhe2STeHHAs+p1Vtuvv8vz76NVPzmm CxiW8Aq6Plj3CP3rgvFomgngVVdrHxBtqUoXN2pMBsw3jzlYd9MqqJ0NXwZT3M2G 57xVuFt+cHRlPt+MJhCma73qFqlyyD3zeNkAsGD0mMR443HOJtvufH39OgLgbAMm XrI01mWP24Usgxc8jNfoHEOEw1xZ2hEYkehqe9hqa1SrBHRKLS/77XB/1KGe9N/U cQYWWWGzvC72pvV+B3BlPxFpwT1HDyV6qS6dTqrg6DpTpEG7T4qSoTk8hB49+z3A AosdVgJs+PxJ4DknkfeqIqBLPgEuEDDlu1E7uT9E3fWHKvPULbs5CRnM3rbNXw20 5utaWgo/fYe7/Q4RVgc77x+P8Wn/EaSEGsRlD0SX3nSpmj0uaYBp3mW9GsVQEltp /PFgfYVOHU8VOG8wCmCxlujmhZrWCquhUWTg1Ykk9CKgPOj320wIMA2vH7/K1fwR 0HRTJBpz48j2TVAhNzrpU0jwhLHdKh5O7vmM5QJxKo9m2eJTB6I7TIdm6f5x7CZI hI3m5BAcTJlKqR9PuB62xEB/yDUQQ2osxZfMwdYmWG5E2CmS7qm0Pizh9o5aRvL4 wxqsxz7Dwyy6expO8WsBuoBTPBhShixYKmWJ8z7z0FCIQwVBKhTOytENes7jv++G mw/hxsJzgLE= =MJIM -----END PGP SIGNATURE----- Tue Jan 9 01:11:20 UTC 2024 I: Checking whether the package is not for us Tue Jan 9 01:11:20 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Tue Jan 9 01:11:20 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Tue Jan 9 01:14:37 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Feb 9 19:34:33 -12 2025 I: pbuilder-time-stamp: 1739172873 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_6.1.7+dfsg-1.dsc] I: copying [./proteinortho_6.1.7+dfsg.orig.tar.xz] I: copying [./proteinortho_6.1.7+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jan 17 15:28:23 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.1.7+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting proteinortho in proteinortho-6.1.7+dfsg dpkg-source: info: unpacking proteinortho_6.1.7+dfsg.orig.tar.xz dpkg-source: info: unpacking proteinortho_6.1.7+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying deb_diamond dpkg-source: info: applying ignore-warnings.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3448296/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=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='da84177b149749c18acb12a1585d14f0' 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='3448296' 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.g8mfuRTn/pbuilderrc_MeZp --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.g8mfuRTn/b1 --logfile b1/build.log proteinortho_6.1.7+dfsg-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 23 2023 more -rwsr-xr-x 1 root root 59704 Mar 23 2023 mount -rwxr-xr-x 1 root root 18744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 23 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3448296/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 ... 18148 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} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack-dev{a} liblapack3{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libpcre3{a} libpipeline1{a} libproc2-0{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx med-config psmisc wget 0 packages upgraded, 56 newly installed, 0 to remove and 0 not upgraded. Need to get 52.1 MB of archives. After unpacking 223 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 diamond-aligner amd64 2.1.3-1 [2434 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libblas-dev amd64 3.11.0-2 [158 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 liblapack-dev amd64 3.11.0-2 [4631 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Fetched 52.1 MB in 1s (77.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 18148 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/proteinortho-6.1.7+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_6.1.7+dfsg-1_source.changes dpkg-buildpackage: info: source package proteinortho dpkg-buildpackage: info: source version 6.1.7+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-6.1.7+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-6.1.7+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-6.1.7+dfsg' CC = cc CCFLAGS = CXX = g++ CXXFLAGS = -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security MTUNEARCHFLAGS = LDFLAGS = -Wl,-z,relro -Wl,-z,now LDLIBS = STATIC = Creating build directory ... 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-6.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-6.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-6.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph src/cleanupblastgraph.cpp -Wl,-z,relro -Wl,-z,now - test max_of_diag() : 1 - test generate_random_vector() : 1 - test get_new_x() : 1 - test makeOrthogonal() : 1 - test normalize() : 1 - test getY() : 1 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-6.1.7+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/proteinortho-6.1.7+dfsg' dh_auto_test --no-parallel make -j1 test make[2]: Entering directory '/build/reproducible-path/proteinortho-6.1.7+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) [1/4] various test functions of proteinortho_clustering (if this fails, try make clean first): passed [2/4] Test proteinortho_clustering using lapack: passed [3/4] Test proteinortho_clustering using power: passed [4/4] Test differences between 'using lapack' and 'using power': 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 [TEST] All tests passed make[2]: Leaving directory '/build/reproducible-path/proteinortho-6.1.7+dfsg' make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.1.7+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-6.1.7+dfsg' mkdir -p /build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin dh_auto_install -- install PREFIX=/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin make -j16 install DESTDIR=/build/reproducible-path/proteinortho-6.1.7\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/build/reproducible-path/proteinortho-6.1.7\+dfsg/debian/proteinortho/usr/bin make[2]: Entering directory '/build/reproducible-path/proteinortho-6.1.7+dfsg' INSTALLING everything to /build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin 'proteinortho6.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl' 'proteinortho' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho' 'src/BUILD/Linux_x86_64/proteinortho_extract_from_graph.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl' 'src/BUILD/Linux_x86_64/proteinortho_formatUsearch.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl' 'src/BUILD/Linux_x86_64/proteinortho_compareProteinorthoGraphs.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl' 'src/BUILD/Linux_x86_64/proteinortho_do_mcl.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl' 'src/BUILD/Linux_x86_64/proteinortho2html.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl' 'src/BUILD/Linux_x86_64/proteinortho2xml.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl' 'src/BUILD/Linux_x86_64/proteinortho_clustering' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering' 'src/BUILD/Linux_x86_64/proteinortho_singletons.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl' 'src/BUILD/Linux_x86_64/proteinortho_ffadj_mcs.py' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py' 'src/BUILD/Linux_x86_64/proteinortho2tree.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl' 'src/BUILD/Linux_x86_64/proteinortho_history.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl' 'src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph' 'src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph' 'src/BUILD/Linux_x86_64/proteinortho_grab_proteins.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl' 'src/BUILD/Linux_x86_64/proteinortho_summary.pl' -> '/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin/proteinortho_summary.pl' Everything installed successfully to /build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin. If needed you can add /build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/build/reproducible-path/proteinortho-6.1.7+dfsg/debian/proteinortho/usr/bin'. make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/reproducible-path/proteinortho-6.1.7+dfsg' make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.1.7+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/proteinortho-6.1.7+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-6.1.7+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-6.1.7+dfsg' dh_fixperms find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.1.7+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-dbgsym' in '../proteinortho-dbgsym_6.1.7+dfsg-1_amd64.deb'. dpkg-deb: building package 'proteinortho' in '../proteinortho_6.1.7+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../proteinortho_6.1.7+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../proteinortho_6.1.7+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/3448296 and its subdirectories I: Current time: Sun Feb 9 19:37:46 -12 2025 I: pbuilder-time-stamp: 1739173066 Tue Jan 9 01:14:37 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Tue Jan 9 01:14:37 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Tue Jan 9 01:20:30 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Tue Jan 9 01:20:31 UTC 2024 I: proteinortho_6.1.7+dfsg-1_amd64.changes: Format: 1.8 Date: Tue, 17 Jan 2023 16:24:44 +0100 Source: proteinortho Binary: proteinortho proteinortho-dbgsym Architecture: amd64 Version: 6.1.7+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 Changes: proteinortho (6.1.7+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 83d86aa978f430168be2d2d82a5b52df6d606573 1324048 proteinortho-dbgsym_6.1.7+dfsg-1_amd64.deb e80a8838ad4bbd2c5d65dfc46809c0a1782e3589 6104 proteinortho_6.1.7+dfsg-1_amd64.buildinfo b6fe9776b7de9a20edd20a36bbb0898a676c24eb 265224 proteinortho_6.1.7+dfsg-1_amd64.deb Checksums-Sha256: 6ba9e06b9763a9b08c72073b3bf2824cff3151714cd4126b02cbaa0ac72ed24d 1324048 proteinortho-dbgsym_6.1.7+dfsg-1_amd64.deb 443858347dc39b9ff20ecedc26206f964ab46e898ac87fd3ff4e9b129608984c 6104 proteinortho_6.1.7+dfsg-1_amd64.buildinfo 186cf596358075f4b2b716ed9f41fd436fde1a121859b8e5284df42b3d003bfb 265224 proteinortho_6.1.7+dfsg-1_amd64.deb Files: cff581b910016e5675fc34fb6fb7036e 1324048 debug optional proteinortho-dbgsym_6.1.7+dfsg-1_amd64.deb 3a04d48b09b6327fce1aee94df39af51 6104 science optional proteinortho_6.1.7+dfsg-1_amd64.buildinfo 3301a7eb9177194598ff3cae694dbefb 265224 science optional proteinortho_6.1.7+dfsg-1_amd64.deb Tue Jan 9 01:20:31 UTC 2024 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.g8mfuRTn/proteinortho_6.1.7+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.g8mfuRTn/proteinortho_6.1.7+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.g8mfuRTn/proteinortho_6.1.7+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.g8mfuRTn/b1/proteinortho_6.1.7+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.g8mfuRTn/b2/proteinortho_6.1.7+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 abc.DotChangesFile ## main (total time: 0.289s) 0.289s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.025s) 0.025s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Tue Jan 9 01:20:32 UTC 2024 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Tue Jan 9 01:20:32 UTC 2024 I: proteinortho from bookworm built successfully and reproducibly on amd64. Tue Jan 9 01:20:33 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Jan 9 01:20:33 UTC 2024 I: Submitting 8.0K b1/proteinortho_6.1.7+dfsg-1_amd64.buildinfo.asc Tue Jan 9 01:20:34 UTC 2024 I: Submitting 8.0K b2/proteinortho_6.1.7+dfsg-1_amd64.buildinfo.asc Tue Jan 9 01:20:35 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jan 9 01:20:35 UTC 2024 I: Done submitting .buildinfo files. Tue Jan 9 01:20:35 UTC 2024 I: Removing signed proteinortho_6.1.7+dfsg-1_amd64.buildinfo.asc files: removed './b1/proteinortho_6.1.7+dfsg-1_amd64.buildinfo.asc' removed './b2/proteinortho_6.1.7+dfsg-1_amd64.buildinfo.asc'