Fri Jul 28 21:06:33 UTC 2023 I: starting to build tm-align/bullseye/amd64 on jenkins on '2023-07-28 21:06' Fri Jul 28 21:06:33 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_17/4854/console.log Fri Jul 28 21:06:33 UTC 2023 I: Downloading source for bullseye/tm-align=20190822+dfsg-2 --2023-07-28 21:06:33-- http://cdn-fastly.deb.debian.org/debian/pool/main/t/tm-align/tm-align_20190822%2bdfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2107 (2.1K) [text/prs.lines.tag] Saving to: ‘tm-align_20190822+dfsg-2.dsc’ 0K .. 100% 24.0M=0s 2023-07-28 21:06:33 (24.0 MB/s) - ‘tm-align_20190822+dfsg-2.dsc’ saved [2107/2107] Fri Jul 28 21:06:33 UTC 2023 I: tm-align_20190822+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: tm-align Binary: tm-align Architecture: any Version: 20190822+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Tim Booth , Andreas Tille Homepage: https://zhanglab.ccmb.med.umich.edu/TM-align/ Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/tm-align Vcs-Git: https://salsa.debian.org/med-team/tm-align.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), gfortran Package-List: tm-align deb science optional arch=any Checksums-Sha1: 3b8f4daf34f2cf76faf07081fe60973f226773fc 52784 tm-align_20190822+dfsg.orig.tar.xz 53f7a5c47c90a68803c12986079c17e925020a94 817920 tm-align_20190822+dfsg-2.debian.tar.xz Checksums-Sha256: b124e9056024e170462b61b01865dc65abad7f41b933a955ba5d84ebaddcac56 52784 tm-align_20190822+dfsg.orig.tar.xz 7359f16763e4d6e277adfa9cd97aef2a397c476d9d50ebcc6734dd2dd6e5ead1 817920 tm-align_20190822+dfsg-2.debian.tar.xz Files: 0556ef655127ae3fe0497026d1bc1c22 52784 tm-align_20190822+dfsg.orig.tar.xz be2d0234d44d3f8658d32190940ec498 817920 tm-align_20190822+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl4BuzYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHmCA//c0MxP/tf4OQOetPqWDouXrEzP9ca6pGK gvY+zlW70PmiJ16Q0YcUZ6NATUs+G4BBUGzUMgdMh4yX/AnGQuJfnEQHf5Q8VBqQ 6NwCjboN8/nSHIY6uhcltaGOn5SUkFdxbwCaerUv6FHKNi230q4/BgQat+871rJj 73hvzTtO/PCYkqzmj0vqvucv3uvGGPQvR5JgY4yZsFWnKrW41CUF4ZWOwagJ4FLj gl8Ns2SVfvd0klKeSULlShZvyswNKp1Ij4U5HUwygqfGgUtHZoK0EGVW2iMj5fr5 f46krx1PpOIizQyRmke/CtSb3mB9Fh/gvytdolCU7BQqeb10QOWw2YS3XYQW/6vr T9Enhvb4u8YXzVReNnm4oC2eX9TAVomzUZksdwN/OLAC9e8T7OTpk4HLM+paiyEq sQ8ovuwLnSfJtlr2fm+pOs+RlFmUdYIWW9ZtWRe8nKUBsDbBBbNoY3OS1yKpeLaG 3h9p1nl69NeplMAwiSJMGUZdqX5XWJ9jjtOPqKbtkUD3QCFXQKFB0X9HsPiSn1qz JMKVPd1f6UvVvzDzIe+mhRy290wB/R/37/To2Tgmjo+ZLUp/YeSbvHkZbmTILpoM grP8/6eG+4a5PSNs6Ai15nwJepcg56YHtEB4MrvC3k2zMG9OeLUZ9iHYSdjlxS05 kH2YomwoVE4= =sEyO -----END PGP SIGNATURE----- Fri Jul 28 21:06:33 UTC 2023 I: Checking whether the package is not for us Fri Jul 28 21:06:33 UTC 2023 I: Starting 1st build on remote node ionos1-amd64.debian.net. Fri Jul 28 21:06:33 UTC 2023 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Fri Jul 28 21:08:16 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Jul 28 09:06:36 -12 2023 I: pbuilder-time-stamp: 1690578396 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [tm-align_20190822+dfsg-2.dsc] I: copying [./tm-align_20190822+dfsg.orig.tar.xz] I: copying [./tm-align_20190822+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.DvnVrud9/trustedkeys.kbx': General error gpgv: Signature made Mon Dec 23 19:16:06 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./tm-align_20190822+dfsg-2.dsc dpkg-source: info: extracting tm-align in tm-align-20190822+dfsg dpkg-source: info: unpacking tm-align_20190822+dfsg.orig.tar.xz dpkg-source: info: unpacking tm-align_20190822+dfsg-2.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2832838/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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,-fixfilepath parallel=15 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d563e5fc2573452fb0d536ea586a52cf' 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='2832838' 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.FcxmE4Uu/pbuilderrc_EsC2 --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FcxmE4Uu/b1 --logfile b1/build.log tm-align_20190822+dfsg-2.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://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-1 (2023-07-14) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 6 21:24 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/2832838/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 (= 12), gfortran dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19707 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran 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} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-10{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran-10-dev{a} libgfortran5{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 29.3 MB of archives. After unpacking 104 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libgfortran-10-dev amd64 10.2.1-6 [769 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 gfortran-10 amd64 10.2.1-6 [9447 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 gfortran amd64 4:10.2.1-1 [1428 B] Fetched 29.3 MB in 1s (30.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19707 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../10-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. 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Setting up libsub-override-perl (0.09-2) ... Setting up libgfortran-10-dev:amd64 (10.2.1-6) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up gfortran-10 (10.2.1-6) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:10.2.1-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/tm-align-20190822+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 > ../tm-align_20190822+dfsg-2_source.changes dpkg-buildpackage: info: source package tm-align dpkg-buildpackage: info: source version 20190822+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/tm-align-20190822+dfsg' for src in `ls *.f` ; do \ rm -f `basename ${src} .f` ; \ done dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/tm-align.substvars debian/files rm -fr -- debian/tm-align/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) make[1]: Leaving directory '/build/tm-align-20190822+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/tm-align.substvars debian/files rm -fr -- debian/tm-align/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/tm-align-20190822+dfsg' for src in `ls *.f` ; do \ gfortran -ffast-math -g -O2 -fdebug-prefix-map=/build/tm-align-20190822+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -o `basename ${src} .f` ${src} ; \ done f951: Warning: command-line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran f951: Warning: command-line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran make[1]: Leaving directory '/build/tm-align-20190822+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep rm -f -- debian/tm-align.substvars rm -fr -- debian/.debhelper/generated/tm-align/ debian/tm-align/ debian/tmp/ dh_install install -d debian/tm-align/usr/bin cp --reflink=auto -a ./TMalign ./TMscore debian/tm-align/usr/bin/ install -d debian/.debhelper/generated/tm-align dh_installdocs install -d debian/tm-align/usr/share/doc/tm-align cp --reflink=auto -a ./debian/tests/run-unit-test debian/tm-align/usr/share/doc/tm-align cp --reflink=auto -a ./debian/README.test debian/tm-align/usr/share/doc/tm-align chown -R 0:0 debian/tm-align/usr/share/doc chmod -R u\+rw,go=rX debian/tm-align/usr/share/doc install -p -m0644 debian/README.Debian debian/tm-align/usr/share/doc/tm-align/README.Debian install -p -m0644 debian/copyright debian/tm-align/usr/share/doc/tm-align/copyright dh_installchangelogs install -p -m0644 debian/changelog debian/tm-align/usr/share/doc/tm-align/changelog.Debian dh_installexamples install -d debian/tm-align/usr/share/doc/tm-align/examples cp --reflink=auto -a ./debian/examples/1ni7.pdb.gz debian/tm-align/usr/share/doc/tm-align/examples cp --reflink=auto -a ./debian/examples/5eep.pdb.gz debian/tm-align/usr/share/doc/tm-align/examples dh_installman install -d debian/tm-align/usr/share/man/man1/ install -p -m0644 ./debian/TMalign.1 debian/tm-align/usr/share/man/man1/TMalign.1 install -p -m0644 ./debian/TMscore.1 debian/tm-align/usr/share/man/man1/TMscore.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tm-align/usr/share/man/man1/TMalign.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tm-align/usr/share/man/man1/TMscore.1 mv debian/tm-align/usr/share/man/man1/TMalign.1.dh-new debian/tm-align/usr/share/man/man1/TMalign.1 chmod 0644 -- debian/tm-align/usr/share/man/man1/TMalign.1 mv debian/tm-align/usr/share/man/man1/TMscore.1.dh-new debian/tm-align/usr/share/man/man1/TMscore.1 chmod 0644 -- debian/tm-align/usr/share/man/man1/TMscore.1 dh_perl dh_link dh_strip_nondeterminism Using 1577171270 as canonical time Normalizing debian/tm-align/usr/share/doc/tm-align/examples/5eep.pdb.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/tm-align/usr/share/doc/tm-align/examples/1ni7.pdb.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/tm-align chmod a-x usr/share/doc/tm-align/changelog.Debian usr/share/man/man1/TMalign.1 usr/share/man/man1/TMscore.1 gzip -9nf usr/share/doc/tm-align/changelog.Debian usr/share/man/man1/TMalign.1 usr/share/man/man1/TMscore.1 cd '/build/tm-align-20190822+dfsg' dh_fixperms find debian/tm-align -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/tm-align ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tm-align/usr/share/doc -type f -a -true -a ! -regex 'debian/tm-align/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tm-align/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tm-align/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tm-align -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tm-align/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz install -d debian/tm-align/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/tm-align/usr/lib/debug/.dwz/x86_64-linux-gnu/tm-align.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/tm-align.debug -- debian/tm-align/usr/bin/TMalign debian/tm-align/usr/bin/TMscore objcopy --compress-debug-sections debian/tm-align/usr/lib/debug/.dwz/x86_64-linux-gnu/tm-align.debug dh_strip install -d debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/4f objcopy --only-keep-debug --compress-debug-sections debian/tm-align/usr/bin/TMscore debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/4f/3b6f30c17cca0e19fe9bf0d796afbaba5a0c68.debug chmod 0644 -- debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/4f/3b6f30c17cca0e19fe9bf0d796afbaba5a0c68.debug chown 0:0 -- debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/4f/3b6f30c17cca0e19fe9bf0d796afbaba5a0c68.debug strip --remove-section=.comment --remove-section=.note debian/tm-align/usr/bin/TMscore objcopy --add-gnu-debuglink debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/4f/3b6f30c17cca0e19fe9bf0d796afbaba5a0c68.debug debian/tm-align/usr/bin/TMscore install -d debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/4e objcopy --only-keep-debug --compress-debug-sections debian/tm-align/usr/bin/TMalign debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/4e/f38cf383c8d85180b8f49730c11fd96a04e4ca.debug chmod 0644 -- debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/4e/f38cf383c8d85180b8f49730c11fd96a04e4ca.debug chown 0:0 -- debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/4e/f38cf383c8d85180b8f49730c11fd96a04e4ca.debug strip --remove-section=.comment --remove-section=.note debian/tm-align/usr/bin/TMalign objcopy --add-gnu-debuglink debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/4e/f38cf383c8d85180b8f49730c11fd96a04e4ca.debug debian/tm-align/usr/bin/TMalign install -d debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tm-align/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tm-align/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/tm-align/usr/lib/debug install -d debian/.debhelper/tm-align/dbgsym-root/usr/share/doc ln -s tm-align debian/.debhelper/tm-align/dbgsym-root/usr/share/doc/tm-align-dbgsym dh_makeshlibs rm -f debian/tm-align/DEBIAN/shlibs dh_shlibdeps install -d debian/tm-align/DEBIAN dpkg-shlibdeps -Tdebian/tm-align.substvars debian/tm-align/usr/bin/TMalign debian/tm-align/usr/bin/TMscore dh_installdeb dh_gencontrol echo misc:Depends= >> debian/tm-align.substvars echo misc:Pre-Depends= >> debian/tm-align.substvars install -d debian/.debhelper/tm-align/dbgsym-root/DEBIAN dpkg-gencontrol -ptm-align -ldebian/changelog -Tdebian/tm-align.substvars -Pdebian/.debhelper/tm-align/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=tm-align-dbgsym "-DDepends=tm-align (= \${binary:Version})" "-DDescription=debug symbols for tm-align" "-DBuild-Ids=4ef38cf383c8d85180b8f49730c11fd96a04e4ca 4f3b6f30c17cca0e19fe9bf0d796afbaba5a0c68" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/tm-align/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/tm-align/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptm-align -ldebian/changelog -Tdebian/tm-align.substvars -Pdebian/tm-align chmod 0644 -- debian/tm-align/DEBIAN/control chown 0:0 -- debian/tm-align/DEBIAN/control dh_md5sums cd debian/tm-align >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/tm-align/DEBIAN/md5sums chown 0:0 -- debian/tm-align/DEBIAN/md5sums cd debian/.debhelper/tm-align/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tm-align/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/tm-align/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/tm-align .. dpkg-deb --build debian/.debhelper/tm-align/dbgsym-root .. dpkg-deb: building package 'tm-align-dbgsym' in '../tm-align-dbgsym_20190822+dfsg-2_amd64.deb'. dpkg-deb: building package 'tm-align' in '../tm-align_20190822+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../tm-align_20190822+dfsg-2_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: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2832838 and its subdirectories I: Current time: Fri Jul 28 09:08:15 -12 2023 I: pbuilder-time-stamp: 1690578495 Fri Jul 28 21:08:17 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Fri Jul 28 21:08:17 UTC 2023 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Fri Jul 28 21:08:55 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Fri Jul 28 21:09:41 UTC 2023 I: tm-align_20190822+dfsg-2_amd64.changes: Format: 1.8 Date: Tue, 24 Dec 2019 08:07:50 +0100 Source: tm-align Binary: tm-align tm-align-dbgsym Architecture: amd64 Version: 20190822+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: tm-align - structural alignment of proteins Closes: 943954 Changes: tm-align (20190822+dfsg-2) unstable; urgency=medium . [ Chris Lamb ] * make the build reproducible Closes: #943954 . [ Andreas Tille ] * Rename autopkgtest script to run-unit-test as in other Debian Med packages * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g Checksums-Sha1: a3746bcb1c0771be9a7db4e7d3eadd15f920c27b 68904 tm-align-dbgsym_20190822+dfsg-2_amd64.deb bdd1fa054a78ead45eb3929ac29c90e779105001 5402 tm-align_20190822+dfsg-2_amd64.buildinfo c44811dd3c980b699ca92db602ba4d93244fdb7d 865176 tm-align_20190822+dfsg-2_amd64.deb Checksums-Sha256: 5aca80e01346e68bfab7285e99d2ffddb71ac3a8a7d5b2bdc3e2f2f55f6992df 68904 tm-align-dbgsym_20190822+dfsg-2_amd64.deb 8f0252043b3baea0c2f6535f6866c5225f859bed9cf85691fb2b8cc54539b157 5402 tm-align_20190822+dfsg-2_amd64.buildinfo 36907a6d964414eb76d2d6ebe496f8188f07671dd8275fc808e3f70d00765f76 865176 tm-align_20190822+dfsg-2_amd64.deb Files: e0615dafe218db0054ed9a3be610ba78 68904 debug optional tm-align-dbgsym_20190822+dfsg-2_amd64.deb 2a42a38b47d67ffc55bfc29050690216 5402 science optional tm-align_20190822+dfsg-2_amd64.buildinfo 02949be57f98bde1f076a12bd905afd7 865176 science optional tm-align_20190822+dfsg-2_amd64.deb Fri Jul 28 21:09:43 UTC 2023 I: W: /var/lib/schroot/session/jenkins-reproducible-bullseye-diffoscope-40ab848e-7cae-4700-8476-011ae1a10f66: Failed to stat file: No such file or directory diffoscope 243 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/r-b-build.FcxmE4Uu/tm-align_20190822+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.FcxmE4Uu/tm-align_20190822+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.FcxmE4Uu/tm-align_20190822+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.FcxmE4Uu/b1/tm-align_20190822+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.FcxmE4Uu/b2/tm-align_20190822+dfsg-2_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: 0.453s) 0.453s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.074s) 0.074s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.003s) 0.003s 1 call specialize Fri Jul 28 21:09:45 UTC 2023 I: W: /var/lib/schroot/session/jenkins-reproducible-bullseye-diffoscope-40ab848e-7cae-4700-8476-011ae1a10f66: Failed to stat file: No such file or directory diffoscope 243 found no differences in the changes files, and a .buildinfo file also exists. Fri Jul 28 21:09:45 UTC 2023 I: tm-align from bullseye built successfully and reproducibly on amd64. Fri Jul 28 21:10:48 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Jul 28 21:10:48 UTC 2023 I: Submitting 8.0K b1/tm-align_20190822+dfsg-2_amd64.buildinfo.asc Fri Jul 28 21:10:49 UTC 2023 I: Submitting 8.0K b2/tm-align_20190822+dfsg-2_amd64.buildinfo.asc Fri Jul 28 21:10:51 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Jul 28 21:10:51 UTC 2023 I: Done submitting .buildinfo files. Fri Jul 28 21:10:51 UTC 2023 I: Removing signed tm-align_20190822+dfsg-2_amd64.buildinfo.asc files: removed './b1/tm-align_20190822+dfsg-2_amd64.buildinfo.asc' removed './b2/tm-align_20190822+dfsg-2_amd64.buildinfo.asc'