Wed May 15 02:56:57 UTC 2024 I: starting to build tm-align/trixie/arm64 on jenkins on '2024-05-15 02:56' Wed May 15 02:56:57 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/11721/console.log Wed May 15 02:56:57 UTC 2024 I: Downloading source for trixie/tm-align=20190822+dfsg-2 --2024-05-15 02:56:57-- http://deb.debian.org/debian/pool/main/t/tm-align/tm-align_20190822%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... 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% 246M=0s 2024-05-15 02:56:57 (246 MB/s) - ‘tm-align_20190822+dfsg-2.dsc’ saved [2107/2107] Wed May 15 02:56:57 UTC 2024 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----- Wed May 15 02:56:57 UTC 2024 I: Checking whether the package is not for us Wed May 15 02:56:57 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Wed May 15 02:56:57 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Wed May 15 02:57:31 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 14 14:57:00 -12 2024 I: pbuilder-time-stamp: 1715741820 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [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: Signature made Tue Dec 24 07:16:06 2019 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 ./tm-align_20190822+dfsg-2.dsc: no acceptable signature found 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/2721212/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='517f1c67abfb4918a7ea11523f2a6eef' 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='2721212' 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.nmJE6mUo/pbuilderrc_qbCI --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nmJE6mUo/b1 --logfile b1/build.log tm-align_20190822+dfsg-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 11:38 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2721212/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 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 ... 19744 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 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-13{a} gfortran-13-aarch64-linux-gnu{a} gfortran-aarch64-linux-gnu{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{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, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 28.7 MB of archives. After unpacking 113 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libgfortran-13-dev arm64 13.2.0-24 [401 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-24 [9297 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 gfortran-13 arm64 13.2.0-24 [12.2 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7 [1288 B] Get: 36 http://deb.debian.org/debian trixie/main arm64 gfortran arm64 4:13.2.0-7 [1428 B] Fetched 28.7 MB in 0s (125 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19744 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../30-libgfortran5_14-20240330-1_arm64.deb ... Unpacking libgfortran5:arm64 (14-20240330-1) ... Selecting previously unselected package libgfortran-13-dev:arm64. Preparing to unpack .../31-libgfortran-13-dev_13.2.0-24_arm64.deb ... Unpacking libgfortran-13-dev:arm64 (13.2.0-24) ... Selecting previously unselected package gfortran-13-aarch64-linux-gnu. Preparing to unpack .../32-gfortran-13-aarch64-linux-gnu_13.2.0-24_arm64.deb ... Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-24) ... Selecting previously unselected package gfortran-13. Preparing to unpack .../33-gfortran-13_13.2.0-24_arm64.deb ... Unpacking gfortran-13 (13.2.0-24) ... Selecting previously unselected package gfortran-aarch64-linux-gnu. Preparing to unpack .../34-gfortran-aarch64-linux-gnu_4%3a13.2.0-7_arm64.deb ... Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7) ... Selecting previously unselected package gfortran. Preparing to unpack .../35-gfortran_4%3a13.2.0-7_arm64.deb ... Unpacking gfortran (4:13.2.0-7) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up libgfortran5:arm64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libgfortran-13-dev:arm64 (13.2.0-24) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up gfortran-13-aarch64-linux-gnu (13.2.0-24) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up gfortran-13 (13.2.0-24) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:13.2.0-7) ... 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 debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-10) ... 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 (1.33-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/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 arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/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 \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) make[1]: Leaving directory '/build/reproducible-path/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 \( -name autom4te.cache -o -name __pycache__ \) -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/reproducible-path/tm-align-20190822+dfsg' for src in `ls *.f` ; do \ gfortran -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tm-align-20190822+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -o `basename ${src} .f` ${src} ; \ done f951: Warning: '-Werror=' argument '-Werror=implicit-function-declaration' 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 f951: Warning: '-Werror=' argument '-Werror=implicit-function-declaration' 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/reproducible-path/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_auto_install --destdir=debian/tm-align/ install -m0755 -d /build/reproducible-path/tm-align-20190822\+dfsg/debian/tm-align dh_install install -m0755 -d debian/tm-align/usr/bin cp --reflink=auto -a ./TMalign ./TMscore debian/tm-align/usr/bin/ dh_installdocs install -m0755 -d debian/tm-align/usr/share/doc/tm-align install -m0755 -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 -m0755 -d debian/tm-align/usr/share/doc/tm-align install -p -m0644 debian/.debhelper/generated/tm-align/dh_installchangelogs.dch.trimmed debian/tm-align/usr/share/doc/tm-align/changelog.Debian dh_installexamples install -m0755 -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 -m0755 -d debian/tm-align/usr/share/man/man1/ install -p -m0644 ./debian/TMalign.1 debian/tm-align/usr/share/man/man1/TMalign.1 install -m0755 -d debian/tm-align/usr/share/man/man1/ 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/reproducible-path/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 -m0755 -d debian/tm-align/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/tm-align/usr/lib/debug/.dwz/aarch64-linux-gnu/tm-align.debug -M/usr/lib/debug/.dwz/aarch64-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/aarch64-linux-gnu/tm-align.debug chmod 0644 -- debian/tm-align/usr/lib/debug/.dwz/aarch64-linux-gnu/tm-align.debug chown 0:0 -- debian/tm-align/usr/lib/debug/.dwz/aarch64-linux-gnu/tm-align.debug dh_strip install -m0755 -d debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/df objcopy --only-keep-debug --compress-debug-sections debian/tm-align/usr/bin/TMalign debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/df/fe54c1c23d87883004991820888bb440db1027.debug chmod 0644 -- debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/df/fe54c1c23d87883004991820888bb440db1027.debug chown 0:0 -- debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/df/fe54c1c23d87883004991820888bb440db1027.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/df/fe54c1c23d87883004991820888bb440db1027.debug debian/tm-align/usr/bin/TMalign install -m0755 -d debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/22 objcopy --only-keep-debug --compress-debug-sections debian/tm-align/usr/bin/TMscore debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/22/c4914753f82259e5a5a9ca0fc60091a9182e37.debug chmod 0644 -- debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/22/c4914753f82259e5a5a9ca0fc60091a9182e37.debug chown 0:0 -- debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.build-id/22/c4914753f82259e5a5a9ca0fc60091a9182e37.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/22/c4914753f82259e5a5a9ca0fc60091a9182e37.debug debian/tm-align/usr/bin/TMscore install -m0755 -d debian/.debhelper/tm-align/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tm-align/usr/lib/debug/.dwz/aarch64-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 -m0755 -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 install -m0755 -d debian/.debhelper/tm-align dh_makeshlibs rm -f debian/tm-align/DEBIAN/shlibs dh_shlibdeps install -m0755 -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 install -m0755 -d debian/tm-align/DEBIAN dh_gencontrol install -m0755 -d debian/tm-align/DEBIAN echo misc:Depends= >> debian/tm-align.substvars echo misc:Pre-Depends= >> debian/tm-align.substvars install -m0755 -d debian/.debhelper/tm-align/dbgsym-root/DEBIAN dpkg-gencontrol -ptm-align -ldebian/changelog -Tdebian/tm-align.substvars -cdebian/control -Pdebian/.debhelper/tm-align/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=tm-align-dbgsym "-DDepends=tm-align (= \${binary:Version})" "-DDescription=debug symbols for tm-align" "-DBuild-Ids=22c4914753f82259e5a5a9ca0fc60091a9182e37 dffe54c1c23d87883004991820888bb440db1027" -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 -cdebian/control -Pdebian/tm-align chmod 0644 -- debian/tm-align/DEBIAN/control chown 0:0 -- debian/tm-align/DEBIAN/control dh_md5sums install -m0755 -d debian/tm-align/DEBIAN 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 install -m0755 -d debian/.debhelper/tm-align/dbgsym-root/DEBIAN 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 --root-owner-group --build debian/.debhelper/tm-align/dbgsym-root .. dpkg-deb: building package 'tm-align' in '../tm-align_20190822+dfsg-2_arm64.deb'. dpkg-deb: building package 'tm-align-dbgsym' in '../tm-align-dbgsym_20190822+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../tm-align_20190822+dfsg-2_arm64.buildinfo dpkg-genchanges --build=binary -O../tm-align_20190822+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2721212 and its subdirectories I: Current time: Tue May 14 14:57:30 -12 2024 I: pbuilder-time-stamp: 1715741850 Wed May 15 02:57:32 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Wed May 15 02:57:32 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Wed May 15 02:58:12 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Wed May 15 02:58:13 UTC 2024 I: tm-align_20190822+dfsg-2_arm64.changes: Format: 1.8 Date: Tue, 24 Dec 2019 08:07:50 +0100 Source: tm-align Binary: tm-align tm-align-dbgsym Architecture: arm64 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: 0e19a2efa5f71c5c32ddb5f933db8442ccd9825c 67936 tm-align-dbgsym_20190822+dfsg-2_arm64.deb 8f9707f196ca5631e7709650bcf005ec5f6bb801 5366 tm-align_20190822+dfsg-2_arm64.buildinfo 70a9320dd5cfc83a5e12ab5133e0d31e594324fc 863020 tm-align_20190822+dfsg-2_arm64.deb Checksums-Sha256: 5145133174724ade066cf72b50a9450a56f0909b8b4aa192ea0ef80fc89061d7 67936 tm-align-dbgsym_20190822+dfsg-2_arm64.deb f12871a95e42b6d650d3b4b35bc523ac9b8eb7e78d1ba0bf50963f3aa59cef7e 5366 tm-align_20190822+dfsg-2_arm64.buildinfo 17e7b8b5f145ea4527b71a16ae11d263eea5cb0d3c7a21bec056a8096f615dc2 863020 tm-align_20190822+dfsg-2_arm64.deb Files: 5c2ab160062327c9a064e5e2e6ccea39 67936 debug optional tm-align-dbgsym_20190822+dfsg-2_arm64.deb 5c34a6200656511a8c9acdbab32f6667 5366 science optional tm-align_20190822+dfsg-2_arm64.buildinfo 63a407d0412d012eb21a156f5cf141e3 863020 science optional tm-align_20190822+dfsg-2_arm64.deb Wed May 15 02:58:14 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_8-11721.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.nmJE6mUo/tm-align_20190822+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.nmJE6mUo/tm-align_20190822+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.nmJE6mUo/tm-align_20190822+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.nmJE6mUo/b1/tm-align_20190822+dfsg-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.nmJE6mUo/b2/tm-align_20190822+dfsg-2_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.377s) 0.377s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.026s) 0.026s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 716ms CPU time consumed: 717ms Wed May 15 02:58:15 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Wed May 15 02:58:15 UTC 2024 I: tm-align from trixie built successfully and reproducibly on arm64. Wed May 15 02:58:16 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 15 02:58:16 UTC 2024 I: Submitting 8.0K b1/tm-align_20190822+dfsg-2_arm64.buildinfo.asc Wed May 15 02:58:17 UTC 2024 I: Submitting 8.0K b2/tm-align_20190822+dfsg-2_arm64.buildinfo.asc Wed May 15 02:58:17 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 15 02:58:17 UTC 2024 I: Done submitting .buildinfo files. Wed May 15 02:58:17 UTC 2024 I: Removing signed tm-align_20190822+dfsg-2_arm64.buildinfo.asc files: removed './b1/tm-align_20190822+dfsg-2_arm64.buildinfo.asc' removed './b2/tm-align_20190822+dfsg-2_arm64.buildinfo.asc'