Running as unit: rb-build-amd64_3-68963.service; invocation ID: 23df479230484f04a9859dccdd778ad6 ==================================================================================== Fri Sep 19 10:43:51 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_3) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Fri Sep 19 10:43:51 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-Cjr2Sm2i" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 19 10:43:51 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Fri Sep 19 10:43:51 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-ckYjo9' Fri Sep 19 10:43:51 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Sep 19 10:43:51 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-YpnYlz' ok, let's check if minimac4 is building anywhere yet… ok, minimac4 is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of minimac4 in unstable on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Fri Sep 19 10:43:58 UTC 2025 I: starting to build minimac4/unstable/amd64 on jenkins on '2025-09-19 10:43' Fri Sep 19 10:43:58 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_3/68963/console.log 1758278638 amd64 unstable minimac4 Fri Sep 19 10:43:58 UTC 2025 I: Downloading source for unstable/minimac4=4.1.6-1 --2025-09-19 10:43:58-- http://deb.debian.org/debian/pool/main/m/minimac4/minimac4_4.1.6-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2288 (2.2K) [text/prs.lines.tag] Saving to: ‘minimac4_4.1.6-1.dsc’ 0K .. 100% 269M=0s 2025-09-19 10:43:58 (269 MB/s) - ‘minimac4_4.1.6-1.dsc’ saved [2288/2288] --2025-09-19 10:43:58-- http://deb.debian.org/debian/pool/main/m/minimac4/minimac4_4.1.6-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2288 (2.2K) [text/prs.lines.tag] Saving to: ‘minimac4_4.1.6-1.dsc’ 0K .. 100% 269M=0s 2025-09-19 10:43:58 (269 MB/s) - ‘minimac4_4.1.6-1.dsc’ saved [2288/2288] Fri Sep 19 10:43:58 UTC 2025 I: minimac4_4.1.6-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: minimac4 Binary: minimac4 Architecture: any Version: 4.1.6-1 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi , Étienne Mollier Homepage: https://genome.sph.umich.edu/wiki/Minimac4 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/minimac4 Vcs-Git: https://salsa.debian.org/med-team/minimac4.git Testsuite: autopkgtest Testsuite-Triggers: bcftools Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libstatgen-dev, libshrinkwrap-dev, libsavvy-dev, libomp-jonathonl-dev, liblzma-dev, libzstd-dev, bcftools Package-List: minimac4 deb science optional arch=any Checksums-Sha1: 190a527edb4cf800a0c3b6ed2cc732442c10ef72 53460 minimac4_4.1.6.orig.tar.gz 8104bc421b8d4b717ca4608f39775675dda37d23 5368 minimac4_4.1.6-1.debian.tar.xz Checksums-Sha256: 0bce8d6edbf5d5d944b19c4e36403d0bc1d18f2d6003d88e01086488c3eb9333 53460 minimac4_4.1.6.orig.tar.gz 994819c4e4ff50247f6f7420ed438e7cd802baaa445beecf3f581ef8ef346b2c 5368 minimac4_4.1.6-1.debian.tar.xz Files: e7c0cfe90add2248fc79824add76253a 53460 minimac4_4.1.6.orig.tar.gz 86de610bf26bb05bae065ea9149df3d1 5368 minimac4_4.1.6-1.debian.tar.xz Dgit: f06073708f98230727f744ec1f0ae2b7a82b38c1 debian archive/debian/4.1.6-1 https://git.dgit.debian.org/minimac4 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmVzCnkUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoxww//VN8VG/iYLukZlL/mut4jDnSvmKn7 HZGN2OojXPMtzVlI7yCROdWICQXaNkzntWKNoP6fc5c6X15lrANtWNziLVHw3fKa RVnN8Z9uEL6QHVHPh+zfXa6sje4nrMiU7Fr5biaXCyeUS0ht30nX/M3L695CQF7b SppP3j4AX0gPpFaj8k/6onJZPbGaNIDj/sTgl67DLsE8k6ht9GJtvyuJs3IGbLg5 ZndqE3I1UQdSzwHs7SXia+kimXN848bUEBfoNi/FBBEpAX11eAEoX75ShKuLcjTW v6mXVQBoUZ99C6oOlqSHLTmPoOD/CuDab8YfIM4OIf7dpcjSdXEL/xQ5TGjnoMGn ncSsDMNqL+fNjWrYN/8LN5YTewK6g5qwxEtpAARdTu6NYfzWW9p2LT6Th+VNvk+o hY8SeYQGNqeOKjcRRD2V1RpRmc5mrq2eAcQ6gIYs0zypq4fozM1rqmcIIKYecago wFtcjn0VEGrPC6PhYjXAAS3DOeBWlRT2luw5mM6uu4zBSyTkpu4EdT4kTemUqO8+ f8mFIZ6fPER9n9Rer50I3IFSVkxn1mb2kHv76jJ1FiOHI7Q9WDEo5h2oiSdSjrZ/ iLAjZHB/Buu9O3cwlnVC6Xz6JxZtmhdp14kaLPkfF1c2Qo+T7MLMNd9uayUJM9b2 qrkjd+gngOl7TF8= =Hdso -----END PGP SIGNATURE----- Fri Sep 19 10:43:58 UTC 2025 I: Checking whether the package is not for us Fri Sep 19 10:43:58 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Fri Sep 19 10:43:58 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Fri Sep 19 10:43:58 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Fri Sep 19 10:43:58 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Ddkek2' ==================================================================================== Fri Sep 19 10:43:59 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 minimac4 unstable /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7 4.1.6-1" as arguments. Fri Sep 19 10:43:59 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-q4mqilPv" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 19 10:43:59 UTC 2025 I: Downloading source for unstable/minimac4=4.1.6-1 Reading package lists... NOTICE: 'minimac4' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/minimac4.git Please use: git clone https://salsa.debian.org/med-team/minimac4.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 61.1 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (dsc) [2288 B] Get:2 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (tar) [53.5 kB] Get:3 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (diff) [5368 B] Fetched 61.1 kB in 0s (1098 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'minimac4' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/minimac4.git Please use: git clone https://salsa.debian.org/med-team/minimac4.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 61.1 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (dsc) [2288 B] Get:2 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (tar) [53.5 kB] Get:3 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (diff) [5368 B] Fetched 61.1 kB in 0s (1098 kB/s) Download complete and in download only mode ============================================================================= Building minimac4 in unstable on amd64 on ionos1-amd64 now. Date: Fri Sep 19 10:44:00 UTC 2025 Date UTC: Fri Sep 19 10:44:00 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 18 22:44:00 -12 2025 I: pbuilder-time-stamp: 1758278640 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [minimac4_4.1.6-1.dsc] I: copying [./minimac4_4.1.6.orig.tar.gz] I: copying [./minimac4_4.1.6-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./minimac4_4.1.6-1.dsc: no acceptable signature found dpkg-source: info: extracting minimac4 in minimac4-4.1.6 dpkg-source: info: unpacking minimac4_4.1.6.orig.tar.gz dpkg-source: info: unpacking minimac4_4.1.6-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Use_shared_zlib.patch dpkg-source: info: applying lzma.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1016826/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=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ba2524757f0c470d9f737a99464982c9' 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='1016826' 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.xt508CP7/pbuilderrc_upmZ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b1 --logfile b1/build.log minimac4_4.1.6-1.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1016826/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), cmake, zlib1g-dev, libstatgen-dev, libshrinkwrap-dev, libsavvy-dev, libomp-jonathonl-dev, liblzma-dev, libzstd-dev, bcftools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libstatgen-dev; however: Package libstatgen-dev is not installed. pbuilder-satisfydepends-dummy depends on libshrinkwrap-dev; however: Package libshrinkwrap-dev is not installed. pbuilder-satisfydepends-dummy depends on libsavvy-dev; however: Package libsavvy-dev is not installed. pbuilder-satisfydepends-dummy depends on libomp-jonathonl-dev; however: Package libomp-jonathonl-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools 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} bcftools{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libomp-jonathonl-dev{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsavvy-dev{a} libshrinkwrap-dev{a} libssh2-1t64{a} libstatgen-dev{a} libstatgen1{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-gffutils python3-matplotlib wget 0 packages upgraded, 74 newly installed, 0 to remove and 0 not upgraded. Need to get 36.0 MB of archives. After unpacking 127 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 30 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.16.0-1 [431 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.22-1 [829 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libomp-jonathonl-dev amd64 1.0.0-1 [7816 B] Get: 69 http://deb.debian.org/debian unstable/main amd64 libshrinkwrap-dev all 1.2.0-2 [12.3 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsavvy-dev all 2.1.0-3 [73.8 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libstatgen1 amd64 1.0.15-8 [316 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libstatgen-dev amd64 1.0.15-8 [122 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 36.0 MB in 1s (42.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. 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Setting up libhtscodecs2:amd64 (1.6.1-2) ... Setting up libexpat1:amd64 (2.7.2-1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libstatgen1:amd64 (1.0.15-8) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-1.1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libuv1t64:amd64 (1.51.0-2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up autotools-dev (20240727.1) ... Setting up libshrinkwrap-dev (1.2.0-2) ... Setting up libjsoncpp26:amd64 (1.9.6-4) ... Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.11.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up procps (2:4.0.4-9) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.15.1-1) ... Setting up libstatgen-dev:amd64 (1.0.15-8) ... Setting up cmake-data (4.1.1+really3.31.6-2) ... Setting up librhash1:amd64 (1.4.6-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libomp-jonathonl-dev (1.0.0-1) ... Setting up libarchive13t64:amd64 (3.7.4-4+b1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libsavvy-dev (2.1.0-3) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Setting up libcurl4t64:amd64 (8.16.0-1) ... Setting up libcurl3t64-gnutls:amd64 (8.16.0-1) ... Setting up debhelper (13.26) ... Setting up cmake (4.1.1+really3.31.6-2) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... Setting up bcftools (1.22-1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/minimac4-4.1.6/ && 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 > ../minimac4_4.1.6-1_source.changes dpkg-buildpackage: info: source package minimac4 dpkg-buildpackage: info: source version 4.1.6-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6' dh_auto_configure -- -DBUILD_TESTS=ON cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_TESTS=ON .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Configuring done (2.0s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6' dh_auto_build cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/minimac4-4.1.6 -B/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' make -f CMakeFiles/minimac4.dir/build.make CMakeFiles/minimac4.dir/depend make[3]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/minimac4-4.1.6 /build/reproducible-path/minimac4-4.1.6 /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/CMakeFiles/minimac4.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' make -f CMakeFiles/minimac4.dir/build.make CMakeFiles/minimac4.dir/build make[3]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' [ 28%] Building CXX object CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o [ 28%] Building CXX object CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o -MF CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o.d -o CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/dosage_writer.cpp [ 42%] Building CXX object CMakeFiles/minimac4.dir/src/input_prep.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o -MF CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o.d -o CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/hidden_markov_model.cpp [ 57%] Building CXX object CMakeFiles/minimac4.dir/src/main.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/input_prep.cpp.o -MF CMakeFiles/minimac4.dir/src/input_prep.cpp.o.d -o CMakeFiles/minimac4.dir/src/input_prep.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/input_prep.cpp [ 71%] Building CXX object CMakeFiles/minimac4.dir/src/recombination.cpp.o [ 85%] Building CXX object CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/recombination.cpp.o -MF CMakeFiles/minimac4.dir/src/recombination.cpp.o.d -o CMakeFiles/minimac4.dir/src/recombination.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/recombination.cpp /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o -MF CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o.d -o CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/unique_haplotype.cpp /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/main.cpp.o -MF CMakeFiles/minimac4.dir/src/main.cpp.o.d -o CMakeFiles/minimac4.dir/src/main.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/main.cpp [100%] Linking CXX executable minimac4 /usr/bin/cmake -E cmake_link_script CMakeFiles/minimac4.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/minimac4.dir/link.d CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o CMakeFiles/minimac4.dir/src/input_prep.cpp.o CMakeFiles/minimac4.dir/src/recombination.cpp.o CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o CMakeFiles/minimac4.dir/src/main.cpp.o -o minimac4 -Wl,-Bstatic -lomp -Wl,-Bdynamic -llzma -lzstd -lz make[3]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' [100%] Built target minimac4 make[2]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' dh_auto_test cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j40 UpdateCTestConfiguration from :/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end Connected to MAKE jobserver test 1 Start 1: simple_test 1: Test command: /build/reproducible-path/minimac4-4.1.6/test/simple-test.sh "/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/minimac4" "m4_simple_test_output" "/build/reproducible-path/minimac4-4.1.6/test/input/ref_panel.vcf" "/build/reproducible-path/minimac4-4.1.6/test/input/tar_panel.vcf" 1: Working Directory: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu 1: Test timeout computed to be: 10000000 test 2 Start 2: haploid_and_diploid_test 2: Test command: /build/reproducible-path/minimac4-4.1.6/test/simple-test.sh "/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/minimac4" "m4_haploid_and_diploid_test_output" "/build/reproducible-path/minimac4-4.1.6/test/input/ref_panel_with_haploid_sample.vcf" "/build/reproducible-path/minimac4-4.1.6/test/input/tar_panel_with_haploid_sample.vcf" 2: Working Directory: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu 2: Test timeout computed to be: 10000000 1: /usr/bin/bcftools 2: /usr/bin/bcftools 1: minimac v4.1.6 1: 2: minimac v4.1.6 2: 2: Mean Compression Ratio: 0.770455 2: Min Compression Ratio: 0.590909 2: Max Compression Ratio: 0.95 1: Mean Compression Ratio: 0.820455 1: Min Compression Ratio: 0.590909 1: Max Compression Ratio: 1.05 1: minimac v4.1.6 1: 2: minimac v4.1.6 2: 2: Imputing chr20:1-10009927 ... 2: Loading target haplotypes ... 2: Loading target haplotypes took 0 seconds 2: Loading reference haplotypes ... 1: Imputing chr20:1-10009927 ... 1: Loading target haplotypes ... 2: Loading reference haplotypes took 0 seconds 2: Typed sites to imputed sites ratio: 0.903226 (28/31) 1: Loading target haplotypes took 0 seconds 1: Loading reference haplotypes ... 2: Running HMM with 1 threads ... 1: Loading reference haplotypes took 0 seconds 1: Typed sites to imputed sites ratio: 0.903226 (28/31) 1: Running HMM with 1 threads ... 2: Completed 2 of 5 samples 2: Completed 4 of 5 samples 1: Completed 2 of 5 samples 1: Completed 4 of 5 samples 2: Completed 5 of 5 samples 2: Running HMM took 0 seconds 2: Writing temp files took 0 seconds 2: Merging temp files ... 2: Merging temp files took 0 seconds 2: 2: Mean ER2: 1 2: 2: Total time for parsing input: 0 seconds 2: Total time for HMM: 0 seconds 2: Total time for writing output: 0 seconds 2: Total wall time (h:mm:ss): 0:00:00 1: Completed 5 of 5 samples 1: Running HMM took 0 seconds 1: Writing temp files took 0 seconds 1: Merging temp files ... 1: Merging temp files took 0 seconds 1: 1: Mean ER2: 1 1 1: 1: Total time for parsing input: 0 seconds 1: Total time for HMM: 0 seconds 1: Total time for writing output: 0 seconds 1: Total wall time (h:mm:ss): 0:00:00 1/2 Test #1: simple_test ...................... Passed 0.15 sec 2/2 Test #2: haploid_and_diploid_test ......... Passed 0.15 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.16 sec make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/minimac4/ cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/minimac4-4.1.6/debian/minimac4 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/minimac4-4.1.6 -B/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/minimac4-4.1.6/debian/minimac4/usr/bin/minimac4 make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'minimac4-dbgsym' in '../minimac4-dbgsym_4.1.6-1_amd64.deb'. dpkg-deb: building package 'minimac4' in '../minimac4_4.1.6-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../minimac4_4.1.6-1_amd64.buildinfo dpkg-genchanges --build=binary -O../minimac4_4.1.6-1_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/1016826 and its subdirectories I: Current time: Thu Sep 18 22:47:03 -12 2025 I: pbuilder-time-stamp: 1758278823 Fri Sep 19 10:47:03 UTC 2025 I: Signing ./b1/minimac4_4.1.6-1_amd64.buildinfo as minimac4_4.1.6-1_amd64.buildinfo.asc Fri Sep 19 10:47:03 UTC 2025 I: Signed ./b1/minimac4_4.1.6-1_amd64.buildinfo as ./b1/minimac4_4.1.6-1_amd64.buildinfo.asc Fri Sep 19 10:47:03 UTC 2025 - build #1 for minimac4/unstable/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Fri Sep 19 10:47:03 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-q4mqilPv, removing. /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 19 10:47 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 19 10:43 b2 -rw-rw-r-- 1 jenkins jenkins 2288 Dec 8 2023 minimac4_4.1.6-1.dsc -rw------- 1 jenkins jenkins 3394 Sep 19 10:43 rbuildlog.ldwKsb4 /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b1: total 5976 -rw-r--r-- 1 jenkins jenkins 46508 Sep 19 10:47 build.log -rw-r--r-- 1 jenkins jenkins 5708520 Sep 19 10:47 minimac4-dbgsym_4.1.6-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 5368 Sep 19 10:47 minimac4_4.1.6-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2288 Sep 19 10:47 minimac4_4.1.6-1.dsc -rw-r--r-- 1 jenkins jenkins 6338 Sep 19 10:47 minimac4_4.1.6-1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7220 Sep 19 10:47 minimac4_4.1.6-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1331 Sep 19 10:47 minimac4_4.1.6-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 265740 Sep 19 10:47 minimac4_4.1.6-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1439 Sep 19 10:47 minimac4_4.1.6-1_source.changes -rw-r--r-- 1 jenkins jenkins 53460 Sep 19 10:47 minimac4_4.1.6.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b2: total 0 Fri Sep 19 10:47:03 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 18 22:44:00 -12 2025 I: pbuilder-time-stamp: 1758278640 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [minimac4_4.1.6-1.dsc] I: copying [./minimac4_4.1.6.orig.tar.gz] I: copying [./minimac4_4.1.6-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./minimac4_4.1.6-1.dsc: no acceptable signature found dpkg-source: info: extracting minimac4 in minimac4-4.1.6 dpkg-source: info: unpacking minimac4_4.1.6.orig.tar.gz dpkg-source: info: unpacking minimac4_4.1.6-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Use_shared_zlib.patch dpkg-source: info: applying lzma.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1016826/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=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ba2524757f0c470d9f737a99464982c9' 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='1016826' 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.xt508CP7/pbuilderrc_upmZ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b1 --logfile b1/build.log minimac4_4.1.6-1.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1016826/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), cmake, zlib1g-dev, libstatgen-dev, libshrinkwrap-dev, libsavvy-dev, libomp-jonathonl-dev, liblzma-dev, libzstd-dev, bcftools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libstatgen-dev; however: Package libstatgen-dev is not installed. pbuilder-satisfydepends-dummy depends on libshrinkwrap-dev; however: Package libshrinkwrap-dev is not installed. pbuilder-satisfydepends-dummy depends on libsavvy-dev; however: Package libsavvy-dev is not installed. pbuilder-satisfydepends-dummy depends on libomp-jonathonl-dev; however: Package libomp-jonathonl-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools 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} bcftools{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libomp-jonathonl-dev{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsavvy-dev{a} libshrinkwrap-dev{a} libssh2-1t64{a} libstatgen-dev{a} libstatgen1{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-gffutils python3-matplotlib wget 0 packages upgraded, 74 newly installed, 0 to remove and 0 not upgraded. Need to get 36.0 MB of archives. After unpacking 127 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 30 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.16.0-1 [431 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.22-1 [829 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libomp-jonathonl-dev amd64 1.0.0-1 [7816 B] Get: 69 http://deb.debian.org/debian unstable/main amd64 libshrinkwrap-dev all 1.2.0-2 [12.3 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsavvy-dev all 2.1.0-3 [73.8 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libstatgen1 amd64 1.0.15-8 [316 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libstatgen-dev amd64 1.0.15-8 [122 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 36.0 MB in 1s (42.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-9_amd64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../18-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../19-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../20-libidn2-0_2.3.8-4_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../21-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../22-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../23-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../24-libgnutls30t64_3.8.10-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.10-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../25-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../26-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../27-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../28-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../29-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../30-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../31-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../32-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/minimac4-4.1.6/ && 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 > ../minimac4_4.1.6-1_source.changes dpkg-buildpackage: info: source package minimac4 dpkg-buildpackage: info: source version 4.1.6-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6' dh_auto_configure -- -DBUILD_TESTS=ON cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_TESTS=ON .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. 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-ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/recombination.cpp.o -MF CMakeFiles/minimac4.dir/src/recombination.cpp.o.d -o CMakeFiles/minimac4.dir/src/recombination.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/recombination.cpp /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o -MF CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o.d -o CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/unique_haplotype.cpp /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/main.cpp.o -MF CMakeFiles/minimac4.dir/src/main.cpp.o.d -o CMakeFiles/minimac4.dir/src/main.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/main.cpp [100%] Linking CXX executable minimac4 /usr/bin/cmake -E cmake_link_script CMakeFiles/minimac4.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/minimac4.dir/link.d CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o CMakeFiles/minimac4.dir/src/input_prep.cpp.o CMakeFiles/minimac4.dir/src/recombination.cpp.o CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o CMakeFiles/minimac4.dir/src/main.cpp.o -o minimac4 -Wl,-Bstatic -lomp -Wl,-Bdynamic -llzma -lzstd -lz make[3]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' [100%] Built target minimac4 make[2]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' dh_auto_test cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j40 UpdateCTestConfiguration from :/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end Connected to MAKE jobserver test 1 Start 1: simple_test 1: Test command: /build/reproducible-path/minimac4-4.1.6/test/simple-test.sh "/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/minimac4" "m4_simple_test_output" "/build/reproducible-path/minimac4-4.1.6/test/input/ref_panel.vcf" "/build/reproducible-path/minimac4-4.1.6/test/input/tar_panel.vcf" 1: Working Directory: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu 1: Test timeout computed to be: 10000000 test 2 Start 2: haploid_and_diploid_test 2: Test command: /build/reproducible-path/minimac4-4.1.6/test/simple-test.sh "/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/minimac4" "m4_haploid_and_diploid_test_output" "/build/reproducible-path/minimac4-4.1.6/test/input/ref_panel_with_haploid_sample.vcf" "/build/reproducible-path/minimac4-4.1.6/test/input/tar_panel_with_haploid_sample.vcf" 2: Working Directory: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu 2: Test timeout computed to be: 10000000 1: /usr/bin/bcftools 2: /usr/bin/bcftools 1: minimac v4.1.6 1: 2: minimac v4.1.6 2: 2: Mean Compression Ratio: 0.770455 2: Min Compression Ratio: 0.590909 2: Max Compression Ratio: 0.95 1: Mean Compression Ratio: 0.820455 1: Min Compression Ratio: 0.590909 1: Max Compression Ratio: 1.05 1: minimac v4.1.6 1: 2: minimac v4.1.6 2: 2: Imputing chr20:1-10009927 ... 2: Loading target haplotypes ... 2: Loading target haplotypes took 0 seconds 2: Loading reference haplotypes ... 1: Imputing chr20:1-10009927 ... 1: Loading target haplotypes ... 2: Loading reference haplotypes took 0 seconds 2: Typed sites to imputed sites ratio: 0.903226 (28/31) 1: Loading target haplotypes took 0 seconds 1: Loading reference haplotypes ... 2: Running HMM with 1 threads ... 1: Loading reference haplotypes took 0 seconds 1: Typed sites to imputed sites ratio: 0.903226 (28/31) 1: Running HMM with 1 threads ... 2: Completed 2 of 5 samples 2: Completed 4 of 5 samples 1: Completed 2 of 5 samples 1: Completed 4 of 5 samples 2: Completed 5 of 5 samples 2: Running HMM took 0 seconds 2: Writing temp files took 0 seconds 2: Merging temp files ... 2: Merging temp files took 0 seconds 2: 2: Mean ER2: 1 2: 2: Total time for parsing input: 0 seconds 2: Total time for HMM: 0 seconds 2: Total time for writing output: 0 seconds 2: Total wall time (h:mm:ss): 0:00:00 1: Completed 5 of 5 samples 1: Running HMM took 0 seconds 1: Writing temp files took 0 seconds 1: Merging temp files ... 1: Merging temp files took 0 seconds 1: 1: Mean ER2: 1 1 1: 1: Total time for parsing input: 0 seconds 1: Total time for HMM: 0 seconds 1: Total time for writing output: 0 seconds 1: Total wall time (h:mm:ss): 0:00:00 1/2 Test #1: simple_test ...................... Passed 0.15 sec 2/2 Test #2: haploid_and_diploid_test ......... Passed 0.15 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.16 sec make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/minimac4/ cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/minimac4-4.1.6/debian/minimac4 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/minimac4-4.1.6 -B/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/minimac4-4.1.6/debian/minimac4/usr/bin/minimac4 make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'minimac4-dbgsym' in '../minimac4-dbgsym_4.1.6-1_amd64.deb'. dpkg-deb: building package 'minimac4' in '../minimac4_4.1.6-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../minimac4_4.1.6-1_amd64.buildinfo dpkg-genchanges --build=binary -O../minimac4_4.1.6-1_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/1016826 and its subdirectories I: Current time: Thu Sep 18 22:47:03 -12 2025 I: pbuilder-time-stamp: 1758278823 Fri Sep 19 10:47:04 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Fri Sep 19 10:47:04 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Fri Sep 19 10:47:04 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Sep 19 10:47:04 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-i1bBhu' ==================================================================================== Thu Oct 22 17:10:04 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 minimac4 unstable /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7 4.1.6-1" as arguments. Thu Oct 22 17:10:04 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-Kv0PetnN" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Oct 22 17:10:04 UTC 2026 I: Downloading source for unstable/minimac4=4.1.6-1 Reading package lists... NOTICE: 'minimac4' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/minimac4.git Please use: git clone https://salsa.debian.org/med-team/minimac4.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 61.1 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (dsc) [2288 B] Get:2 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (tar) [53.5 kB] Get:3 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (diff) [5368 B] Fetched 61.1 kB in 0s (3408 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'minimac4' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/minimac4.git Please use: git clone https://salsa.debian.org/med-team/minimac4.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 61.1 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (dsc) [2288 B] Get:2 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (tar) [53.5 kB] Get:3 http://deb.debian.org/debian unstable/main minimac4 4.1.6-1 (diff) [5368 B] Fetched 61.1 kB in 0s (3408 kB/s) Download complete and in download only mode ============================================================================= Re-Building minimac4 in unstable on amd64 on ionos15-amd64 now. Date: Thu Oct 22 17:10:05 UTC 2026 Date UTC: Thu Oct 22 17:10:05 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/pbuilderrc_32bc + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' minimac4 = debian-installer -o minimac4 = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' minimac4 = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/pbuilderrc_32bc --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b2 --logfile b2/build.log minimac4_4.1.6-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 23 07:10:05 +14 2026 I: pbuilder-time-stamp: 1792689005 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [minimac4_4.1.6-1.dsc] I: copying [./minimac4_4.1.6.orig.tar.gz] I: copying [./minimac4_4.1.6-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./minimac4_4.1.6-1.dsc: no acceptable signature found dpkg-source: info: extracting minimac4 in minimac4-4.1.6 dpkg-source: info: unpacking minimac4_4.1.6.orig.tar.gz dpkg-source: info: unpacking minimac4_4.1.6-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Use_shared_zlib.patch dpkg-source: info: applying lzma.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 22 17:10 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=217a1baaf3334e2e83b2c0bc552d2846 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2894658 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/pbuilderrc_32bc --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b2 --logfile b2/build.log minimac4_4.1.6-1.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2894658/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), cmake, zlib1g-dev, libstatgen-dev, libshrinkwrap-dev, libsavvy-dev, libomp-jonathonl-dev, liblzma-dev, libzstd-dev, bcftools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libstatgen-dev; however: Package libstatgen-dev is not installed. pbuilder-satisfydepends-dummy depends on libshrinkwrap-dev; however: Package libshrinkwrap-dev is not installed. pbuilder-satisfydepends-dummy depends on libsavvy-dev; however: Package libsavvy-dev is not installed. pbuilder-satisfydepends-dummy depends on libomp-jonathonl-dev; however: Package libomp-jonathonl-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools 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} bcftools{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libomp-jonathonl-dev{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsavvy-dev{a} libshrinkwrap-dev{a} libssh2-1t64{a} libstatgen-dev{a} libstatgen1{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-gffutils python3-matplotlib wget 0 packages upgraded, 74 newly installed, 0 to remove and 0 not upgraded. Need to get 36.0 MB of archives. After unpacking 127 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 30 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.16.0-1 [431 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.22-1 [829 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libomp-jonathonl-dev amd64 1.0.0-1 [7816 B] Get: 69 http://deb.debian.org/debian unstable/main amd64 libshrinkwrap-dev all 1.2.0-2 [12.3 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsavvy-dev all 2.1.0-3 [73.8 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libstatgen1 amd64 1.0.15-8 [316 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libstatgen-dev amd64 1.0.15-8 [122 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 36.0 MB in 11s (3388 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-9_amd64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../18-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../19-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../20-libidn2-0_2.3.8-4_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../21-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../22-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../23-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../24-libgnutls30t64_3.8.10-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.10-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../25-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../26-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../27-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../28-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../29-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../30-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../31-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../32-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../33-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../34-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../35-libnghttp3-9_1.11.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../36-libngtcp2-16_1.15.1-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.15.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../37-libngtcp2-crypto-gnutls8_1.15.1-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../38-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../39-librtmp1_2.4+20151223.gitfa8646d.1-3_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../40-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../41-libcurl3t64-gnutls_8.16.0-1_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.16.0-1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../42-libdeflate0_1.23-2_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-2) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../43-libhtscodecs2_1.6.1-2_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.1-2) ... Selecting previously unselected package libhts3t64:amd64. Preparing to unpack .../44-libhts3t64_1.22.1+ds2-1_amd64.deb ... Unpacking libhts3t64:amd64 (1.22.1+ds2-1) ... Selecting previously unselected package bcftools. Preparing to unpack .../45-bcftools_1.22-1_amd64.deb ... Unpacking bcftools (1.22-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../46-cmake-data_4.1.1+really3.31.6-2_all.deb ... Unpacking cmake-data (4.1.1+really3.31.6-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../47-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../48-libarchive13t64_3.7.4-4+b1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-4+b1) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../49-libcurl4t64_8.16.0-1_amd64.deb ... Unpacking libcurl4t64:amd64 (8.16.0-1) ... Selecting previously unselected package libjsoncpp26:amd64. Preparing to unpack .../50-libjsoncpp26_1.9.6-4_amd64.deb ... Unpacking libjsoncpp26:amd64 (1.9.6-4) ... Selecting previously unselected package librhash1:amd64. Preparing to unpack .../51-librhash1_1.4.6-1_amd64.deb ... Unpacking librhash1:amd64 (1.4.6-1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../52-libuv1t64_1.51.0-2_amd64.deb ... Unpacking libuv1t64:amd64 (1.51.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../53-cmake_4.1.1+really3.31.6-2_amd64.deb ... Unpacking cmake (4.1.1+really3.31.6-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../54-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../55-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/minimac4-4.1.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../minimac4_4.1.6-1_source.changes dpkg-buildpackage: info: source package minimac4 dpkg-buildpackage: info: source version 4.1.6-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6' dh_auto_configure -- -DBUILD_TESTS=ON cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_TESTS=ON .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. 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-DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/main.cpp.o -MF CMakeFiles/minimac4.dir/src/main.cpp.o.d -o CMakeFiles/minimac4.dir/src/main.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/main.cpp [100%] Linking CXX executable minimac4 /usr/bin/cmake -E cmake_link_script CMakeFiles/minimac4.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/minimac4.dir/link.d CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o CMakeFiles/minimac4.dir/src/input_prep.cpp.o CMakeFiles/minimac4.dir/src/recombination.cpp.o CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o CMakeFiles/minimac4.dir/src/main.cpp.o -o minimac4 -Wl,-Bstatic -lomp -Wl,-Bdynamic -llzma -lzstd -lz make[3]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' [100%] Built target minimac4 make[2]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' dh_auto_test cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end Connected to MAKE jobserver test 1 Start 1: simple_test 1: Test command: /build/reproducible-path/minimac4-4.1.6/test/simple-test.sh "/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/minimac4" "m4_simple_test_output" "/build/reproducible-path/minimac4-4.1.6/test/input/ref_panel.vcf" "/build/reproducible-path/minimac4-4.1.6/test/input/tar_panel.vcf" 1: Working Directory: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu 1: Test timeout computed to be: 10000000 test 2 Start 2: haploid_and_diploid_test 2: Test command: /build/reproducible-path/minimac4-4.1.6/test/simple-test.sh "/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/minimac4" "m4_haploid_and_diploid_test_output" "/build/reproducible-path/minimac4-4.1.6/test/input/ref_panel_with_haploid_sample.vcf" "/build/reproducible-path/minimac4-4.1.6/test/input/tar_panel_with_haploid_sample.vcf" 2: Working Directory: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu 2: Test timeout computed to be: 10000000 1: /usr/bin/bcftools 2: /usr/bin/bcftools 2: minimac v4.1.6 2: 1: minimac v4.1.6 1: 2: Mean Compression Ratio: 0.770455 2: Min Compression Ratio: 0.590909 2: Max Compression Ratio: 0.95 1: Mean Compression Ratio: 0.820455 1: Min Compression Ratio: 0.590909 1: Max Compression Ratio: 1.05 1: minimac v4.1.6 1: 2: minimac v4.1.6 2: 2: Imputing chr20:1-10009927 ... 2: Loading target haplotypes ... 1: Imputing chr20:1-10009927 ... 1: Loading target haplotypes ... 1: Loading target haplotypes took 0 seconds 1: Loading reference haplotypes ... 2: Loading target haplotypes took 0 seconds 2: Loading reference haplotypes ... 2: Loading reference haplotypes took 0 seconds 2: Typed sites to imputed sites ratio: 0.903226 (28/31) 2: Running HMM with 1 threads ... 1: Loading reference haplotypes took 0 seconds 1: Typed sites to imputed sites ratio: 0.903226 (28/31) 1: Running HMM with 1 threads ... 1: Completed 2 of 5 samples 2: Completed 2 of 5 samples 1: Completed 4 of 5 samples 2: Completed 4 of 5 samples 2: Completed 5 of 5 samples 1: Completed 5 of 5 samples 2: Running HMM took 0 seconds 2: Writing temp files took 0 seconds 2: Merging temp files ... 1: Running HMM took 0 seconds 1: Writing temp files took 0 seconds 1: Merging temp files ... 2: Merging temp files took 0 seconds 2: 2: Mean ER2: 1 2: 2: Total time for parsing input: 0 seconds 2: Total time for HMM: 0 seconds 2: Total time for writing output: 0 seconds 2: Total wall time (h:mm:ss): 0:00:00 1: Merging temp files took 0 seconds 1: 1: Mean ER2: 1 1 1: 1: Total time for parsing input: 0 seconds 1: Total time for HMM: 0 seconds 1: Total time for writing output: 0 seconds 1: Total wall time (h:mm:ss): 0:00:00 1/2 Test #1: simple_test ...................... Passed 1.58 sec 2/2 Test #2: haploid_and_diploid_test ......... Passed 1.58 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 1.67 sec make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/minimac4/ cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/minimac4-4.1.6/debian/minimac4 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/minimac4-4.1.6 -B/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/minimac4-4.1.6/debian/minimac4/usr/bin/minimac4 make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'minimac4' in '../minimac4_4.1.6-1_amd64.deb'. dpkg-deb: building package 'minimac4-dbgsym' in '../minimac4-dbgsym_4.1.6-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../minimac4_4.1.6-1_amd64.buildinfo dpkg-genchanges --build=binary -O../minimac4_4.1.6-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2894658 and its subdirectories I: Current time: Fri Oct 23 07:14:08 +14 2026 I: pbuilder-time-stamp: 1792689248 + false + set +x Thu Oct 22 17:14:08 UTC 2026 I: Signing ./b2/minimac4_4.1.6-1_amd64.buildinfo as minimac4_4.1.6-1_amd64.buildinfo.asc Thu Oct 22 17:14:08 UTC 2026 I: Signed ./b2/minimac4_4.1.6-1_amd64.buildinfo as ./b2/minimac4_4.1.6-1_amd64.buildinfo.asc Thu Oct 22 17:14:08 UTC 2026 - build #2 for minimac4/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Thu Oct 22 17:14:08 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-Kv0PetnN, removing. /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7: total 68 drwxrwxr-x 2 jenkins jenkins 4096 Sep 19 10:47 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 19 10:51 b2 -rw-rw-r-- 1 jenkins jenkins 2288 Dec 8 2023 minimac4_4.1.6-1.dsc -rw------- 1 jenkins jenkins 50190 Sep 19 10:47 rbuildlog.ldwKsb4 /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b1: total 5996 -rw-r--r-- 1 jenkins jenkins 46508 Sep 19 10:47 build.log -rw-r--r-- 1 jenkins jenkins 5708520 Sep 19 10:47 minimac4-dbgsym_4.1.6-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 5368 Sep 19 10:47 minimac4_4.1.6-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2288 Sep 19 10:47 minimac4_4.1.6-1.dsc -rw-r--r-- 1 jenkins jenkins 6338 Sep 19 10:47 minimac4_4.1.6-1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7220 Sep 19 10:47 minimac4_4.1.6-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1331 Sep 19 10:47 minimac4_4.1.6-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 265740 Sep 19 10:47 minimac4_4.1.6-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1439 Sep 19 10:47 minimac4_4.1.6-1_source.changes -rw-r--r-- 1 jenkins jenkins 53460 Sep 19 10:47 minimac4_4.1.6.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b2: total 5976 -rw-rw-r-- 1 jenkins jenkins 48440 Sep 19 10:51 build.log -rw-r--r-- 1 jenkins jenkins 5708520 Sep 19 10:51 minimac4-dbgsym_4.1.6-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 5368 Sep 19 10:51 minimac4_4.1.6-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2288 Sep 19 10:51 minimac4_4.1.6-1.dsc -rw-rw-r-- 1 jenkins jenkins 6338 Sep 19 10:51 minimac4_4.1.6-1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7220 Sep 19 10:51 minimac4_4.1.6-1_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1331 Sep 19 10:51 minimac4_4.1.6-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 265740 Sep 19 10:51 minimac4_4.1.6-1_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1439 Sep 19 10:51 minimac4_4.1.6-1_source.changes -rw-r--r-- 1 jenkins jenkins 53460 Sep 19 10:51 minimac4_4.1.6.orig.tar.gz Fri Sep 19 10:51:11 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Fri Sep 19 10:51:11 UTC 2025 I: minimac4_4.1.6-1_amd64.changes: Format: 1.8 Date: Fri, 08 Dec 2023 13:14:00 +0100 Source: minimac4 Binary: minimac4 minimac4-dbgsym Architecture: amd64 Version: 4.1.6-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: minimac4 - Fast Imputation Based on State Space Reduction HMM Changes: minimac4 (4.1.6-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 88b7d6e2468c4bc7d1961f08d53059c89c6936ff 5708520 minimac4-dbgsym_4.1.6-1_amd64.deb 9cb1c4a2b1b7ac8ab9c55014231ff9762f802f17 6338 minimac4_4.1.6-1_amd64.buildinfo 0413eb2311cfad152e99eb6e01dceef0192588a4 265740 minimac4_4.1.6-1_amd64.deb Checksums-Sha256: 174a9a9a521f416d98fa07adedc2b2fbd9489b8ec5591be8c047b60abd7b5297 5708520 minimac4-dbgsym_4.1.6-1_amd64.deb ab9274649a4a22a9ab57ef88269b40ceb11321b8dda1f3b46003023df038ee10 6338 minimac4_4.1.6-1_amd64.buildinfo 86afdc2d11f03332d58ed0f483bed5a5d21fc978f88e5ddf1ff12347c088e19b 265740 minimac4_4.1.6-1_amd64.deb Files: 5cd2522a9d77e190ebcb123144b2a92a 5708520 debug optional minimac4-dbgsym_4.1.6-1_amd64.deb 5773444a168dde341ae7ee6c638681d8 6338 science optional minimac4_4.1.6-1_amd64.buildinfo 5b7489c13a91c5667efedbe878c84fd2 265740 science optional minimac4_4.1.6-1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/minimac4_4.1.6-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/minimac4_4.1.6-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/minimac4_4.1.6-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/minimac4_4.1.6-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/minimac4_4.1.6-1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/minimac4_4.1.6-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-19 10:47:03.918466381 +0000 +++ b2/build.log 2025-09-19 10:51:11.570777286 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Sep 18 22:44:00 -12 2025 -I: pbuilder-time-stamp: 1758278640 +I: Current time: Fri Oct 23 07:10:05 +14 2026 +I: pbuilder-time-stamp: 1792689005 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,53 +25,85 @@ dpkg-source: info: applying lzma.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1016826/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 22 17:10 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2894658/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=40 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='ba2524757f0c470d9f737a99464982c9' - 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='1016826' - PS1='# ' - PS2='> ' + INVOCATION_ID=217a1baaf3334e2e83b2c0bc552d2846 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2894658 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.xt508CP7/pbuilderrc_upmZ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b1 --logfile b1/build.log minimac4_4.1.6-1.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/pbuilderrc_32bc --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b2 --logfile b2/build.log minimac4_4.1.6-1.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1016826/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -199,7 +231,7 @@ Get: 72 http://deb.debian.org/debian unstable/main amd64 libstatgen-dev amd64 1.0.15-8 [122 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 36.0 MB in 1s (42.4 MB/s) +Fetched 36.0 MB in 11s (3388 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -510,7 +542,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/minimac4-4.1.6/ && 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 > ../minimac4_4.1.6-1_source.changes +I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/minimac4-4.1.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../minimac4_4.1.6-1_source.changes dpkg-buildpackage: info: source package minimac4 dpkg-buildpackage: info: source version 4.1.6-1 dpkg-buildpackage: info: source distribution unstable @@ -552,7 +588,7 @@ -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE --- Configuring done (2.0s) +-- Configuring done (0.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -569,7 +605,7 @@ -- Build files have been written to: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6' dh_auto_build - cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/minimac4-4.1.6 -B/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -581,17 +617,17 @@ make[3]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' make -f CMakeFiles/minimac4.dir/build.make CMakeFiles/minimac4.dir/build make[3]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' -[ 28%] Building CXX object CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o -[ 28%] Building CXX object CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o +[ 57%] Building CXX object CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o +[ 57%] Building CXX object CMakeFiles/minimac4.dir/src/recombination.cpp.o +[ 57%] Building CXX object CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o +[ 57%] Building CXX object CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o +[ 85%] Building CXX object CMakeFiles/minimac4.dir/src/input_prep.cpp.o +[ 85%] Building CXX object CMakeFiles/minimac4.dir/src/main.cpp.o +/usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o -MF CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o.d -o CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/unique_haplotype.cpp /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o -MF CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o.d -o CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/dosage_writer.cpp -[ 42%] Building CXX object CMakeFiles/minimac4.dir/src/input_prep.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o -MF CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o.d -o CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/hidden_markov_model.cpp -[ 57%] Building CXX object CMakeFiles/minimac4.dir/src/main.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/input_prep.cpp.o -MF CMakeFiles/minimac4.dir/src/input_prep.cpp.o.d -o CMakeFiles/minimac4.dir/src/input_prep.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/input_prep.cpp -[ 71%] Building CXX object CMakeFiles/minimac4.dir/src/recombination.cpp.o -[ 85%] Building CXX object CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/recombination.cpp.o -MF CMakeFiles/minimac4.dir/src/recombination.cpp.o.d -o CMakeFiles/minimac4.dir/src/recombination.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/recombination.cpp -/usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o -MF CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o.d -o CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/unique_haplotype.cpp /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/main.cpp.o -MF CMakeFiles/minimac4.dir/src/main.cpp.o.d -o CMakeFiles/minimac4.dir/src/main.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/main.cpp [100%] Linking CXX executable minimac4 /usr/bin/cmake -E cmake_link_script CMakeFiles/minimac4.dir/link.txt --verbose=1 @@ -602,10 +638,10 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' dh_auto_test - cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 + cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j40 +/usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu @@ -630,10 +666,10 @@ 2: Test timeout computed to be: 10000000 1: /usr/bin/bcftools 2: /usr/bin/bcftools -1: minimac v4.1.6 -1: 2: minimac v4.1.6 2: +1: minimac v4.1.6 +1: 2: Mean Compression Ratio: 0.770455 2: Min Compression Ratio: 0.590909 2: Max Compression Ratio: 0.95 @@ -646,26 +682,30 @@ 2: 2: Imputing chr20:1-10009927 ... 2: Loading target haplotypes ... -2: Loading target haplotypes took 0 seconds -2: Loading reference haplotypes ... 1: Imputing chr20:1-10009927 ... 1: Loading target haplotypes ... -2: Loading reference haplotypes took 0 seconds -2: Typed sites to imputed sites ratio: 0.903226 (28/31) 1: Loading target haplotypes took 0 seconds 1: Loading reference haplotypes ... +2: Loading target haplotypes took 0 seconds +2: Loading reference haplotypes ... +2: Loading reference haplotypes took 0 seconds +2: Typed sites to imputed sites ratio: 0.903226 (28/31) 2: Running HMM with 1 threads ... 1: Loading reference haplotypes took 0 seconds 1: Typed sites to imputed sites ratio: 0.903226 (28/31) 1: Running HMM with 1 threads ... -2: Completed 2 of 5 samples -2: Completed 4 of 5 samples 1: Completed 2 of 5 samples +2: Completed 2 of 5 samples 1: Completed 4 of 5 samples +2: Completed 4 of 5 samples 2: Completed 5 of 5 samples +1: Completed 5 of 5 samples 2: Running HMM took 0 seconds 2: Writing temp files took 0 seconds 2: Merging temp files ... +1: Running HMM took 0 seconds +1: Writing temp files took 0 seconds +1: Merging temp files ... 2: Merging temp files took 0 seconds 2: 2: Mean ER2: 1 @@ -674,10 +714,6 @@ 2: Total time for HMM: 0 seconds 2: Total time for writing output: 0 seconds 2: Total wall time (h:mm:ss): 0:00:00 -1: Completed 5 of 5 samples -1: Running HMM took 0 seconds -1: Writing temp files took 0 seconds -1: Merging temp files ... 1: Merging temp files took 0 seconds 1: 1: Mean ER2: 1 1 @@ -686,17 +722,17 @@ 1: Total time for HMM: 0 seconds 1: Total time for writing output: 0 seconds 1: Total wall time (h:mm:ss): 0:00:00 -1/2 Test #1: simple_test ...................... Passed 0.15 sec -2/2 Test #2: haploid_and_diploid_test ......... Passed 0.15 sec +1/2 Test #1: simple_test ...................... Passed 1.58 sec +2/2 Test #2: haploid_and_diploid_test ......... Passed 1.58 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 0.16 sec +Total Test time (real) = 1.67 sec make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/minimac4/ - cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/minimac4-4.1.6/debian/minimac4 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/minimac4-4.1.6/debian/minimac4 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/minimac4-4.1.6 -B/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -726,8 +762,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'minimac4-dbgsym' in '../minimac4-dbgsym_4.1.6-1_amd64.deb'. dpkg-deb: building package 'minimac4' in '../minimac4_4.1.6-1_amd64.deb'. +dpkg-deb: building package 'minimac4-dbgsym' in '../minimac4-dbgsym_4.1.6-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../minimac4_4.1.6-1_amd64.buildinfo dpkg-genchanges --build=binary -O../minimac4_4.1.6-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -735,12 +771,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2894658/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1016826 and its subdirectories -I: Current time: Thu Sep 18 22:47:03 -12 2025 -I: pbuilder-time-stamp: 1758278823 +I: removing directory /srv/workspace/pbuilder/2894658 and its subdirectories +I: Current time: Fri Oct 23 07:14:08 +14 2026 +I: pbuilder-time-stamp: 1792689248 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/minimac4_4.1.6-1.diff: 75.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/minimac4_4.1.6-1.diff.gz b2/build.log: 79.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 79.6% -- replaced with stdout Fri Sep 19 10:51:12 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_minimac4_unstable_amd64_1758279072 + touch /var/log/reproducible-builds/diffoscope_stamp_minimac4_unstable_amd64_1758279072 + RESULT=0 + systemd-run '--description=diffoscope on minimac4/4.1.6-1 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_3-68963 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7 --run-session -c jenkins-reproducible-unstable-diffoscope-b0a28379-2f34-4939-8d39-5ff1f83ea3fe -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/dbd-tmp-xYmiP7B ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/minimac4_4.1.6-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/minimac4_4.1.6-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/minimac4_4.1.6-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b1/minimac4_4.1.6-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b2/minimac4_4.1.6-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_3-68963.service; invocation ID: 6360bc7ce0d443b69049964367822f71 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/minimac4_4.1.6-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/minimac4_4.1.6-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/minimac4_4.1.6-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b1/minimac4_4.1.6-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.xt508CP7/b2/minimac4_4.1.6-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 199ms CPU time consumed: 175ms Memory peak: 18M (swap: 0B) _ _ _ _ _ __ ___ (_)_ __ (_)_ __ ___ __ _ ___| || | | '_ ` _ \| | '_ \| | '_ ` _ \ / _` |/ __| || |_ | | | | | | | | | | | | | | | | (_| | (__|__ _| |_| |_| |_|_|_| |_|_|_| |_| |_|\__,_|\___| |_| Fri Sep 19 10:51:13 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Fri Sep 19 10:51:13 UTC 2025 I: minimac4 from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-19 10:51:13] INFO: Starting at 2025-09-19 10:51:13.497952 [2025-09-19 10:51:13] INFO: Generating the pages of 1 package(s) [2025-09-19 10:51:14] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/minimac4 didn't produce a buildlog, even though it has been built. [2025-09-19 10:51:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/minimac4_4.1.6-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/minimac4_4.1.6-1.diff.gz is missing [2025-09-19 10:51:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/minimac4_4.1.6-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/minimac4_4.1.6-1.diff.gz is missing [2025-09-19 10:51:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/minimac4_4.1.6-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/minimac4_4.1.6-1.diff.gz is missing [2025-09-19 10:51:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/minimac4_4.1.2-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/minimac4_4.1.2-1.diff.gz is missing [2025-09-19 10:51:14] INFO: Finished at 2025-09-19 10:51:14.119000, took: 0:00:00.621051 Fri Sep 19 10:51:14 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/minimac4.html Fri Sep 19 10:51:14 UTC 2025 I: Removing signed minimac4_4.1.6-1_amd64.buildinfo.asc files: removed './b1/minimac4_4.1.6-1_amd64.buildinfo.asc' removed './b2/minimac4_4.1.6-1_amd64.buildinfo.asc' 1758279074 amd64 unstable minimac4 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/minimac4_4.1.6-1.rbuild.log: 76.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/minimac4_4.1.6-1.rbuild.log.gz [2025-09-19 10:51:14] INFO: Starting at 2025-09-19 10:51:14.446923 [2025-09-19 10:51:14] INFO: Generating the pages of 1 package(s) [2025-09-19 10:51:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/minimac4_4.1.6-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/minimac4_4.1.6-1.diff.gz is missing [2025-09-19 10:51:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/minimac4_4.1.6-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/minimac4_4.1.6-1.diff.gz is missing [2025-09-19 10:51:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/minimac4_4.1.6-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/minimac4_4.1.6-1.diff.gz is missing [2025-09-19 10:51:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/minimac4_4.1.2-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/minimac4_4.1.2-1.diff.gz is missing [2025-09-19 10:51:14] INFO: Finished at 2025-09-19 10:51:14.959893, took: 0:00:00.512973 All cleanup done. Fri Sep 19 10:51:15 UTC 2025 - total duration: 0h 7m 22s. Fri Sep 19 10:51:15 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Cjr2Sm2i, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 7min 23.943s CPU time consumed: 3.756s Memory peak: 72.6M (swap: 0B)