Thu Jun 1 22:53:23 UTC 2023 I: starting to build minimac4/bookworm/amd64 on jenkins on '2023-06-01 22:53' Thu Jun 1 22:53:23 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_26/76/console.log Thu Jun 1 22:53:23 UTC 2023 I: Downloading source for bookworm/minimac4=4.1.2-1 --2023-06-01 22:53:23-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/minimac4/minimac4_4.1.2-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2170 (2.1K) [text/prs.lines.tag] Saving to: ‘minimac4_4.1.2-1.dsc’ 0K .. 100% 189M=0s 2023-06-01 22:53:23 (189 MB/s) - ‘minimac4_4.1.2-1.dsc’ saved [2170/2170] Thu Jun 1 22:53:23 UTC 2023 I: minimac4_4.1.2-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: minimac4 Binary: minimac4 Architecture: any Version: 4.1.2-1 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: dc804dc0ffb188dc609350116a4b1d8d79a8920c 47645 minimac4_4.1.2.orig.tar.gz 8dac62ed540e62406487337ce62fea41b8ab8910 5216 minimac4_4.1.2-1.debian.tar.xz Checksums-Sha256: 66c26c99461ed5a32b09c044633d5cf2da1507850f8b81e375b83301a4bee265 47645 minimac4_4.1.2.orig.tar.gz c8a1331515146a2b0d1a7b44debc2778e558b54fa88230f5ef5975cb990d506c 5216 minimac4_4.1.2-1.debian.tar.xz Files: 8c5de19a54528301e561d0de22e6f237 47645 minimac4_4.1.2.orig.tar.gz fb428608f1ab57a67b2fc38cf241521e 5216 minimac4_4.1.2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPQK8QRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEurg/8Cx+toJ0X6ZB2QW5t8DN1DxXq9cSBbUP7 uwnbSW4aOhlie0CJi1culzljx3aPwaury1akLkxpLNqdfXt2iEKDocn4p012ibYg +p1myIbpXy2xka+ePUVWTZBbuHu6KJRmMVhBmXj9BKMcY67r1w6noh+TzPKCwBaf BA/vEKpJ/7cdhJA1C0A7kbxBKPoD8fHGOVmWiPKurxFoPm9wE3RO+0NWJ0OjBC2B hsHXHbuYgyeQDB88Lnr0FYyIfQVvyXva8mM14fP/h2BgHDZoFhpGP/Nuk0VknexQ Qv+UpDvzEZZMbc+KBO4rkzJZfQjqI6cv2Yua/JSI4cSQG3H6Z5R7uEVzHcqhWZ4A nDHVsuZ4ULwTqPwssUP/035lScEJL5H3dj+Jutqd5NzaEzOUM5vCwZNdgEaBUhq7 Sd/ir/DoP/xbT5qUoobPTqNKmTqCCDX6idqLZUb6kS3fYL+PDCauSc0Ukosf1bvV 7XG/NmvMofU2SZRpLJzkn1683XesxzaHiucdcKIjOJYr6dcBYwURm2rnhoiJ2krR t+R++MCwNipyWc8YFh+g0BLRzYh18tZ/Bc/wQhFG1mMXMqkBVgS9qvb2y+tDzq/n hD8Yg4Y/za2Fx7KjpBioqVK/yBEQORoPhddYkAD9ZdEBIrDv41ExHW62CyPbSE3S QLShr7E6PI4= =lsyM -----END PGP SIGNATURE----- Thu Jun 1 22:53:23 UTC 2023 I: Checking whether the package is not for us Thu Jun 1 22:53:23 UTC 2023 I: Starting 1st build on remote node ionos5-amd64.debian.net. Thu Jun 1 22:53:23 UTC 2023 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Thu Jun 1 22:55:18 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 3 17:16:25 -12 2024 I: pbuilder-time-stamp: 1720070185 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel: time stamp 2025-08-04 08:27:02 is 34269029.663172201 s in the future tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel.other: time stamp 2025-08-04 08:27:02 is 34269029.662942855 s in the future tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples: time stamp 2025-08-04 08:27:02 is 34269029.662911155 s in the future tar: ./usr/share/doc/adduser/examples: time stamp 2025-08-04 08:27:02 is 34269029.662884526 s in the future tar: ./usr/share/doc/adduser: time stamp 2025-08-04 08:27:02 is 34269029.662858021 s in the future tar: ./usr/share/locale/ca/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.57508348 s in the future tar: ./usr/share/locale/cs/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.553837452 s in the future tar: ./usr/share/locale/da/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.533053878 s in the future tar: ./usr/share/locale/de/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.510304864 s in the future tar: ./usr/share/locale/es/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.463514067 s in the future tar: ./usr/share/locale/eu/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.458184674 s in the future tar: ./usr/share/locale/fr/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.391015919 s in the future tar: ./usr/share/locale/gl/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.383749481 s in the future tar: ./usr/share/locale/hu/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.370501718 s in the future tar: ./usr/share/locale/it/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.352479456 s in the future tar: ./usr/share/locale/ja/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.327681422 s in the future tar: ./usr/share/locale/ko/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.309633776 s in the future tar: ./usr/share/locale/nb/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.286758127 s in the future tar: ./usr/share/locale/nl/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.262749546 s in the future tar: ./usr/share/locale/pl/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.241915582 s in the future tar: ./usr/share/locale/pt/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.215991198 s in the future tar: ./usr/share/locale/pt_BR/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.198126662 s in the future tar: ./usr/share/locale/ru/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.13869402 s in the future tar: ./usr/share/locale/sk/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.127198232 s in the future tar: ./usr/share/locale/sv/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.077468301 s in the future tar: ./usr/share/locale/uk/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269029.004789375 s in the future tar: ./usr/share/locale/vi/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269028.98114044 s in the future tar: ./usr/share/locale/zh_CN/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34269028.96071452 s in the future tar: ./usr/share/man/de/man5: time stamp 2025-08-04 08:27:02 is 34269028.827198471 s in the future tar: ./usr/share/man/fr/man5: time stamp 2025-08-04 08:27:02 is 34269028.819867908 s in the future tar: ./usr/share/man/man5: time stamp 2025-08-04 08:27:02 is 34269028.79463453 s in the future tar: ./usr/share/man/nl/man5: time stamp 2025-08-04 08:27:02 is 34269028.783788469 s in the future tar: ./usr/share/man/nl/man8: time stamp 2025-08-04 08:27:02 is 34269028.782795348 s in the future tar: ./usr/share/man/pt/man5: time stamp 2025-08-04 08:27:02 is 34269028.77738613 s in the future tar: ./usr/share/man/pt/man8: time stamp 2025-08-04 08:27:02 is 34269028.776419256 s in the future tar: ./usr/share/perl5/Debian: time stamp 2025-08-04 08:27:02 is 34269028.740998188 s in the future tar: ./var/lib/dpkg/info/adduser.list: time stamp 2025-08-04 08:27:02 is 34269026.749334798 s in the future tar: ./usr/sbin: time stamp 2025-08-04 08:27:02 is 34269026.570773671 s in the future tar: ./usr/share/man/man8: time stamp 2025-08-04 08:27:02 is 34269026.569619803 s in the future tar: ./usr/share/man/fr/man8: time stamp 2025-08-04 08:27:02 is 34269026.569394071 s in the future tar: ./usr/share/man/de/man8: time stamp 2025-08-04 08:27:02 is 34269026.569247566 s in the future 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_4.1.2-1.dsc] I: copying [./minimac4_4.1.2.orig.tar.gz] I: copying [./minimac4_4.1.2-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jan 24 07:04:36 2023 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./minimac4_4.1.2-1.dsc: no acceptable signature found dpkg-source: info: extracting minimac4 in minimac4-4.1.2 dpkg-source: info: unpacking minimac4_4.1.2.orig.tar.gz dpkg-source: info: unpacking minimac4_4.1.2-1.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/3257906/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='a0fabf2946484168a91642470e61466b' 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='3257906' 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.QppFXRZm/pbuilderrc_USoP --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QppFXRZm/b1 --logfile b1/build.log minimac4_4.1.2-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/3257906/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 ... 19591 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} libarchive13{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libomp-jonathonl-dev{a} libpipeline1{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsavvy-dev{a} libshrinkwrap-dev{a} libssh2-1{a} libstatgen-dev{a} libstatgen1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 61 newly installed, 0 to remove and 0 not upgraded. Need to get 36.0 MB of archives. After unpacking 131 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10 [381 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 bcftools amd64 1.16-1 [692 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10 [386 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libomp-jonathonl-dev amd64 1.0.0-1 [7816 B] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libshrinkwrap-dev all 1.2.0-2 [12.3 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libsavvy-dev all 2.1.0-2 [73.6 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libstatgen1 amd64 1.0.15-6 [317 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libstatgen-dev amd64 1.0.15-6 [122 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libzstd-dev amd64 1.5.4+dfsg2-5 [354 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 36.0 MB in 1s (37.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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 ... 19591 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../04-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../07-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... 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Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../27-libhtscodecs2_1.3.0-4_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.3.0-4) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../28-libhts3_1.16+ds-3_amd64.deb ... Unpacking libhts3:amd64 (1.16+ds-3) ... Selecting previously unselected package bcftools. Preparing to unpack .../29-bcftools_1.16-1_amd64.deb ... Unpacking bcftools (1.16-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../30-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../31-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../32-libarchive13_3.6.2-1_amd64.deb ... Unpacking libarchive13:amd64 (3.6.2-1) ... 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Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libshrinkwrap-dev (1.2.0-2) ... Setting up libuv1:amd64 (1.44.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up librhash0:amd64 (1.4.3-3) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libstatgen-dev:amd64 (1.0.15-6) ... Setting up cmake-data (3.25.1-1) ... Setting up libomp-jonathonl-dev (1.0.0-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libsavvy-dev (2.1.0-2) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:amd64 (3.6.2-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libcurl4:amd64 (7.88.1-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up cmake (3.25.1-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up bcftools (1.16-1) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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/minimac4-4.1.2/ && 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_4.1.2-1_source.changes dpkg-buildpackage: info: source package minimac4 dpkg-buildpackage: info: source version 4.1.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/minimac4-4.1.2' dh_auto_configure -- -DBUILD_TESTS=ON cd obj-x86_64-linux-gnu && 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 .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- 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 -- Generating done 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/minimac4-4.1.2/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/minimac4-4.1.2' dh_auto_build cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/minimac4-4.1.2 -B/build/minimac4-4.1.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/minimac4-4.1.2/obj-x86_64-linux-gnu/CMakeFiles /build/minimac4-4.1.2/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' make -f CMakeFiles/minimac4.dir/build.make CMakeFiles/minimac4.dir/depend make[3]: Entering directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' cd /build/minimac4-4.1.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/minimac4-4.1.2 /build/minimac4-4.1.2 /build/minimac4-4.1.2/obj-x86_64-linux-gnu /build/minimac4-4.1.2/obj-x86_64-linux-gnu /build/minimac4-4.1.2/obj-x86_64-linux-gnu/CMakeFiles/minimac4.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' make -f CMakeFiles/minimac4.dir/build.make CMakeFiles/minimac4.dir/build make[3]: Entering directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' [ 14%] Building CXX object CMakeFiles/minimac4.dir/src/input_prep.cpp.o [ 42%] Building CXX object CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o [ 42%] Building CXX object CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.2\" -g -O2 -ffile-prefix-map=/build/minimac4-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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/minimac4-4.1.2/src/input_prep.cpp /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.2\" -g -O2 -ffile-prefix-map=/build/minimac4-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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/minimac4-4.1.2/src/dosage_writer.cpp [ 57%] Building CXX object CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.2\" -g -O2 -ffile-prefix-map=/build/minimac4-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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/minimac4-4.1.2/src/hidden_markov_model.cpp [ 71%] Building CXX object CMakeFiles/minimac4.dir/src/recombination.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.2\" -g -O2 -ffile-prefix-map=/build/minimac4-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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/minimac4-4.1.2/src/recombination.cpp /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.2\" -g -O2 -ffile-prefix-map=/build/minimac4-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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/minimac4-4.1.2/src/unique_haplotype.cpp [ 85%] Building CXX object CMakeFiles/minimac4.dir/src/main.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.2\" -g -O2 -ffile-prefix-map=/build/minimac4-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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/minimac4-4.1.2/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/minimac4-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -Wl,-z,relro -Wl,-z,now -rdynamic 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/minimac4-4.1.2/obj-x86_64-linux-gnu' [100%] Built target minimac4 make[2]: Leaving directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/minimac4-4.1.2/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' dh_auto_test cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 make[1]: Entering directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j16 UpdateCTestConfiguration from :/build/minimac4-4.1.2/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/minimac4-4.1.2/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/minimac4-4.1.2/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 test 1 Start 1: simple_test 1: Test command: /build/minimac4-4.1.2/test/simple-test.sh "/build/minimac4-4.1.2/obj-x86_64-linux-gnu/minimac4" "m4_simple_test_output" "/build/minimac4-4.1.2/test/input/ref_panel.vcf" "/build/minimac4-4.1.2/test/input/tar_panel.vcf" 1: Working Directory: /build/minimac4-4.1.2/obj-x86_64-linux-gnu 1: Test timeout computed to be: 10000000 test 2 Start 2: haploid_and_diploid_test 2: Test command: /build/minimac4-4.1.2/test/simple-test.sh "/build/minimac4-4.1.2/obj-x86_64-linux-gnu/minimac4" "m4_haploid_and_diploid_test_output" "/build/minimac4-4.1.2/test/input/ref_panel_with_haploid_sample.vcf" "/build/minimac4-4.1.2/test/input/tar_panel_with_haploid_sample.vcf" 2: Working Directory: /build/minimac4-4.1.2/obj-x86_64-linux-gnu 2: Test timeout computed to be: 10000000 2: /usr/bin/bcftools 1: /usr/bin/bcftools 2: minimac v4.1.2 2: 1: minimac v4.1.2 1: 2: minimac v4.1.2 2: 2: Imputing chr20:1-10009927 ... 2: Loading target 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: Loading switch probabilities ... 2: Loading switch probabilities took 0 seconds 2: Running HMM with 1 threads ... 2: Running HMM took 0 seconds 2: Writing output ... 2: Writing output 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: minimac v4.1.2 1: 1: Imputing chr20:1-10009927 ... 1: Loading target haplotypes ... 1: Loading target haplotypes took 0 seconds 1: Loading reference haplotypes ... 1: Loading reference haplotypes took 0 seconds 1: Typed sites to imputed sites ratio: 0.903226 (28/31) 1: Loading switch probabilities ... 1: Loading switch probabilities took 0 seconds 1: Running HMM with 1 threads ... 1: Running HMM took 0 seconds 1: Writing output ... 1: Writing output 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 0.21 sec 2/2 Test #2: haploid_and_diploid_test ......... Passed 0.19 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.22 sec make[1]: Leaving directory '/build/minimac4-4.1.2/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 -j16 install DESTDIR=/build/minimac4-4.1.2/debian/minimac4 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/minimac4-4.1.2 -B/build/minimac4-4.1.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/minimac4-4.1.2/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/minimac4-4.1.2/debian/minimac4/usr/bin/minimac4 make[1]: Leaving directory '/build/minimac4-4.1.2/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_4.1.2-1_amd64.deb'. dpkg-deb: building package 'minimac4' in '../minimac4_4.1.2-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../minimac4_4.1.2-1_amd64.buildinfo dpkg-genchanges --build=binary -O../minimac4_4.1.2-1_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/3257906 and its subdirectories I: Current time: Wed Jul 3 17:18:18 -12 2024 I: pbuilder-time-stamp: 1720070298 Thu Jun 1 22:55:19 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu Jun 1 22:55:19 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu Jun 1 23:00:18 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu Jun 1 23:00:19 UTC 2023 I: minimac4_4.1.2-1_amd64.changes: Format: 1.8 Date: Tue, 24 Jan 2023 20:01:52 +0100 Source: minimac4 Binary: minimac4 minimac4-dbgsym Architecture: amd64 Version: 4.1.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: minimac4 - Fast Imputation Based on State Space Reduction HMM Changes: minimac4 (4.1.2-1) unstable; urgency=medium . * Team upload. * New upstream version * Build-Depends: libsavvy-dev, libomp-jonathonl-dev, libzstd-dev * Standards-Version: 4.6.2 (routine-update) * Rename autopkgtest script to run-unit-test * Switch on build tests provided upstream * Build-Depends bcftools needed for build tests * Adapt autopkgtest to build time test Checksums-Sha1: d82d1f44c2147f02006fd83500004375ca499587 5633132 minimac4-dbgsym_4.1.2-1_amd64.deb 0137c6252712617d75d5673283495b5066a345df 6202 minimac4_4.1.2-1_amd64.buildinfo 1ce9ee912dc44c6260eecd3b008a2d1f9f750e67 240408 minimac4_4.1.2-1_amd64.deb Checksums-Sha256: 32b89e10a266217ebbbbebced3b8cdd1a8e0c92980705eb4f9e3bc8845be2f46 5633132 minimac4-dbgsym_4.1.2-1_amd64.deb f77fd412ebcb78149d55a8268b7c0b135b07be9aec0200ce3ff7dfd3faa1e619 6202 minimac4_4.1.2-1_amd64.buildinfo 070767c0e996d20753eaaecf3b959d247bb517d60da94c69c74e33cdcca2dd75 240408 minimac4_4.1.2-1_amd64.deb Files: fcb90542ad37000d028081a5a6ec1c49 5633132 debug optional minimac4-dbgsym_4.1.2-1_amd64.deb 1d2aae97b94820a7eac9f5cc9014a147 6202 science optional minimac4_4.1.2-1_amd64.buildinfo 69130f1edca7ce3b441cb4618aa8e36c 240408 science optional minimac4_4.1.2-1_amd64.deb Thu Jun 1 23:00:20 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QppFXRZm/minimac4_4.1.2-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QppFXRZm/minimac4_4.1.2-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QppFXRZm/minimac4_4.1.2-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QppFXRZm/b1/minimac4_4.1.2-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.QppFXRZm/b2/minimac4_4.1.2-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.378s) 0.378s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.075s) 0.075s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Thu Jun 1 23:00:35 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Thu Jun 1 23:00:35 UTC 2023 I: minimac4 from bookworm built successfully and reproducibly on amd64. Thu Jun 1 23:00:38 UTC 2023 I: Submitting .buildinfo files to external archives: Thu Jun 1 23:00:39 UTC 2023 I: Submitting 8.0K b1/minimac4_4.1.2-1_amd64.buildinfo.asc Thu Jun 1 23:00:40 UTC 2023 I: Submitting 8.0K b2/minimac4_4.1.2-1_amd64.buildinfo.asc Thu Jun 1 23:00:40 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jun 1 23:00:40 UTC 2023 I: Done submitting .buildinfo files. Thu Jun 1 23:00:40 UTC 2023 I: Removing signed minimac4_4.1.2-1_amd64.buildinfo.asc files: removed './b1/minimac4_4.1.2-1_amd64.buildinfo.asc' removed './b2/minimac4_4.1.2-1_amd64.buildinfo.asc'