Diff of the two buildlogs: -- --- b1/build.log 2024-07-05 11:23:30.818024632 +0000 +++ b2/build.log 2024-07-05 11:31:27.937715266 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 4 23:11:29 -12 2024 -I: pbuilder-time-stamp: 1720177889 +I: Current time: Fri Aug 8 07:46:31 +14 2025 +I: pbuilder-time-stamp: 1754588791 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./gemma_0.98.4+dfsg-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.HIAcHKVd/trustedkeys.kbx': General error -gpgv: Signature made Fri Jul 30 17:19:48 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.0lo6UW9f/trustedkeys.kbx': General error +gpgv: Signature made Sat Jul 31 19:19:48 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,135 +33,166 @@ dpkg-source: info: applying Makefile.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/561431/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/538655/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Aug 8 07:46 /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/538655/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/538655/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,-fixfilepath parallel=20 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=42 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f7b77b78ce0244b6a33b0ea60dd7f222' - 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='561431' - PS1='# ' - PS2='> ' + INVOCATION_ID=5045483f93b3409c97ab5fc6c881552f + 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=538655 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.MALss73v/pbuilderrc_XThn --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MALss73v/b1 --logfile b1/build.log gemma_0.98.4+dfsg-4.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.MALss73v/pbuilderrc_qhyJ --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MALss73v/b2 --logfile b2/build.log gemma_0.98.4+dfsg-4.dsc' + SUDO_GID=110 + SUDO_UID=105 + 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 ionos11-amd64 6.1.0-22-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.94-1 (2024-06-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Mar 27 22:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 22:09 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Mar 27 22:09 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Mar 27 22:09 more - -rwsr-xr-x 1 root root 55528 Mar 27 22:09 mount - -rwxr-xr-x 1 root root 18664 Mar 27 22:09 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 6 21:25 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Mar 27 22:09 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 21:59 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Mar 27 22:09 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 22:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/561431/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Mar 29 2024 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 2024 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Mar 29 2024 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Mar 29 2024 more + -rwsr-xr-x 1 root root 55528 Mar 29 2024 mount + -rwxr-xr-x 1 root root 18664 Mar 29 2024 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Aug 8 07:46 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Mar 29 2024 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 2024 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Mar 29 2024 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 2024 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/538655/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -259,7 +290,7 @@ Get: 46 http://deb.debian.org/debian bullseye/main amd64 libopenblas-dev amd64 0.3.13+ds-3+deb11u1 [44.2 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 shunit2 all 2.1.6-1.2 [39.7 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] -Fetched 44.6 MB in 1s (62.7 MB/s) +Fetched 44.6 MB in 1s (47.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19711 files and directories currently installed.) @@ -476,7 +507,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gemma-0.98.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gemma_0.98.4+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/538655/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/538655/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gemma-0.98.4+dfsg/ && 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 > ../gemma_0.98.4+dfsg-4_source.changes dpkg-buildpackage: info: source package gemma dpkg-buildpackage: info: source version 0.98.4+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -487,7 +522,7 @@ dh clean dh_auto_clean install -d /build/reproducible-path/gemma-0.98.4\+dfsg/debian/.debhelper/generated/_source/home - make -j20 clean + make -j42 clean make[1]: Entering directory '/build/reproducible-path/gemma-0.98.4+dfsg' rm -vf ./src/*.o rm -vf ./src/*~ @@ -521,7 +556,7 @@ dh_auto_configure install -d /build/reproducible-path/gemma-0.98.4\+dfsg/debian/.debhelper/generated/_source/home dh_auto_build - make -j20 "INSTALL=install --strip-program=true" + make -j42 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/gemma-0.98.4+dfsg' g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmm.o src/bslmm.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmmdap.o src/bslmmdap.cpp @@ -621,8 +656,8 @@ cd test && ./dev_test_suite.sh | tee ../dev_test.log run system shunit2 testLinearModel -GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 +GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... ## number of total individuals = 1940 @@ -633,14 +668,14 @@ ## number of analyzed SNPs = 10768 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. -## total computation time = 0.0946074 min +## total computation time = 0.11503 min testBXDStandardRelatednessMatrixKSingularError -GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=100 -GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 -Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. GSL ERROR: matrix is singular in lu.c at line 449 errno 1 +GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 +GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 +Reading Files ... testBXDStandardRelatednessMatrixK GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=100 @@ -655,13 +690,15 @@ ## number of analyzed SNPs = 7317 Calculating Relatedness Matrix ... 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% +Mismatch coordinates (2,0)0:0! +**** WARNING: K is not symmetric! in src/gemma.cpp at line 1912 in BatchRun **** INFO: Done. testBXDLMLikelihoodRatio -GSL_RNG_SEED=100 -**** INFO: no intercept term is found in the cvt file: a column of 1s is added. GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 +GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... +**** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 @@ -672,10 +709,10 @@ **** INFO: Done. testBXDLMMLikelihoodRatio GSL_RNG_SEED=100 +**** INFO: no intercept term is found in the cvt file: a column of 1s is added. GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... -**** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 @@ -740,8 +777,8 @@ 0% ========================= 50% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixKLOCO1 -GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 +GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** TEST MODE: trim individuals from 1940 to 400 @@ -758,8 +795,10 @@ ## number of analyzed SNPs = 889 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% +**** WARNING: Mismatch coordinates (4,0)0:0! +K is not symmetric! in src/gemma.cpp at line 1912 in BatchRun **** INFO: Done. -## total computation time = 0.151471 min +## total computation time = 0.539521 min testUnivariateLinearMixedModelLOCO1 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=100 @@ -780,9 +819,9 @@ Start Eigen-Decomposition... pve estimate =0.678775 se(pve) =0.0717914 - 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% -**** INFO: Done. -## total computation time = 0.103368 min + 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. +================================================== 100% +## total computation time = 0.213058 min testPlinkCenteredRelatednessMatrixKLOCO1 testPlinkUnivariateLinearMixedModelLOCO1 testCorrelatedPhenotypesMvLLM @@ -822,30 +861,30 @@ 0.0266 0.0186 0.0215 0.0242 0.0208 REMLE likelihood = -3813.3258 MLE estimate for Vg in the null model: -0.8082 -0.1434 0.0660 --0.1455 -0.0664 0.1165 -0.0906 0.0362 -0.0830 0.0639 --0.5528 -0.0984 0.1170 -0.0764 0.4127 +0.8086 +0.1436 0.0660 +-0.1456 -0.0665 0.1167 +0.0907 0.0362 -0.0831 0.0640 +-0.5531 -0.0985 0.1171 -0.0765 0.4130 se(Vg): -0.0735 -0.0355 0.0298 -0.0420 0.0264 0.0421 +0.0736 +0.0355 0.0299 +0.0421 0.0264 0.0422 0.0443 0.0278 0.0430 0.0478 -0.0515 0.0254 0.0295 0.0313 0.0388 +0.0516 0.0254 0.0295 0.0313 0.0389 MLE estimate for Ve in the null model: -0.0334 +0.0335 0.0267 0.4497 --0.0529 -0.0882 0.5997 -0.0682 0.1412 -0.6495 0.8392 --0.0128 -0.0040 -0.0705 0.0879 0.0418 +-0.0528 -0.0881 0.5996 +0.0682 0.1411 -0.6494 0.8391 +-0.0128 -0.0040 -0.0705 0.0879 0.0417 se(Ve): 0.0378 0.0252 0.0329 0.0298 0.0281 0.0455 -0.0331 0.0318 0.0493 0.0582 -0.0265 0.0185 0.0215 0.0242 0.0207 -MLE likelihood = -3814.3913 +0.0332 0.0318 0.0493 0.0582 +0.0266 0.0186 0.0215 0.0242 0.0208 +MLE likelihood = -3814.3903 0% ================================================== 100% **** INFO: Done. @@ -909,8 +948,8 @@ 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm3 -GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 +GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 1 (option 1); first value = 1791095845 Reading Files ... ## number of total individuals = 1940 @@ -930,8 +969,8 @@ 0% 0.00 ==== 9% 0.22 ========= 18% 0.22 ============= 27% 0.21 ================== 36% 0.21 ====================== 45% 0.21 =========================== 55% 0.21 =============================== 64% 0.21 ==================================== 73% 0.21 ======================================== 82% 0.21 ============================================= 91% 0.21 ================================================== 100% 0.21 **** INFO: Done. testBslmm4 -GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 +GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 @@ -953,9 +992,9 @@ ## number of phenotypes = 1 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. -GSL_RNG_SEED=10 testCenteredRelatednessMatrixKFullLOCO1 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 +GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 @@ -989,7 +1028,7 @@ se(pve) =0.0332587 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. -## total computation time = 0.760059 min +## total computation time = 1.39779 min testCenteredRelatednessMatrixK GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 @@ -1005,8 +1044,8 @@ 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testUnivariateLinearMixedModel -GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 +GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 @@ -1020,7 +1059,7 @@ se(pve) =0.032774 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. -## total computation time = 0.985195 min +## total computation time = 1.4643 min testLinearMixedModelPhenotypes GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 @@ -1098,7 +1137,7 @@ OK tail -n 1 test.log | grep -q 'OK' test.log make[2]: Leaving directory '/build/reproducible-path/gemma-0.98.4+dfsg' - rm -fr -- /tmp/dh-xdg-rundir-6XWPjfmc + rm -fr -- /tmp/dh-xdg-rundir-GuWWuNwV make[1]: Leaving directory '/build/reproducible-path/gemma-0.98.4+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -1135,20 +1174,20 @@ cd debian/gemma cd debian/gemma-doc chmod a-x usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian + gzip -9nf usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian chmod a-x usr/share/doc/gemma-doc/changelog.Debian usr/share/doc/gemma/example/BXD_snps.txt usr/share/doc/gemma/example/HLC.bed usr/share/doc/gemma/example/HLC.bim usr/share/doc/gemma/example/HLC.fam usr/share/doc/gemma/example/HLC.simu.pheno.txt usr/share/doc/gemma/example/demo.txt usr/share/doc/gemma/example/mouse_hs1940.anno.txt usr/share/doc/gemma/example/mouse_hs1940.bed usr/share/doc/gemma/example/mouse_hs1940.bim usr/share/doc/gemma/example/mouse_hs1940.fam usr/share/doc/gemma/example/mouse_hs1940.pheno.txt usr/share/doc/gemma/example/mouse_hs1940_snps.txt usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt gzip -9nf usr/share/doc/gemma-doc/changelog.Debian usr/share/doc/gemma/example/BXD_snps.txt usr/share/doc/gemma/example/HLC.bed usr/share/doc/gemma/example/HLC.bim usr/share/doc/gemma/example/HLC.fam usr/share/doc/gemma/example/HLC.simu.pheno.txt usr/share/doc/gemma/example/demo.txt usr/share/doc/gemma/example/mouse_hs1940.anno.txt usr/share/doc/gemma/example/mouse_hs1940.bed usr/share/doc/gemma/example/mouse_hs1940.bim usr/share/doc/gemma/example/mouse_hs1940.fam usr/share/doc/gemma/example/mouse_hs1940.pheno.txt usr/share/doc/gemma/example/mouse_hs1940_snps.txt usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt - gzip -9nf usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian cd '/build/reproducible-path/gemma-0.98.4+dfsg' cd '/build/reproducible-path/gemma-0.98.4+dfsg' dh_fixperms find debian/gemma ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/gemma-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/gemma/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/gemma-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/gemma/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/gemma-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/gemma-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/gemma -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/gemma-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a @@ -1181,8 +1220,8 @@ dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -Pdebian/gemma chmod 0644 -- debian/gemma/DEBIAN/control dh_md5sums - cd debian/gemma >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/gemma-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + cd debian/gemma >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/gemma/DEBIAN/md5sums cd debian/.debhelper/gemma/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/md5sums @@ -1192,8 +1231,8 @@ dpkg-deb --root-owner-group --build debian/.debhelper/gemma/dbgsym-root .. dpkg-deb --root-owner-group --build debian/gemma-doc .. dpkg-deb: building package 'gemma-dbgsym' in '../gemma-dbgsym_0.98.4+dfsg-4_amd64.deb'. -dpkg-deb: building package 'gemma-doc' in '../gemma-doc_0.98.4+dfsg-4_all.deb'. dpkg-deb: building package 'gemma' in '../gemma_0.98.4+dfsg-4_amd64.deb'. +dpkg-deb: building package 'gemma-doc' in '../gemma-doc_0.98.4+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gemma_0.98.4+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1201,12 +1240,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/538655/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/538655/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/561431 and its subdirectories -I: Current time: Thu Jul 4 23:23:30 -12 2024 -I: pbuilder-time-stamp: 1720178610 +I: removing directory /srv/workspace/pbuilder/538655 and its subdirectories +I: Current time: Fri Aug 8 07:54:24 +14 2025 +I: pbuilder-time-stamp: 1754589264