Diff of the two buildlogs: -- --- b1/build.log 2023-04-30 23:50:25.772131021 +0000 +++ b2/build.log 2023-05-01 00:01:29.551032271 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 1 18:07:17 -12 2024 -I: pbuilder-time-stamp: 1717308437 +I: Current time: Mon May 1 13:50:29 +14 2023 +I: pbuilder-time-stamp: 1682898629 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./gemma_0.98.5+dfsg.orig.tar.xz] I: copying [./gemma_0.98.5+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Nov 17 23:18:27 2022 -12 +gpgv: Signature made Sat Nov 19 01:18:27 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,167 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2462765/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/301067/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 May 1 13:50 /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/301067/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/301067/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' + 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]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=15' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='78c0a915dcd54812b3834edf75ae6937' - 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='2462765' - PS1='# ' - PS2='> ' + INVOCATION_ID=8c476e227eb14e77961a9662d8b2036c + 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=301067 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.VZ5ufHHM/pbuilderrc_lO7l --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.VZ5ufHHM/b1 --logfile b1/build.log gemma_0.98.5+dfsg-2.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://85.184.249.68:3128' + 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.VZ5ufHHM/pbuilderrc_sPjI --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VZ5ufHHM/b2 --logfile b2/build.log --extrapackages usrmerge gemma_0.98.5+dfsg-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) 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/2462765/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 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 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 1 13:50 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 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 6460 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 8103 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/301067/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -278,7 +310,7 @@ Get: 64 http://deb.debian.org/debian bookworm/main amd64 libruby amd64 1:3.1 [4972 B] Get: 65 http://deb.debian.org/debian bookworm/main amd64 shunit2 all 2.1.8-3 [33.6 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] -Fetched 55.2 MB in 1s (78.6 MB/s) +Fetched 55.2 MB in 2s (32.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) @@ -571,8 +603,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/gemma-0.98.5+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_0.98.5+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/301067/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/301067/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/gemma-0.98.5+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_0.98.5+dfsg-2_source.changes dpkg-buildpackage: info: source package gemma dpkg-buildpackage: info: source version 0.98.5+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -582,7 +625,7 @@ debian/rules clean dh clean dh_auto_clean - make -j16 clean + make -j15 clean make[1]: Entering directory '/build/gemma-0.98.5+dfsg' rm -vf ./src/*.o rm -vf ./src/*~ @@ -615,7 +658,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j16 "INSTALL=install --strip-program=true" + make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/gemma-0.98.5+dfsg' g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.5+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 -ffile-prefix-map=/build/gemma-0.98.5+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 @@ -697,12 +740,41 @@ rm -vf output/* ruby -Eutf-8 -Itest ./test/dev_tests.rb | tee ./dev_test.log -Run options: --seed 41349 +Run options: --seed 63747 # Running: +GSL_RNG_SEED=100 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 +GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 +Reading Files ... +## number of total individuals = 427 +## number of analyzed individuals = 427 +## number of covariates = 1 +## number of phenotypes = 1 +## number of total SNPs/var = 358499 +## number of analyzed SNPs = 273349 +Calculating Relatedness Matrix ... + 0% 0% 1% 1% 1% 1% 2% 2% = 2% = 3% = 3% = 3% = 3% = 4% = 4% == 4% == 4% == 5% == 5% == 5% == 6% == 6% === 6% === 6% === 7% === 7% === 7% === 8% === 8% ==== 8% ==== 8% ==== 9% ==== 9% ==== 9% ==== 9% ==== 10% ===== 10% ===== 10% ===== 11% ===== 11% ===== 11% ===== 11% ===== 12% ===== 12% ====== 12% ====== 13% ====== 13% ====== 13% ====== 13% ====== 14% ====== 14% ======= 14% ======= 15% ======= 15% ======= 15% ======= 15% ======= 16% ======= 16% ======== 16% ======== 16% ======== 17% ======== 17% ======== 17% ======== 18% ======== 18% ========= 18% ========= 18% ========= 19% ========= 19% ========= 19% ========= 20% ========= 20% ========== 20% ========== 20% ========== 21% ========== 21% ========== 21% ========== 21% ========== 22% =========== 22% =========== 22% =========== 23% =========== 23% =========== 23% =========== 23% =========== 24% =========== 24% ============ 24% ============ 25% ============ 25% ============ 25% ============ 25% ============ 26% ============ 26% ============= 26% ============= 26% ============= 27% ============= 27% ============= 27% ============= 28% ============= 28% ============== 28% ============== 28% ============== 29% ============== 29% ============== 29% ============== 30% ============== 30% =============== 30% =============== 30% =============== 31% =============== 31% =============== 31% =============== 32% =============== 32% ================ 32% ================ 32% ================ 33% ================ 33% ================ 33% ================ 33% ================ 34% ================= 34% ================= 34% ================= 35% ================= 35% ================= 35% ================= 35% ================= 36% ================= 36% ================== 36% ================== 37% ================== 37% ================== 37% ================== 37% ================== 38% ================== 38% =================== 38% =================== 38% =================== 39% =================== 39% =================== 39% =================== 40% 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================================================ 97% ================================================ 97% ================================================ 97% ================================================ 98% ================================================ 98% ================================================= 98% ================================================= 98% ================================================= 99% ================================================= 99% ================================================= 99% ================================================= 100% ================================================= 100% ================================================== 100% +**** INFO: Done. GSL_RNG_SEED=100 +GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins 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 = 427 +## number of analyzed individuals = 427 +## number of covariates = 2 +## number of phenotypes = 1 +## number of total SNPs/var = 358499 +## number of analyzed SNPs = 223242 +Start Eigen-Decomposition... +pve estimate =0.365545 +se(pve) =0.47481 + 0% 0% 1% 1% 1% 1% 2% 2% = 2% = 3% = 3% = 3% = 3% = 4% = 4% == 4% == 4% == 5% == 5% == 5% == 6% == 6% === 6% === 6% === 7% === 7% === 7% === 8% === 8% ==== 8% ==== 8% ==== 9% ==== 9% ==== 9% ==== 9% ==== 10% ===== 10% ===== 10% ===== 11% ===== 11% ===== 11% ===== 11% ===== 12% ===== 12% ====== 12% ====== 13% ====== 13% ====== 13% ====== 13% ====== 14% ====== 14% ======= 14% ======= 15% ======= 15% ======= 15% ======= 15% ======= 16% ======= 16% ======== 16% ======== 16% ======== 17% ======== 17% ======== 17% ======== 18% ======== 18% ========= 18% ========= 18% ========= 19% ========= 19% ========= 19% ========= 20% ========= 20% ========== 20% ========== 20% ========== 21% ========== 21% ========== 21% ========== 21% ========== 22% =========== 22% =========== 22% =========== 23% =========== 23% =========== 23% =========== 23% =========== 24% =========== 24% ============ 24% ============ 25% ============ 25% ============ 25% ============ 25% ============ 26% ============ 26% ============= 26% ============= 26% ============= 27% ============= 27% ============= 27% ============= 28% ============= 28% ============== 28% ============== 28% ============== 29% ============== 29% ============== 29% ============== 30% ============== 30% =============== 30% =============== 30% =============== 31% =============== 31% =============== 31% =============== 32% =============== 32% ================ 32% ================ 32% 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62% =============================== 62% =============================== 62% =============================== 63% =============================== 63% =============================== 63% =============================== 64% =============================== 64% ================================ 64% ================================ 64% ================================ 65% ================================ 65% ================================ 65% ================================ 66% ================================ 66% ================================= 66% ================================= 66% ================================= 67% ================================= 67% ================================= 67% ================================= 68% ================================= 68% ================================== 68% ================================== 68% ================================== 69% ================================== 69% ================================== 69% ================================== 69% ================================== 70% =================================== 70% =================================== 70% =================================== 71% =================================== 71% =================================== 71% =================================== 71% =================================== 72% =================================== 72% ==================================== 72% ==================================== 73% ==================================== 73% ==================================== 73% ==================================== 73% ==================================== 74% ==================================== 74% ===================================== 74% ===================================== 74% ===================================== 75% ===================================== 75% ===================================== 75% ===================================== 76% ===================================== 76% 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========================================= 82% ========================================= 83% ========================================= 83% ========================================= 83% ========================================= 83% ========================================= 84% ========================================= 84% ========================================== 84% ========================================== 85% ========================================== 85% ========================================== 85% ========================================== 85% ========================================== 86% ========================================== 86% =========================================== 86% =========================================== 86% =========================================== 87% =========================================== 87% =========================================== 87% =========================================== 88% =========================================== 88% ============================================ 88% ============================================ 88% ============================================ 89% ============================================ 89% ============================================ 89% ============================================ 90% ============================================ 90% ============================================= 90% ============================================= 90% ============================================= 91% ============================================= 91% ============================================= 91% ============================================= 91% ============================================= 92% ============================================== 92% ============================================== 92% ============================================== 93% ============================================== 93% ============================================== 93% ============================================== 93% ============================================== 94% =============================================== 94% =============================================== 94% =============================================== 95% =============================================== 95% =============================================== 95% =============================================== 95% =============================================== 96% =============================================== 96% ================================================ 96% ================================================ 97% ================================================ 97% ================================================ 97% ================================================ 97% ================================================ 98% ================================================ 98% ================================================= 98% ================================================= 98% ================================================= 99% ================================================= 99% ================================================= 99% ================================================= 100% ================================================= 100% ================================================== 100% +**** INFO: Done. +.GSL_RNG_SEED=100 +GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins 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. @@ -715,8 +787,8 @@ Calculating Relatedness Matrix ... 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% **** INFO: Done. -GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 +GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins 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. @@ -728,7 +800,7 @@ ## number of analyzed SNPs = 7317 Start Eigen-Decomposition... pve estimate =0.00100086 -se(pve) =0.204166 +se(pve) =0.204165 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% **** INFO: Done. GSL_RNG_SEED=100 @@ -744,11 +816,23 @@ ## number of analyzed SNPs = 7317 Start Eigen-Decomposition... pve estimate =0.00100086 -se(pve) =0.204166 +se(pve) =0.204165 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% **** INFO: Done. -.GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 -GSL_RNG_SEED=100 +.GSL_RNG_SEED=100 +GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 +GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 +Reading Files ... +## number of total individuals = 1940 +## number of analyzed individuals = 1410 +## number of covariates = 1 +## number of phenotypes = 1 +## number of total SNPs/var = 12226 +## number of analyzed SNPs = 10768 + 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% +**** INFO: Done. +.GSL_RNG_SEED=100 +GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** TEST MODE: trim individuals from 1940 to 400 @@ -766,8 +850,8 @@ Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. -GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 +GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** TEST MODE: trim individuals from 1940 to 400 @@ -787,54 +871,13 @@ se(pve) =0.0717914 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. -.GSL_RNG_SEED=100 -GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 -GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 -Reading Files ... -## number of total individuals = 427 -## number of analyzed individuals = 427 -## number of covariates = 1 -## number of phenotypes = 1 -## number of total SNPs/var = 358499 -## number of analyzed SNPs = 273349 -Calculating Relatedness Matrix ... - 0% 0% 1% 1% 1% 1% 2% 2% = 2% = 3% = 3% = 3% = 3% = 4% = 4% == 4% == 4% == 5% == 5% == 5% == 6% == 6% === 6% === 6% === 7% === 7% === 7% === 8% === 8% ==== 8% ==== 8% ==== 9% ==== 9% ==== 9% ==== 9% ==== 10% ===== 10% ===== 10% ===== 11% ===== 11% ===== 11% ===== 11% ===== 12% ===== 12% ====== 12% ====== 13% ====== 13% ====== 13% ====== 13% ====== 14% ====== 14% ======= 14% ======= 15% ======= 15% ======= 15% ======= 15% ======= 16% ======= 16% ======== 16% ======== 16% ======== 17% ======== 17% ======== 17% ======== 18% ======== 18% ========= 18% ========= 18% ========= 19% ========= 19% ========= 19% ========= 20% ========= 20% ========== 20% ========== 20% ========== 21% ========== 21% ========== 21% ========== 21% ========== 22% =========== 22% =========== 22% =========== 23% =========== 23% =========== 23% =========== 23% =========== 24% =========== 24% ============ 24% ============ 25% ============ 25% ============ 25% ============ 25% ============ 26% ============ 26% ============= 26% ============= 26% ============= 27% ============= 27% ============= 27% ============= 28% ============= 28% ============== 28% ============== 28% ============== 29% ============== 29% ============== 29% ============== 30% ============== 30% =============== 30% =============== 30% =============== 31% =============== 31% =============== 31% =============== 32% =============== 32% ================ 32% 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============================== 62% =============================== 62% =============================== 62% =============================== 63% =============================== 63% =============================== 63% =============================== 64% =============================== 64% ================================ 64% ================================ 64% ================================ 65% ================================ 65% ================================ 65% ================================ 66% ================================ 66% ================================= 66% ================================= 66% ================================= 67% ================================= 67% ================================= 67% ================================= 68% ================================= 68% ================================== 68% ================================== 68% ================================== 69% ================================== 69% 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=========================================== 88% ============================================ 88% ============================================ 88% ============================================ 89% ============================================ 89% ============================================ 89% ============================================ 90% ============================================ 90% ============================================= 90% ============================================= 90% ============================================= 91% ============================================= 91% ============================================= 91% ============================================= 91% ============================================= 92% ============================================== 92% ============================================== 92% ============================================== 93% ============================================== 93% ============================================== 93% ============================================== 93% ============================================== 94% =============================================== 94% =============================================== 94% =============================================== 95% =============================================== 95% =============================================== 95% =============================================== 95% =============================================== 96% =============================================== 96% ================================================ 96% ================================================ 97% ================================================ 97% ================================================ 97% ================================================ 97% ================================================ 98% ================================================ 98% ================================================= 98% ================================================= 98% ================================================= 99% ================================================= 99% ================================================= 99% ================================================= 100% ================================================= 100% ================================================== 100% -**** INFO: Done. -GSL_RNG_SEED=100 -GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins 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 = 427 -## number of analyzed individuals = 427 -## number of covariates = 2 -## number of phenotypes = 1 -## number of total SNPs/var = 358499 -## number of analyzed SNPs = 223242 -Start Eigen-Decomposition... -pve estimate =0.365545 -se(pve) =0.47481 - 0% 0% 1% 1% 1% 1% 2% 2% = 2% = 3% = 3% = 3% = 3% = 4% = 4% == 4% == 4% == 5% == 5% == 5% == 6% == 6% === 6% === 6% === 7% === 7% === 7% === 8% === 8% ==== 8% ==== 8% ==== 9% ==== 9% ==== 9% ==== 9% ==== 10% ===== 10% ===== 10% ===== 11% ===== 11% ===== 11% ===== 11% ===== 12% ===== 12% ====== 12% ====== 13% ====== 13% ====== 13% ====== 13% ====== 14% ====== 14% ======= 14% ======= 15% ======= 15% ======= 15% ======= 15% ======= 16% ======= 16% ======== 16% ======== 16% ======== 17% ======== 17% ======== 17% ======== 18% ======== 18% ========= 18% ========= 18% ========= 19% ========= 19% ========= 19% ========= 20% ========= 20% ========== 20% ========== 20% ========== 21% ========== 21% ========== 21% ========== 21% ========== 22% =========== 22% =========== 22% =========== 23% =========== 23% =========== 23% =========== 23% =========== 24% =========== 24% ============ 24% ============ 25% ============ 25% ============ 25% ============ 25% ============ 26% ============ 26% ============= 26% ============= 26% ============= 27% ============= 27% ============= 27% ============= 28% ============= 28% ============== 28% ============== 28% ============== 29% ============== 29% ============== 29% ============== 30% ============== 30% =============== 30% =============== 30% =============== 31% =============== 31% =============== 31% =============== 32% =============== 32% ================ 32% ================ 32% ================ 33% ================ 33% ================ 33% ================ 33% ================ 34% ================= 34% ================= 34% ================= 35% ================= 35% ================= 35% ================= 35% ================= 36% ================= 36% ================== 36% ================== 37% ================== 37% ================== 37% ================== 37% ================== 38% ================== 38% =================== 38% =================== 38% =================== 39% =================== 39% =================== 39% =================== 40% =================== 40% ==================== 40% 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========================================== 86% =========================================== 86% =========================================== 86% =========================================== 87% =========================================== 87% =========================================== 87% =========================================== 88% =========================================== 88% ============================================ 88% ============================================ 88% ============================================ 89% ============================================ 89% ============================================ 89% ============================================ 90% ============================================ 90% ============================================= 90% ============================================= 90% ============================================= 91% ============================================= 91% ============================================= 91% ============================================= 91% ============================================= 92% ============================================== 92% ============================================== 92% ============================================== 93% ============================================== 93% ============================================== 93% ============================================== 93% ============================================== 94% =============================================== 94% =============================================== 94% =============================================== 95% =============================================== 95% =============================================== 95% =============================================== 95% =============================================== 96% =============================================== 96% ================================================ 96% ================================================ 97% ================================================ 97% ================================================ 97% ================================================ 97% ================================================ 98% ================================================ 98% ================================================= 98% ================================================= 98% ================================================= 99% ================================================= 99% ================================================= 99% ================================================= 100% ================================================= 100% ================================================== 100% -**** INFO: Done. -.GSL_RNG_SEED=100 -GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 -GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 -Reading Files ... -## number of total individuals = 1940 -## number of analyzed individuals = 1410 -## number of covariates = 1 -## number of phenotypes = 1 -## number of total SNPs/var = 12226 -## number of analyzed SNPs = 10768 - 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% -**** INFO: Done. . -Finished in 246.628638s, 0.0162 runs/s, 0.0851 assertions/s. +Finished in 371.627956s, 0.0108 runs/s, 0.0565 assertions/s. 4 runs, 21 assertions, 0 failures, 0 errors, 0 skips make[2]: Leaving directory '/build/gemma-0.98.5+dfsg' - rm -fr -- /tmp/dh-xdg-rundir-0ODrQeYh + rm -fr -- /tmp/dh-xdg-rundir-QpFVIrA3 make[1]: Leaving directory '/build/gemma-0.98.5+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -858,10 +901,10 @@ chmod -R u\+rw,go=rX debian/gemma-doc/usr/share/doc install -p -m0644 debian/copyright debian/gemma-doc/usr/share/doc/gemma-doc/copyright dh_installchangelogs - install -m0755 -d debian/gemma/usr/share/doc/gemma - install -p -m0644 debian/.debhelper/generated/gemma/dh_installchangelogs.dch.trimmed debian/gemma/usr/share/doc/gemma/changelog.Debian install -m0755 -d debian/gemma-doc/usr/share/doc/gemma-doc install -p -m0644 debian/.debhelper/generated/gemma-doc/dh_installchangelogs.dch.trimmed debian/gemma-doc/usr/share/doc/gemma-doc/changelog.Debian + install -m0755 -d debian/gemma/usr/share/doc/gemma + install -p -m0644 debian/.debhelper/generated/gemma/dh_installchangelogs.dch.trimmed debian/gemma/usr/share/doc/gemma/changelog.Debian dh_perl dh_link dh_strip_nondeterminism @@ -872,16 +915,16 @@ 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 - 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/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian - 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 cd '/build/gemma-0.98.5+dfsg' + 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 cd '/build/gemma-0.98.5+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 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s 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/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/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 @@ -908,22 +951,22 @@ install -m0755 -d debian/gemma/DEBIAN install -m0755 -d debian/gemma-doc/DEBIAN dh_gencontrol + install -m0755 -d debian/gemma-doc/DEBIAN + echo misc:Depends= >> debian/gemma-doc.substvars + echo misc:Pre-Depends= >> debian/gemma-doc.substvars + dpkg-gencontrol -pgemma-doc -ldebian/changelog -Tdebian/gemma-doc.substvars -Pdebian/gemma-doc install -m0755 -d debian/gemma/DEBIAN echo misc:Depends= >> debian/gemma.substvars echo misc:Pre-Depends= >> debian/gemma.substvars install -m0755 -d debian/.debhelper/gemma/dbgsym-root/DEBIAN dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -Pdebian/.debhelper/gemma/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=gemma-dbgsym "-DDepends=gemma (= \${binary:Version})" "-DDescription=debug symbols for gemma" -DBuild-Ids=78e6b0ccc6c77899fa35c8c0c4efc9d0c9152304 -DSection=debug -UMulti-Arch -UReplaces -UBreaks - install -m0755 -d debian/gemma-doc/DEBIAN - echo misc:Depends= >> debian/gemma-doc.substvars - echo misc:Pre-Depends= >> debian/gemma-doc.substvars - dpkg-gencontrol -pgemma-doc -ldebian/changelog -Tdebian/gemma-doc.substvars -Pdebian/gemma-doc - chmod 0644 -- debian/gemma-doc/DEBIAN/control chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/control dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -Pdebian/gemma + chmod 0644 -- debian/gemma-doc/DEBIAN/control chmod 0644 -- debian/gemma/DEBIAN/control dh_md5sums - install -m0755 -d debian/gemma/DEBIAN install -m0755 -d debian/gemma-doc/DEBIAN + install -m0755 -d debian/gemma/DEBIAN 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 chmod 0644 -- debian/gemma/DEBIAN/md5sums @@ -932,11 +975,11 @@ chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/gemma-doc/DEBIAN/md5sums dh_builddeb + dpkg-deb --root-owner-group --build debian/gemma-doc .. dpkg-deb --root-owner-group --build debian/gemma .. 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' in '../gemma_0.98.5+dfsg-2_amd64.deb'. dpkg-deb: building package 'gemma-doc' in '../gemma-doc_0.98.5+dfsg-2_all.deb'. +dpkg-deb: building package 'gemma' in '../gemma_0.98.5+dfsg-2_amd64.deb'. dpkg-deb: building package 'gemma-dbgsym' in '../gemma-dbgsym_0.98.5+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gemma_0.98.5+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gemma_0.98.5+dfsg-2_amd64.changes @@ -945,12 +988,14 @@ 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/301067/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/301067/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/2462765 and its subdirectories -I: Current time: Sat Jun 1 18:13:26 -12 2024 -I: pbuilder-time-stamp: 1717308806 +I: removing directory /srv/workspace/pbuilder/301067 and its subdirectories +I: Current time: Mon May 1 14:01:29 +14 2023 +I: pbuilder-time-stamp: 1682899289