Diff of the two buildlogs: -- --- b1/build.log 2023-06-04 05:46:06.320076657 +0000 +++ b2/build.log 2023-06-04 05:55:19.391858106 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 3 17:37:22 -12 2023 -I: pbuilder-time-stamp: 1685857042 +I: Current time: Sun Jun 4 19:46:49 +14 2023 +I: pbuilder-time-stamp: 1685857609 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 [./reapr_1.0.18+dfsg.orig.tar.gz] I: copying [./reapr_1.0.18+dfsg-5.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Dec 26 18:26:11 2019 -12 +gpgv: Signature made Fri Dec 27 20:26:11 2019 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,167 @@ dpkg-source: info: applying ld_as_needed I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22776/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/24360/tmp/hooks/D01_modify_environment starting +debug: Running on virt32b. +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 Jun 4 19:47 /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/24360/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/24360/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='c60c1188ef77440698d4cdf7a4a0de2f' - 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='22776' - PS1='# ' - PS2='> ' + INVOCATION_ID=2d25e8876c194f3ba7e5438b84e6fc95 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=24360 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.ErqpT5bu/pbuilderrc_43e8 --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.ErqpT5bu/b1 --logfile b1/build.log reapr_1.0.18+dfsg-5.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.ErqpT5bu/pbuilderrc_kIhI --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.ErqpT5bu/b2 --logfile b2/build.log --extrapackages usrmerge reapr_1.0.18+dfsg-5.dsc' + SUDO_GID=112 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64b 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 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 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 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 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/22776/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 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 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 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 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 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 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 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 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 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 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Jun 4 19:47 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 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/24360/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -369,7 +401,7 @@ Get: 147 http://deb.debian.org/debian bookworm/main armhf smalt armhf 0.7.6-12 [98.4 kB] Get: 148 http://deb.debian.org/debian bookworm/main armhf snpomatic armhf 1.0-6 [71.1 kB] Get: 149 http://deb.debian.org/debian bookworm/main armhf tabix armhf 1.16+ds-3 [388 kB] -Fetched 94.1 MB in 9s (10.9 MB/s) +Fetched 94.1 MB in 9s (9967 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (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 ... 19324 files and directories currently installed.) @@ -1001,10 +1033,17 @@ Reading package lists... Building dependency tree... Reading state information... +usrmerge is already the newest version (35). fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reapr-1.0.18+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 > ../reapr_1.0.18+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/24360/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/24360/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reapr-1.0.18+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 > ../reapr_1.0.18+dfsg-5_source.changes dpkg-buildpackage: info: source package reapr dpkg-buildpackage: info: source version 1.0.18+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -1302,7 +1341,7 @@ make[1]: Entering directory '/build/reapr-1.0.18+dfsg' mkdir /build/reapr-1.0.18+dfsg/debian/test ln -s /build/reapr-1.0.18+dfsg/src/reapr.pl /build/reapr-1.0.18+dfsg/debian/test/reapr -PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/build/reapr-1.0.18+dfsg/src:/build/reapr-1.0.18+dfsg/debian/test /build/reapr-1.0.18+dfsg/debian/tests/test-example +PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path:/build/reapr-1.0.18+dfsg/src:/build/reapr-1.0.18+dfsg/debian/test /build/reapr-1.0.18+dfsg/debian/tests/test-example [wgsim] seed = 42 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 1 sequences, total length: 1000111 @@ -2283,8 +2322,8 @@ foo 994610 C Y + foo 998107 - T + foo 999725 G R + -[REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.7457.smaltmap.smalt_index foo1.fasta -# Command line: smalt index -k 13 -s 2 out.bam.tmp.7457.smaltmap.smalt_index foo1.fasta +[REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.32362.smaltmap.smalt_index foo1.fasta +# Command line: smalt index -k 13 -s 2 out.bam.tmp.32362.smaltmap.smalt_index foo1.fasta # Reading sequences ... # Writing sequence set ... # Setting up hash index with collisions ... @@ -2307,9 +2346,9 @@ # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Writing table to file ... -# smalt: Total elapsed wall clock time: 1 seconds -[REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.7457.smaltmap.smalt_sample out.bam.tmp.7457.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq -# Command line: smalt sample -u 1000 -o out.bam.tmp.7457.smaltmap.smalt_sample out.bam.tmp.7457.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq +# smalt: Total elapsed wall clock time: 0 seconds +[REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.32362.smaltmap.smalt_sample out.bam.tmp.32362.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq +# Command line: smalt sample -u 1000 -o out.bam.tmp.32362.smaltmap.smalt_sample out.bam.tmp.32362.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Opening read files ... # Reading reference sequences ... # Reading hash table ... @@ -2328,10 +2367,10 @@ # Sampling insert size distribution ... # Processed 9999 read pairs. # smalt: Time spent setting up hash index:0 seconds -# smalt: Time spent mapping reads:7 seconds -# smalt: Total elapsed wall clock time: 7 seconds -[REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.7457.smaltmap.smalt_sample -f samsoft out.bam.tmp.7457.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.7457.smaltmap.raw.bam -# Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.7457.smaltmap.smalt_sample -f samsoft out.bam.tmp.7457.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq +# smalt: Time spent mapping reads:9 seconds +# smalt: Total elapsed wall clock time: 9 seconds +[REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.32362.smaltmap.smalt_sample -f samsoft out.bam.tmp.32362.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.32362.smaltmap.raw.bam +# Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.32362.smaltmap.smalt_sample -f samsoft out.bam.tmp.32362.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Reading distribution of insert sizes from file ... # Sampled histogram # Smoothed histogram @@ -2351,17 +2390,17 @@ # Processing query reads ... # Processed 10000 read pairs. # smalt: Time spent setting up hash index:0 seconds -# smalt: Time spent mapping reads:39 seconds -# smalt: Total elapsed wall clock time: 39 seconds -[REAPR smaltmap] Running: samtools sort out.bam.tmp.7457.smaltmap.raw.bam -O bam -o out.bam.tmp.7457.smaltmap.raw.bam.sort.bam -[REAPR smaltmap] Running: samtools rmdup out.bam.tmp.7457.smaltmap.raw.bam.sort.bam out.bam.tmp.7457.smaltmap.rmdup.bam +# smalt: Time spent mapping reads:40 seconds +# smalt: Total elapsed wall clock time: 40 seconds +[REAPR smaltmap] Running: samtools sort out.bam.tmp.32362.smaltmap.raw.bam -O bam -o out.bam.tmp.32362.smaltmap.raw.bam.sort.bam +[REAPR smaltmap] Running: samtools rmdup out.bam.tmp.32362.smaltmap.raw.bam.sort.bam out.bam.tmp.32362.smaltmap.rmdup.bam [bam_rmdup_core] processing reference foo... [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' -[REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.7457.smaltmap.header -[REAPR smaltmap] Running: samtools view -H out.bam.tmp.7457.smaltmap.rmdup.bam >> out.bam.tmp.7457.smaltmap.header -[REAPR smaltmap] Running: samtools reheader out.bam.tmp.7457.smaltmap.header out.bam.tmp.7457.smaltmap.rmdup.bam > out.bam +[REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.32362.smaltmap.header +[REAPR smaltmap] Running: samtools view -H out.bam.tmp.32362.smaltmap.rmdup.bam >> out.bam.tmp.32362.smaltmap.header +[REAPR smaltmap] Running: samtools reheader out.bam.tmp.32362.smaltmap.header out.bam.tmp.32362.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam -[REAPR smaltmap] Running: rm out.bam.tmp.7457.smaltmap.* +[REAPR smaltmap] Running: rm out.bam.tmp.32362.smaltmap.* Running reapr version 1.0.18 pipeline: reapr foo1.fasta out.bam result [REAPR pipeline] Running facheck @@ -2418,27 +2457,27 @@ dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_fcdrate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/fa2gaps contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/n50 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_score contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/bam2fcdEstimate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/bam2fragCov contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_stats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/bam2perfect contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/bam2insert contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/fa2gc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_gapresize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_break contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/fa2gc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/fa2gaps contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_stats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/bam2perfect contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/make_plots contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/bam2fcdEstimate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/scaff2contig contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_break contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/n50 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/bam2fragCov contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'reapr-dbgsym' in '../reapr-dbgsym_1.0.18+dfsg-5_armhf.deb'. dpkg-deb: building package 'reapr' in '../reapr_1.0.18+dfsg-5_armhf.deb'. +dpkg-deb: building package 'reapr-dbgsym' in '../reapr-dbgsym_1.0.18+dfsg-5_armhf.deb'. dpkg-genbuildinfo --build=binary -O../reapr_1.0.18+dfsg-5_armhf.buildinfo dpkg-genchanges --build=binary -O../reapr_1.0.18+dfsg-5_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2446,12 +2485,14 @@ 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/24360/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/24360/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/22776 and its subdirectories -I: Current time: Sat Jun 3 17:45:58 -12 2023 -I: pbuilder-time-stamp: 1685857558 +I: removing directory /srv/workspace/pbuilder/24360 and its subdirectories +I: Current time: Sun Jun 4 19:55:11 +14 2023 +I: pbuilder-time-stamp: 1685858111