Diff of the two buildlogs: -- --- b1/build.log 2023-01-06 01:20:06.498051979 +0000 +++ b2/build.log 2023-01-06 01:36:42.248566217 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 7 19:39:35 -12 2024 -I: pbuilder-time-stamp: 1707377975 +I: Current time: Fri Jan 6 15:20:10 +14 2023 +I: pbuilder-time-stamp: 1672968010 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 [./ariba_2.14.6+ds-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.PHYSq33b/trustedkeys.kbx': General error -gpgv: Signature made Sun Sep 13 05:03:27 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.JVLANQ5R/trustedkeys.kbx': General error +gpgv: Signature made Mon Sep 14 07:03:27 2020 +14 gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ariba_2.14.6+ds-1.dsc @@ -34,135 +34,170 @@ dpkg-source: info: applying run-debian-spades-wrapper.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22017/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3674194/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +lrwxrwxrwx 1 root root 4 Jan 6 15:20 /bin/sh -> 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/3674194/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3674194/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,-fixfilepath parallel=16' - 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 + 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=15' + 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='767a22aece51445fb53a9f43b0d42f96' - 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='22017' - PS1='# ' - PS2='> ' + INVOCATION_ID=81c0c54d910644c39923213b4c51cf0c + 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=3674194 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.u4MSBO5l/pbuilderrc_Yu8w --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.u4MSBO5l/b1 --logfile b1/build.log ariba_2.14.6+ds-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.u4MSBO5l/pbuilderrc_pWWX --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.u4MSBO5l/b2 --logfile b2/build.log ariba_2.14.6+ds-1.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://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 6.0.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.0.12-1~bpo11+1 (2022-12-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) 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 Jan 20 2022 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 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 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 Jan 20 2022 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 Jan 20 2022 more - -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount - -rwxr-xr-x 1 root root 18664 Jan 20 2022 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 Jan 23 03:47 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 Jan 20 2022 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 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 Jan 20 2022 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 Jan 20 2022 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/22017/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 Jan 21 2022 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 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 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 Jan 21 2022 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 Jan 21 2022 more + -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount + -rwxr-xr-x 1 root root 18664 Jan 21 2022 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 4 Jan 6 15:20 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 21 23:24 sh.distrib -> dash + -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 Jan 21 2022 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 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 Jan 21 2022 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 Jan 21 2022 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/3674194/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -416,7 +451,7 @@ Get: 174 http://deb.debian.org/debian bullseye/main amd64 python3-tk amd64 3.9.2-1 [101 kB] Get: 175 http://deb.debian.org/debian bullseye/main amd64 python3-yaml amd64 5.3.1-5 [138 kB] Get: 176 http://deb.debian.org/debian bullseye/main amd64 spades amd64 3.13.1+dfsg-2+b2 [4777 kB] -Fetched 80.2 MB in 1s (76.8 MB/s) +Fetched 80.2 MB in 5s (15.6 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 ... 19704 files and directories currently installed.) @@ -1156,7 +1191,11 @@ fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/ariba-2.14.6+ds/ && 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 > ../ariba_2.14.6+ds-1_source.changes +I: user script /srv/workspace/pbuilder/3674194/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/3674194/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/ariba-2.14.6+ds/ && 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 > ../ariba_2.14.6+ds-1_source.changes dpkg-buildpackage: info: source package ariba dpkg-buildpackage: info: source version 2.14.6+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -2073,7 +2112,7 @@ System information: SPAdes version: 3.13.1 Python version: 3.9.2 - OS: Linux-6.0.0-0.deb11.6-amd64-x86_64-with-glibc2.31 + OS: Linux-5.10.0-20-amd64-x86_64-with-glibc2.31 Output dir: /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/tmp.test_assemble_with_spades_fail/Assemble Mode: ONLY assembling (without read error correction) @@ -2118,65 +2157,65 @@ 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 - 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) - 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads - 0:00:00.120 68M / 132M INFO General (binary_converter.hpp : 117) 1 reads written - 0:00:00.120 4M / 132M INFO General (read_converter.hpp : 87) Converting single reads - 0:00:00.369 132M / 260M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.369 4M / 260M INFO General (read_converter.hpp : 95) Converting merged reads - 0:00:00.611 132M / 260M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.611 4M / 260M INFO General (construction.cpp : 111) Max read length 67 - 0:00:00.611 4M / 260M INFO General (construction.cpp : 117) Average read length 67 - 0:00:00.611 4M / 260M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.611 4M / 260M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1 files using 1 threads. This might take a while. - 0:00:00.612 4M / 260M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.612 4M / 260M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 15.6654 Gb - 0:00:00.612 4M / 260M INFO General (kmer_splitters.hpp : 97) Using cell size of 67108864 - 0:00:00.612 568M / 1G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:00.612 4M / 1G INFO General (kmer_splitters.hpp : 308) Used 4 reads - 0:00:00.612 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:00.613 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 46 kmers in total. - 0:00:00.613 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:00.613 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:00.613 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:00.613 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. - 0:00:00.613 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.613 4M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 15.6654 Gb - 0:00:00.613 4M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304 - 0:00:00.622 580M / 1G INFO General (kmer_splitters.hpp : 385) Used 46 kmers. - 0:00:00.622 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:00.629 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 47 kmers in total. - 0:00:00.629 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:00.629 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:00.709 4M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:00.709 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9000 bytes occupied (1531.91 bits per kmer). - 0:00:00.709 4M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:00.709 4M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:00.709 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:00.709 4M / 1G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:00.709 4M / 1G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:00.710 4M / 1G INFO Early tip clipping (early_simplification.hpp : 184) 0 22-mers were removed by early tip clipper - 0:00:00.710 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:00.710 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:00.710 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:00.710 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:00.710 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:00.710 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:00.710 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:00.710 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:00.717 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 608 bytes occupied (105.739 bits per kmer). - 0:00:00.717 4M / 1G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:00.718 4M / 1G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:00.718 4M / 1G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction + 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) + 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads + 0:00:00.383 68M / 132M INFO General (binary_converter.hpp : 117) 1 reads written + 0:00:00.401 4M / 132M INFO General (read_converter.hpp : 87) Converting single reads + 0:00:01.572 132M / 260M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:01.641 4M / 260M INFO General (read_converter.hpp : 95) Converting merged reads + 0:00:02.916 132M / 260M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:02.982 4M / 260M INFO General (construction.cpp : 111) Max read length 67 + 0:00:02.982 4M / 260M INFO General (construction.cpp : 117) Average read length 67 + 0:00:02.982 4M / 260M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting + 0:00:02.982 4M / 260M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1 files using 1 threads. This might take a while. + 0:00:02.982 4M / 260M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:02.982 4M / 260M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 15.6654 Gb + 0:00:02.982 4M / 260M INFO General (kmer_splitters.hpp : 97) Using cell size of 67108864 + 0:00:02.992 568M / 1G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:02.992 4M / 1G INFO General (kmer_splitters.hpp : 308) Used 4 reads + 0:00:02.992 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:02.993 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 46 kmers in total. + 0:00:02.993 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.993 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:02.993 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:02.993 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. + 0:00:02.993 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:02.993 4M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 15.6654 Gb + 0:00:02.993 4M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304 + 0:00:03.034 580M / 1G INFO General (kmer_splitters.hpp : 385) Used 46 kmers. + 0:00:03.034 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:03.070 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 47 kmers in total. + 0:00:03.070 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:03.080 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:08.167 4M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:08.168 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9000 bytes occupied (1531.91 bits per kmer). + 0:00:08.168 4M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:08.168 4M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:08.168 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:08.168 4M / 1G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:08.168 4M / 1G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:08.168 4M / 1G INFO Early tip clipping (early_simplification.hpp : 184) 0 22-mers were removed by early tip clipper + 0:00:08.168 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:08.168 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:08.168 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:08.168 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:08.168 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:08.168 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:08.168 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:08.168 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:08.483 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 608 bytes occupied (105.739 bits per kmer). + 0:00:08.483 4M / 1G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:08.483 4M / 1G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:08.484 4M / 1G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding === Stack Trace === -/usr/lib/spades/bin/spades-core(_ZN14coverage_model17KMerCoverageModel3FitEv+0xc2) [0x558c7d094622] -/usr/lib/spades/bin/spades-core(_ZN14debruijn_graph17GenomicInfoFiller3runERNS_10graph_packINS_13DeBruijnGraphEEEPKc+0x687) [0x558c7d02e8e7] -/usr/lib/spades/bin/spades-core(_ZN6spades12StageManager3runERN14debruijn_graph10graph_packINS1_13DeBruijnGraphEEEPKc+0x10d) [0x558c7d00212d] -/usr/lib/spades/bin/spades-core(_ZN6spades15assemble_genomeEv+0xccf) [0x558c7ce9f80f] -/usr/lib/spades/bin/spades-core(main+0x3ce) [0x558c7ce9716e] -/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xea) [0x7f35f11eed0a] -/usr/lib/spades/bin/spades-core(_start+0x2a) [0x558c7ce9ce5a] +/usr/lib/spades/bin/spades-core(_ZN14coverage_model17KMerCoverageModel3FitEv+0xc2) [0x562b24b57622] +/usr/lib/spades/bin/spades-core(_ZN14debruijn_graph17GenomicInfoFiller3runERNS_10graph_packINS_13DeBruijnGraphEEEPKc+0x687) [0x562b24af18e7] +/usr/lib/spades/bin/spades-core(_ZN6spades12StageManager3runERN14debruijn_graph10graph_packINS1_13DeBruijnGraphEEEPKc+0x10d) [0x562b24ac512d] +/usr/lib/spades/bin/spades-core(_ZN6spades15assemble_genomeEv+0xccf) [0x562b2496280f] +/usr/lib/spades/bin/spades-core(main+0x3ce) [0x562b2495a16e] +/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xea) [0x7f3239f36d0a] +/usr/lib/spades/bin/spades-core(_start+0x2a) [0x562b2495fe5a] Verification of expression 'cov_.size() > 10' failed in function 'void coverage_model::KMerCoverageModel::Fit()'. In file '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp' on line 187. Message 'Invalid kmer coverage histogram, make sure that the coverage is indeed uniform'. Verification of expression 'cov_.size() > 10' failed in function 'void coverage_model::KMerCoverageModel::Fit()'. In file '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp' on line 187. Message 'Invalid kmer coverage histogram, make sure that the coverage is indeed uniform'. spades-core: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:187: void coverage_model::KMerCoverageModel::Fit(): Assertion `cov_.size() > 10' failed. @@ -2559,7 +2598,7 @@ test run ... ok ---------------------------------------------------------------------- -Ran 356 tests in 120.703s +Ran 356 tests in 491.051s OK create-stamp debian/debhelper-build-stamp @@ -3636,12 +3675,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3674194/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3674194/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/22017 and its subdirectories -I: Current time: Wed Feb 7 19:43:07 -12 2024 -I: pbuilder-time-stamp: 1707378187 +I: removing directory /srv/workspace/pbuilder/3674194 and its subdirectories +I: Current time: Fri Jan 6 15:36:40 +14 2023 +I: pbuilder-time-stamp: 1672969000