Diff of the two buildlogs: -- --- b1/build.log 2020-07-21 01:52:20.287838091 +0000 +++ b2/build.log 2020-07-21 02:27:45.986233280 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jul 20 12:38:42 -12 2020 -I: pbuilder-time-stamp: 1595291922 +I: Current time: Tue Jul 21 15:52:35 +14 2020 +I: pbuilder-time-stamp: 1595296355 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Sat Jul 28 17:47:00 2018 -12 +gpgv: Signature made Sun Jul 29 19:47:00 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,136 +30,170 @@ dpkg-source: info: applying adapt_path_to_perl_scripts.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/13610/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27951/tmp/hooks/D01_modify_environment starting +debug: Running on ff2b. +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' +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/27951/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27951/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='' - HOME='/root' - HOST_ARCH='armhf' + 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]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.0.3(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= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='649b2f8651cd41248d83de8b66e37c5c' - 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='13610' - PS1='# ' - PS2='> ' + INVOCATION_ID=f2563af76046445fbec77b3771477ba2 + 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=27951 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/tmp.e1Z5e4uiAN/pbuilderrc_414y --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.e1Z5e4uiAN/b1 --logfile b1/build.log art-nextgen-simulation-tools_20160605+dfsg-3.dsc' - SUDO_GID='115' - SUDO_UID='111' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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/tmp.e1Z5e4uiAN/pbuilderrc_nmBL --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.e1Z5e4uiAN/b2 --logfile b2/build.log art-nextgen-simulation-tools_20160605+dfsg-3.dsc' + SUDO_GID=114 + SUDO_UID=109 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux wbq0 4.19.0-9-armmp #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux + Linux i-capture-the-hostname 4.19.0-9-armmp-lpae #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux I: ls -l /bin total 3328 - -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat - -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown - -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp - -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash - -rwxr-xr-x 1 root root 71648 Feb 28 2019 date - -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd - -rwxr-xr-x 1 root root 55672 Feb 28 2019 df - -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir - -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 18260 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln - -rwxr-xr-x 1 root root 34932 Jul 26 2018 login - -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls - -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 26024 Jan 9 2019 more - -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount - -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm - -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 19 20:26 sh -> dash - -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty - -rwsr-xr-x 1 root root 42472 Jan 9 2019 su - -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync - -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar - -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch - -rwxr-xr-x 1 root root 18260 Feb 28 2019 true - -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount - -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/13610/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat + -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown + -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp + -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash + -rwxr-xr-x 1 root root 71648 Mar 1 2019 date + -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd + -rwxr-xr-x 1 root root 55672 Mar 1 2019 df + -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir + -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 18260 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln + -rwxr-xr-x 1 root root 34932 Jul 27 2018 login + -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls + -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 26024 Jan 10 2019 more + -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount + -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm + -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 21 15:53 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 19 22:37 sh.distrib -> dash + -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty + -rwsr-xr-x 1 root root 42472 Jan 10 2019 su + -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync + -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar + -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch + -rwxr-xr-x 1 root root 18260 Mar 1 2019 true + -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount + -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/27951/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -233,7 +267,7 @@ Get: 34 http://deb.debian.org/debian buster/main armhf libgslcblas0 armhf 2.5+dfsg-6 [79.1 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libgsl23 armhf 2.5+dfsg-6 [718 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libgsl-dev armhf 2.5+dfsg-6 [903 kB] -Fetched 19.9 MB in 9s (2175 kB/s) +Fetched 19.9 MB in 10s (2031 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) @@ -400,7 +434,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/art-nextgen-simulation-tools-20160605+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/art-nextgen-simulation-tools-20160605+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package art-nextgen-simulation-tools dpkg-buildpackage: info: source version 20160605+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -476,13 +510,16 @@ config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' make all-am make[2]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/art_illumina.o art_illumina_src/art_illumina.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/art_qual_scale.o art_illumina_src/art_qual_scale.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/empdist.o art_illumina_src/empdist.cpp +g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/readSeqFile.o art_illumina_src/readSeqFile.cpp +g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/seqRead.o art_illumina_src/seqRead.cpp +g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/samRead.o art_illumina_src/samRead.cpp In file included from /usr/include/c++/8/vector:69, from art_illumina_src/art.h:34, from art_illumina_src/art_illumina.cpp:32: @@ -497,9 +534,6 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/readSeqFile.o art_illumina_src/readSeqFile.cpp -g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/seqRead.o art_illumina_src/seqRead.cpp -g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/samRead.o art_illumina_src/samRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/art_454.o art_454_src/art_454.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/art.o art_454_src/art.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/read_profile.o art_454_src/read_profile.cpp @@ -548,9 +582,9 @@ Single-end simulation -Total CPU time used: 0.59297 +Total CPU time used: 0.205296 -The random seed for the run: 1595292179 +The random seed for the run: 1595296466 Parameters Settings number of flow cycles: 100 @@ -581,9 +615,9 @@ Paired-end simulation -Total CPU time used: 0.571105 +Total CPU time used: 0.145611 -The random seed for the run: 1595292180 +The random seed for the run: 1595296467 Parameters Settings number of flow cycles: 100 @@ -619,9 +653,9 @@ Paired-end simulation -Total CPU time used: 0.591451 +Total CPU time used: 0.15666 -The random seed for the run: 1595292181 +The random seed for the run: 1595296467 Parameters Settings number of flow cycles: 200 @@ -657,9 +691,9 @@ Amplicon 5'-end sequencing with single-end reads -Total CPU time used: 90.5419 +Total CPU time used: 32.72 -The random seed for the run: 1595292182 +The random seed for the run: 1595296467 Parameters Settings number of flow cycles: 100 @@ -690,9 +724,9 @@ Amplicon two-end sequencing with paired-end reads -Total CPU time used: 70.194 +Total CPU time used: 24.2338 -The random seed for the run: 1595292274 +The random seed for the run: 1595296502 Parameters Settings number of flow cycles: 100 @@ -725,7 +759,7 @@ Single-end simulation -Total CPU time used: 0.530909 +Total CPU time used: 0.195015 The random seed for the run: 777 @@ -758,7 +792,7 @@ Single-end simulation -Total CPU time used: 0.526653 +Total CPU time used: 0.201767 The random seed for the run: 777 @@ -792,9 +826,9 @@ Single-end simulation -Total CPU time used: 0.835313 +Total CPU time used: 0.307294 -The random seed for the run: 1595292347 +The random seed for the run: 1595296528 Parameters Settings fold of read coverage: 10X @@ -824,9 +858,9 @@ Single-end simulation -Total CPU time used: 0.993322 +Total CPU time used: 0.375637 -The random seed for the run: 1595292348 +The random seed for the run: 1595296528 Parameters Settings fold of read coverage: 20X @@ -854,9 +888,9 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 1.36173 +Total CPU time used: 0.494112 -The random seed for the run: 1595292349 +The random seed for the run: 1595296529 Parameters Settings fold of read coverage: 20X @@ -894,7 +928,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.617819 +Total CPU time used: 0.227515 The random seed for the run: 777 @@ -932,7 +966,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.614375 +Total CPU time used: 0.227545 The random seed for the run: 777 @@ -975,9 +1009,9 @@ Paired-end (F3-F5) simulation -Total CPU time used: 2.03865 +Total CPU time used: 0.796457 -The random seed for the run: 1595292352 +The random seed for the run: 1595296530 Parameters Settings fold of read coverage: 50X @@ -1011,9 +1045,9 @@ Amplicon single-end sequencing simulation -Total CPU time used: 2000.33 +Total CPU time used: 824.748 -The random seed for the run: 1595292354 +The random seed for the run: 1595296531 Parameters Settings # reads per amplion: 100 @@ -1043,9 +1077,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 1083.97 +Total CPU time used: 463.474 -The random seed for the run: 1595294364 +The random seed for the run: 1595297591 Parameters Settings # read pairs per amplion: 80 @@ -1076,9 +1110,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 741.784 +Total CPU time used: 298.029 -The random seed for the run: 1595295457 +The random seed for the run: 1595298072 Parameters Settings # read pairs per amplion: 50 @@ -1110,9 +1144,9 @@ Single-end Simulation -Total CPU time used: 0.621948 +Total CPU time used: 0.184179 -The random seed for the run: 1595296205 +The random seed for the run: 1595298383 Parameters used during run Read Length: 35 @@ -1144,9 +1178,9 @@ Single-end Simulation -Total CPU time used: 0.423072 +Total CPU time used: 0.156262 -The random seed for the run: 1595296206 +The random seed for the run: 1595298383 Parameters used during run Read Length: 50 @@ -1178,9 +1212,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.261596 +Total CPU time used: 0.093667 -The random seed for the run: 1595296206 +The random seed for the run: 1595298383 Parameters used during run Read Length: 150 @@ -1217,9 +1251,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.501931 +Total CPU time used: 0.159148 -The random seed for the run: 1595296207 +The random seed for the run: 1595298383 Parameters used during run Read Length: 100 @@ -1256,9 +1290,9 @@ Matepair-end sequencing simulation -Total CPU time used: 0.336554 +Total CPU time used: 0.119272 -The random seed for the run: 1595296207 +The random seed for the run: 1595298384 Parameters used during run Read Length: 100 @@ -1295,9 +1329,9 @@ Amplicon 5'-end sequencing simulation -Total CPU time used: 3.32996 +Total CPU time used: 1.1108 -The random seed for the run: 1595296208 +The random seed for the run: 1595298384 Parameters used during run Read Length: 100 @@ -1329,9 +1363,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 3.64154 +Total CPU time used: 1.21067 -The random seed for the run: 1595296212 +The random seed for the run: 1595298385 Parameters used during run Read Length: 100 @@ -1366,9 +1400,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 4.32504 +Total CPU time used: 1.39811 -The random seed for the run: 1595296216 +The random seed for the run: 1595298387 Parameters used during run Read Length: 100 @@ -1403,7 +1437,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.303323 +Total CPU time used: 0.112193 The random seed for the run: 777 @@ -1442,7 +1476,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.314171 +Total CPU time used: 0.105867 The random seed for the run: 777 @@ -1481,9 +1515,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.391407 +Total CPU time used: 0.120241 -The random seed for the run: 1595296222 +The random seed for the run: 1595298389 Parameters used during run Read Length: 100 @@ -1522,9 +1556,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.356888 +Total CPU time used: 0.119403 -The random seed for the run: 1595296222 +The random seed for the run: 1595298389 Parameters used during run Read Length: 75 @@ -1560,11 +1594,11 @@ dh_testroot dh_prep dh_auto_install - make -j3 install DESTDIR=/build/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' -make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' +make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/install -c art_illumina art_454 art_SOLiD '/build/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/install -c aln2bed.pl map2bed.pl ART_profiler_454/art_profiler_454 ART_profiler_illumina/combinedAvg.pl ART_profiler_illumina/fastqReadAvg.pl ART_profiler_illumina/art_profiler_illumina ART_profiler_illumina/empDist.pl ART_profiler_illumina/summation.pl '/build/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' @@ -1612,9 +1646,9 @@ dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/art-nextgen-simulation-tools/usr/bin/art_454 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/art-nextgen-simulation-tools/usr/bin/art_SOLiD contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/art-nextgen-simulation-tools/usr/bin/art_illumina contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/art-nextgen-simulation-tools/usr/bin/art_454 debian/art-nextgen-simulation-tools/usr/bin/art_SOLiD debian/art-nextgen-simulation-tools/usr/bin/art_illumina were not linked against libgslcblas.so.0 (they use none of the library's symbols) +dpkg-shlibdeps: warning: debian/art-nextgen-simulation-tools/usr/bin/art_SOLiD contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/art-nextgen-simulation-tools/usr/bin/art_454 debian/art-nextgen-simulation-tools/usr/bin/art_illumina debian/art-nextgen-simulation-tools/usr/bin/art_SOLiD were not linked against libgslcblas.so.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package art-nextgen-simulation-tools-profiles: substitution variable ${perl:Depends} unused, but is defined @@ -1622,21 +1656,23 @@ dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-3_armhf.deb'. -dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-3_all.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-3_armhf.deb'. +dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-3_all.deb'. +dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-3_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../art-nextgen-simulation-tools_20160605+dfsg-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/27951/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27951/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/13610 and its subdirectories -I: Current time: Mon Jul 20 13:51:39 -12 2020 -I: pbuilder-time-stamp: 1595296299 +I: removing directory /srv/workspace/pbuilder/27951 and its subdirectories +I: Current time: Tue Jul 21 16:27:04 +14 2020 +I: pbuilder-time-stamp: 1595298424