Diff of the two buildlogs: -- --- b1/build.log 2021-09-07 01:20:38.124415097 +0000 +++ b2/build.log 2021-09-07 01:22:48.291744831 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 6 13:18:51 -12 2021 -I: pbuilder-time-stamp: 1630977531 +I: Current time: Tue Sep 7 15:20:53 +14 2021 +I: pbuilder-time-stamp: 1630977653 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./pirs_2.0.2+dfsg-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.lytNO94y/trustedkeys.kbx': General error -gpgv: Signature made Fri Dec 4 23:14:30 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.e7nEmDnH/trustedkeys.kbx': General error +gpgv: Signature made Sun Dec 6 01:14:30 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,169 @@ dpkg-source: info: applying Remove-mtune-compiler-flag.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/19022/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/12383/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +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/12383/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/12383/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,-fixfilepath 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]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath 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='bef8e329423845d6aabda36945360582' - 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='19022' - PS1='# ' - PS2='> ' + INVOCATION_ID=8a2aa0df716b4893a1b1929f7bc3edfc + 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=12383 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.RBFbQ6aCyz/pbuilderrc_Novg --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RBFbQ6aCyz/b1 --logfile b1/build.log pirs_2.0.2+dfsg-9.dsc' - SUDO_GID='114' - SUDO_UID='108' - 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.RBFbQ6aCyz/pbuilderrc_csRw --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RBFbQ6aCyz/b2 --logfile b2/build.log pirs_2.0.2+dfsg-9.dsc' + SUDO_GID=113 + SUDO_UID=107 + 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 jtx1c 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 20 21:24 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 2021 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/19022/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Jul 29 09:09 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 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 7 15:21 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 21 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 2021 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/12383/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -238,7 +272,7 @@ Get: 34 http://deb.debian.org/debian bullseye/main armhf libgzstream0 armhf 1.5+dfsg-5 [6268 B] Get: 35 http://deb.debian.org/debian bullseye/main armhf libgzstream-dev armhf 1.5+dfsg-5 [6700 B] Get: 36 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] -Fetched 27.4 MB in 3s (10.4 MB/s) +Fetched 27.4 MB in 2s (13.0 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 ... 19398 files and directories currently installed.) @@ -398,7 +432,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/pirs-2.0.2+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 > ../pirs_2.0.2+dfsg-9_source.changes +hostname: Name or service not known +I: Running cd /build/pirs-2.0.2+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 > ../pirs_2.0.2+dfsg-9_source.changes dpkg-buildpackage: info: source package pirs dpkg-buildpackage: info: source version 2.0.2+dfsg-9 dpkg-buildpackage: info: source distribution unstable @@ -484,12 +519,12 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/pirs-2.0.2+dfsg' dh_auto_build - cd src && make -j3 + cd src && make -j4 make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src' -(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash '/build/pirs-2.0.2+dfsg/src/missing' autoheader) +(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh '/build/pirs-2.0.2+dfsg/src/missing' autoheader) rm -f stamp-h1 touch config.h.in -cd . && /bin/bash ./config.status config.h +cd . && /bin/sh ./config.status config.h config.status: creating config.h config.status: config.h is unchanged make all-recursive @@ -499,25 +534,18 @@ g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InputStream.o InputStream.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o OutputStream.o OutputStream.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.o util.cpp main.cpp:18:19: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" | ^~~~~~~~ main.cpp:18:38: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" | ^~~~~~~~ -In file included from InputStream.cpp:1: -InputStream.h: In constructor 'InputStream::InputStream()': -InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 50 | memset(this, 0, sizeof(*this)); - | ^ In file included from OutputStream.cpp:1: OutputStream.h: In constructor 'OutputStream::OutputStream()': OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 54 | memset(this, 0, sizeof(*this)); | ^ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ @@ -528,6 +556,14 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ +In file included from InputStream.cpp:1: +InputStream.h: In constructor 'InputStream::InputStream()': +InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 50 | memset(this, 0, sizeof(*this)); + | ^ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ InputStream.h: In constructor 'InputStream::InputStream(const char*)': InputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 54 | memset(this, 0, sizeof(*this)); @@ -535,10 +571,41 @@ InputStream.h:25:7: note: 'class InputStream' declared here 25 | class InputStream { | ^~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.o util.cpp +In file included from util.cpp:18: +InputStream.h: In constructor 'InputStream::InputStream()': +InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 50 | memset(this, 0, sizeof(*this)); + | ^ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ +InputStream.h: In constructor 'InputStream::InputStream(const char*)': +InputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ^ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ +util.cpp: In function 'void* xmalloc(size_t)': +util.cpp:192:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 192 | fatal_error("Out of memory: tried to allocate %lu bytes", size); + | ~~^ ~~~~ + | | | + | | size_t {aka unsigned int} + | long unsigned int + | %u +util.cpp: In function 'void* xrealloc(void*, size_t)': +util.cpp:200:53: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 200 | fatal_error("Out of memory: tried to reallocate %lu bytes", size); + | ~~^ ~~~~ + | | | + | | size_t {aka unsigned int} + | long unsigned int + | %u g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mt19937-64.o mt19937-64.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_diploid.o pirs_diploid.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o BaseCallingProfile.o BaseCallingProfile.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GCBiasProfile.o GCBiasProfile.cpp pirs_diploid.cpp:639:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 639 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n", | ^ @@ -560,7 +627,10 @@ pirs_diploid.cpp:643:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 643 | info(" %#"PRIx64"]\n", het_type_tab[6]); | ^ -In file included from util.cpp:18: +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IndelProfile.o IndelProfile.cpp +In file included from SimulationParameters.h:6, + from BaseCallingProfile.h:7, + from BaseCallingProfile.cpp:5: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 50 | memset(this, 0, sizeof(*this)); @@ -575,22 +645,23 @@ InputStream.h:25:7: note: 'class InputStream' declared here 25 | class InputStream { | ^~~~~~~~~~~ -util.cpp: In function 'void* xmalloc(size_t)': -util.cpp:192:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 192 | fatal_error("Out of memory: tried to allocate %lu bytes", size); - | ~~^ ~~~~ - | | | - | | size_t {aka unsigned int} - | long unsigned int - | %u -util.cpp: In function 'void* xrealloc(void*, size_t)': -util.cpp:200:53: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 200 | fatal_error("Out of memory: tried to reallocate %lu bytes", size); - | ~~^ ~~~~ - | | | - | | size_t {aka unsigned int} - | long unsigned int - | %u +In file included from SimulationParameters.h:7, + from BaseCallingProfile.h:7, + from BaseCallingProfile.cpp:5: +OutputStream.h: In constructor 'OutputStream::OutputStream()': +OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ^ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ +OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': +OutputStream.h:58:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 58 | memset(this, 0, sizeof(*this)); + | ^ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ In file included from pirs_diploid.cpp:11: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] @@ -643,42 +714,6 @@ | | | uint64_t {aka long long unsigned int} In file included from SimulationParameters.h:6, - from BaseCallingProfile.h:7, - from BaseCallingProfile.cpp:5: -InputStream.h: In constructor 'InputStream::InputStream()': -InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 50 | memset(this, 0, sizeof(*this)); - | ^ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ -InputStream.h: In constructor 'InputStream::InputStream(const char*)': -InputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ^ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ -In file included from SimulationParameters.h:7, - from BaseCallingProfile.h:7, - from BaseCallingProfile.cpp:5: -OutputStream.h: In constructor 'OutputStream::OutputStream()': -OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ^ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': -OutputStream.h:58:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 58 | memset(this, 0, sizeof(*this)); - | ^ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GCBiasProfile.o GCBiasProfile.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IndelProfile.o IndelProfile.cpp -In file included from SimulationParameters.h:6, from GCBiasProfile.h:5, from GCBiasProfile.cpp:5: InputStream.h: In constructor 'InputStream::InputStream()': @@ -712,6 +747,18 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from GCBiasProfile.cpp:3: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from GCBiasProfile.cpp:3: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from SimulationParameters.h:6, from IndelProfile.cpp:2: InputStream.h: In constructor 'InputStream::InputStream()': @@ -775,18 +822,6 @@ | long unsigned int | %llu g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskQvalsByEamss.o MaskQvalsByEamss.cpp -In file included from /usr/include/c++/10/vector:72, - from GCBiasProfile.cpp:3: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from GCBiasProfile.cpp:3: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Profile.o Profile.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_simulate.o pirs_simulate.cpp pirs_simulate.cpp:168:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] @@ -932,7 +967,7 @@ make[3]: Leaving directory '/build/pirs-2.0.2+dfsg/src' make[2]: Leaving directory '/build/pirs-2.0.2+dfsg/src' dh_auto_build --sourcedirectory=src/stator/gcContCvgBias -- CC='$(CXX)' - cd src/stator/gcContCvgBias && make -j3 "INSTALL=install --strip-program=true" CC=\$\(CXX\) + cd src/stator/gcContCvgBias && make -j4 "INSTALL=install --strip-program=true" CC=\$\(CXX\) make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src/stator/gcContCvgBias' g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal self_util.cpp self_util.h g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal main.cpp @@ -1357,7 +1392,7 @@ make[2]: Leaving directory '/build/pirs-2.0.2+dfsg/src/stator/gcContCvgBias' make[1]: Leaving directory '/build/pirs-2.0.2+dfsg' dh_auto_test -O--sourcedirectory=src - cd src && make -j3 check VERBOSE=1 + cd src && make -j4 check VERBOSE=1 make[1]: Entering directory '/build/pirs-2.0.2+dfsg/src' Making check in pirs make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src/pirs' @@ -1422,17 +1457,17 @@ dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src -dpkg-shlibdeps: warning: debian/pirs/usr/bin/gc_coverage_bias contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/pirs/usr/bin/pirs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/pirs/usr/bin/gc_coverage_bias contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dpkg-gencontrol: warning: package pirs: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package pirs: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'pirs-profiles' in '../pirs-profiles_2.0.2+dfsg-9_all.deb'. -dpkg-deb: building package 'pirs' in '../pirs_2.0.2+dfsg-9_armhf.deb'. dpkg-deb: building package 'pirs-dbgsym' in '../pirs-dbgsym_2.0.2+dfsg-9_armhf.deb'. +dpkg-deb: building package 'pirs' in '../pirs_2.0.2+dfsg-9_armhf.deb'. +dpkg-deb: building package 'pirs-profiles' in '../pirs-profiles_2.0.2+dfsg-9_all.deb'. dpkg-deb: building package 'pirs-examples' in '../pirs-examples_2.0.2+dfsg-9_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pirs_2.0.2+dfsg-9_armhf.changes @@ -1441,12 +1476,14 @@ 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/12383/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/12383/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/19022 and its subdirectories -I: Current time: Mon Sep 6 13:20:34 -12 2021 -I: pbuilder-time-stamp: 1630977634 +I: removing directory /srv/workspace/pbuilder/12383 and its subdirectories +I: Current time: Tue Sep 7 15:22:44 +14 2021 +I: pbuilder-time-stamp: 1630977764