Diff of the two buildlogs: -- --- b1/build.log 2021-08-24 00:52:47.915180030 +0000 +++ b2/build.log 2021-08-24 00:55:12.053786234 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 23 12:50:12 -12 2021 -I: pbuilder-time-stamp: 1629766212 +I: Current time: Tue Aug 24 14:53:07 +14 2021 +I: pbuilder-time-stamp: 1629766387 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 [./probcons_1.12-13.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.5LsOOHKR/trustedkeys.kbx': General error -gpgv: Signature made Sun Nov 15 21:17:20 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.uRRUE_8R/trustedkeys.kbx': General error +gpgv: Signature made Mon Nov 16 23:17:20 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -34,135 +34,169 @@ dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3630/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/25937/tmp/hooks/D01_modify_environment starting +debug: Running on jtx1a. +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/25937/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/25937/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='24aae173e7064143a9830262163e73c0' - 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='3630' - PS1='# ' - PS2='> ' + INVOCATION_ID=3a1fbb4cd365464eac3c429fefb9fc40 + 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=25937 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.HR83T5rztL/pbuilderrc_3aiR --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.HR83T5rztL/b1 --logfile b1/build.log probcons_1.12-13.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.HR83T5rztL/pbuilderrc_CKqk --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.HR83T5rztL/b2 --logfile b2/build.log probcons_1.12-13.dsc' + SUDO_GID=114 + SUDO_UID=108 + 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 virt32a 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 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 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 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 21:25 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 04:12 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 11:30 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 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/3630/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 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 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 Aug 24 14:53 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 21 23:26 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 06:12 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 13:30 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 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/25937/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -229,7 +263,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] -Fetched 17.7 MB in 2s (10.5 MB/s) +Fetched 17.7 MB in 14s (1231 kB/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.) @@ -369,7 +403,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/probcons-1.12/ && 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 > ../probcons_1.12-13_source.changes +hostname: Name or service not known +I: Running cd /build/probcons-1.12/ && 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 > ../probcons_1.12-13_source.changes dpkg-buildpackage: info: source package probcons dpkg-buildpackage: info: source version 1.12-13 dpkg-buildpackage: info: source distribution unstable @@ -379,7 +414,7 @@ debian/rules clean dh clean dh_auto_clean - make -j3 clean + make -j4 clean make[1]: Entering directory '/build/probcons-1.12' rm -f probcons probcons-RNA pc-compare pc-project pc-makegnuplot make[1]: Leaving directory '/build/probcons-1.12' @@ -398,55 +433,74 @@ sed -i s/Defaults.h/Defaults-RNA.h/ Main-RNA.cc cp debian/Defaults-RNA.h Defaults-RNA.h dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/probcons-1.12' g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -lm -o probcons Main.cc -Wl,-z,relro -Wl,-z,now g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -lm -o probcons-RNA Main-RNA.cc -Wl,-z,relro -Wl,-z,now g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -o pc-compare CompareToRef.cc -Wl,-z,relro -Wl,-z,now +g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -o pc-project ProjectPairwise.cc -Wl,-z,relro -Wl,-z,now In file included from MultiSequence.h:18, - from Main-RNA.cc:8: + from ProjectPairwise.cc:9: Sequence.h: In member function 'Sequence* Sequence::Clone() const': Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ -In file included from Main-RNA.cc:7: +In file included from ProjectPairwise.cc:8: SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from MultiSequence.h:18, + from Main-RNA.cc:8: +Sequence.h: In member function 'Sequence* Sequence::Clone() const': +Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] + 293 | *(ret->data) = *data; + | ^~~~ +In file included from MultiSequence.h:18, from CompareToRef.cc:9: Sequence.h: In member function 'Sequence* Sequence::Clone() const': Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ -In file included from CompareToRef.cc:8: -SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' - 29 | SafeVector (const SafeVector &source) : std::vector(source) {} - | ^~~~~~~~~~ In file included from MultiSequence.h:18, from Main.cc:8: Sequence.h: In member function 'Sequence* Sequence::Clone() const': Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ +In file included from Main-RNA.cc:7: +SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' + 29 | SafeVector (const SafeVector &source) : std::vector(source) {} + | ^~~~~~~~~~ In file included from Main.cc:7: SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ +In file included from CompareToRef.cc:8: +SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' + 29 | SafeVector (const SafeVector &source) : std::vector(source) {} + | ^~~~~~~~~~ In file included from Main-RNA.cc:11: ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const': ProbabilisticModel.h:493:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 493 | if (enableTrainEmissions && i != 1 || j != 1){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ -ProbabilisticModel.h: In member function 'VF* ProbabilisticModel::BuildPosterior(MultiSequence*, MultiSequence*, const SafeVector >&, float) const': -ProbabilisticModel.h:1027:18: warning: variable 'postPtr' set but not used [-Wunused-but-set-variable] - 1027 | VF::iterator postPtr = posterior.begin(); - | ^~~~~~~ In file included from Main.cc:11: ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const': ProbabilisticModel.h:493:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 493 | if (enableTrainEmissions && i != 1 || j != 1){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ +ProbabilisticModel.h: In member function 'VF* ProbabilisticModel::BuildPosterior(MultiSequence*, MultiSequence*, const SafeVector >&, float) const': +ProbabilisticModel.h:1027:18: warning: variable 'postPtr' set but not used [-Wunused-but-set-variable] + 1027 | VF::iterator postPtr = posterior.begin(); + | ^~~~~~~ +ProbabilisticModel.h: In member function 'VF* ProbabilisticModel::BuildPosterior(MultiSequence*, MultiSequence*, const SafeVector >&, float) const': +ProbabilisticModel.h:1027:18: warning: variable 'postPtr' set but not used [-Wunused-but-set-variable] + 1027 | VF::iterator postPtr = posterior.begin(); + | ^~~~~~~ +Main.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': +Main.cc:282:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] + 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); + | ^~~ Main-RNA.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': Main-RNA.cc:282:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); @@ -454,15 +508,30 @@ Main-RNA.cc:282:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~~~~~ +Main.cc:282:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' + 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); + | ^~~~~~~ Main-RNA.cc:283:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~ +Main.cc:283:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] + 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); + | ^~~ Main-RNA.cc:283:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~~~~~ +Main.cc:283:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' + 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); + | ^~~~~~~ Main-RNA.cc:284:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~ +Main.cc:284:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] + 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); + | ^~~ +Main.cc:284:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' + 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); + | ^~~~~~~ Main-RNA.cc:284:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~~~~~ @@ -473,44 +542,6 @@ Main-RNA.cc:403:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 403 | delete alignment.first; | ^~~~~~ -ProbabilisticModel.h: In member function 'VF* ProbabilisticModel::BuildPosterior(MultiSequence*, MultiSequence*, const SafeVector >&, float) const': -ProbabilisticModel.h:1027:18: warning: variable 'postPtr' set but not used [-Wunused-but-set-variable] - 1027 | VF::iterator postPtr = posterior.begin(); - | ^~~~~~~ -Main-RNA.cc: In function 'void ReadParameters()': -Main-RNA.cc:893:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] - 893 | emitPairs = VVF (256, VF (256, 1e-10)); - | ^ -In file included from Main-RNA.cc:7: -SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' - 29 | SafeVector (const SafeVector &source) : std::vector(source) {} - | ^~~~~~~~~~ -Main-RNA.cc:894:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] - 894 | emitSingle = VF (256, 1e-5); - | ^ -In file included from Main-RNA.cc:7: -SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = float]' - 29 | SafeVector (const SafeVector &source) : std::vector(source) {} - | ^~~~~~~~~~ -Main.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': -Main.cc:282:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] - 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); - | ^~~ -Main.cc:282:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' - 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); - | ^~~~~~~ -Main.cc:283:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] - 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); - | ^~~ -Main.cc:283:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' - 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); - | ^~~~~~~ -Main.cc:284:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] - 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); - | ^~~ -Main.cc:284:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' - 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); - | ^~~~~~~ Main.cc: In function 'MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)': Main.cc:400:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 400 | if (enableVerbose) @@ -518,6 +549,10 @@ Main.cc:403:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 403 | delete alignment.first; | ^~~~~~ +Main-RNA.cc: In function 'void ReadParameters()': +Main-RNA.cc:893:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] + 893 | emitPairs = VVF (256, VF (256, 1e-10)); + | ^ Main.cc: In function 'void ReadParameters()': Main.cc:893:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] 893 | emitPairs = VVF (256, VF (256, 1e-10)); @@ -526,22 +561,22 @@ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ +In file included from Main-RNA.cc:7: +SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' + 29 | SafeVector (const SafeVector &source) : std::vector(source) {} + | ^~~~~~~~~~ Main.cc:894:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 894 | emitSingle = VF (256, 1e-5); | ^ +Main-RNA.cc:894:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] + 894 | emitSingle = VF (256, 1e-5); + | ^ In file included from Main.cc:7: SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = float]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ -g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -o pc-project ProjectPairwise.cc -Wl,-z,relro -Wl,-z,now -In file included from MultiSequence.h:18, - from ProjectPairwise.cc:9: -Sequence.h: In member function 'Sequence* Sequence::Clone() const': -Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] - 293 | *(ret->data) = *data; - | ^~~~ -In file included from ProjectPairwise.cc:8: -SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' +In file included from Main-RNA.cc:7: +SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = float]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -o pc-makegnuplot MakeGnuPlot.cc -Wl,-z,relro -Wl,-z,now @@ -571,19 +606,19 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/probcons/usr/bin/probcons contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/probcons/usr/bin/probcons-RNA contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/probcons-extra/usr/bin/pc-project contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/probcons-extra/usr/bin/pc-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/probcons-extra/usr/bin/pc-makegnuplot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/probcons-extra/usr/bin/pc-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/probcons/usr/bin/probcons-RNA contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/probcons/usr/bin/probcons contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'probcons' in '../probcons_1.12-13_armhf.deb'. dpkg-deb: building package 'probcons-extra' in '../probcons-extra_1.12-13_armhf.deb'. -dpkg-deb: building package 'probcons-extra-dbgsym' in '../probcons-extra-dbgsym_1.12-13_armhf.deb'. dpkg-deb: building package 'probcons-dbgsym' in '../probcons-dbgsym_1.12-13_armhf.deb'. +dpkg-deb: building package 'probcons-extra-dbgsym' in '../probcons-extra-dbgsym_1.12-13_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../probcons_1.12-13_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -591,12 +626,14 @@ 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/25937/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/25937/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/3630 and its subdirectories -I: Current time: Mon Aug 23 12:52:42 -12 2021 -I: pbuilder-time-stamp: 1629766362 +I: removing directory /srv/workspace/pbuilder/25937 and its subdirectories +I: Current time: Tue Aug 24 14:55:05 +14 2021 +I: pbuilder-time-stamp: 1629766505