Diff of the two buildlogs: -- --- b1/build.log 2021-08-10 14:19:08.129148950 +0000 +++ b2/build.log 2021-08-10 14:25:26.775098198 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 12 08:36:00 -12 2022 -I: pbuilder-time-stamp: 1663014960 +I: Current time: Wed Aug 11 04:19:12 +14 2021 +I: pbuilder-time-stamp: 1628605152 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 [./parsinsert_1.04-10.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.JyG1M7uD/trustedkeys.kbx': General error -gpgv: Signature made Tue Jan 19 07:51:44 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.zLxJDrvy/trustedkeys.kbx': General error +gpgv: Signature made Wed Jan 20 09:51:44 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -30,135 +30,169 @@ dpkg-source: info: applying 020_hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9912/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/17376/tmp/hooks/D01_modify_environment starting +debug: Running on codethink12-arm64. +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/17376/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/17376/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='9912' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=17376 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.7A5raRPd3B/pbuilderrc_3Ec2 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7A5raRPd3B/b1 --logfile b1/build.log parsinsert_1.04-10.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.7A5raRPd3B/pbuilderrc_HVOy --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7A5raRPd3B/b2 --logfile b2/build.log --extrapackages usrmerge parsinsert_1.04-10.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink9-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jul 28 2021 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 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 178400 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 93744 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 2021 more - -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount - -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 12 03:47 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 2021 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jul 28 2021 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/9912/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 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 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 178400 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 93744 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 09:09 more + -rwsr-xr-x 1 root root 51360 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 14496 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 134808 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 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 11 04:19 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 10 01:21 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 09:09 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 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/17376/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -225,7 +259,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] -Fetched 17.9 MB in 0s (40.4 MB/s) +Fetched 17.9 MB in 4s (4766 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 ... 19646 files and directories currently installed.) @@ -364,8 +398,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (2031 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 21522 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/parsinsert-1.04/ && 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 > ../parsinsert_1.04-10_source.changes +hostname: Temporary failure in name resolution +I: Running cd /build/parsinsert-1.04/ && 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 > ../parsinsert_1.04-10_source.changes dpkg-buildpackage: info: source package parsinsert dpkg-buildpackage: info: source version 1.04-10 dpkg-buildpackage: info: source distribution unstable @@ -419,8 +490,35 @@ ParsInsert.cpp:416:25: note: in expansion of macro 'VERSION' 416 | DisplayT(USAGE, VERSION, APPNAME); | ^~~~~~~ -In file included from ParsInsert.h:29, - from ParsInsert.cpp:34: +AttrList.cpp: In member function 'int CAttrList::AddHex(const char*, long unsigned int)': +AttrList.cpp:173:21: warning: format '%X' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 173 | sprintf(buf, "0x%08X", value); + | ~~~^ ~~~~~ + | | | + | | long unsigned int + | unsigned int + | %08lX +In file included from PNode.h:31, + from PNode.cpp:27: +ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': +ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 429 | DisplayL("%s [", label); + | ^~~~~~ +ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 431 | DisplayL(" %3d", segCounts[k]); + | ^~~~~~ +ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 432 | DisplayL("]\n"); + | ^~~~~ +PNode.cpp: In member function 'void CPTree::Parse(const char*)': +PNode.cpp:299:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 299 | DisplayL("Could not process all the chars in NEWICK file\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +PNode.cpp:304:11: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 304 | DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from PNode.h:31, + from SeqList.cpp:27: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 429 | DisplayL("%s [", label); @@ -435,14 +533,45 @@ Taxonomy.cpp:96:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | DisplayL("%s[%s] %d\n", leader, name.c_str(), count); | ^~~~~~~~~~~~~ -AttrList.cpp: In member function 'int CAttrList::AddHex(const char*, long unsigned int)': -AttrList.cpp:173:21: warning: format '%X' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 173 | sprintf(buf, "0x%08X", value); - | ~~~^ ~~~~~ - | | | - | | long unsigned int - | unsigned int - | %08lX +SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceIndexFile(const char*)': +SeqList.cpp:490:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 490 | DisplayT("Loading sequence %d [%s]\n", count, name); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp:492:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 492 | DisplayT("Loading sequence %d\n", count); + | ^~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp:496:11: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 496 | DisplayT("Loaded %d sequences from [%s]\n", count, filename); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp: In member function 'int CSequenceFile::ReadTaxonomyFile()': +SeqList.cpp:529:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 529 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp:531:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 531 | DisplayT("Loading sequence %d\n", seqCount); + | ^~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceFile(int)': +SeqList.cpp:565:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 565 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp:580:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 580 | DisplayL("Duplicate sequence found [%s]\n", seq->name.c_str()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp:605:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 605 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ParsInsert.h:29, + from ParsInsert.cpp:34: +ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': +ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 429 | DisplayL("%s [", label); + | ^~~~~~ +ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 431 | DisplayL(" %3d", segCounts[k]); + | ^~~~~~ +ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 432 | DisplayL("]\n"); + | ^~~~~ ParsInsert.cpp: At global scope: ParsInsert.cpp:92:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 92 | char *statsName = "PI_Results.log"; @@ -456,18 +585,14 @@ ParsInsert.cpp:95:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 95 | char *seqFilename = "PI_Tree.fasta"; | ^~~~~~~~~~~~~~~ -In file included from PNode.h:31, - from SeqList.cpp:27: -ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': -ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 429 | DisplayL("%s [", label); - | ^~~~~~ -ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 431 | DisplayL(" %3d", segCounts[k]); - | ^~~~~~ -ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 432 | DisplayL("]\n"); - | ^~~~~ +SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqHeader(FILE*)': +SeqList.cpp:202:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 202 | fgets(buffer, sizeof(buffer)-1, f); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqData(FILE*)': +SeqList.cpp:229:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 229 | fgets(buffer, sizeof(buffer)-1, f); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: In function 'int main(int, char**)': ParsInsert.cpp:247:11: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 247 | DisplayL("%s\n", COPYRIGHT); @@ -593,18 +718,6 @@ ParsInsert.cpp:623:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 623 | DisplayL("[%d sec elapsed] Insert Locations Completed: %d sec\n", time(NULL)-start, time(NULL)-stage); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from PNode.h:31, - from PNode.cpp:27: -ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': -ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 429 | DisplayL("%s [", label); - | ^~~~~~ -ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 431 | DisplayL(" %3d", segCounts[k]); - | ^~~~~~ -ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 432 | DisplayL("]\n"); - | ^~~~~ ParsInsert.cpp:641:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 641 | DisplayL("Writing Newick tree file: [%s]\n", treename.c_str()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -757,36 +870,12 @@ ParsInsert.cpp:1892:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1892 | DisplayL("\tNO MATCHES found\n"); | ^~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceIndexFile(const char*)': -SeqList.cpp:490:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 490 | DisplayT("Loading sequence %d [%s]\n", count, name); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp:492:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 492 | DisplayT("Loading sequence %d\n", count); - | ^~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp:496:11: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 496 | DisplayT("Loaded %d sequences from [%s]\n", count, filename); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp:1939:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1939 | DisplayL("%c(%3d%%) %6d (%4d diffs, %4d partials, %4d indels) [%12s][%s]\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp: In member function 'int CSequenceFile::ReadTaxonomyFile()': -SeqList.cpp:529:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 529 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp:531:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 531 | DisplayT("Loading sequence %d\n", seqCount); - | ^~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceFile(int)': -SeqList.cpp:565:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 565 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp:1975:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1975 | DisplayL("\nInsertion [%5d sites] [%20.20s] %6d (%4d diffs, %4d partials, %4d indels)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp:580:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 580 | DisplayL("Duplicate sequence found [%s]\n", seq->name.c_str()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp:1989:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1989 | DisplayL("%12.12s\t Seq[%s]\n", marker.c_str(), tax.c_str()); | ^~~~~~~~~~~~~~~~~~~~~~ @@ -799,9 +888,6 @@ ParsInsert.cpp:1993:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1993 | DisplayL("\tFirst[%s]\n", taxFirst.c_str()); | ^~~~~~~~~~~~~~~ -SeqList.cpp:605:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 605 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: In function 'void DisplayBestInsertLocations(CInsertPos*, int)': ParsInsert.cpp:2010:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2010 | DisplayL("======================================================================\n"); @@ -874,13 +960,6 @@ ParsInsert.cpp:2407:11: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2407 | DisplayL("Taxonomies List:\n"); | ^~~~~~~~~~~~~~~~~~~~ -PNode.cpp: In member function 'void CPTree::Parse(const char*)': -PNode.cpp:299:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 299 | DisplayL("Could not process all the chars in NEWICK file\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -PNode.cpp:304:11: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 304 | DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: In function 'int BuildInsertTree(CTreeInserts*, CPTree*)': ParsInsert.cpp:2647:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2647 | DisplayL("[%s] at %d%% does not meet threshold (%d%%)\n", in->seq->name.c_str(), score, 100-scoreThresh); @@ -922,14 +1001,6 @@ ParsInsert.cpp:3077:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 3077 | DisplayL("Newick Tree Read Completed: %d taxa\n", (fullTree->nodeList.size()+1)/2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqHeader(FILE*)': -SeqList.cpp:202:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 202 | fgets(buffer, sizeof(buffer)-1, f); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqData(FILE*)': -SeqList.cpp:229:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 229 | fgets(buffer, sizeof(buffer)-1, f); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -o ParsInsert AttrList.o Knox_Stddef.o PNode.o SeqList.o Taxonomy.o ParsInsert.o -lm -lc -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/parsinsert-1.04' mv ParsInsert parsinsert @@ -972,7 +1043,7 @@ Newick Tree Read Completed: 10143 taxa, 0 sec Tree Sequence Reading: [core_rdp.fasta] Loading sequence 10143 [51224] -Tree Sequence Read Completed: 10143 sequences, 0 sec +Tree Sequence Read Completed: 10143 sequences, 1 sec Reading sequences for insertion: [set1000.fasta] Duplicate sequence found [175015] Duplicate sequence found [290252] @@ -1065,8 +1136,8 @@ Calculating Parsimony ... CalcParsimony 20000 nodes remaining CalcParsimony 19000 nodes remaining CalcParsimony 18000 nodes remaining CalcParsimony 17000 nodes remaining CalcParsimony 16000 nodes remaining CalcParsimony 15000 nodes remaining CalcParsimony 14000 nodes remaining CalcParsimony 13000 nodes remaining CalcParsimony 12000 nodes remaining CalcParsimony 11000 nodes remaining CalcParsimony 10000 nodes remaining CalcParsimony 9000 nodes remaining CalcParsimony 8000 nodes remaining CalcParsimony 7000 nodes remaining CalcParsimony 6000 nodes remaining CalcParsimony 5000 nodes remaining CalcParsimony 4000 nodes remaining CalcParsimony 3000 nodes remaining CalcParsimony 2000 nodes remaining CalcParsimony 1000 nodes remaining CalcParsimony 0 nodes remaining Applying parsimonious selections back down the tree. 10147 nodes were modified -Processed 20285 nodes in 8 seconds, 2536 nodes per sec -Parsimony Calculation Completed: 7 sec +Processed 20285 nodes in 7 seconds, 2898 nodes per sec +Parsimony Calculation Completed: 6 sec [14 sec elapsed] Searching for insertion points: **** Sequence is already in core tree: 100403 **** Sequence is already in core tree: 100628 @@ -2066,17 +2137,17 @@ **** Sequence is already in core tree: 9947 Insert [ 99538](len=7683) [ 1184 sites] (137 - 6427) [Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae;Chryseobacterium] Insert [ 99764](len=7683) [ 1261 sites] (130 - 6790) [Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Brucellaceae;Brucella] -Searching for position to insert 957 sequences in tree of 20285 nodes. {Setup: 1 sec} +Searching for position to insert 957 sequences in tree of 20285 nodes. {Setup: 2 sec} [ 1000/20285] {22 sec} [I_1000] [ 2000/20285] {43 sec} [7996] [ 3000/20285] {62 sec} [39961] -[ 4000/20285] {81 sec} [81358] +[ 4000/20285] {80 sec} [81358] [ 5000/20285] {99 sec} [I_5000] -[ 6000/20285] {118 sec} [4546] -[ 7000/20285] {134 sec} [67802] -[ 8000/20285] {150 sec} [135894] -[ 9000/20285] {162 sec} [I_9000] -[ 10000/20285] {174 sec} [137100] +[ 6000/20285] {117 sec} [4546] +[ 7000/20285] {133 sec} [67802] +[ 8000/20285] {149 sec} [135894] +[ 9000/20285] {161 sec} [I_9000] +[ 10000/20285] {173 sec} [137100] [ 11000/20285] {186 sec} [I_11000] [ 12000/20285] {198 sec} [63458] [ 13000/20285] {210 sec} [47043] @@ -9322,8 +9393,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-10_arm64.deb'. -dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-10_all.deb'. dpkg-deb: building package 'parsinsert-dbgsym' in '../parsinsert-dbgsym_1.04-10_arm64.deb'. +dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-10_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../parsinsert_1.04-10_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -9331,12 +9402,14 @@ 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/17376/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/17376/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/9912 and its subdirectories -I: Current time: Mon Sep 12 08:42:06 -12 2022 -I: pbuilder-time-stamp: 1663015326 +I: removing directory /srv/workspace/pbuilder/17376 and its subdirectories +I: Current time: Wed Aug 11 04:25:25 +14 2021 +I: pbuilder-time-stamp: 1628605525