Diff of the two buildlogs: -- --- b1/build.log 2023-06-01 17:01:02.298114106 +0000 +++ b2/build.log 2023-06-01 17:03:07.208635230 +0000 @@ -1,49 +1,8 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 3 11:22:37 -12 2024 -I: pbuilder-time-stamp: 1720048957 +I: Current time: Fri Jun 2 07:01:04 +14 2023 +I: pbuilder-time-stamp: 1685638864 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] -tar: ./usr/share/perl5/Debian: time stamp 2025-08-04 08:27:04 is 34290261.410146914 s in the future -tar: ./usr/share/man/pt/man8: time stamp 2025-08-04 08:27:04 is 34290261.326138757 s in the future -tar: ./usr/share/man/pt/man5: time stamp 2025-08-04 08:27:04 is 34290261.323296613 s in the future -tar: ./usr/share/man/nl/man8: time stamp 2025-08-04 08:27:04 is 34290261.317020905 s in the future -tar: ./usr/share/man/nl/man5: time stamp 2025-08-04 08:27:04 is 34290261.314263038 s in the future -tar: ./usr/share/man/man5: time stamp 2025-08-04 08:27:04 is 34290261.295121654 s in the future -tar: ./usr/share/man/fr/man5: time stamp 2025-08-04 08:27:04 is 34290261.282628225 s in the future -tar: ./usr/share/man/de/man5: time stamp 2025-08-04 08:27:04 is 34290261.270285322 s in the future -tar: ./usr/share/locale/zh_CN/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.967499936 s in the future -tar: ./usr/share/locale/vi/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.942044695 s in the future -tar: ./usr/share/locale/uk/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.899006457 s in the future -tar: ./usr/share/locale/sv/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.863698502 s in the future -tar: ./usr/share/locale/sk/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.851015315 s in the future -tar: ./usr/share/locale/ru/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.809402398 s in the future -tar: ./usr/share/locale/pt_BR/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.78878888 s in the future -tar: ./usr/share/locale/pt/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.759322979 s in the future -tar: ./usr/share/locale/pl/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.73806084 s in the future -tar: ./usr/share/locale/nl/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.714478087 s in the future -tar: ./usr/share/locale/nb/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.698874356 s in the future -tar: ./usr/share/locale/ko/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.68383455 s in the future -tar: ./usr/share/locale/ja/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.659010828 s in the future -tar: ./usr/share/locale/it/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.639625626 s in the future -tar: ./usr/share/locale/hu/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.625397947 s in the future -tar: ./usr/share/locale/gl/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.617319982 s in the future -tar: ./usr/share/locale/fr/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.574024574 s in the future -tar: ./usr/share/locale/eu/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.567629846 s in the future -tar: ./usr/share/locale/es/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.532718585 s in the future -tar: ./usr/share/locale/de/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.50495591 s in the future -tar: ./usr/share/locale/da/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.48440713 s in the future -tar: ./usr/share/locale/cs/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.463335818 s in the future -tar: ./usr/share/locale/ca/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34290260.442015133 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel.other: time stamp 2025-08-04 08:27:04 is 34290260.227440203 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel: time stamp 2025-08-04 08:27:04 is 34290260.227231957 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples: time stamp 2025-08-04 08:27:04 is 34290260.227128005 s in the future -tar: ./usr/share/doc/adduser/examples: time stamp 2025-08-04 08:27:04 is 34290260.226000391 s in the future -tar: ./usr/share/doc/adduser: time stamp 2025-08-04 08:27:04 is 34290260.225110956 s in the future -tar: ./var/lib/dpkg/info/adduser.list: time stamp 2025-08-04 08:27:04 is 34290252.81889884 s in the future -tar: ./usr/share/man/de/man8: time stamp 2025-08-04 08:27:04 is 34290252.11573012 s in the future -tar: ./usr/share/man/fr/man8: time stamp 2025-08-04 08:27:04 is 34290252.115612922 s in the future -tar: ./usr/share/man/man8: time stamp 2025-08-04 08:27:04 is 34290252.115550796 s in the future -tar: ./usr/sbin: time stamp 2025-08-04 08:27:04 is 34290252.114506487 s in the future I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem @@ -57,7 +16,7 @@ I: copying [./maq_0.7.1.orig.tar.gz] I: copying [./maq_0.7.1-9.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Nov 15 22:45:18 2020 -12 +gpgv: Signature made Tue Nov 17 00:45:18 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -71,135 +30,167 @@ dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2627759/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2684211/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 2 07:01 /bin/sh -> /bin/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/2684211/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2684211/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3e6c02ac0dd948a7b939faf2a50bfad0' - 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='2627759' - PS1='# ' - PS2='> ' + INVOCATION_ID=6ce5350e733145f0acc16396974ed61d + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2684211 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.tBeKj3eA/pbuilderrc_sMAE --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tBeKj3eA/b1 --logfile b1/build.log maq_0.7.1-9.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.tBeKj3eA/pbuilderrc_hY3M --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tBeKj3eA/b2 --logfile b2/build.log --extrapackages usrmerge maq_0.7.1-9.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2627759/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Jun 2 07:01 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/2684211/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -268,7 +259,7 @@ Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] -Fetched 19.6 MB in 1s (36.6 MB/s) +Fetched 19.6 MB in 0s (44.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19591 files and directories currently installed.) @@ -406,8 +397,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/maq-0.7.1/ && 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 > ../maq_0.7.1-9_source.changes +I: user script /srv/workspace/pbuilder/2684211/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/2684211/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/maq-0.7.1/ && 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 > ../maq_0.7.1-9_source.changes dpkg-buildpackage: info: source package maq dpkg-buildpackage: info: source version 0.7.1-9 dpkg-buildpackage: info: source distribution unstable @@ -442,7 +444,7 @@ ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -472,15 +474,15 @@ checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for zlib.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h dh_auto_build - make -j16 + make -j15 make[1]: Entering directory '/build/maq-0.7.1' make all-am make[2]: Entering directory '/build/maq-0.7.1' @@ -497,35 +499,9 @@ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_mapping.o sort_mapping.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pileup.o pileup.cc -bfa.c: In function 'nst_load_bfa1': -bfa.c:31:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 31 | fread(bfa1->name, sizeof(char), len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:32:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 32 | fread(&bfa1->ori_len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:33:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 33 | fread(&bfa1->len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:35:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 35 | fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:37:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 37 | fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c: In function 'nst_bfa_len': -bfa.c:46:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 46 | fread(&len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:48:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 48 | fread(&len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mapcheck.o mapcheck.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_pos.o get_pos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assopt.o assopt.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aux_utils.o aux_utils.c -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rbcc.o rbcc.cc -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o subsnp.o subsnp.cc fastq2bfq.c: In function 'fastq2bfq': fastq2bfq.c:30:12: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 30 | fp = gzopen(str, "w"); @@ -583,16 +559,35 @@ /usr/include/zlib.h:1631:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1631 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ +bfa.c: In function 'nst_load_bfa1': +bfa.c:31:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 31 | fread(bfa1->name, sizeof(char), len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:32:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 32 | fread(&bfa1->ori_len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:33:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 33 | fread(&bfa1->len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:35:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 35 | fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:37:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 37 | fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c: In function 'nst_bfa_len': +bfa.c:46:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 46 | fread(&len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:48:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 48 | fread(&len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aux_utils.o aux_utils.c +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rbcc.o rbcc.cc +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o subsnp.o subsnp.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_stat.o pair_stat.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_soa.o indel_soa.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o maqmap.o maqmap.c -sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)': -sort_mapping.cc:59:75: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses] - 59 | p->i1 = (((m1->i1>>24)+(m2->i1>>24))<<24) | (m1->i1^m2->i1&0xffffff); - | ~~~~~~^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o maqmap_conv.o maqmap_conv.c -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o altchr.o altchr.cc -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o submap.o submap.c indel_soa.cc: In function 'void fill_counter(bit32_t*, int, nst_bfa1_t*, gzFile)': indel_soa.cc:42:61: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] 42 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; @@ -600,6 +595,11 @@ indel_soa.cc:56:61: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] 56 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; | ~~^~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o maqmap_conv.o maqmap_conv.c +sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)': +sort_mapping.cc:59:75: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses] + 59 | p->i1 = (((m1->i1>>24)+(m2->i1>>24))<<24) | (m1->i1^m2->i1&0xffffff); + | ~~~~~~^~~~~~~~~ match.cc: In function 'int alt_cal_mm(bit64_t)': match.cc:58:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 58 | x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; @@ -625,14 +625,23 @@ match.cc:292:17: warning: variable 'n_reads' set but not used [-Wunused-but-set-variable] 292 | bit32_t n_reads; | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rmdup.o rmdup.cc -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simulate.o simulate.c +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o altchr.o altchr.cc +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o submap.o submap.c mapcheck.cc: In function 'int ma_mapcheck(int, char**)': mapcheck.cc:60:24: warning: variable 'fpout' set but not used [-Wunused-but-set-variable] 60 | FILE *fp_bfa, *fpout; | ^~~~~ +assemble.cc: In function 'base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)': +assemble.cc:106:77: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] + 106 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; + | ~~~~^~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rmdup.o rmdup.cc +match.cc: In function 'int ma_match(int, char**)': +match.cc:525:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fscanf(tmpfp, "%s", adaptor); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simulate.o simulate.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o genran.o genran.c -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_pe.o indel_pe.cc subsnp.cc: In function 'hash_map_char* ma_load_snp(FILE*)': subsnp.cc:20:34: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 20 | sprintf(key, "%s.%d", name, pos); @@ -648,14 +657,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -match.cc: In function 'int ma_match(int, char**)': -match.cc:525:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fscanf(tmpfp, "%s", adaptor); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ subsnp.cc: In function 'hash_set_char* ma_load_snp_set(FILE*)': subsnp.cc:35:34: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 35 | sprintf(key, "%s.%d", name, pos); | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'hash_set_char* ma_load_snp_set(FILE*)' at subsnp.cc:35:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ simulate.c: In function 'maq_simutrain': simulate.c:83:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 83 | fpout = gzopen(argv[1], "w"); @@ -678,21 +692,13 @@ /usr/include/zlib.h:1631:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1631 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'hash_set_char* ma_load_snp_set(FILE*)' at subsnp.cc:35:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_pe.o indel_pe.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stdaln.o stdaln.c -assemble.cc: In function 'base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)': -assemble.cc:106:77: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] - 106 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; - | ~~~~^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_call.o indel_call.cc +stdaln.c: In function 'aln_local_core': +stdaln.c:534:32: warning: variable 'b' set but not used [-Wunused-but-set-variable] + 534 | int gap_open, gap_ext, b; + | ^ rbcc.cc: In function 'hash_map_char* cns_load_dbSNP(FILE*)': rbcc.cc:21:35: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 21 | sprintf(str1, "%s.%d", name, pos); @@ -722,13 +728,8 @@ simulate.c:381:19: note: 'tc' declared here 381 | int i, k, tc[2][2]; | ^~ -stdaln.c: In function 'aln_local_core': -stdaln.c:534:32: warning: variable 'b' set but not used [-Wunused-but-set-variable] - 534 | int gap_open, gap_ext, b; - | ^ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eland2maq.o eland2maq.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o csmap2ntmap.o csmap2ntmap.cc -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o break_pair.o break_pair.c subsnp.cc: In function 'void maq_simucns_core(FILE*, gzFile, FILE*)': subsnp.cc:190:42: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 190 | sprintf(key, "%s.%d", name, pos); @@ -757,12 +758,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from break_pair.c:2: -break_pair.c: In function 'breakpair': -break_pair.c:16:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 16 | assert(fp = gzopen(str, "r")); - | ^~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o glfgen.o glfgen.cc +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o break_pair.o break_pair.c rmdup.cc: In function 'void maq_rmdup_core(gzFile, gzFile)': rmdup.cc:46:32: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-truncation] 46 | strncpy(buf, name, tl-1); @@ -793,6 +789,12 @@ rmdup.cc:42:40: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o glfgen.o glfgen.cc +In file included from break_pair.c:2: +break_pair.c: In function 'breakpair': +break_pair.c:16:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 16 | assert(fp = gzopen(str, "r")); + | ^~ glfgen.cc: In function 'glf1_t* glfgen1_core(assemble_pos_t*, const assemble_aux_t*, bit8_t)': glfgen.cc:43:77: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 43 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; @@ -840,18 +842,18 @@ make[2]: Leaving directory '/build/maq-0.7.1' make[1]: Leaving directory '/build/maq-0.7.1' dh_auto_test - make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 + make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/maq-0.7.1' make[1]: Leaving directory '/build/maq-0.7.1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/maq/ - make -j16 install DESTDIR=/build/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no + make -j15 install DESTDIR=/build/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/maq-0.7.1' make[2]: Entering directory '/build/maq-0.7.1' - /bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' + /usr/bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' + /usr/bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' make[2]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c maq '/build/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c scripts/maq.pl scripts/farm-run.pl scripts/maq_plot.pl scripts/maq_eval.pl '/build/maq-0.7.1/debian/maq/usr/bin' make[2]: Leaving directory '/build/maq-0.7.1' @@ -896,12 +898,14 @@ 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/2684211/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2684211/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/2627759 and its subdirectories -I: Current time: Wed Jul 3 11:24:02 -12 2024 -I: pbuilder-time-stamp: 1720049042 +I: removing directory /srv/workspace/pbuilder/2684211 and its subdirectories +I: Current time: Fri Jun 2 07:03:06 +14 2023 +I: pbuilder-time-stamp: 1685638986