Diff of the two buildlogs: -- --- b1/build.log 2024-06-30 15:31:08.456795779 +0000 +++ b2/build.log 2024-06-30 15:44:15.663386403 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Aug 2 09:38:36 -12 2025 -I: pbuilder-time-stamp: 1754170716 +I: Current time: Mon Jul 1 05:31:11 +14 2024 +I: pbuilder-time-stamp: 1719761471 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./biobambam2_2.0.179+ds-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.54aeqZeq/trustedkeys.kbx': General error -gpgv: Signature made Sat Jan 2 22:19:42 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.5JkhYjIc/trustedkeys.kbx': General error +gpgv: Signature made Mon Jan 4 00:19:42 2021 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./biobambam2_2.0.179+ds-1.dsc @@ -30,134 +30,165 @@ dpkg-source: info: applying spelling-error-in-binary.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3637637/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/748683/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 Jul 1 05:31 /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/748683/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/748683/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - 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]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + 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,-fixfilepath parallel=12 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3af3724fcd3147b7b8d5354bf340ba9a' - 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='3637637' - PS1='# ' - PS2='> ' + INVOCATION_ID=984bc89c2132477b932946f8c3c3f9b3 + 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=748683 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.nuRBzbmr/pbuilderrc_pX1Z --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nuRBzbmr/b1 --logfile b1/build.log biobambam2_2.0.179+ds-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.nuRBzbmr/pbuilderrc_gwIr --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nuRBzbmr/b2 --logfile b2/build.log biobambam2_2.0.179+ds-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-22-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.94-1 (2024-06-21) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Mar 27 2024 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 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 2024 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 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 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Mar 27 2024 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Mar 27 2024 more - -rwsr-xr-x 1 root root 55528 Mar 27 2024 mount - -rwxr-xr-x 1 root root 18664 Mar 27 2024 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 10 03:47 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Mar 27 2024 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 2024 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Mar 27 2024 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 2024 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 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 5898 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 8049 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/3637637/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 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 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 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 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Mar 29 00:09 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 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 00:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 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 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Mar 29 00:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Mar 29 00:09 more + -rwsr-xr-x 1 root root 55528 Mar 29 00:09 mount + -rwxr-xr-x 1 root root 18664 Mar 29 00:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Jul 1 05:31 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Mar 29 00:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 23:59 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Mar 29 00:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 00:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 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 5898 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 8049 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/748683/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -253,7 +284,7 @@ Get: 54 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libmaus2-dev amd64 2.0.768+dfsg-2 [3500 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] -Fetched 33.7 MB in 3s (11.9 MB/s) +Fetched 33.7 MB in 1s (29.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19711 files and directories currently installed.) @@ -494,7 +525,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/biobambam2-2.0.179+ds/ && 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 > ../biobambam2_2.0.179+ds-1_source.changes +I: user script /srv/workspace/pbuilder/748683/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/748683/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/biobambam2-2.0.179+ds/ && 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 > ../biobambam2_2.0.179+ds-1_source.changes dpkg-buildpackage: info: source package biobambam2 dpkg-buildpackage: info: source version 2.0.179+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -666,7 +701,6 @@ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bamtofastq-bamtofastq.o `test -f 'programs/bamtofastq.cpp' || echo './'`programs/bamtofastq.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bammarkduplicates-bammarkduplicates.o `test -f 'programs/bammarkduplicates.cpp' || echo './'`programs/bammarkduplicates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bamsort-bamsort.o `test -f 'programs/bamsort.cpp' || echo './'`programs/bamsort.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bammaskflags-bammaskflags.o `test -f 'programs/bammaskflags.cpp' || echo './'`programs/bammaskflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bammaskflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bamrecompress-bamrecompress.o `test -f 'programs/bamrecompress.cpp' || echo './'`programs/bamrecompress.cpp @@ -821,12 +855,12 @@ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamreplacechecksums-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o `test -f 'biobambam2/UpdateNumericalIndex.cpp' || echo './'`biobambam2/UpdateNumericalIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bamfastcat-bamfastcat.o `test -f 'programs/bamfastcat.cpp' || echo './'`programs/bamfastcat.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamfastcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamfastcat-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp programs/bamrefextract.cpp: In function 'void handle(libmaus2::sorting::SerialisingSortingBufferedOutputFile::unique_ptr_type&, int64_t, const libmaus2::bambam::BamHeader&)': programs/bamrefextract.cpp:106:28: warning: 'GP.libmaus2::aio::GenericPeeker > >::slot.Element::p' may be used uninitialized in this function [-Wmaybe-uninitialized] 106 | while ( GP.peekNext(EL) && EL.p == p ) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamfastcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamfastcat-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamfastcat-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/populaterefcache-populaterefcache.o `test -f 'programs/populaterefcache.cpp' || echo './'`programs/populaterefcache.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/populaterefcache-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp @@ -935,12 +969,12 @@ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamsimpledepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bamdepthmerge-bamdepthmerge.o `test -f 'programs/bamdepthmerge.cpp' || echo './'`programs/bamdepthmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamdepthmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bamcountflags-bamcountflags.o `test -f 'programs/bamcountflags.cpp' || echo './'`programs/bamcountflags.cpp In file included from programs/bamdepthmerge.cpp:23: ./biobambam2/DepthIntervalGetter.hpp: In member function 'uint64_t biobambam2::DepthIntervalGetterMerge::getNext(uint64_t&, uint64_t&, libmaus2::autoarray::AutoArray >&)': ./biobambam2/DepthIntervalGetter.hpp:210:25: warning: unused variable 'HE' [-Wunused-variable] 210 | HeapElement const & HE = H.top(); | ^~ +g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bamcountflags-bamcountflags.o `test -f 'programs/bamcountflags.cpp' || echo './'`programs/bamcountflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamcountflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/vcffilterfilterflags-vcffilterfilterflags.o `test -f 'programs/vcffilterfilterflags.cpp' || echo './'`programs/vcffilterfilterflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/vcffilterfilterflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp @@ -955,227 +989,228 @@ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamaddne-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamtofastq-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bammarkduplicates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsort programs/bamsort-bamsort.o biobambam2/bamsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz -libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsort programs/bamsort-bamsort.o biobambam2/bamsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxsort programs/bamauxsort-bamauxsort.o biobambam2/bamauxsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxsort programs/bamauxsort-bamauxsort.o biobambam2/bamauxsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterclip programs/bamadapterclip-bamadapterclip.o biobambam2/bamadapterclip-Licensing.o biobambam2/bamadapterclip-ClipAdapters.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 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-Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamheap3 programs/bamheap3-bamheap3.o biobambam2/bamheap3-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobampar programs/fastqtobampar-fastqtobampar.o biobambam2/fastqtobampar-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtagconversion programs/bamtagconversion-bamtagconversion.o biobambam2/bamtagconversion-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobampar programs/fastqtobampar-fastqtobampar.o biobambam2/fastqtobampar-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bambisect programs/bambisect-bambisect.o biobambam2/bambisect-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bambisect programs/bambisect-bambisect.o biobambam2/bambisect-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 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programs/bamconsensus-bamconsensus.o biobambam2/bamconsensus-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcountflags programs/bamcountflags-bamcountflags.o biobambam2/bamcountflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamconsensus programs/bamconsensus-bamconsensus.o biobambam2/bamconsensus-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcountflags programs/bamcountflags-bamcountflags.o biobambam2/bamcountflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamconsensus programs/bamconsensus-bamconsensus.o biobambam2/bamconsensus-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamexondepth programs/bamexondepth-bamexondepth.o biobambam2/bamexondepth-Licensing.o biobambam2/bamexondepth-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamexondepth programs/bamexondepth-bamexondepth.o biobambam2/bamexondepth-Licensing.o biobambam2/bamexondepth-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamexondepth programs/bamexondepth-bamexondepth.o biobambam2/bamexondepth-Licensing.o biobambam2/bamexondepth-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcountflags programs/bamcountflags-bamcountflags.o biobambam2/bamcountflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz -libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcountflags programs/bamcountflags-bamcountflags.o biobambam2/bamcountflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamaddne programs/bamaddne-bamaddne.o biobambam2/bamaddne-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamaddne programs/bamaddne-bamaddne.o biobambam2/bamaddne-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamaddne programs/bamaddne-bamaddne.o biobambam2/bamaddne-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicatesoptdist programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o biobambam2/bammarkduplicatesoptdist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicatesoptdist programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o biobambam2/bammarkduplicatesoptdist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammarkduplicatesoptdist programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o biobambam2/bammarkduplicatesoptdist-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.179+ds/src' Making all in test @@ -1199,8 +1234,8 @@ make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.179+ds/test' g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o bamcmp-bamcmp.o `test -f 'bamcmp.cpp' || echo './'`bamcmp.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o bamtosam-bamtosam.o `test -f 'bamtosam.cpp' || echo './'`bamtosam.cpp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtosam bamtosam-bamtosam.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcmp bamcmp-bamcmp.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtosam bamtosam-bamtosam.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcmp bamcmp-bamcmp.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtosam bamtosam-bamtosam.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcmp bamcmp-bamcmp.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.179+ds/test' @@ -1239,7 +1274,7 @@ make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.179+ds/src' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.179+ds/src' /bin/mkdir -p '/build/reproducible-path/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress bamadapterfind bamfilteraux bamauxsort bamadapterclip bamcollate2 bam12auxmerge bam12split bam12strip bamreset bamrank bamclipreinsert bamclipXT bamzztoname bamindex bamfilterflags bamfilterrg bamdownsamplerandom bammarkduplicates2 bamcat bammerge bamsplit bamfastsplit bamsplitdiv bamchecksort fastqtobam bamfixmateinformation bamseqchksum normalisefasta bamfilterheader bamfilterheader2 bammdnm bammapdist bamvalidate bamflagsplit bamintervalcomment bamintervalcommenthist bamstreamingmarkduplicates bamalignfrac bamfilternames bamsormadup bamexplode bamexploderef bamfastexploderef bamfastnumextract bamranksort fastaexplod bamrecalculatecigar bamfiltermc bamnumericalindex bamnumericalindexstats bammarkduplicatesopt bamfilterlength bamauxmerge bamrefinterval bamscrapcount bamfilterrefid bamfillquery bamrefextract fastqtobam2 bamauxmerge2 bamreheader bamreplacechecksums bamfastcat populaterefcache bamfiltereofblocks bamdepth bamdepthintersect bamfilterk bamfixpairinfo bamdifference bamfeaturecount '/build/reproducible-path/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress bamadapterfind bamfilteraux bamauxsort bamadapterclip bamcollate2 bam12auxmerge bam12split bam12strip bamreset bamrank bamclipreinsert bamclipXT bamzztoname bamindex bamfilterflags bamfilterrg bamdownsamplerandom bammarkduplicates2 bamcat bammerge bamsplit bamfastsplit bamsplitdiv bamchecksort fastqtobam bamfixmateinformation bamseqchksum normalisefasta bamfilterheader bamfilterheader2 bammdnm bammapdist bamvalidate bamflagsplit bamintervalcomment bamintervalcommenthist bamstreamingmarkduplicates bamalignfrac bamfilternames bamsormadup bamexplode bamexploderef bamfastexploderef bamfastnumextract bamranksort fastaexplod bamrecalculatecigar bamfiltermc bamnumericalindex bamnumericalindexstats bammarkduplicatesopt bamfilterlength bamauxmerge bamrefinterval bamscrapcount bamfilterrefid bamfillquery bamrefextract fastqtobam2 bamauxmerge2 bamreheader bamreplacechecksums bamfastcat populaterefcache bamfiltereofblocks bamdepth bamdepthintersect bamfilterk bamfixpairinfo bamdifference bamfeaturecount '/build/reproducible-path/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin' libtool: install: /usr/bin/install -c bamtofastq /build/reproducible-path/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamtofastq libtool: install: /usr/bin/install -c bammarkduplicates /build/reproducible-path/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bammarkduplicates libtool: install: /usr/bin/install -c bamsort /build/reproducible-path/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamsort @@ -1349,14 +1384,14 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/biobambam2/usr/bin/bammerge debian/biobambam2/usr/bin/bamnumericalindex debian/biobambam2/usr/bin/bamdepth debian/biobambam2/usr/bin/bamexplode debian/biobambam2/usr/bin/bamfilterheader debian/biobambam2/usr/bin/bamsormadup debian/biobambam2/usr/bin/fastqtobam debian/biobambam2/usr/bin/bamreplacechecksums debian/biobambam2/usr/bin/bamintervalcommenthist debian/biobambam2/usr/bin/bamfeaturecount debian/biobambam2/usr/bin/bamdownsamplerandom debian/biobambam2/usr/bin/bamrank debian/biobambam2/usr/bin/bamfilterlength debian/biobambam2/usr/bin/bamrefinterval debian/biobambam2/usr/bin/bammapdist debian/biobambam2/usr/bin/bamcat debian/biobambam2/usr/bin/bamalignfrac debian/biobambam2/usr/bin/bammarkduplicatesopt debian/biobambam2/usr/bin/bamcollate2 debian/biobambam2/usr/bin/bamflagsplit debian/biobambam2/usr/bin/bamseqchksum debian/biobambam2/usr/bin/bamreheader debian/biobambam2/usr/bin/bamdifference debian/biobambam2/usr/bin/bammarkduplicates2 debian/biobambam2/usr/bin/bamfastexploderef debian/biobambam2/usr/bin/bamdepthintersect debian/biobambam2/usr/bin/bammaskflags debian/biobambam2/usr/bin/populaterefcache debian/biobambam2/usr/bin/bamrecompress debian/biobambam2/usr/bin/fastqtobam2 debian/biobambam2/usr/bin/bamreset debian/biobambam2/usr/bin/bamauxmerge2 debian/biobambam2/usr/bin/bamindex debian/biobambam2/usr/bin/bamrefextract debian/biobambam2/usr/bin/bam12strip debian/biobambam2/usr/bin/bamadapterfind debian/biobambam2/usr/bin/bamfilterflags debian/biobambam2/usr/bin/bamvalidate debian/biobambam2/usr/bin/bamclipreinsert debian/biobambam2/usr/bin/bamadapterclip debian/biobambam2/usr/bin/bamtofastq debian/biobambam2/usr/bin/bamsort debian/biobambam2/usr/bin/bamauxmerge debian/biobambam2/usr/bin/bam12auxmerge debian/biobambam2/usr/bin/bamscrapcount debian/biobambam2/usr/bin/bammdnm debian/biobambam2/usr/bin/bamfastcat debian/biobambam2/usr/bin/bamintervalcomment debian/biobambam2/usr/bin/bamclipXT debian/biobambam2/usr/bin/bammarkduplicates debian/biobambam2/usr/bin/bamfilterrefid debian/biobambam2/usr/bin/bamfiltereofblocks debian/biobambam2/usr/bin/bamranksort debian/biobambam2/usr/bin/bamchecksort debian/biobambam2/usr/bin/bamfilterrg debian/biobambam2/usr/bin/bamsplitdiv debian/biobambam2/usr/bin/bamzztoname debian/biobambam2/usr/bin/normalisefasta debian/biobambam2/usr/bin/bamfixpairinfo debian/biobambam2/usr/bin/bamnumericalindexstats debian/biobambam2/usr/bin/bamfilternames debian/biobambam2/usr/bin/bamstreamingmarkduplicates debian/biobambam2/usr/bin/bamfilteraux debian/biobambam2/usr/bin/bamauxsort debian/biobambam2/usr/bin/bamfastsplit debian/biobambam2/usr/bin/bamfillquery debian/biobambam2/usr/bin/bamfastnumextract debian/biobambam2/usr/bin/fastaexplod debian/biobambam2/usr/bin/bam12split debian/biobambam2/usr/bin/bamfilterk debian/biobambam2/usr/bin/bamfiltermc debian/biobambam2/usr/bin/bamsplit debian/biobambam2/usr/bin/bamfixmateinformation debian/biobambam2/usr/bin/bamexploderef debian/biobambam2/usr/bin/bamfilterheader2 debian/biobambam2/usr/bin/bamrecalculatecigar were not linked against libmaus2_simd_align_256.so.2 (they use none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/biobambam2/usr/bin/bammerge debian/biobambam2/usr/bin/bamnumericalindex debian/biobambam2/usr/bin/bamdepth debian/biobambam2/usr/bin/bamexplode debian/biobambam2/usr/bin/bamfilterheader debian/biobambam2/usr/bin/bamsormadup debian/biobambam2/usr/bin/fastqtobam debian/biobambam2/usr/bin/bamreplacechecksums debian/biobambam2/usr/bin/bamintervalcommenthist debian/biobambam2/usr/bin/bamfeaturecount debian/biobambam2/usr/bin/bamdownsamplerandom debian/biobambam2/usr/bin/bamrank debian/biobambam2/usr/bin/bamfilterlength debian/biobambam2/usr/bin/bamrefinterval debian/biobambam2/usr/bin/bammapdist debian/biobambam2/usr/bin/bamcat debian/biobambam2/usr/bin/bamalignfrac debian/biobambam2/usr/bin/bammarkduplicatesopt debian/biobambam2/usr/bin/bamcollate2 debian/biobambam2/usr/bin/bamflagsplit debian/biobambam2/usr/bin/bamseqchksum debian/biobambam2/usr/bin/bamreheader debian/biobambam2/usr/bin/bamdifference debian/biobambam2/usr/bin/bammarkduplicates2 debian/biobambam2/usr/bin/bamfastexploderef debian/biobambam2/usr/bin/bamdepthintersect debian/biobambam2/usr/bin/bammaskflags debian/biobambam2/usr/bin/populaterefcache debian/biobambam2/usr/bin/bamrecompress debian/biobambam2/usr/bin/fastqtobam2 debian/biobambam2/usr/bin/bamreset debian/biobambam2/usr/bin/bamauxmerge2 debian/biobambam2/usr/bin/bamindex debian/biobambam2/usr/bin/bamrefextract debian/biobambam2/usr/bin/bam12strip debian/biobambam2/usr/bin/bamadapterfind debian/biobambam2/usr/bin/bamfilterflags debian/biobambam2/usr/bin/bamvalidate debian/biobambam2/usr/bin/bamclipreinsert debian/biobambam2/usr/bin/bamadapterclip debian/biobambam2/usr/bin/bamtofastq debian/biobambam2/usr/bin/bamsort debian/biobambam2/usr/bin/bamauxmerge debian/biobambam2/usr/bin/bam12auxmerge debian/biobambam2/usr/bin/bamscrapcount debian/biobambam2/usr/bin/bammdnm debian/biobambam2/usr/bin/bamfastcat debian/biobambam2/usr/bin/bamintervalcomment debian/biobambam2/usr/bin/bamclipXT debian/biobambam2/usr/bin/bammarkduplicates debian/biobambam2/usr/bin/bamfilterrefid debian/biobambam2/usr/bin/bamfiltereofblocks debian/biobambam2/usr/bin/bamranksort debian/biobambam2/usr/bin/bamchecksort debian/biobambam2/usr/bin/bamfilterrg debian/biobambam2/usr/bin/bamsplitdiv debian/biobambam2/usr/bin/bamzztoname debian/biobambam2/usr/bin/normalisefasta debian/biobambam2/usr/bin/bamfixpairinfo debian/biobambam2/usr/bin/bamnumericalindexstats debian/biobambam2/usr/bin/bamfilternames debian/biobambam2/usr/bin/bamstreamingmarkduplicates debian/biobambam2/usr/bin/bamfilteraux debian/biobambam2/usr/bin/bamauxsort debian/biobambam2/usr/bin/bamfastsplit debian/biobambam2/usr/bin/bamfillquery debian/biobambam2/usr/bin/bamfastnumextract debian/biobambam2/usr/bin/fastaexplod debian/biobambam2/usr/bin/bam12split debian/biobambam2/usr/bin/bamfilterk debian/biobambam2/usr/bin/bamfiltermc debian/biobambam2/usr/bin/bamsplit debian/biobambam2/usr/bin/bamfixmateinformation debian/biobambam2/usr/bin/bamexploderef debian/biobambam2/usr/bin/bamfilterheader2 debian/biobambam2/usr/bin/bamrecalculatecigar were not linked against libmaus2_simd_align_128.so.2 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/biobambam2/usr/bin/bamfilterheader2 debian/biobambam2/usr/bin/bamexplode debian/biobambam2/usr/bin/bamsormadup debian/biobambam2/usr/bin/bamsplit debian/biobambam2/usr/bin/fastaexplod debian/biobambam2/usr/bin/fastqtobam debian/biobambam2/usr/bin/bamfastexploderef debian/biobambam2/usr/bin/bamalignfrac debian/biobambam2/usr/bin/bamdepth debian/biobambam2/usr/bin/bammarkduplicates debian/biobambam2/usr/bin/bamfeaturecount debian/biobambam2/usr/bin/bamfixmateinformation debian/biobambam2/usr/bin/bamcat debian/biobambam2/usr/bin/bamnumericalindex debian/biobambam2/usr/bin/bammerge debian/biobambam2/usr/bin/bamfiltermc debian/biobambam2/usr/bin/bamchecksort debian/biobambam2/usr/bin/bamauxmerge2 debian/biobambam2/usr/bin/bamrank debian/biobambam2/usr/bin/bamflagsplit debian/biobambam2/usr/bin/bamfilterk debian/biobambam2/usr/bin/bamreheader debian/biobambam2/usr/bin/bammarkduplicatesopt debian/biobambam2/usr/bin/bamauxmerge debian/biobambam2/usr/bin/bamstreamingmarkduplicates debian/biobambam2/usr/bin/bamcollate2 debian/biobambam2/usr/bin/bamreplacechecksums debian/biobambam2/usr/bin/bamrecalculatecigar debian/biobambam2/usr/bin/bammapdist debian/biobambam2/usr/bin/bamdifference debian/biobambam2/usr/bin/bamauxsort debian/biobambam2/usr/bin/bamfilterlength debian/biobambam2/usr/bin/bamfilterflags debian/biobambam2/usr/bin/bamclipreinsert debian/biobambam2/usr/bin/bamdepthintersect debian/biobambam2/usr/bin/bam12split debian/biobambam2/usr/bin/bamadapterclip debian/biobambam2/usr/bin/bammdnm debian/biobambam2/usr/bin/bamrefextract debian/biobambam2/usr/bin/bamintervalcommenthist debian/biobambam2/usr/bin/bammaskflags debian/biobambam2/usr/bin/bamfastnumextract debian/biobambam2/usr/bin/bamfillquery debian/biobambam2/usr/bin/bamfiltereofblocks debian/biobambam2/usr/bin/bammarkduplicates2 debian/biobambam2/usr/bin/bamreset debian/biobambam2/usr/bin/bamfilterrefid debian/biobambam2/usr/bin/bamfastcat debian/biobambam2/usr/bin/bamdownsamplerandom debian/biobambam2/usr/bin/populaterefcache debian/biobambam2/usr/bin/bamtofastq debian/biobambam2/usr/bin/bamfilternames debian/biobambam2/usr/bin/bam12strip debian/biobambam2/usr/bin/bamadapterfind debian/biobambam2/usr/bin/bamrecompress debian/biobambam2/usr/bin/bamfilteraux debian/biobambam2/usr/bin/bam12auxmerge debian/biobambam2/usr/bin/bamvalidate debian/biobambam2/usr/bin/bamfixpairinfo debian/biobambam2/usr/bin/bamscrapcount debian/biobambam2/usr/bin/bamclipXT debian/biobambam2/usr/bin/fastqtobam2 debian/biobambam2/usr/bin/bamsort debian/biobambam2/usr/bin/bamsplitdiv debian/biobambam2/usr/bin/bamranksort debian/biobambam2/usr/bin/bamseqchksum debian/biobambam2/usr/bin/bamnumericalindexstats debian/biobambam2/usr/bin/normalisefasta debian/biobambam2/usr/bin/bamrefinterval debian/biobambam2/usr/bin/bamfastsplit debian/biobambam2/usr/bin/bamindex debian/biobambam2/usr/bin/bamintervalcomment debian/biobambam2/usr/bin/bamzztoname debian/biobambam2/usr/bin/bamexploderef debian/biobambam2/usr/bin/bamfilterheader debian/biobambam2/usr/bin/bamfilterrg were not linked against libmaus2_simd_align_128.so.2 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/biobambam2/usr/bin/bamfilterheader2 debian/biobambam2/usr/bin/bamexplode debian/biobambam2/usr/bin/bamsormadup debian/biobambam2/usr/bin/bamsplit debian/biobambam2/usr/bin/fastaexplod debian/biobambam2/usr/bin/fastqtobam debian/biobambam2/usr/bin/bamfastexploderef debian/biobambam2/usr/bin/bamalignfrac debian/biobambam2/usr/bin/bamdepth debian/biobambam2/usr/bin/bammarkduplicates debian/biobambam2/usr/bin/bamfeaturecount debian/biobambam2/usr/bin/bamfixmateinformation debian/biobambam2/usr/bin/bamcat debian/biobambam2/usr/bin/bamnumericalindex debian/biobambam2/usr/bin/bammerge debian/biobambam2/usr/bin/bamfiltermc debian/biobambam2/usr/bin/bamchecksort debian/biobambam2/usr/bin/bamauxmerge2 debian/biobambam2/usr/bin/bamrank debian/biobambam2/usr/bin/bamflagsplit debian/biobambam2/usr/bin/bamfilterk debian/biobambam2/usr/bin/bamreheader debian/biobambam2/usr/bin/bammarkduplicatesopt debian/biobambam2/usr/bin/bamauxmerge debian/biobambam2/usr/bin/bamstreamingmarkduplicates debian/biobambam2/usr/bin/bamcollate2 debian/biobambam2/usr/bin/bamreplacechecksums debian/biobambam2/usr/bin/bamrecalculatecigar debian/biobambam2/usr/bin/bammapdist debian/biobambam2/usr/bin/bamdifference debian/biobambam2/usr/bin/bamauxsort debian/biobambam2/usr/bin/bamfilterlength debian/biobambam2/usr/bin/bamfilterflags debian/biobambam2/usr/bin/bamclipreinsert debian/biobambam2/usr/bin/bamdepthintersect debian/biobambam2/usr/bin/bam12split debian/biobambam2/usr/bin/bamadapterclip debian/biobambam2/usr/bin/bammdnm debian/biobambam2/usr/bin/bamrefextract debian/biobambam2/usr/bin/bamintervalcommenthist debian/biobambam2/usr/bin/bammaskflags debian/biobambam2/usr/bin/bamfastnumextract debian/biobambam2/usr/bin/bamfillquery debian/biobambam2/usr/bin/bamfiltereofblocks debian/biobambam2/usr/bin/bammarkduplicates2 debian/biobambam2/usr/bin/bamreset debian/biobambam2/usr/bin/bamfilterrefid debian/biobambam2/usr/bin/bamfastcat debian/biobambam2/usr/bin/bamdownsamplerandom debian/biobambam2/usr/bin/populaterefcache debian/biobambam2/usr/bin/bamtofastq debian/biobambam2/usr/bin/bamfilternames debian/biobambam2/usr/bin/bam12strip debian/biobambam2/usr/bin/bamadapterfind debian/biobambam2/usr/bin/bamrecompress debian/biobambam2/usr/bin/bamfilteraux debian/biobambam2/usr/bin/bam12auxmerge debian/biobambam2/usr/bin/bamvalidate debian/biobambam2/usr/bin/bamfixpairinfo debian/biobambam2/usr/bin/bamscrapcount debian/biobambam2/usr/bin/bamclipXT debian/biobambam2/usr/bin/fastqtobam2 debian/biobambam2/usr/bin/bamsort debian/biobambam2/usr/bin/bamsplitdiv debian/biobambam2/usr/bin/bamranksort debian/biobambam2/usr/bin/bamseqchksum debian/biobambam2/usr/bin/bamnumericalindexstats debian/biobambam2/usr/bin/normalisefasta debian/biobambam2/usr/bin/bamrefinterval debian/biobambam2/usr/bin/bamfastsplit debian/biobambam2/usr/bin/bamindex debian/biobambam2/usr/bin/bamintervalcomment debian/biobambam2/usr/bin/bamzztoname debian/biobambam2/usr/bin/bamexploderef debian/biobambam2/usr/bin/bamfilterheader debian/biobambam2/usr/bin/bamfilterrg were not linked against libmaus2_simd_align_256.so.2 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'biobambam2' in '../biobambam2_2.0.179+ds-1_amd64.deb'. dpkg-deb: building package 'biobambam2-dbgsym' in '../biobambam2-dbgsym_2.0.179+ds-1_amd64.deb'. +dpkg-deb: building package 'biobambam2' in '../biobambam2_2.0.179+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biobambam2_2.0.179+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1364,12 +1399,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/748683/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/748683/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/3637637 and its subdirectories -I: Current time: Sat Aug 2 09:54:05 -12 2025 -I: pbuilder-time-stamp: 1754171645 +I: removing directory /srv/workspace/pbuilder/748683 and its subdirectories +I: Current time: Mon Jul 1 05:44:12 +14 2024 +I: pbuilder-time-stamp: 1719762252