Diff of the two buildlogs: -- --- b1/build.log 2024-07-18 20:15:25.715757723 +0000 +++ b2/build.log 2024-07-18 20:22:52.492745114 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Aug 20 14:36:56 -12 2025 -I: pbuilder-time-stamp: 1755743816 +I: Current time: Fri Jul 19 10:15:28 +14 2024 +I: pbuilder-time-stamp: 1721333728 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 [./samtools_1.11-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.4NVfn1i4/trustedkeys.kbx': General error -gpgv: Signature made Thu Oct 1 02:52:01 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.b1YP3jBH/trustedkeys.kbx': General error +gpgv: Signature made Fri Oct 2 04:52:01 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,135 +28,166 @@ dpkg-source: info: unpacking samtools_1.11-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/381713/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1626967/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 19 10:15 /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/1626967/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1626967/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=42 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + 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=20 ' + 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='24fbd3edcab648c0b308ba3ba3287095' - 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='381713' - PS1='# ' - PS2='> ' + INVOCATION_ID=928d8851b0c84a16925ab897b2881882 + 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=1626967 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.TPfftu0I/pbuilderrc_bdHX --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.TPfftu0I/b1 --logfile b1/build.log samtools_1.11-1.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://213.165.73.152:3128' + 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.TPfftu0I/pbuilderrc_4e0t --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.TPfftu0I/b2 --logfile b2/build.log samtools_1.11-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-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 6.1.0-23-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) 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 Aug 9 03:46 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/381713/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 19 10:15 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/1626967/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -271,7 +302,7 @@ Get: 55 http://deb.debian.org/debian bullseye/main amd64 libncurses5-dev amd64 6.2+20201114-2+deb11u2 [948 B] Get: 56 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 tabix amd64 1.11-4 [339 kB] -Fetched 28.2 MB in 4s (7390 kB/s) +Fetched 28.2 MB in 1s (34.6 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.) @@ -516,7 +547,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/samtools-1.11/ && 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 > ../samtools_1.11-1_source.changes +I: user script /srv/workspace/pbuilder/1626967/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1626967/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/samtools-1.11/ && 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 > ../samtools_1.11-1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.11-1 dpkg-buildpackage: info: source distribution unstable @@ -532,7 +567,7 @@ touch config.mk dh_auto_clean -- install -d /build/reproducible-path/samtools-1.11/debian/.debhelper/generated/_source/home - make -j42 distclean + make -j20 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.11' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai @@ -636,47 +671,54 @@ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" - make -j42 "CFLAGS=-g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" + make -j20 "CFLAGS=-g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.11' gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c +cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c +cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.11"' > version.h cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c +cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c +cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -684,95 +726,88 @@ cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c -cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c +cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c +cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c +cc1: warning: command-line option '-frelease' is valid for D but not for C ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o ar: `u' modifier ignored since `D' is the default (see `U') +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread -gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c -cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread +gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o ./lz4/lz4.o libbam.a libst.a -lhts -lcurses -lm -lz -lpthread gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c @@ -780,91 +815,91 @@ cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/reproducible-path/samtools-1.11' make[1]: Leaving directory '/build/reproducible-path/samtools-1.11' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/samtools-1.11' dh_auto_test -- BGZIP=/usr/bin/bgzip - make -j42 test VERBOSE=1 BGZIP=/usr/bin/bgzip + make -j20 test VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/reproducible-path/samtools-1.11' test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} -/usr/bin/bgzip -c -b 65272 -s 5 /tmp/0VbifrUoEO/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/d4gSebVaAF/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/0VbifrUoEO/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/d4gSebVaAF/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/0VbifrUoEO/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/d4gSebVaAF/bgzip.dat.gz .. ok -/build/reproducible-path/samtools-1.11/samtools faidx /tmp/0VbifrUoEO/faidx.fa 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.11/samtools faidx /tmp/d4gSebVaAF/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.11/samtools faidx /tmp/0VbifrUoEO/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.11/samtools faidx /tmp/d4gSebVaAF/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.11/samtools faidx /tmp/0VbifrUoEO/faidx.fa 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.11/samtools faidx /tmp/d4gSebVaAF/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.11/samtools faidx /tmp/0VbifrUoEO/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.11/samtools faidx /tmp/d4gSebVaAF/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.11/samtools faidx /tmp/0VbifrUoEO/faidx.fa 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.11/samtools faidx /tmp/d4gSebVaAF/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.11/samtools faidx /tmp/0VbifrUoEO/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.11/samtools faidx /tmp/d4gSebVaAF/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.11/samtools faidx /tmp/0VbifrUoEO/faidx.fa 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.11/samtools faidx /tmp/d4gSebVaAF/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.11/samtools faidx /tmp/0VbifrUoEO/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.11/samtools faidx /tmp/d4gSebVaAF/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/0VbifrUoEO/fqidx.fq 3:11-13 +/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/d4gSebVaAF/fqidx.fq 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/0VbifrUoEO/fqidx.fq.gz 3:11-13 +/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/d4gSebVaAF/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/0VbifrUoEO/fqidx.fq 2:998-1003 +/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/d4gSebVaAF/fqidx.fq 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/0VbifrUoEO/fqidx.fq.gz 2:998-1003 +/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/d4gSebVaAF/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/0VbifrUoEO/fqidx.fq 1:100-104 +/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/d4gSebVaAF/fqidx.fq 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/0VbifrUoEO/fqidx.fq.gz 1:100-104 +/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/d4gSebVaAF/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/0VbifrUoEO/fqidx.fq 1:99998-100007 +/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/d4gSebVaAF/fqidx.fq 1:99998-100007 .. ok .. ok -/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/0VbifrUoEO/fqidx.fq.gz 1:99998-100007 +/build/reproducible-path/samtools-1.11/samtools fqidx /tmp/d4gSebVaAF/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -874,7 +909,7 @@ .. ok test_dict: - /build/reproducible-path/samtools-1.11/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/0VbifrUoEO/dict.fa.gz + /build/reproducible-path/samtools-1.11/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/d4gSebVaAF/dict.fa.gz .. ok test_dict: @@ -886,11 +921,11 @@ .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools view /tmp/0VbifrUoEO/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.11/samtools view /tmp/d4gSebVaAF/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools view /tmp/0VbifrUoEO/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.11/samtools view /tmp/d4gSebVaAF/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -898,31 +933,31 @@ .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools view -X /build/reproducible-path/samtools-1.11/test/dat/test_input_1_b.bam /tmp/0VbifrUoEO/test_input_1_b.bam.bai ref2 + /build/reproducible-path/samtools-1.11/samtools view -X /build/reproducible-path/samtools-1.11/test/dat/test_input_1_b.bam /tmp/d4gSebVaAF/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.11/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/0VbifrUoEO/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.11/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.11/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/d4gSebVaAF/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools index -c /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/0VbifrUoEO/auto_indexed.csi && cat /tmp/0VbifrUoEO/auto_indexed.csi + /build/reproducible-path/samtools-1.11/samtools index -c /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/d4gSebVaAF/auto_indexed.csi && cat /tmp/d4gSebVaAF/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools index /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/0VbifrUoEO/auto_indexed.crai && cat /tmp/0VbifrUoEO/auto_indexed.crai + /build/reproducible-path/samtools-1.11/samtools index /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/d4gSebVaAF/auto_indexed.crai && cat /tmp/d4gSebVaAF/auto_indexed.crai .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools index -c /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/0VbifrUoEO/auto_indexed.csi && cat /tmp/0VbifrUoEO/auto_indexed.csi + /build/reproducible-path/samtools-1.11/samtools index -c /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/d4gSebVaAF/auto_indexed.csi && cat /tmp/d4gSebVaAF/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools view -@ 2 /tmp/0VbifrUoEO/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.11/samtools view -@ 2 /tmp/d4gSebVaAF/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools view -@ 2 /tmp/0VbifrUoEO/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.11/samtools view -@ 2 /tmp/d4gSebVaAF/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -930,63 +965,63 @@ .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools view -@ 2 -X /build/reproducible-path/samtools-1.11/test/dat/test_input_1_b.bam /tmp/0VbifrUoEO/test_input_1_b.bam.bai ref2 + /build/reproducible-path/samtools-1.11/samtools view -@ 2 -X /build/reproducible-path/samtools-1.11/test/dat/test_input_1_b.bam /tmp/d4gSebVaAF/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.11/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/0VbifrUoEO/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.11/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.11/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/d4gSebVaAF/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools index -@ 2 -c /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/0VbifrUoEO/auto_indexed.csi && cat /tmp/0VbifrUoEO/auto_indexed.csi + /build/reproducible-path/samtools-1.11/samtools index -@ 2 -c /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/d4gSebVaAF/auto_indexed.csi && cat /tmp/d4gSebVaAF/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools index -@ 2 /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/0VbifrUoEO/auto_indexed.crai && cat /tmp/0VbifrUoEO/auto_indexed.crai + /build/reproducible-path/samtools-1.11/samtools index -@ 2 /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/d4gSebVaAF/auto_indexed.crai && cat /tmp/d4gSebVaAF/auto_indexed.crai .. ok test_index: - /build/reproducible-path/samtools-1.11/samtools index -@ 2 -c /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/0VbifrUoEO/auto_indexed.csi && cat /tmp/0VbifrUoEO/auto_indexed.csi + /build/reproducible-path/samtools-1.11/samtools index -@ 2 -c /build/reproducible-path/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/d4gSebVaAF/auto_indexed.csi && cat /tmp/d4gSebVaAF/auto_indexed.csi .. ok test_mpileup: - /build/reproducible-path/samtools-1.11/samtools mpileup -b /tmp/0VbifrUoEO/mpileup.bam.list -f /tmp/0VbifrUoEO/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.11/samtools mpileup -b /tmp/d4gSebVaAF/mpileup.bam.list -f /tmp/d4gSebVaAF/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.11/samtools mpileup -b /tmp/0VbifrUoEO/mpileup.cram.list -f /tmp/0VbifrUoEO/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.11/samtools mpileup -b /tmp/d4gSebVaAF/mpileup.cram.list -f /tmp/d4gSebVaAF/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.11/samtools mpileup -b /tmp/0VbifrUoEO/mpileup.bam.urllist -f /tmp/0VbifrUoEO/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.11/samtools mpileup -b /tmp/d4gSebVaAF/mpileup.bam.urllist -f /tmp/d4gSebVaAF/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.11/samtools mpileup -b /tmp/0VbifrUoEO/mpileup.cram.urllist -f /tmp/0VbifrUoEO/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.11/samtools mpileup -b /tmp/d4gSebVaAF/mpileup.cram.urllist -f /tmp/d4gSebVaAF/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.11/samtools mpileup -uvDV -b /tmp/0VbifrUoEO/mpileup.bam.list -f /tmp/0VbifrUoEO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/reproducible-path/samtools-1.11/samtools mpileup -uvDV -b /tmp/d4gSebVaAF/mpileup.bam.list -f /tmp/d4gSebVaAF/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/reproducible-path/samtools-1.11/samtools mpileup -uvDV -b /tmp/0VbifrUoEO/mpileup.cram.list -f /tmp/0VbifrUoEO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/reproducible-path/samtools-1.11/samtools mpileup -uvDV -b /tmp/d4gSebVaAF/mpileup.cram.list -f /tmp/d4gSebVaAF/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/reproducible-path/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/0VbifrUoEO/mpileup.cram.list -f /tmp/0VbifrUoEO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/reproducible-path/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/d4gSebVaAF/mpileup.cram.list -f /tmp/d4gSebVaAF/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/reproducible-path/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/0VbifrUoEO/mpileup.cram.list -f /tmp/0VbifrUoEO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/reproducible-path/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/d4gSebVaAF/mpileup.cram.list -f /tmp/d4gSebVaAF/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/reproducible-path/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/0VbifrUoEO/mpileup.ref.fa.gz -r17:1050-1060 /tmp/0VbifrUoEO/mpileup.1.bam | grep -v mpileup + /build/reproducible-path/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/d4gSebVaAF/mpileup.ref.fa.gz -r17:1050-1060 /tmp/d4gSebVaAF/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/reproducible-path/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/0VbifrUoEO/mpileup.ref.fa.gz -r17:1050-1060 /tmp/0VbifrUoEO/mpileup.1.cram | grep -v mpileup + /build/reproducible-path/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/d4gSebVaAF/mpileup.ref.fa.gz -r17:1050-1060 /tmp/d4gSebVaAF/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: @@ -1254,41 +1289,41 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/0VbifrUoEO/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/d4gSebVaAF/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/0VbifrUoEO/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/d4gSebVaAF/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/0VbifrUoEO/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/d4gSebVaAF/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/0VbifrUoEO/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/d4gSebVaAF/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/0VbifrUoEO/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/d4gSebVaAF/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/0VbifrUoEO/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/d4gSebVaAF/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/0VbifrUoEO/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/d4gSebVaAF/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/0VbifrUoEO/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/d4gSebVaAF/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/0VbifrUoEO/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/d4gSebVaAF/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/0VbifrUoEO/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/d4gSebVaAF/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/0VbifrUoEO/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/d4gSebVaAF/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/0VbifrUoEO/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/d4gSebVaAF/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/0VbifrUoEO/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/d4gSebVaAF/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/0VbifrUoEO/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/d4gSebVaAF/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/0VbifrUoEO/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/d4gSebVaAF/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/0VbifrUoEO/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/d4gSebVaAF/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/0VbifrUoEO/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/d4gSebVaAF/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/0VbifrUoEO/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/d4gSebVaAF/view.001.fogn (CRAM input).. ok 67: Filter -d BC:TGCA (SAM input) .. ok @@ -1302,53 +1337,53 @@ 72: Count -d BC:TGCA (CRAM input) .. ok - 73: Filter -D BC:/tmp/0VbifrUoEO/view.001.fobc (SAM input) .. ok + 73: Filter -D BC:/tmp/d4gSebVaAF/view.001.fobc (SAM input) .. ok - 74: Count -D BC:/tmp/0VbifrUoEO/view.001.fobc (SAM input) .. ok + 74: Count -D BC:/tmp/d4gSebVaAF/view.001.fobc (SAM input) .. ok - 75: Filter -D BC:/tmp/0VbifrUoEO/view.001.fobc (BAM input) .. ok + 75: Filter -D BC:/tmp/d4gSebVaAF/view.001.fobc (BAM input) .. ok - 76: Count -D BC:/tmp/0VbifrUoEO/view.001.fobc (BAM input) .. ok + 76: Count -D BC:/tmp/d4gSebVaAF/view.001.fobc (BAM input) .. ok - 77: Filter -D BC:/tmp/0VbifrUoEO/view.001.fobc (CRAM input) .. ok + 77: Filter -D BC:/tmp/d4gSebVaAF/view.001.fobc (CRAM input) .. ok - 78: Count -D BC:/tmp/0VbifrUoEO/view.001.fobc (CRAM input) .. ok + 78: Count -D BC:/tmp/d4gSebVaAF/view.001.fobc (CRAM input) .. ok - 79: Filter -D BC:/tmp/0VbifrUoEO/view.001.fobc -d BC:TGCA (SAM input).. ok + 79: Filter -D BC:/tmp/d4gSebVaAF/view.001.fobc -d BC:TGCA (SAM input).. ok - 80: Count -D BC:/tmp/0VbifrUoEO/view.001.fobc -d BC:TGCA (SAM input).. ok + 80: Count -D BC:/tmp/d4gSebVaAF/view.001.fobc -d BC:TGCA (SAM input).. ok - 81: Filter -D BC:/tmp/0VbifrUoEO/view.001.fobc -d BC:TGCA (BAM input).. ok + 81: Filter -D BC:/tmp/d4gSebVaAF/view.001.fobc -d BC:TGCA (BAM input).. ok - 82: Count -D BC:/tmp/0VbifrUoEO/view.001.fobc -d BC:TGCA (BAM input).. ok + 82: Count -D BC:/tmp/d4gSebVaAF/view.001.fobc -d BC:TGCA (BAM input).. ok - 83: Filter -D BC:/tmp/0VbifrUoEO/view.001.fobc -d BC:TGCA (CRAM input).. ok + 83: Filter -D BC:/tmp/d4gSebVaAF/view.001.fobc -d BC:TGCA (CRAM input).. ok - 84: Count -D BC:/tmp/0VbifrUoEO/view.001.fobc -d BC:TGCA (CRAM input).. ok + 84: Count -D BC:/tmp/d4gSebVaAF/view.001.fobc -d BC:TGCA (CRAM input).. ok - 85: Filter -d BC:TGCA -D BC:/tmp/0VbifrUoEO/view.001.fobc (SAM input).. ok + 85: Filter -d BC:TGCA -D BC:/tmp/d4gSebVaAF/view.001.fobc (SAM input).. ok - 86: Count -d BC:TGCA -D BC:/tmp/0VbifrUoEO/view.001.fobc (SAM input).. ok + 86: Count -d BC:TGCA -D BC:/tmp/d4gSebVaAF/view.001.fobc (SAM input).. ok - 87: Filter -d BC:TGCA -D BC:/tmp/0VbifrUoEO/view.001.fobc (BAM input).. ok + 87: Filter -d BC:TGCA -D BC:/tmp/d4gSebVaAF/view.001.fobc (BAM input).. ok - 88: Count -d BC:TGCA -D BC:/tmp/0VbifrUoEO/view.001.fobc (BAM input).. ok + 88: Count -d BC:TGCA -D BC:/tmp/d4gSebVaAF/view.001.fobc (BAM input).. ok - 89: Filter -d BC:TGCA -D BC:/tmp/0VbifrUoEO/view.001.fobc (CRAM input).. ok + 89: Filter -d BC:TGCA -D BC:/tmp/d4gSebVaAF/view.001.fobc (CRAM input).. ok - 90: Count -d BC:TGCA -D BC:/tmp/0VbifrUoEO/view.001.fobc (CRAM input).. ok + 90: Count -d BC:TGCA -D BC:/tmp/d4gSebVaAF/view.001.fobc (CRAM input).. ok - 91: Filter -D RG:/tmp/0VbifrUoEO/view.001.fogn (SAM input) .. ok + 91: Filter -D RG:/tmp/d4gSebVaAF/view.001.fogn (SAM input) .. ok - 92: Count -D RG:/tmp/0VbifrUoEO/view.001.fogn (SAM input) .. ok + 92: Count -D RG:/tmp/d4gSebVaAF/view.001.fogn (SAM input) .. ok - 93: Filter -D RG:/tmp/0VbifrUoEO/view.001.fogn (BAM input) .. ok + 93: Filter -D RG:/tmp/d4gSebVaAF/view.001.fogn (BAM input) .. ok - 94: Count -D RG:/tmp/0VbifrUoEO/view.001.fogn (BAM input) .. ok + 94: Count -D RG:/tmp/d4gSebVaAF/view.001.fogn (BAM input) .. ok - 95: Filter -D RG:/tmp/0VbifrUoEO/view.001.fogn (CRAM input) .. ok + 95: Filter -D RG:/tmp/d4gSebVaAF/view.001.fogn (CRAM input) .. ok - 96: Count -D RG:/tmp/0VbifrUoEO/view.001.fogn (CRAM input) .. ok + 96: Count -D RG:/tmp/d4gSebVaAF/view.001.fogn (CRAM input) .. ok 97: Filter -d NE:TGCA (SAM input) .. ok @@ -1364,126 +1399,126 @@ 103: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -o /tmp/0VbifrUoEO/view.test103.sam -h -d TGCA /tmp/0VbifrUoEO/view.001.sam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -o /tmp/d4gSebVaAF/view.test103.sam -h -d TGCA /tmp/d4gSebVaAF/view.001.sam --no-PG .. expected failure 104: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -c -d TGCA /tmp/0VbifrUoEO/view.001.sam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -c -d TGCA /tmp/d4gSebVaAF/view.001.sam --no-PG .. expected failure 105: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -o /tmp/0VbifrUoEO/view.test105.sam -h -d TGCA /tmp/0VbifrUoEO/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -o /tmp/d4gSebVaAF/view.test105.sam -h -d TGCA /tmp/d4gSebVaAF/view.test001.bam --no-PG .. expected failure 106: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -c -d TGCA /tmp/0VbifrUoEO/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -c -d TGCA /tmp/d4gSebVaAF/view.test001.bam --no-PG .. expected failure 107: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -o /tmp/0VbifrUoEO/view.test107.sam -h -d TGCA /tmp/0VbifrUoEO/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.11/samtools view -o /tmp/d4gSebVaAF/view.test107.sam -h -d TGCA /tmp/d4gSebVaAF/view.test006.cram --no-PG .. expected failure 108: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -c -d TGCA /tmp/0VbifrUoEO/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.11/samtools view -c -d TGCA /tmp/d4gSebVaAF/view.test006.cram --no-PG .. expected failure - 109: Filter -D BClong:/tmp/0VbifrUoEO/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/0VbifrUoEO/view.001.fobc" + 109: Filter -D BClong:/tmp/d4gSebVaAF/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/d4gSebVaAF/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -o /tmp/0VbifrUoEO/view.test109.sam -h -D BClong:/tmp/0VbifrUoEO/view.001.fobc /tmp/0VbifrUoEO/view.001.sam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -o /tmp/d4gSebVaAF/view.test109.sam -h -D BClong:/tmp/d4gSebVaAF/view.001.fobc /tmp/d4gSebVaAF/view.001.sam --no-PG .. expected failure - 110: Count -D BClong:/tmp/0VbifrUoEO/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/0VbifrUoEO/view.001.fobc" + 110: Count -D BClong:/tmp/d4gSebVaAF/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/d4gSebVaAF/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -c -D BClong:/tmp/0VbifrUoEO/view.001.fobc /tmp/0VbifrUoEO/view.001.sam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -c -D BClong:/tmp/d4gSebVaAF/view.001.fobc /tmp/d4gSebVaAF/view.001.sam --no-PG .. expected failure - 111: Filter -D BClong:/tmp/0VbifrUoEO/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/0VbifrUoEO/view.001.fobc" + 111: Filter -D BClong:/tmp/d4gSebVaAF/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/d4gSebVaAF/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -o /tmp/0VbifrUoEO/view.test111.sam -h -D BClong:/tmp/0VbifrUoEO/view.001.fobc /tmp/0VbifrUoEO/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -o /tmp/d4gSebVaAF/view.test111.sam -h -D BClong:/tmp/d4gSebVaAF/view.001.fobc /tmp/d4gSebVaAF/view.test001.bam --no-PG .. expected failure - 112: Count -D BClong:/tmp/0VbifrUoEO/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/0VbifrUoEO/view.001.fobc" + 112: Count -D BClong:/tmp/d4gSebVaAF/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/d4gSebVaAF/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -c -D BClong:/tmp/0VbifrUoEO/view.001.fobc /tmp/0VbifrUoEO/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -c -D BClong:/tmp/d4gSebVaAF/view.001.fobc /tmp/d4gSebVaAF/view.test001.bam --no-PG .. expected failure - 113: Filter -D BClong:/tmp/0VbifrUoEO/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/0VbifrUoEO/view.001.fobc" + 113: Filter -D BClong:/tmp/d4gSebVaAF/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/d4gSebVaAF/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -o /tmp/0VbifrUoEO/view.test113.sam -h -D BClong:/tmp/0VbifrUoEO/view.001.fobc /tmp/0VbifrUoEO/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.11/samtools view -o /tmp/d4gSebVaAF/view.test113.sam -h -D BClong:/tmp/d4gSebVaAF/view.001.fobc /tmp/d4gSebVaAF/view.test006.cram --no-PG .. expected failure - 114: Count -D BClong:/tmp/0VbifrUoEO/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/0VbifrUoEO/view.001.fobc" + 114: Count -D BClong:/tmp/d4gSebVaAF/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/d4gSebVaAF/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -c -D BClong:/tmp/0VbifrUoEO/view.001.fobc /tmp/0VbifrUoEO/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.11/samtools view -c -D BClong:/tmp/d4gSebVaAF/view.001.fobc /tmp/d4gSebVaAF/view.test006.cram --no-PG .. expected failure 115: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -o /tmp/0VbifrUoEO/view.test115.sam -h -d BC:ACGT -d RG:grp2 /tmp/0VbifrUoEO/view.001.sam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -o /tmp/d4gSebVaAF/view.test115.sam -h -d BC:ACGT -d RG:grp2 /tmp/d4gSebVaAF/view.001.sam --no-PG .. expected failure 116: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/0VbifrUoEO/view.001.sam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/d4gSebVaAF/view.001.sam --no-PG .. expected failure 117: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -o /tmp/0VbifrUoEO/view.test117.sam -h -d BC:ACGT -d RG:grp2 /tmp/0VbifrUoEO/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -o /tmp/d4gSebVaAF/view.test117.sam -h -d BC:ACGT -d RG:grp2 /tmp/d4gSebVaAF/view.test001.bam --no-PG .. expected failure 118: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/0VbifrUoEO/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/d4gSebVaAF/view.test001.bam --no-PG .. expected failure 119: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -o /tmp/0VbifrUoEO/view.test119.sam -h -d BC:ACGT -d RG:grp2 /tmp/0VbifrUoEO/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.11/samtools view -o /tmp/d4gSebVaAF/view.test119.sam -h -d BC:ACGT -d RG:grp2 /tmp/d4gSebVaAF/view.test006.cram --no-PG .. expected failure 120: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/0VbifrUoEO/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/d4gSebVaAF/view.test006.cram --no-PG .. expected failure @@ -2077,7 +2112,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.11/samtools fastq -N -s /tmp/0VbifrUoEO/bam2fq.discard.s.fq -0 /tmp/0VbifrUoEO/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.11/test/dat/bam2fq.001.sam + /build/reproducible-path/samtools-1.11/samtools fastq -N -s /tmp/d4gSebVaAF/bam2fq.discard.s.fq -0 /tmp/d4gSebVaAF/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2178,7 +2213,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.11/samtools fastq -@ 2 -N -s /tmp/0VbifrUoEO/bam2fq.discard.s.fq -0 /tmp/0VbifrUoEO/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.11/test/dat/bam2fq.001.sam + /build/reproducible-path/samtools-1.11/samtools fastq -@ 2 -N -s /tmp/d4gSebVaAF/bam2fq.discard.s.fq -0 /tmp/d4gSebVaAF/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2339,7 +2374,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.11/samtools merge -s 1 -O sam -b /tmp/lLOZQjfdBS - /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam + /build/reproducible-path/samtools-1.11/samtools merge -s 1 -O sam -b /tmp/q0CQafYqOL - /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2359,11 +2394,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.11/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/0VbifrUoEO/merge.tag.1.bam /tmp/0VbifrUoEO/merge.tag.2.bam + /build/reproducible-path/samtools-1.11/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/d4gSebVaAF/merge.tag.1.bam /tmp/d4gSebVaAF/merge.tag.2.bam .. ok test_merge: - /build/reproducible-path/samtools-1.11/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/0VbifrUoEO/merge.tag.3.bam /tmp/0VbifrUoEO/merge.tag.4.bam + /build/reproducible-path/samtools-1.11/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/d4gSebVaAF/merge.tag.3.bam /tmp/d4gSebVaAF/merge.tag.4.bam .. ok test_merge: @@ -2371,7 +2406,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.11/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.11/test/merge/merge.bed - /tmp/0VbifrUoEO/merge.bed.1.bam /tmp/0VbifrUoEO/merge.bed.2.bam + /build/reproducible-path/samtools-1.11/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.11/test/merge/merge.bed - /tmp/d4gSebVaAF/merge.bed.1.bam /tmp/d4gSebVaAF/merge.bed.2.bam .. ok test_merge: @@ -2383,7 +2418,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.11/samtools merge -@ 2 -s 1 -O sam -b /tmp/pf3RrKOnKz - /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam + /build/reproducible-path/samtools-1.11/samtools merge -@ 2 -s 1 -O sam -b /tmp/6OBgQkiJri - /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2403,11 +2438,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/0VbifrUoEO/merge.tag.1.bam /tmp/0VbifrUoEO/merge.tag.2.bam + /build/reproducible-path/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/d4gSebVaAF/merge.tag.1.bam /tmp/d4gSebVaAF/merge.tag.2.bam .. ok test_merge: - /build/reproducible-path/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/0VbifrUoEO/merge.tag.3.bam /tmp/0VbifrUoEO/merge.tag.4.bam + /build/reproducible-path/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/d4gSebVaAF/merge.tag.3.bam /tmp/d4gSebVaAF/merge.tag.4.bam .. ok test_merge: @@ -2415,19 +2450,19 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.11/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.11/test/merge/merge.bed - /tmp/0VbifrUoEO/merge.bed.1.bam /tmp/0VbifrUoEO/merge.bed.2.bam + /build/reproducible-path/samtools-1.11/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.11/test/merge/merge.bed - /tmp/d4gSebVaAF/merge.bed.1.bam /tmp/d4gSebVaAF/merge.bed.2.bam .. ok test_sort: - /build/reproducible-path/samtools-1.11/samtools sort /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/0VbifrUoEO/sortout + /build/reproducible-path/samtools-1.11/samtools sort /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/d4gSebVaAF/sortout .. ok test_sort: - /build/reproducible-path/samtools-1.11/samtools sort -f /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/0VbifrUoEO/sortout.bam + /build/reproducible-path/samtools-1.11/samtools sort -f /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/d4gSebVaAF/sortout.bam .. ok test_sort: - /build/reproducible-path/samtools-1.11/samtools sort -o /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/0VbifrUoEO/sorttmp + /build/reproducible-path/samtools-1.11/samtools sort -o /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/d4gSebVaAF/sorttmp .. ok test_sort: @@ -2455,15 +2490,15 @@ .. ok test_sort: - /build/reproducible-path/samtools-1.11/samtools sort -@ 2 /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/0VbifrUoEO/sortout + /build/reproducible-path/samtools-1.11/samtools sort -@ 2 /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/d4gSebVaAF/sortout .. ok test_sort: - /build/reproducible-path/samtools-1.11/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/0VbifrUoEO/sortout.bam + /build/reproducible-path/samtools-1.11/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/d4gSebVaAF/sortout.bam .. ok test_sort: - /build/reproducible-path/samtools-1.11/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/0VbifrUoEO/sorttmp + /build/reproducible-path/samtools-1.11/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.11/test/dat/test_input_1_a.bam /tmp/d4gSebVaAF/sorttmp .. ok test_sort: @@ -2871,15 +2906,15 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.11/samtools view -h --no-PG /tmp/0VbifrUoEO/longref.sam.gz + /build/reproducible-path/samtools-1.11/samtools view -h --no-PG /tmp/d4gSebVaAF/longref.sam.gz .. ok test_large_positions: - /build/reproducible-path/samtools-1.11/samtools view -h --no-PG /tmp/0VbifrUoEO/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 + /build/reproducible-path/samtools-1.11/samtools view -h --no-PG /tmp/d4gSebVaAF/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: - /build/reproducible-path/samtools-1.11/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.11/test/large_pos/test.bed /tmp/0VbifrUoEO/longref.sam.gz + /build/reproducible-path/samtools-1.11/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.11/test/large_pos/test.bed /tmp/d4gSebVaAF/longref.sam.gz .. ok test_large_positions: @@ -2899,7 +2934,7 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.11/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/0VbifrUoEO/longref.sam.gz + /build/reproducible-path/samtools-1.11/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/d4gSebVaAF/longref.sam.gz .. ok test_large_positions: @@ -3012,7 +3047,7 @@ Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/reproducible-path/samtools-1.11' - rm -fr -- /tmp/dh-xdg-rundir-aOnuSBFA + rm -fr -- /tmp/dh-xdg-rundir-vG9Ppu1W make[1]: Leaving directory '/build/reproducible-path/samtools-1.11' create-stamp debian/debhelper-build-stamp dh_prep @@ -3024,7 +3059,7 @@ dh_auto_install -- \ prefix=/usr install -d /build/reproducible-path/samtools-1.11/debian/tmp - make -j42 install DESTDIR=/build/reproducible-path/samtools-1.11/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr + make -j20 install DESTDIR=/build/reproducible-path/samtools-1.11/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.11' mkdir -p -m 755 /build/reproducible-path/samtools-1.11/debian/tmp/usr/bin /build/reproducible-path/samtools-1.11/debian/tmp/usr/bin /build/reproducible-path/samtools-1.11/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.11/debian/tmp/usr/bin @@ -3091,114 +3126,78 @@ dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-index.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-sort.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 - mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 - mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-bedcov.1 - mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-split.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-cat.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 - mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-calmd.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-collate.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-view.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools.1 - mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-dict.1 - mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depth.1 - mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-coverage.1 - mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/wgsim.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-faidx.1 + mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 + mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 + mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 + mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 + mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 + mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 + mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-flags.1 - mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-index.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 + mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 + mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 + mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 + mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 + mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 + mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 + mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 + mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 + mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 + mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 + mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 + mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fqidx.1 - mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fasta.1 - mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-idxstats.1 - mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-merge.1 - mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-markdup.1 - mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-phase.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-quickcheck.1 - mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-mpileup.1 - mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reheader.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 + mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 + mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-sort.1 - mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-stats.1 - mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-tview.1 - mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-targetcut.1 - mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.pl.1 - mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/wgsim.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 dh_lintian install -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools @@ -3216,8 +3215,8 @@ Using 1601563342 as canonical time Normalizing debian/samtools-test/usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz using File::StripNondeterminism::handlers::gzip dh_compress - cd debian/samtools cd debian/samtools-test + cd debian/samtools chmod a-x usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian chmod a-x usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian @@ -3232,10 +3231,10 @@ find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a @@ -3244,26 +3243,16 @@ dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 661293 new size 684194 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug dh_strip -a - install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0/1b3f86afa31b6ee71a2c01b3b64d7d668c5254.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0/1b3f86afa31b6ee71a2c01b3b64d7d668c5254.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0/1b3f86afa31b6ee71a2c01b3b64d7d668c5254.debug debian/samtools/usr/bin/samtools - install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09/684418342c8a9ab01523eb5f887869b0d12730.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09/684418342c8a9ab01523eb5f887869b0d12730.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09/684418342c8a9ab01523eb5f887869b0d12730.debug debian/samtools/usr/bin/maq2sam-long - install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da/27c69a3352779b39b452c02e87cd398cc134ad.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da/27c69a3352779b39b452c02e87cd398cc134ad.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da/27c69a3352779b39b452c02e87cd398cc134ad.debug debian/samtools/usr/bin/wgsim install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f7 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f7/b656becd4af76539de264916eea2f0bed5b3e6.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f7/b656becd4af76539de264916eea2f0bed5b3e6.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f7/b656becd4af76539de264916eea2f0bed5b3e6.debug debian/samtools/usr/bin/ace2sam + install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0/1b3f86afa31b6ee71a2c01b3b64d7d668c5254.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0/1b3f86afa31b6ee71a2c01b3b64d7d668c5254.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0/1b3f86afa31b6ee71a2c01b3b64d7d668c5254.debug debian/samtools/usr/bin/samtools install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8c objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8c/faee18231d062d7062c595c2172ea8c9351b33.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8c/faee18231d062d7062c595c2172ea8c9351b33.debug @@ -3279,6 +3268,16 @@ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2a/e22e10784afaf12da4f258960dd589a998c5e8.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2a/e22e10784afaf12da4f258960dd589a998c5e8.debug debian/samtools/usr/bin/md5fa + install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09/684418342c8a9ab01523eb5f887869b0d12730.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09/684418342c8a9ab01523eb5f887869b0d12730.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09/684418342c8a9ab01523eb5f887869b0d12730.debug debian/samtools/usr/bin/maq2sam-long + install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da/27c69a3352779b39b452c02e87cd398cc134ad.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da/27c69a3352779b39b452c02e87cd398cc134ad.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da/27c69a3352779b39b452c02e87cd398cc134ad.debug debian/samtools/usr/bin/wgsim install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz @@ -3289,7 +3288,7 @@ rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -d debian/samtools/DEBIAN - dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa + dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim dh_installdeb install -d debian/samtools-test/DEBIAN dh_gencontrol @@ -3308,8 +3307,8 @@ dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums - cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums @@ -3318,9 +3317,9 @@ dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools-test .. +dpkg-deb: building package 'samtools-test' in '../samtools-test_1.11-1_all.deb'. dpkg-deb: building package 'samtools' in '../samtools_1.11-1_amd64.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.11-1_amd64.deb'. -dpkg-deb: building package 'samtools-test' in '../samtools-test_1.11-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../samtools_1.11-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3329,12 +3328,14 @@ 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/1626967/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1626967/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/381713 and its subdirectories -I: Current time: Wed Aug 20 14:38:24 -12 2025 -I: pbuilder-time-stamp: 1755743905 +I: removing directory /srv/workspace/pbuilder/1626967 and its subdirectories +I: Current time: Fri Jul 19 10:22:51 +14 2024 +I: pbuilder-time-stamp: 1721334171