Diff of the two buildlogs: -- --- b1/build.log 2021-12-15 06:50:39.752253372 +0000 +++ b2/build.log 2021-12-15 06:57:20.183795289 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 17 01:11:56 -12 2023 -I: pbuilder-time-stamp: 1673961116 +I: Current time: Wed Dec 15 20:50:41 +14 2021 +I: pbuilder-time-stamp: 1639551041 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Feb 21 05:35:10 2019 -12 +gpgv: Signature made Fri Feb 22 07:35:10 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,136 +30,170 @@ dpkg-source: info: applying sort-tests-memory-limit.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1882377/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/586548/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/586548/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/586548/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='' - 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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='ad73610aac984d0e85d8e9b332d3d992' - 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='1882377' - PS1='# ' - PS2='> ' + INVOCATION_ID=33c4353788e243f1a90f6d532b17a607 + 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=586548 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.cjLObFpaCN/pbuilderrc_Drmc --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.cjLObFpaCN/b1 --logfile b1/build.log samtools_1.9-4.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.cjLObFpaCN/pbuilderrc_swBk --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.cjLObFpaCN/b2 --logfile b2/build.log samtools_1.9-4.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 10 16:20 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/1882377/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 15 20:50 sh -> bash + lrwxrwxrwx 1 root root 4 Nov 8 11:58 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/586548/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -273,7 +307,7 @@ Get: 58 http://deb.debian.org/debian buster/main amd64 libncurses5-dev amd64 6.1+20181013-2+deb10u2 [948 B] Get: 59 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 tabix amd64 1.9-12~deb10u1 [292 kB] -Fetched 29.3 MB in 0s (79.3 MB/s) +Fetched 29.3 MB in 1s (28.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -536,7 +570,8 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/samtools-1.9/ && 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_1.9-4_source.changes +hostname: Name or service not known +I: Running cd /build/samtools-1.9/ && 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_1.9-4_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.9-4 dpkg-buildpackage: info: source distribution unstable @@ -551,7 +586,7 @@ rm -f config.mk touch config.mk dh_auto_clean -- - make -j16 distclean + make -j15 distclean make[2]: Entering directory '/build/samtools-1.9' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai @@ -649,7 +684,7 @@ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" - make -j16 "CFLAGS=-g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" + make -j15 "CFLAGS=-g -O2 -ffile-prefix-map=/build/samtools-1.9=. -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/samtools-1.9' gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c @@ -704,33 +739,33 @@ gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c -gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c -gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c -ar -rcs libst.a sam_opts.o sam_utils.o -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -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 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread +gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c +gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c +ar -rcs libst.a sam_opts.o sam_utils.o 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 -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 ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.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/wgsim misc/wgsim.o -lm -lhts -lz 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 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -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_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 test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread +gcc -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.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 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 ./lz4/lz4.o libbam.a libst.a -lhts -lcurses -lm -lz -lpthread gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.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 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_trans_tbl_init test/merge/test_trans_tbl_init.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/samtools-1.9' make[1]: Leaving directory '/build/samtools-1.9' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log @@ -738,78 +773,78 @@ make[1]: Entering directory '/build/samtools-1.9' dh_auto_test -- \ BGZIP=/usr/bin/bgzip - make -j16 test VERBOSE=1 BGZIP=/usr/bin/bgzip + make -j15 test VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/samtools-1.9' REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} -/usr/bin/bgzip -c -b 65272 -s 5 /tmp/vwAFHEfE6l/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/7Q6OZGRcBQ/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/vwAFHEfE6l/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/7Q6OZGRcBQ/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/vwAFHEfE6l/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/7Q6OZGRcBQ/bgzip.dat.gz .. ok -/build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa 3:11-13 | grep -v '^>' +/build/samtools-1.9/samtools faidx /tmp/7Q6OZGRcBQ/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/samtools-1.9/samtools faidx /tmp/7Q6OZGRcBQ/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa 2:998-1003 | grep -v '^>' +/build/samtools-1.9/samtools faidx /tmp/7Q6OZGRcBQ/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/samtools-1.9/samtools faidx /tmp/7Q6OZGRcBQ/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa 1:100-104 | grep -v '^>' +/build/samtools-1.9/samtools faidx /tmp/7Q6OZGRcBQ/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/samtools-1.9/samtools faidx /tmp/7Q6OZGRcBQ/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa 1:99998-100007 | grep -v '^>' +/build/samtools-1.9/samtools faidx /tmp/7Q6OZGRcBQ/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/samtools-1.9/samtools faidx /tmp/7Q6OZGRcBQ/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq 3:11-13 +/build/samtools-1.9/samtools fqidx /tmp/7Q6OZGRcBQ/fqidx.fq 3:11-13 .. ok .. ok -/build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq.gz 3:11-13 +/build/samtools-1.9/samtools fqidx /tmp/7Q6OZGRcBQ/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq 2:998-1003 +/build/samtools-1.9/samtools fqidx /tmp/7Q6OZGRcBQ/fqidx.fq 2:998-1003 .. ok .. ok -/build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq.gz 2:998-1003 +/build/samtools-1.9/samtools fqidx /tmp/7Q6OZGRcBQ/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq 1:100-104 +/build/samtools-1.9/samtools fqidx /tmp/7Q6OZGRcBQ/fqidx.fq 1:100-104 .. ok .. ok -/build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq.gz 1:100-104 +/build/samtools-1.9/samtools fqidx /tmp/7Q6OZGRcBQ/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq 1:99998-100007 +/build/samtools-1.9/samtools fqidx /tmp/7Q6OZGRcBQ/fqidx.fq 1:99998-100007 .. ok .. ok -/build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq.gz 1:99998-100007 +/build/samtools-1.9/samtools fqidx /tmp/7Q6OZGRcBQ/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -819,7 +854,7 @@ .. ok test_dict: - /build/samtools-1.9/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/vwAFHEfE6l/dict.fa.gz + /build/samtools-1.9/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/7Q6OZGRcBQ/dict.fa.gz .. ok test_dict: @@ -827,11 +862,11 @@ .. ok test_index: - /build/samtools-1.9/samtools view /tmp/vwAFHEfE6l/large_chrom.bam ref2 + /build/samtools-1.9/samtools view /tmp/7Q6OZGRcBQ/large_chrom.bam ref2 .. ok test_index: - /build/samtools-1.9/samtools view /tmp/vwAFHEfE6l/large_chrom.bam ref2:1-541556283 + /build/samtools-1.9/samtools view /tmp/7Q6OZGRcBQ/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -839,11 +874,11 @@ .. ok test_index: - /build/samtools-1.9/samtools view -@ 2 /tmp/vwAFHEfE6l/large_chrom.bam ref2 + /build/samtools-1.9/samtools view -@ 2 /tmp/7Q6OZGRcBQ/large_chrom.bam ref2 .. ok test_index: - /build/samtools-1.9/samtools view -@ 2 /tmp/vwAFHEfE6l/large_chrom.bam ref2:1-541556283 + /build/samtools-1.9/samtools view -@ 2 /tmp/7Q6OZGRcBQ/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -851,43 +886,43 @@ .. ok test_mpileup: - /build/samtools-1.9/samtools mpileup -b /tmp/vwAFHEfE6l/mpileup.bam.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.9/samtools mpileup -b /tmp/7Q6OZGRcBQ/mpileup.bam.list -f /tmp/7Q6OZGRcBQ/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.9/samtools mpileup -b /tmp/vwAFHEfE6l/mpileup.cram.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.9/samtools mpileup -b /tmp/7Q6OZGRcBQ/mpileup.cram.list -f /tmp/7Q6OZGRcBQ/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.9/samtools mpileup -b /tmp/vwAFHEfE6l/mpileup.bam.urllist -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.9/samtools mpileup -b /tmp/7Q6OZGRcBQ/mpileup.bam.urllist -f /tmp/7Q6OZGRcBQ/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.9/samtools mpileup -b /tmp/vwAFHEfE6l/mpileup.cram.urllist -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.9/samtools mpileup -b /tmp/7Q6OZGRcBQ/mpileup.cram.urllist -f /tmp/7Q6OZGRcBQ/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.9/samtools mpileup -uvDV -b /tmp/vwAFHEfE6l/mpileup.bam.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/samtools-1.9/samtools mpileup -uvDV -b /tmp/7Q6OZGRcBQ/mpileup.bam.list -f /tmp/7Q6OZGRcBQ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/samtools-1.9/samtools mpileup -uvDV -b /tmp/vwAFHEfE6l/mpileup.cram.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/samtools-1.9/samtools mpileup -uvDV -b /tmp/7Q6OZGRcBQ/mpileup.cram.list -f /tmp/7Q6OZGRcBQ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/samtools-1.9/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/vwAFHEfE6l/mpileup.cram.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/samtools-1.9/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/7Q6OZGRcBQ/mpileup.cram.list -f /tmp/7Q6OZGRcBQ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/samtools-1.9/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/vwAFHEfE6l/mpileup.cram.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/samtools-1.9/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/7Q6OZGRcBQ/mpileup.cram.list -f /tmp/7Q6OZGRcBQ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/samtools-1.9/samtools mpileup -B --ff 0x14 -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:1050-1060 /tmp/vwAFHEfE6l/mpileup.1.bam | grep -v mpileup + /build/samtools-1.9/samtools mpileup -B --ff 0x14 -f /tmp/7Q6OZGRcBQ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/7Q6OZGRcBQ/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/samtools-1.9/samtools mpileup -B --ff 0x14 -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:1050-1060 /tmp/vwAFHEfE6l/mpileup.1.cram | grep -v mpileup + /build/samtools-1.9/samtools mpileup -B --ff 0x14 -f /tmp/7Q6OZGRcBQ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/7Q6OZGRcBQ/mpileup.1.cram | grep -v mpileup .. ok test_usage: @@ -1137,41 +1172,41 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/vwAFHEfE6l/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/7Q6OZGRcBQ/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/vwAFHEfE6l/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/7Q6OZGRcBQ/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/vwAFHEfE6l/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/7Q6OZGRcBQ/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/vwAFHEfE6l/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/7Q6OZGRcBQ/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/vwAFHEfE6l/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/7Q6OZGRcBQ/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/vwAFHEfE6l/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/7Q6OZGRcBQ/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/7Q6OZGRcBQ/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/7Q6OZGRcBQ/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/7Q6OZGRcBQ/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/7Q6OZGRcBQ/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/7Q6OZGRcBQ/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/7Q6OZGRcBQ/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/7Q6OZGRcBQ/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/7Q6OZGRcBQ/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/7Q6OZGRcBQ/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/7Q6OZGRcBQ/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/7Q6OZGRcBQ/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/7Q6OZGRcBQ/view.001.fogn (CRAM input).. ok 67: Filter -l Library 2 (SAM input) .. ok @@ -1928,7 +1963,7 @@ .. ok test_merge: - /build/samtools-1.9/samtools merge -s 1 -O sam -b /tmp/VV6jbpNvW5 - /build/samtools-1.9/test/dat/test_input_1_a.bam + /build/samtools-1.9/samtools merge -s 1 -O sam -b /tmp/rfB5C_w2ou - /build/samtools-1.9/test/dat/test_input_1_a.bam .. ok test_merge: @@ -1948,11 +1983,11 @@ .. ok test_merge: - /build/samtools-1.9/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/vwAFHEfE6l/merge.tag.1.bam /tmp/vwAFHEfE6l/merge.tag.2.bam + /build/samtools-1.9/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/7Q6OZGRcBQ/merge.tag.1.bam /tmp/7Q6OZGRcBQ/merge.tag.2.bam .. ok test_merge: - /build/samtools-1.9/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/vwAFHEfE6l/merge.tag.3.bam /tmp/vwAFHEfE6l/merge.tag.4.bam + /build/samtools-1.9/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/7Q6OZGRcBQ/merge.tag.3.bam /tmp/7Q6OZGRcBQ/merge.tag.4.bam .. ok test_merge: @@ -1964,7 +1999,7 @@ .. ok test_merge: - /build/samtools-1.9/samtools merge -@ 2 -s 1 -O sam -b /tmp/t8UAISCSB1 - /build/samtools-1.9/test/dat/test_input_1_a.bam + /build/samtools-1.9/samtools merge -@ 2 -s 1 -O sam -b /tmp/rSYOJqLTfP - /build/samtools-1.9/test/dat/test_input_1_a.bam .. ok test_merge: @@ -1984,23 +2019,23 @@ .. ok test_merge: - /build/samtools-1.9/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/vwAFHEfE6l/merge.tag.1.bam /tmp/vwAFHEfE6l/merge.tag.2.bam + /build/samtools-1.9/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/7Q6OZGRcBQ/merge.tag.1.bam /tmp/7Q6OZGRcBQ/merge.tag.2.bam .. ok test_merge: - /build/samtools-1.9/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/vwAFHEfE6l/merge.tag.3.bam /tmp/vwAFHEfE6l/merge.tag.4.bam + /build/samtools-1.9/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/7Q6OZGRcBQ/merge.tag.3.bam /tmp/7Q6OZGRcBQ/merge.tag.4.bam .. ok test_sort: - /build/samtools-1.9/samtools sort /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sortout + /build/samtools-1.9/samtools sort /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/7Q6OZGRcBQ/sortout .. ok test_sort: - /build/samtools-1.9/samtools sort -f /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sortout.bam + /build/samtools-1.9/samtools sort -f /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/7Q6OZGRcBQ/sortout.bam .. ok test_sort: - /build/samtools-1.9/samtools sort -o /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sorttmp + /build/samtools-1.9/samtools sort -o /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/7Q6OZGRcBQ/sorttmp .. ok test_sort: @@ -2028,15 +2063,15 @@ .. ok test_sort: - /build/samtools-1.9/samtools sort -@ 2 /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sortout + /build/samtools-1.9/samtools sort -@ 2 /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/7Q6OZGRcBQ/sortout .. ok test_sort: - /build/samtools-1.9/samtools sort -@ 2 -f /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sortout.bam + /build/samtools-1.9/samtools sort -@ 2 -f /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/7Q6OZGRcBQ/sortout.bam .. ok test_sort: - /build/samtools-1.9/samtools sort -@ 2 -o /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sorttmp + /build/samtools-1.9/samtools sort -@ 2 -o /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/7Q6OZGRcBQ/sorttmp .. ok test_sort: @@ -2451,7 +2486,7 @@ dh_auto_install -- \ prefix=/usr install -d /build/samtools-1.9/debian/tmp - make -j16 install DESTDIR=/build/samtools-1.9/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr + make -j15 install DESTDIR=/build/samtools-1.9/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/samtools-1.9' mkdir -p -m 755 /build/samtools-1.9/debian/tmp/usr/bin /build/samtools-1.9/debian/tmp/usr/bin /build/samtools-1.9/debian/tmp/usr/share/man/man1 install -p samtools /build/samtools-1.9/debian/tmp/usr/bin @@ -2502,12 +2537,12 @@ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/samtools-1.9' dh_installchangelogs NEWS - install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian - install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian - install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog install -p -m0644 debian/changelog debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian install -p -m0644 debian/NEWS debian/samtools-test/usr/share/doc/samtools-test/NEWS.Debian install -p -m0644 NEWS debian/samtools-test/usr/share/doc/samtools-test/changelog + install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian + install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian + install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog make[1]: Leaving directory '/build/samtools-1.9' dh_installexamples install -d debian/samtools/usr/share/doc/samtools/examples @@ -2517,18 +2552,18 @@ cp --reflink=auto -a ./examples/toy.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.sam debian/samtools/usr/share/doc/samtools/examples dh_installman - man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/samtools.pl.1 > debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/ace2sam.1 > debian/samtools/usr/share/man/man1/ace2sam.1.dh-new man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/wgsim.1 > debian/samtools/usr/share/man/man1/wgsim.1.dh-new + man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/samtools.pl.1 > debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/samtools.1 > debian/samtools/usr/share/man/man1/samtools.1.dh-new - 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/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.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 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 + 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.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.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 @@ -2546,10 +2581,10 @@ dh_compress cd debian/samtools cd debian/samtools-test - 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.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 gzip -9nf 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.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 + chmod a-x usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian + gzip -9nf usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian cd '/build/samtools-1.9' cd '/build/samtools-1.9' dh_fixperms @@ -2557,8 +2592,8 @@ find debian/samtools-test -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s 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/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s + find debian/samtools/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 -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 @@ -2659,9 +2694,9 @@ dpkg-deb --build debian/samtools .. dpkg-deb --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --build debian/samtools-test .. +dpkg-deb: building package 'samtools' in '../samtools_1.9-4_amd64.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.9-4_amd64.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.9-4_all.deb'. -dpkg-deb: building package 'samtools' in '../samtools_1.9-4_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../samtools_1.9-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2670,12 +2705,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/586548/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/586548/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/1882377 and its subdirectories -I: Current time: Tue Jan 17 01:13:41 -12 2023 -I: pbuilder-time-stamp: 1673961221 +I: removing directory /srv/workspace/pbuilder/586548 and its subdirectories +I: Current time: Wed Dec 15 20:57:19 +14 2021 +I: pbuilder-time-stamp: 1639551439