Diff of the two buildlogs: -- --- b1/build.log 2021-07-29 02:55:03.237930712 +0000 +++ b2/build.log 2021-07-29 03:01:26.023515067 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 28 14:41:41 -12 2021 -I: pbuilder-time-stamp: 1627526501 +I: Current time: Thu Jul 29 16:55:24 +14 2021 +I: pbuilder-time-stamp: 1627527324 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./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._1Od2Uic/trustedkeys.kbx': General error -gpgv: Signature made Thu Oct 1 02:52:01 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.ZTDcevGl/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 @@ -27,135 +27,169 @@ 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/1103/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/12083/tmp/hooks/D01_modify_environment starting +debug: Running on virt64c. +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/12083/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/12083/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='80006e4c458c43ae98adf3f8907cd1ed' - 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='1103' - PS1='# ' - PS2='> ' + INVOCATION_ID=03fafc15b39643608fd1779e36218e26 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=12083 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.Rsa8oGtFuV/pbuilderrc_oQgG --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Rsa8oGtFuV/b1 --logfile b1/build.log samtools_1.11-1.dsc' - SUDO_GID='116' - SUDO_UID='112' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.Rsa8oGtFuV/pbuilderrc_IoUZ --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Rsa8oGtFuV/b2 --logfile b2/build.log --extrapackages usrmerge samtools_1.11-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux cbxi4b 5.10.0-8-armmp #1 SMP Debian 5.10.46-2 (2021-07-20) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-arm64 #1 SMP Debian 5.10.46-2 (2021-07-20) aarch64 GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Feb 7 02:38 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 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more - -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 24 21:29 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/1103/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Feb 8 04:38 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 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more + -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 29 16:55 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 26 23:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/12083/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -270,7 +304,7 @@ Get: 55 http://deb.debian.org/debian bullseye/main armhf libncurses5-dev armhf 6.2+20201114-2 [936 B] Get: 56 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf tabix armhf 1.11-4 [306 kB] -Fetched 27.0 MB in 2s (11.8 MB/s) +Fetched 27.0 MB in 2s (13.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) @@ -514,8 +548,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (377 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23613 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/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 +hostname: Name or service not known +I: Running cd /build/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 @@ -531,7 +602,7 @@ touch config.mk dh_auto_clean -- install -d /build/samtools-1.11/debian/.debhelper/generated/_source/home - make -j3 distclean + make -j4 distclean make[2]: Entering directory '/build/samtools-1.11' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai @@ -609,7 +680,7 @@ checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed -checking for grep that handles long lines and -e... /bin/grep +checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 @@ -635,15 +706,15 @@ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" - make -j3 "CFLAGS=-g -O2 -fdebug-prefix-map=/build/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 -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/build/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/samtools-1.11' gcc -g -O2 -fdebug-prefix-map=/build/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/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 gcc -g -O2 -fdebug-prefix-map=/build/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 +gcc -g -O2 -fdebug-prefix-map=/build/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 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/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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/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 @@ -683,9 +754,9 @@ gcc -g -O2 -fdebug-prefix-map=/build/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/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/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 gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/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 @@ -743,9 +814,9 @@ gcc -g -O2 -fdebug-prefix-map=/build/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/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 gcc -g -O2 -fdebug-prefix-map=/build/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 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/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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/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 @@ -773,97 +844,97 @@ 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 misc/wgsim misc/wgsim.o -lm -lhts -lz -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 -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/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_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_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_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 test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread 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 -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 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_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 test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/samtools-1.11' make[1]: Leaving directory '/build/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/samtools-1.11' dh_auto_test -- BGZIP=/usr/bin/bgzip - make -j3 test VERBOSE=1 BGZIP=/usr/bin/bgzip + make -j4 test VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/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/bbvDPfW4Fn/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/xWaIZqXfN5/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/bbvDPfW4Fn/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/xWaIZqXfN5/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/bbvDPfW4Fn/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/xWaIZqXfN5/bgzip.dat.gz .. ok -/build/samtools-1.11/samtools faidx /tmp/bbvDPfW4Fn/faidx.fa 3:11-13 | grep -v '^>' +/build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/samtools-1.11/samtools faidx /tmp/bbvDPfW4Fn/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/samtools-1.11/samtools faidx /tmp/bbvDPfW4Fn/faidx.fa 2:998-1003 | grep -v '^>' +/build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/samtools-1.11/samtools faidx /tmp/bbvDPfW4Fn/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/samtools-1.11/samtools faidx /tmp/bbvDPfW4Fn/faidx.fa 1:100-104 | grep -v '^>' +/build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/samtools-1.11/samtools faidx /tmp/bbvDPfW4Fn/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/samtools-1.11/samtools faidx /tmp/bbvDPfW4Fn/faidx.fa 1:99998-100007 | grep -v '^>' +/build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/samtools-1.11/samtools faidx /tmp/bbvDPfW4Fn/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/samtools-1.11/samtools fqidx /tmp/bbvDPfW4Fn/fqidx.fq 3:11-13 +/build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq 3:11-13 .. ok .. ok -/build/samtools-1.11/samtools fqidx /tmp/bbvDPfW4Fn/fqidx.fq.gz 3:11-13 +/build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/samtools-1.11/samtools fqidx /tmp/bbvDPfW4Fn/fqidx.fq 2:998-1003 +/build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq 2:998-1003 .. ok .. ok -/build/samtools-1.11/samtools fqidx /tmp/bbvDPfW4Fn/fqidx.fq.gz 2:998-1003 +/build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/samtools-1.11/samtools fqidx /tmp/bbvDPfW4Fn/fqidx.fq 1:100-104 +/build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq 1:100-104 .. ok .. ok -/build/samtools-1.11/samtools fqidx /tmp/bbvDPfW4Fn/fqidx.fq.gz 1:100-104 +/build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/samtools-1.11/samtools fqidx /tmp/bbvDPfW4Fn/fqidx.fq 1:99998-100007 +/build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq 1:99998-100007 .. ok .. ok -/build/samtools-1.11/samtools fqidx /tmp/bbvDPfW4Fn/fqidx.fq.gz 1:99998-100007 +/build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -873,7 +944,7 @@ .. ok test_dict: - /build/samtools-1.11/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/bbvDPfW4Fn/dict.fa.gz + /build/samtools-1.11/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/xWaIZqXfN5/dict.fa.gz .. ok test_dict: @@ -885,11 +956,11 @@ .. ok test_index: - /build/samtools-1.11/samtools view /tmp/bbvDPfW4Fn/large_chrom.bam ref2 + /build/samtools-1.11/samtools view /tmp/xWaIZqXfN5/large_chrom.bam ref2 .. ok test_index: - /build/samtools-1.11/samtools view /tmp/bbvDPfW4Fn/large_chrom.bam ref2:1-541556283 + /build/samtools-1.11/samtools view /tmp/xWaIZqXfN5/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -897,31 +968,31 @@ .. ok test_index: - /build/samtools-1.11/samtools view -X /build/samtools-1.11/test/dat/test_input_1_b.bam /tmp/bbvDPfW4Fn/test_input_1_b.bam.bai ref2 + /build/samtools-1.11/samtools view -X /build/samtools-1.11/test/dat/test_input_1_b.bam /tmp/xWaIZqXfN5/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/samtools-1.11/samtools merge -O sam - -X -cp -R ref2 /build/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/bbvDPfW4Fn/test_input_1_b.bam.bai + /build/samtools-1.11/samtools merge -O sam - -X -cp -R ref2 /build/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/xWaIZqXfN5/test_input_1_b.bam.bai .. ok test_index: - /build/samtools-1.11/samtools index -c /build/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/bbvDPfW4Fn/auto_indexed.csi && cat /tmp/bbvDPfW4Fn/auto_indexed.csi + /build/samtools-1.11/samtools index -c /build/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/xWaIZqXfN5/auto_indexed.csi && cat /tmp/xWaIZqXfN5/auto_indexed.csi .. ok test_index: - /build/samtools-1.11/samtools index /build/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/bbvDPfW4Fn/auto_indexed.crai && cat /tmp/bbvDPfW4Fn/auto_indexed.crai + /build/samtools-1.11/samtools index /build/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/xWaIZqXfN5/auto_indexed.crai && cat /tmp/xWaIZqXfN5/auto_indexed.crai .. ok test_index: - /build/samtools-1.11/samtools index -c /build/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/bbvDPfW4Fn/auto_indexed.csi && cat /tmp/bbvDPfW4Fn/auto_indexed.csi + /build/samtools-1.11/samtools index -c /build/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/xWaIZqXfN5/auto_indexed.csi && cat /tmp/xWaIZqXfN5/auto_indexed.csi .. ok test_index: - /build/samtools-1.11/samtools view -@ 2 /tmp/bbvDPfW4Fn/large_chrom.bam ref2 + /build/samtools-1.11/samtools view -@ 2 /tmp/xWaIZqXfN5/large_chrom.bam ref2 .. ok test_index: - /build/samtools-1.11/samtools view -@ 2 /tmp/bbvDPfW4Fn/large_chrom.bam ref2:1-541556283 + /build/samtools-1.11/samtools view -@ 2 /tmp/xWaIZqXfN5/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -929,63 +1000,63 @@ .. ok test_index: - /build/samtools-1.11/samtools view -@ 2 -X /build/samtools-1.11/test/dat/test_input_1_b.bam /tmp/bbvDPfW4Fn/test_input_1_b.bam.bai ref2 + /build/samtools-1.11/samtools view -@ 2 -X /build/samtools-1.11/test/dat/test_input_1_b.bam /tmp/xWaIZqXfN5/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/samtools-1.11/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/bbvDPfW4Fn/test_input_1_b.bam.bai + /build/samtools-1.11/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/xWaIZqXfN5/test_input_1_b.bam.bai .. ok test_index: - /build/samtools-1.11/samtools index -@ 2 -c /build/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/bbvDPfW4Fn/auto_indexed.csi && cat /tmp/bbvDPfW4Fn/auto_indexed.csi + /build/samtools-1.11/samtools index -@ 2 -c /build/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/xWaIZqXfN5/auto_indexed.csi && cat /tmp/xWaIZqXfN5/auto_indexed.csi .. ok test_index: - /build/samtools-1.11/samtools index -@ 2 /build/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/bbvDPfW4Fn/auto_indexed.crai && cat /tmp/bbvDPfW4Fn/auto_indexed.crai + /build/samtools-1.11/samtools index -@ 2 /build/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/xWaIZqXfN5/auto_indexed.crai && cat /tmp/xWaIZqXfN5/auto_indexed.crai .. ok test_index: - /build/samtools-1.11/samtools index -@ 2 -c /build/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/bbvDPfW4Fn/auto_indexed.csi && cat /tmp/bbvDPfW4Fn/auto_indexed.csi + /build/samtools-1.11/samtools index -@ 2 -c /build/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/xWaIZqXfN5/auto_indexed.csi && cat /tmp/xWaIZqXfN5/auto_indexed.csi .. ok test_mpileup: - /build/samtools-1.11/samtools mpileup -b /tmp/bbvDPfW4Fn/mpileup.bam.list -f /tmp/bbvDPfW4Fn/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.11/samtools mpileup -b /tmp/xWaIZqXfN5/mpileup.bam.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.11/samtools mpileup -b /tmp/bbvDPfW4Fn/mpileup.cram.list -f /tmp/bbvDPfW4Fn/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.11/samtools mpileup -b /tmp/xWaIZqXfN5/mpileup.cram.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.11/samtools mpileup -b /tmp/bbvDPfW4Fn/mpileup.bam.urllist -f /tmp/bbvDPfW4Fn/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.11/samtools mpileup -b /tmp/xWaIZqXfN5/mpileup.bam.urllist -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.11/samtools mpileup -b /tmp/bbvDPfW4Fn/mpileup.cram.urllist -f /tmp/bbvDPfW4Fn/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.11/samtools mpileup -b /tmp/xWaIZqXfN5/mpileup.cram.urllist -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.11/samtools mpileup -uvDV -b /tmp/bbvDPfW4Fn/mpileup.bam.list -f /tmp/bbvDPfW4Fn/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/samtools-1.11/samtools mpileup -uvDV -b /tmp/xWaIZqXfN5/mpileup.bam.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/samtools-1.11/samtools mpileup -uvDV -b /tmp/bbvDPfW4Fn/mpileup.cram.list -f /tmp/bbvDPfW4Fn/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/samtools-1.11/samtools mpileup -uvDV -b /tmp/xWaIZqXfN5/mpileup.cram.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/bbvDPfW4Fn/mpileup.cram.list -f /tmp/bbvDPfW4Fn/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/xWaIZqXfN5/mpileup.cram.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/bbvDPfW4Fn/mpileup.cram.list -f /tmp/bbvDPfW4Fn/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref + /build/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/xWaIZqXfN5/mpileup.cram.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: - /build/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/bbvDPfW4Fn/mpileup.ref.fa.gz -r17:1050-1060 /tmp/bbvDPfW4Fn/mpileup.1.bam | grep -v mpileup + /build/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:1050-1060 /tmp/xWaIZqXfN5/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/bbvDPfW4Fn/mpileup.ref.fa.gz -r17:1050-1060 /tmp/bbvDPfW4Fn/mpileup.1.cram | grep -v mpileup + /build/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:1050-1060 /tmp/xWaIZqXfN5/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: @@ -1253,41 +1324,41 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/bbvDPfW4Fn/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/xWaIZqXfN5/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/bbvDPfW4Fn/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/xWaIZqXfN5/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/bbvDPfW4Fn/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/xWaIZqXfN5/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/bbvDPfW4Fn/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/xWaIZqXfN5/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/bbvDPfW4Fn/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/xWaIZqXfN5/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/bbvDPfW4Fn/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/xWaIZqXfN5/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/bbvDPfW4Fn/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/bbvDPfW4Fn/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/bbvDPfW4Fn/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/bbvDPfW4Fn/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/bbvDPfW4Fn/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/bbvDPfW4Fn/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/bbvDPfW4Fn/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/bbvDPfW4Fn/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/bbvDPfW4Fn/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/bbvDPfW4Fn/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/bbvDPfW4Fn/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/bbvDPfW4Fn/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (CRAM input).. ok 67: Filter -d BC:TGCA (SAM input) .. ok @@ -1301,53 +1372,53 @@ 72: Count -d BC:TGCA (CRAM input) .. ok - 73: Filter -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (SAM input) .. ok + 73: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc (SAM input) .. ok - 74: Count -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (SAM input) .. ok + 74: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc (SAM input) .. ok - 75: Filter -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (BAM input) .. ok + 75: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc (BAM input) .. ok - 76: Count -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (BAM input) .. ok + 76: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc (BAM input) .. ok - 77: Filter -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (CRAM input) .. ok + 77: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input) .. ok - 78: Count -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (CRAM input) .. ok + 78: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input) .. ok - 79: Filter -D BC:/tmp/bbvDPfW4Fn/view.001.fobc -d BC:TGCA (SAM input).. ok + 79: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (SAM input).. ok - 80: Count -D BC:/tmp/bbvDPfW4Fn/view.001.fobc -d BC:TGCA (SAM input).. ok + 80: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (SAM input).. ok - 81: Filter -D BC:/tmp/bbvDPfW4Fn/view.001.fobc -d BC:TGCA (BAM input).. ok + 81: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (BAM input).. ok - 82: Count -D BC:/tmp/bbvDPfW4Fn/view.001.fobc -d BC:TGCA (BAM input).. ok + 82: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (BAM input).. ok - 83: Filter -D BC:/tmp/bbvDPfW4Fn/view.001.fobc -d BC:TGCA (CRAM input).. ok + 83: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (CRAM input).. ok - 84: Count -D BC:/tmp/bbvDPfW4Fn/view.001.fobc -d BC:TGCA (CRAM input).. ok + 84: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (CRAM input).. ok - 85: Filter -d BC:TGCA -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (SAM input).. ok + 85: Filter -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (SAM input).. ok - 86: Count -d BC:TGCA -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (SAM input).. ok + 86: Count -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (SAM input).. ok - 87: Filter -d BC:TGCA -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (BAM input).. ok + 87: Filter -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (BAM input).. ok - 88: Count -d BC:TGCA -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (BAM input).. ok + 88: Count -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (BAM input).. ok - 89: Filter -d BC:TGCA -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (CRAM input).. ok + 89: Filter -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input).. ok - 90: Count -d BC:TGCA -D BC:/tmp/bbvDPfW4Fn/view.001.fobc (CRAM input).. ok + 90: Count -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input).. ok - 91: Filter -D RG:/tmp/bbvDPfW4Fn/view.001.fogn (SAM input) .. ok + 91: Filter -D RG:/tmp/xWaIZqXfN5/view.001.fogn (SAM input) .. ok - 92: Count -D RG:/tmp/bbvDPfW4Fn/view.001.fogn (SAM input) .. ok + 92: Count -D RG:/tmp/xWaIZqXfN5/view.001.fogn (SAM input) .. ok - 93: Filter -D RG:/tmp/bbvDPfW4Fn/view.001.fogn (BAM input) .. ok + 93: Filter -D RG:/tmp/xWaIZqXfN5/view.001.fogn (BAM input) .. ok - 94: Count -D RG:/tmp/bbvDPfW4Fn/view.001.fogn (BAM input) .. ok + 94: Count -D RG:/tmp/xWaIZqXfN5/view.001.fogn (BAM input) .. ok - 95: Filter -D RG:/tmp/bbvDPfW4Fn/view.001.fogn (CRAM input) .. ok + 95: Filter -D RG:/tmp/xWaIZqXfN5/view.001.fogn (CRAM input) .. ok - 96: Count -D RG:/tmp/bbvDPfW4Fn/view.001.fogn (CRAM input) .. ok + 96: Count -D RG:/tmp/xWaIZqXfN5/view.001.fogn (CRAM input) .. ok 97: Filter -d NE:TGCA (SAM input) .. ok @@ -1363,126 +1434,126 @@ 103: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.11/samtools view -o /tmp/bbvDPfW4Fn/view.test103.sam -h -d TGCA /tmp/bbvDPfW4Fn/view.001.sam --no-PG + /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test103.sam -h -d TGCA /tmp/xWaIZqXfN5/view.001.sam --no-PG .. expected failure 104: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.11/samtools view -c -d TGCA /tmp/bbvDPfW4Fn/view.001.sam --no-PG + /build/samtools-1.11/samtools view -c -d TGCA /tmp/xWaIZqXfN5/view.001.sam --no-PG .. expected failure 105: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.11/samtools view -o /tmp/bbvDPfW4Fn/view.test105.sam -h -d TGCA /tmp/bbvDPfW4Fn/view.test001.bam --no-PG + /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test105.sam -h -d TGCA /tmp/xWaIZqXfN5/view.test001.bam --no-PG .. expected failure 106: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.11/samtools view -c -d TGCA /tmp/bbvDPfW4Fn/view.test001.bam --no-PG + /build/samtools-1.11/samtools view -c -d TGCA /tmp/xWaIZqXfN5/view.test001.bam --no-PG .. expected failure 107: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.11/samtools view -o /tmp/bbvDPfW4Fn/view.test107.sam -h -d TGCA /tmp/bbvDPfW4Fn/view.test006.cram --no-PG + /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test107.sam -h -d TGCA /tmp/xWaIZqXfN5/view.test006.cram --no-PG .. expected failure 108: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.11/samtools view -c -d TGCA /tmp/bbvDPfW4Fn/view.test006.cram --no-PG + /build/samtools-1.11/samtools view -c -d TGCA /tmp/xWaIZqXfN5/view.test006.cram --no-PG .. expected failure - 109: Filter -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/bbvDPfW4Fn/view.001.fobc" + 109: Filter -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: - /build/samtools-1.11/samtools view -o /tmp/bbvDPfW4Fn/view.test109.sam -h -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc /tmp/bbvDPfW4Fn/view.001.sam --no-PG + /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test109.sam -h -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.001.sam --no-PG .. expected failure - 110: Count -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/bbvDPfW4Fn/view.001.fobc" + 110: Count -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: - /build/samtools-1.11/samtools view -c -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc /tmp/bbvDPfW4Fn/view.001.sam --no-PG + /build/samtools-1.11/samtools view -c -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.001.sam --no-PG .. expected failure - 111: Filter -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/bbvDPfW4Fn/view.001.fobc" + 111: Filter -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: - /build/samtools-1.11/samtools view -o /tmp/bbvDPfW4Fn/view.test111.sam -h -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc /tmp/bbvDPfW4Fn/view.test001.bam --no-PG + /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test111.sam -h -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.test001.bam --no-PG .. expected failure - 112: Count -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/bbvDPfW4Fn/view.001.fobc" + 112: Count -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: - /build/samtools-1.11/samtools view -c -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc /tmp/bbvDPfW4Fn/view.test001.bam --no-PG + /build/samtools-1.11/samtools view -c -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.test001.bam --no-PG .. expected failure - 113: Filter -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/bbvDPfW4Fn/view.001.fobc" + 113: Filter -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: - /build/samtools-1.11/samtools view -o /tmp/bbvDPfW4Fn/view.test113.sam -h -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc /tmp/bbvDPfW4Fn/view.test006.cram --no-PG + /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test113.sam -h -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.test006.cram --no-PG .. expected failure - 114: Count -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/bbvDPfW4Fn/view.001.fobc" + 114: Count -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: - /build/samtools-1.11/samtools view -c -D BClong:/tmp/bbvDPfW4Fn/view.001.fobc /tmp/bbvDPfW4Fn/view.test006.cram --no-PG + /build/samtools-1.11/samtools view -c -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/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/samtools-1.11/samtools view -o /tmp/bbvDPfW4Fn/view.test115.sam -h -d BC:ACGT -d RG:grp2 /tmp/bbvDPfW4Fn/view.001.sam --no-PG + /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test115.sam -h -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/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/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/bbvDPfW4Fn/view.001.sam --no-PG + /build/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/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/samtools-1.11/samtools view -o /tmp/bbvDPfW4Fn/view.test117.sam -h -d BC:ACGT -d RG:grp2 /tmp/bbvDPfW4Fn/view.test001.bam --no-PG + /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test117.sam -h -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/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/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/bbvDPfW4Fn/view.test001.bam --no-PG + /build/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/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/samtools-1.11/samtools view -o /tmp/bbvDPfW4Fn/view.test119.sam -h -d BC:ACGT -d RG:grp2 /tmp/bbvDPfW4Fn/view.test006.cram --no-PG + /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test119.sam -h -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/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/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/bbvDPfW4Fn/view.test006.cram --no-PG + /build/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/view.test006.cram --no-PG .. expected failure @@ -2076,7 +2147,7 @@ .. ok test_bam2fq: - /build/samtools-1.11/samtools fastq -N -s /tmp/bbvDPfW4Fn/bam2fq.discard.s.fq -0 /tmp/bbvDPfW4Fn/bam2fq.discard.0.fq /build/samtools-1.11/test/dat/bam2fq.001.sam + /build/samtools-1.11/samtools fastq -N -s /tmp/xWaIZqXfN5/bam2fq.discard.s.fq -0 /tmp/xWaIZqXfN5/bam2fq.discard.0.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2177,7 +2248,7 @@ .. ok test_bam2fq: - /build/samtools-1.11/samtools fastq -@ 2 -N -s /tmp/bbvDPfW4Fn/bam2fq.discard.s.fq -0 /tmp/bbvDPfW4Fn/bam2fq.discard.0.fq /build/samtools-1.11/test/dat/bam2fq.001.sam + /build/samtools-1.11/samtools fastq -@ 2 -N -s /tmp/xWaIZqXfN5/bam2fq.discard.s.fq -0 /tmp/xWaIZqXfN5/bam2fq.discard.0.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2338,7 +2409,7 @@ .. ok test_merge: - /build/samtools-1.11/samtools merge -s 1 -O sam -b /tmp/VqAqIqJjqY - /build/samtools-1.11/test/dat/test_input_1_a.bam + /build/samtools-1.11/samtools merge -s 1 -O sam -b /tmp/dg9Xw1qrec - /build/samtools-1.11/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2358,11 +2429,11 @@ .. ok test_merge: - /build/samtools-1.11/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/bbvDPfW4Fn/merge.tag.1.bam /tmp/bbvDPfW4Fn/merge.tag.2.bam + /build/samtools-1.11/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/xWaIZqXfN5/merge.tag.1.bam /tmp/xWaIZqXfN5/merge.tag.2.bam .. ok test_merge: - /build/samtools-1.11/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/bbvDPfW4Fn/merge.tag.3.bam /tmp/bbvDPfW4Fn/merge.tag.4.bam + /build/samtools-1.11/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/xWaIZqXfN5/merge.tag.3.bam /tmp/xWaIZqXfN5/merge.tag.4.bam .. ok test_merge: @@ -2370,7 +2441,7 @@ .. ok test_merge: - /build/samtools-1.11/samtools merge --no-PG -O SAM -L /build/samtools-1.11/test/merge/merge.bed - /tmp/bbvDPfW4Fn/merge.bed.1.bam /tmp/bbvDPfW4Fn/merge.bed.2.bam + /build/samtools-1.11/samtools merge --no-PG -O SAM -L /build/samtools-1.11/test/merge/merge.bed - /tmp/xWaIZqXfN5/merge.bed.1.bam /tmp/xWaIZqXfN5/merge.bed.2.bam .. ok test_merge: @@ -2382,7 +2453,7 @@ .. ok test_merge: - /build/samtools-1.11/samtools merge -@ 2 -s 1 -O sam -b /tmp/48BCqH_zSX - /build/samtools-1.11/test/dat/test_input_1_a.bam + /build/samtools-1.11/samtools merge -@ 2 -s 1 -O sam -b /tmp/7EwXKV13fC - /build/samtools-1.11/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2402,11 +2473,11 @@ .. ok test_merge: - /build/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/bbvDPfW4Fn/merge.tag.1.bam /tmp/bbvDPfW4Fn/merge.tag.2.bam + /build/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/xWaIZqXfN5/merge.tag.1.bam /tmp/xWaIZqXfN5/merge.tag.2.bam .. ok test_merge: - /build/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/bbvDPfW4Fn/merge.tag.3.bam /tmp/bbvDPfW4Fn/merge.tag.4.bam + /build/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/xWaIZqXfN5/merge.tag.3.bam /tmp/xWaIZqXfN5/merge.tag.4.bam .. ok test_merge: @@ -2414,19 +2485,19 @@ .. ok test_merge: - /build/samtools-1.11/samtools merge -@ 2 --no-PG -O SAM -L /build/samtools-1.11/test/merge/merge.bed - /tmp/bbvDPfW4Fn/merge.bed.1.bam /tmp/bbvDPfW4Fn/merge.bed.2.bam + /build/samtools-1.11/samtools merge -@ 2 --no-PG -O SAM -L /build/samtools-1.11/test/merge/merge.bed - /tmp/xWaIZqXfN5/merge.bed.1.bam /tmp/xWaIZqXfN5/merge.bed.2.bam .. ok test_sort: - /build/samtools-1.11/samtools sort /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/bbvDPfW4Fn/sortout + /build/samtools-1.11/samtools sort /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sortout .. ok test_sort: - /build/samtools-1.11/samtools sort -f /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/bbvDPfW4Fn/sortout.bam + /build/samtools-1.11/samtools sort -f /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sortout.bam .. ok test_sort: - /build/samtools-1.11/samtools sort -o /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/bbvDPfW4Fn/sorttmp + /build/samtools-1.11/samtools sort -o /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sorttmp .. ok test_sort: @@ -2454,15 +2525,15 @@ .. ok test_sort: - /build/samtools-1.11/samtools sort -@ 2 /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/bbvDPfW4Fn/sortout + /build/samtools-1.11/samtools sort -@ 2 /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sortout .. ok test_sort: - /build/samtools-1.11/samtools sort -@ 2 -f /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/bbvDPfW4Fn/sortout.bam + /build/samtools-1.11/samtools sort -@ 2 -f /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sortout.bam .. ok test_sort: - /build/samtools-1.11/samtools sort -@ 2 -o /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/bbvDPfW4Fn/sorttmp + /build/samtools-1.11/samtools sort -@ 2 -o /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sorttmp .. ok test_sort: @@ -2870,15 +2941,15 @@ .. ok test_large_positions: - /build/samtools-1.11/samtools view -h --no-PG /tmp/bbvDPfW4Fn/longref.sam.gz + /build/samtools-1.11/samtools view -h --no-PG /tmp/xWaIZqXfN5/longref.sam.gz .. ok test_large_positions: - /build/samtools-1.11/samtools view -h --no-PG /tmp/bbvDPfW4Fn/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 + /build/samtools-1.11/samtools view -h --no-PG /tmp/xWaIZqXfN5/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: - /build/samtools-1.11/samtools view -h --no-PG -L /build/samtools-1.11/test/large_pos/test.bed /tmp/bbvDPfW4Fn/longref.sam.gz + /build/samtools-1.11/samtools view -h --no-PG -L /build/samtools-1.11/test/large_pos/test.bed /tmp/xWaIZqXfN5/longref.sam.gz .. ok test_large_positions: @@ -2898,7 +2969,7 @@ .. ok test_large_positions: - /build/samtools-1.11/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/bbvDPfW4Fn/longref.sam.gz + /build/samtools-1.11/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/xWaIZqXfN5/longref.sam.gz .. ok test_large_positions: @@ -3011,7 +3082,7 @@ Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/samtools-1.11' - rm -fr -- /tmp/dh-xdg-rundir-Qd7ZAE4R + rm -fr -- /tmp/dh-xdg-rundir-zkrLiXgy make[1]: Leaving directory '/build/samtools-1.11' create-stamp debian/debhelper-build-stamp dh_prep @@ -3023,7 +3094,7 @@ dh_auto_install -- \ prefix=/usr install -d /build/samtools-1.11/debian/tmp - make -j3 install DESTDIR=/build/samtools-1.11/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr + make -j4 install DESTDIR=/build/samtools-1.11/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/samtools-1.11' mkdir -p -m 755 /build/samtools-1.11/debian/tmp/usr/bin /build/samtools-1.11/debian/tmp/usr/bin /build/samtools-1.11/debian/tmp/usr/share/man/man1 install -p samtools /build/samtools-1.11/debian/tmp/usr/bin @@ -3090,9 +3161,10 @@ 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/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 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-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.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 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 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/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 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-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 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/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 @@ -3102,13 +3174,7 @@ mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.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 - 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/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 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-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 - mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.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/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.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 @@ -3118,20 +3184,27 @@ mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.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/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 - mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new 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 - mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new 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 - mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new 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-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.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 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 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-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 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-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 + mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.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-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 + mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.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 + mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new 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 + mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new 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 + mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new 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-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.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 @@ -3152,9 +3225,9 @@ 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 + gzip -9nf 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/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 cd '/build/samtools-1.11' cd '/build/samtools-1.11' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz @@ -3162,13 +3235,13 @@ dh_fixperms 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-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s + 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 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/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/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/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/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 -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 @@ -3177,20 +3250,6 @@ dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 586252 new size 607065 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a - install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/925ea5765600fca317e280a0b6eb655a9e71d4.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/925ea5765600fca317e280a0b6eb655a9e71d4.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/925ea5765600fca317e280a0b6eb655a9e71d4.debug debian/samtools/usr/bin/maq2sam-short - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/25677a2ac9ec55e3028473c9ce4813820da8e4.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/25677a2ac9ec55e3028473c9ce4813820da8e4.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/91/25677a2ac9ec55e3028473c9ce4813820da8e4.debug debian/samtools/usr/bin/samtools - install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/30243c9cbcb20002b282bf848cefc9d9aef8fd.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/30243c9cbcb20002b282bf848cefc9d9aef8fd.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/30243c9cbcb20002b282bf848cefc9d9aef8fd.debug debian/samtools/usr/bin/md5sum-lite install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/57 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/57/bb9880f18ecf7667ce5534ef530a6bf35e1a6a.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/57/bb9880f18ecf7667ce5534ef530a6bf35e1a6a.debug @@ -3201,16 +3260,30 @@ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c/e8bcfeca4939d768b51d712defa0da18dad300.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/1c/e8bcfeca4939d768b51d712defa0da18dad300.debug debian/samtools/usr/bin/ace2sam - install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0b - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0b/7c9879235c025a48c0b5df5b53a7e1e12b2e3e.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0b/7c9879235c025a48c0b5df5b53a7e1e12b2e3e.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/0b/7c9879235c025a48c0b5df5b53a7e1e12b2e3e.debug debian/samtools/usr/bin/maq2sam-long install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bc objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bc/f849a1727409ffe3ad7d810b11f4f03f9d27b5.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bc/f849a1727409ffe3ad7d810b11f4f03f9d27b5.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/bc/f849a1727409ffe3ad7d810b11f4f03f9d27b5.debug debian/samtools/usr/bin/md5fa + install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0b + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0b/7c9879235c025a48c0b5df5b53a7e1e12b2e3e.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0b/7c9879235c025a48c0b5df5b53a7e1e12b2e3e.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/0b/7c9879235c025a48c0b5df5b53a7e1e12b2e3e.debug debian/samtools/usr/bin/maq2sam-long + install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/25677a2ac9ec55e3028473c9ce4813820da8e4.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/25677a2ac9ec55e3028473c9ce4813820da8e4.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/91/25677a2ac9ec55e3028473c9ce4813820da8e4.debug debian/samtools/usr/bin/samtools + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/925ea5765600fca317e280a0b6eb655a9e71d4.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/925ea5765600fca317e280a0b6eb655a9e71d4.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/925ea5765600fca317e280a0b6eb655a9e71d4.debug debian/samtools/usr/bin/maq2sam-short + install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/30243c9cbcb20002b282bf848cefc9d9aef8fd.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/30243c9cbcb20002b282bf848cefc9d9aef8fd.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/30243c9cbcb20002b282bf848cefc9d9aef8fd.debug debian/samtools/usr/bin/md5sum-lite install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz @@ -3221,7 +3294,7 @@ rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -d debian/samtools/DEBIAN - dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa + dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite dh_installdeb install -d debian/samtools-test/DEBIAN dh_gencontrol @@ -3261,12 +3334,14 @@ 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/12083/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/12083/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/1103 and its subdirectories -I: Current time: Wed Jul 28 14:54:59 -12 2021 -I: pbuilder-time-stamp: 1627527299 +I: removing directory /srv/workspace/pbuilder/12083 and its subdirectories +I: Current time: Thu Jul 29 17:01:22 +14 2021 +I: pbuilder-time-stamp: 1627527682