Diff of the two buildlogs: -- --- b1/build.log 2023-05-23 10:03:29.034042498 +0000 +++ b2/build.log 2023-05-23 10:25:52.971213308 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 22 21:54:52 -12 2023 -I: pbuilder-time-stamp: 1684835692 +I: Current time: Wed May 24 00:04:58 +14 2023 +I: pbuilder-time-stamp: 1684836298 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./samtools_1.16.1.orig.tar.gz] I: copying [./samtools_1.16.1-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Sep 29 21:55:42 2022 -12 +gpgv: Signature made Fri Sep 30 23:55:42 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,135 +29,167 @@ dpkg-source: info: applying samtools-fasta-q-whatis.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9163/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30201/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 24 00:06 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/30201/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30201/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 parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='df3c4f0252094b8f8354faa76ccd5525' - 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='9163' - PS1='# ' - PS2='> ' + INVOCATION_ID=c9ba4320257f4a82bf7aa6e9f9ca203c + 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=30201 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HZLk05aI/pbuilderrc_XFc6 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HZLk05aI/b1 --logfile b1/build.log samtools_1.16.1-1.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HZLk05aI/pbuilderrc_FFGX --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HZLk05aI/b2 --logfile b2/build.log --extrapackages usrmerge samtools_1.16.1-1.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://10.0.0.15:3142/ I: uname -a - Linux jtx1a 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/9163/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 24 00:06 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/30201/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -274,7 +306,7 @@ Get: 57 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf tabix armhf 1.16+ds-3 [388 kB] -Fetched 24.8 MB in 2s (10.9 MB/s) +Fetched 24.8 MB in 3s (8914 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (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 ... 19329 files and directories currently installed.) @@ -524,8 +556,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/samtools-1.16.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../samtools_1.16.1-1_source.changes +I: user script /srv/workspace/pbuilder/30201/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/30201/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/samtools-1.16.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../samtools_1.16.1-1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.16.1-1 dpkg-buildpackage: info: source distribution unstable @@ -540,7 +583,7 @@ rm -f config.mk touch config.mk dh_auto_clean -- - make -j3 distclean + make -j4 distclean make[2]: Entering directory '/build/samtools-1.16.1' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai @@ -602,7 +645,7 @@ checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 @@ -628,15 +671,15 @@ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" - make -j3 "CFLAGS=-g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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-1.16.1' gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c cc1: warning: command-line option '-frelease' is valid for D but not for C 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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 @@ -647,9 +690,9 @@ gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c @@ -670,17 +713,17 @@ echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h sed -i -e 's@/build/samtools-1.16.1@«BUILDPATH»@g' version.h gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c @@ -690,9 +733,9 @@ gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c @@ -706,9 +749,9 @@ gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c @@ -724,9 +767,9 @@ gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c @@ -752,9 +795,9 @@ gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c @@ -778,22 +821,22 @@ 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_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.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 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 bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o ./lz4/lz4.o 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_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 make[2]: Leaving directory '/build/samtools-1.16.1' make[1]: Leaving directory '/build/samtools-1.16.1' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/samtools-1.16.1' dh_auto_test -- BGZIP=/usr/bin/bgzip - make -j3 test "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip + make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/samtools-1.16.1' test/split/test_count_rg test/split/test_expand_format_string @@ -832,75 +875,75 @@ /build/samtools-1.16.1/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok -/usr/bin/bgzip -c -b 65272 -s 5 /tmp/K12zu0h1CL/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/8XFqOIQ9QB/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/K12zu0h1CL/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/8XFqOIQ9QB/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/K12zu0h1CL/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/8XFqOIQ9QB/bgzip.dat.gz .. ok -/build/samtools-1.16.1/samtools faidx /tmp/K12zu0h1CL/faidx.fa 3:11-13 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/K12zu0h1CL/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/K12zu0h1CL/faidx.fa 2:998-1003 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/K12zu0h1CL/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/K12zu0h1CL/faidx.fa 1:100-104 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/K12zu0h1CL/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/K12zu0h1CL/faidx.fa 1:99998-100007 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/K12zu0h1CL/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/K12zu0h1CL/fqidx.fq 3:11-13 +/build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq 3:11-13 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/K12zu0h1CL/fqidx.fq.gz 3:11-13 +/build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/K12zu0h1CL/fqidx.fq 2:998-1003 +/build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq 2:998-1003 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/K12zu0h1CL/fqidx.fq.gz 2:998-1003 +/build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/K12zu0h1CL/fqidx.fq 1:100-104 +/build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq 1:100-104 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/K12zu0h1CL/fqidx.fq.gz 1:100-104 +/build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/K12zu0h1CL/fqidx.fq 1:99998-100007 +/build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq 1:99998-100007 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/K12zu0h1CL/fqidx.fq.gz 1:99998-100007 +/build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -910,7 +953,7 @@ .. ok test_dict: - /build/samtools-1.16.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/K12zu0h1CL/dict.fa.gz + /build/samtools-1.16.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/8XFqOIQ9QB/dict.fa.gz .. ok test_dict: @@ -926,11 +969,11 @@ .. ok test_index: - /build/samtools-1.16.1/samtools view /tmp/K12zu0h1CL/large_chrom.bam ref2 + /build/samtools-1.16.1/samtools view /tmp/8XFqOIQ9QB/large_chrom.bam ref2 .. ok test_index: - /build/samtools-1.16.1/samtools view /tmp/K12zu0h1CL/large_chrom.bam ref2:1-541556283 + /build/samtools-1.16.1/samtools view /tmp/8XFqOIQ9QB/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -938,15 +981,15 @@ .. ok test_index: - /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/K12zu0h1CL/test_input_1_b.bam.bai ref2 + /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/8XFqOIQ9QB/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/samtools-1.16.1/samtools merge -O sam - -X -cp -R ref2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai /tmp/K12zu0h1CL/test_input_1_b.bam.bai + /build/samtools-1.16.1/samtools merge -O sam - -X -cp -R ref2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai /tmp/8XFqOIQ9QB/test_input_1_b.bam.bai .. ok test_index: - /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/K12zu0h1CL/test_input_1_b_opt.bam.bai ref2 + /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/8XFqOIQ9QB/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -962,23 +1005,23 @@ .. ok test_index: - /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/K12zu0h1CL/auto_indexed.csi && cat /tmp/K12zu0h1CL/auto_indexed.csi + /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/8XFqOIQ9QB/auto_indexed.csi && cat /tmp/8XFqOIQ9QB/auto_indexed.csi .. ok test_index: - /build/samtools-1.16.1/samtools index /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/K12zu0h1CL/auto_indexed.crai && cat /tmp/K12zu0h1CL/auto_indexed.crai + /build/samtools-1.16.1/samtools index /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/8XFqOIQ9QB/auto_indexed.crai && cat /tmp/8XFqOIQ9QB/auto_indexed.crai .. ok test_index: - /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/K12zu0h1CL/auto_indexed.csi && cat /tmp/K12zu0h1CL/auto_indexed.csi + /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/8XFqOIQ9QB/auto_indexed.csi && cat /tmp/8XFqOIQ9QB/auto_indexed.csi .. ok test_index: - /build/samtools-1.16.1/samtools view -@ 2 /tmp/K12zu0h1CL/large_chrom.bam ref2 + /build/samtools-1.16.1/samtools view -@ 2 /tmp/8XFqOIQ9QB/large_chrom.bam ref2 .. ok test_index: - /build/samtools-1.16.1/samtools view -@ 2 /tmp/K12zu0h1CL/large_chrom.bam ref2:1-541556283 + /build/samtools-1.16.1/samtools view -@ 2 /tmp/8XFqOIQ9QB/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -986,15 +1029,15 @@ .. ok test_index: - /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/K12zu0h1CL/test_input_1_b.bam.bai ref2 + /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/8XFqOIQ9QB/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/samtools-1.16.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai /tmp/K12zu0h1CL/test_input_1_b.bam.bai + /build/samtools-1.16.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai /tmp/8XFqOIQ9QB/test_input_1_b.bam.bai .. ok test_index: - /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/K12zu0h1CL/test_input_1_b_opt.bam.bai ref2 + /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/8XFqOIQ9QB/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -1010,39 +1053,39 @@ .. ok test_index: - /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/K12zu0h1CL/auto_indexed.csi && cat /tmp/K12zu0h1CL/auto_indexed.csi + /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/8XFqOIQ9QB/auto_indexed.csi && cat /tmp/8XFqOIQ9QB/auto_indexed.csi .. ok test_index: - /build/samtools-1.16.1/samtools index -@ 2 /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/K12zu0h1CL/auto_indexed.crai && cat /tmp/K12zu0h1CL/auto_indexed.crai + /build/samtools-1.16.1/samtools index -@ 2 /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/8XFqOIQ9QB/auto_indexed.crai && cat /tmp/8XFqOIQ9QB/auto_indexed.crai .. ok test_index: - /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/K12zu0h1CL/auto_indexed.csi && cat /tmp/K12zu0h1CL/auto_indexed.csi + /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/8XFqOIQ9QB/auto_indexed.csi && cat /tmp/8XFqOIQ9QB/auto_indexed.csi .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/K12zu0h1CL/mpileup.bam.list -f /tmp/K12zu0h1CL/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/8XFqOIQ9QB/mpileup.bam.list -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/K12zu0h1CL/mpileup.cram.list -f /tmp/K12zu0h1CL/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/8XFqOIQ9QB/mpileup.cram.list -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/K12zu0h1CL/mpileup.bam.urllist -f /tmp/K12zu0h1CL/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/8XFqOIQ9QB/mpileup.bam.urllist -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/K12zu0h1CL/mpileup.cram.urllist -f /tmp/K12zu0h1CL/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/8XFqOIQ9QB/mpileup.cram.urllist -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/K12zu0h1CL/mpileup.ref.fa.gz -r17:1050-1060 /tmp/K12zu0h1CL/mpileup.1.bam | grep -v mpileup + /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/8XFqOIQ9QB/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/K12zu0h1CL/mpileup.ref.fa.gz -r17:1050-1060 /tmp/K12zu0h1CL/mpileup.1.cram | grep -v mpileup + /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/8XFqOIQ9QB/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: @@ -1328,53 +1371,53 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/K12zu0h1CL/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/K12zu0h1CL/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/8XFqOIQ9QB/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/K12zu0h1CL/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/K12zu0h1CL/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/8XFqOIQ9QB/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/K12zu0h1CL/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/K12zu0h1CL/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/8XFqOIQ9QB/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/K12zu0h1CL/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/K12zu0h1CL/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/K12zu0h1CL/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/K12zu0h1CL/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/K12zu0h1CL/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/K12zu0h1CL/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/K12zu0h1CL/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/K12zu0h1CL/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/K12zu0h1CL/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/K12zu0h1CL/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/K12zu0h1CL/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/K12zu0h1CL/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (CRAM input).. ok - 67: Filter -N /tmp/K12zu0h1CL/view.001.forn (SAM input) .. ok + 67: Filter -N /tmp/8XFqOIQ9QB/view.001.forn (SAM input) .. ok - 68: Count -N /tmp/K12zu0h1CL/view.001.forn (SAM input) .. ok + 68: Count -N /tmp/8XFqOIQ9QB/view.001.forn (SAM input) .. ok - 69: Filter -N /tmp/K12zu0h1CL/view.001.forn (BAM input) .. ok + 69: Filter -N /tmp/8XFqOIQ9QB/view.001.forn (BAM input) .. ok - 70: Count -N /tmp/K12zu0h1CL/view.001.forn (BAM input) .. ok + 70: Count -N /tmp/8XFqOIQ9QB/view.001.forn (BAM input) .. ok - 71: Filter -N /tmp/K12zu0h1CL/view.001.forn (CRAM input) .. ok + 71: Filter -N /tmp/8XFqOIQ9QB/view.001.forn (CRAM input) .. ok - 72: Count -N /tmp/K12zu0h1CL/view.001.forn (CRAM input) .. ok + 72: Count -N /tmp/8XFqOIQ9QB/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok @@ -1400,53 +1443,53 @@ 84: Count -d BC:TGCA (CRAM input) .. ok - 85: Filter -D BC:/tmp/K12zu0h1CL/view.001.fobc (SAM input) .. ok + 85: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input) .. ok - 86: Count -D BC:/tmp/K12zu0h1CL/view.001.fobc (SAM input) .. ok + 86: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input) .. ok - 87: Filter -D BC:/tmp/K12zu0h1CL/view.001.fobc (BAM input) .. ok + 87: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input) .. ok - 88: Count -D BC:/tmp/K12zu0h1CL/view.001.fobc (BAM input) .. ok + 88: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input) .. ok - 89: Filter -D BC:/tmp/K12zu0h1CL/view.001.fobc (CRAM input) .. ok + 89: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input) .. ok - 90: Count -D BC:/tmp/K12zu0h1CL/view.001.fobc (CRAM input) .. ok + 90: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input) .. ok - 91: Filter -D BC:/tmp/K12zu0h1CL/view.001.fobc -d BC:TGCA (SAM input).. ok + 91: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (SAM input).. ok - 92: Count -D BC:/tmp/K12zu0h1CL/view.001.fobc -d BC:TGCA (SAM input).. ok + 92: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (SAM input).. ok - 93: Filter -D BC:/tmp/K12zu0h1CL/view.001.fobc -d BC:TGCA (BAM input).. ok + 93: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (BAM input).. ok - 94: Count -D BC:/tmp/K12zu0h1CL/view.001.fobc -d BC:TGCA (BAM input).. ok + 94: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (BAM input).. ok - 95: Filter -D BC:/tmp/K12zu0h1CL/view.001.fobc -d BC:TGCA (CRAM input).. ok + 95: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (CRAM input).. ok - 96: Count -D BC:/tmp/K12zu0h1CL/view.001.fobc -d BC:TGCA (CRAM input).. ok + 96: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (CRAM input).. ok - 97: Filter -d BC:TGCA -D BC:/tmp/K12zu0h1CL/view.001.fobc (SAM input).. ok + 97: Filter -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input).. ok - 98: Count -d BC:TGCA -D BC:/tmp/K12zu0h1CL/view.001.fobc (SAM input).. ok + 98: Count -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input).. ok - 99: Filter -d BC:TGCA -D BC:/tmp/K12zu0h1CL/view.001.fobc (BAM input).. ok + 99: Filter -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input).. ok - 100: Count -d BC:TGCA -D BC:/tmp/K12zu0h1CL/view.001.fobc (BAM input).. ok + 100: Count -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input).. ok - 101: Filter -d BC:TGCA -D BC:/tmp/K12zu0h1CL/view.001.fobc (CRAM input).. ok + 101: Filter -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input).. ok - 102: Count -d BC:TGCA -D BC:/tmp/K12zu0h1CL/view.001.fobc (CRAM input).. ok + 102: Count -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input).. ok - 103: Filter -D RG:/tmp/K12zu0h1CL/view.001.fogn (SAM input) .. ok + 103: Filter -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (SAM input) .. ok - 104: Count -D RG:/tmp/K12zu0h1CL/view.001.fogn (SAM input) .. ok + 104: Count -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (SAM input) .. ok - 105: Filter -D RG:/tmp/K12zu0h1CL/view.001.fogn (BAM input) .. ok + 105: Filter -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (BAM input) .. ok - 106: Count -D RG:/tmp/K12zu0h1CL/view.001.fogn (BAM input) .. ok + 106: Count -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (BAM input) .. ok - 107: Filter -D RG:/tmp/K12zu0h1CL/view.001.fogn (CRAM input).. ok + 107: Filter -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (CRAM input).. ok - 108: Count -D RG:/tmp/K12zu0h1CL/view.001.fogn (CRAM input) .. ok + 108: Count -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok @@ -1462,126 +1505,126 @@ 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/K12zu0h1CL/view.test115.sam -h -d TGCA /tmp/K12zu0h1CL/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test115.sam -h -d TGCA /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/K12zu0h1CL/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/K12zu0h1CL/view.test117.sam -h -d TGCA /tmp/K12zu0h1CL/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test117.sam -h -d TGCA /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/K12zu0h1CL/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/K12zu0h1CL/view.test119.sam -h -d TGCA /tmp/K12zu0h1CL/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test119.sam -h -d TGCA /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/K12zu0h1CL/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure - 121: Filter -D BClong:/tmp/K12zu0h1CL/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/K12zu0h1CL/view.001.fobc" + 121: Filter -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/K12zu0h1CL/view.test121.sam -h -D BClong:/tmp/K12zu0h1CL/view.001.fobc /tmp/K12zu0h1CL/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test121.sam -h -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure - 122: Count -D BClong:/tmp/K12zu0h1CL/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/K12zu0h1CL/view.001.fobc" + 122: Count -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/K12zu0h1CL/view.001.fobc /tmp/K12zu0h1CL/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure - 123: Filter -D BClong:/tmp/K12zu0h1CL/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/K12zu0h1CL/view.001.fobc" + 123: Filter -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/K12zu0h1CL/view.test123.sam -h -D BClong:/tmp/K12zu0h1CL/view.001.fobc /tmp/K12zu0h1CL/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test123.sam -h -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure - 124: Count -D BClong:/tmp/K12zu0h1CL/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/K12zu0h1CL/view.001.fobc" + 124: Count -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/K12zu0h1CL/view.001.fobc /tmp/K12zu0h1CL/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure - 125: Filter -D BClong:/tmp/K12zu0h1CL/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/K12zu0h1CL/view.001.fobc" + 125: Filter -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/K12zu0h1CL/view.test125.sam -h -D BClong:/tmp/K12zu0h1CL/view.001.fobc /tmp/K12zu0h1CL/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test125.sam -h -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure - 126: Count -D BClong:/tmp/K12zu0h1CL/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/K12zu0h1CL/view.001.fobc" + 126: Count -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/K12zu0h1CL/view.001.fobc /tmp/K12zu0h1CL/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/K12zu0h1CL/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/K12zu0h1CL/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/K12zu0h1CL/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/K12zu0h1CL/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/K12zu0h1CL/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/K12zu0h1CL/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/K12zu0h1CL/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/K12zu0h1CL/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/K12zu0h1CL/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure @@ -2455,7 +2498,7 @@ .. ok test_bam2fq: - /build/samtools-1.16.1/samtools fastq -N -s /tmp/K12zu0h1CL/bam2fq.discard.s.fq -0 /tmp/K12zu0h1CL/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam + /build/samtools-1.16.1/samtools fastq -N -s /tmp/8XFqOIQ9QB/bam2fq.discard.s.fq -0 /tmp/8XFqOIQ9QB/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2576,7 +2619,7 @@ .. ok test_bam2fq: - /build/samtools-1.16.1/samtools fastq -@ 2 -N -s /tmp/K12zu0h1CL/bam2fq.discard.s.fq -0 /tmp/K12zu0h1CL/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam + /build/samtools-1.16.1/samtools fastq -@ 2 -N -s /tmp/8XFqOIQ9QB/bam2fq.discard.s.fq -0 /tmp/8XFqOIQ9QB/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2769,7 +2812,7 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -s 1 -O sam -b /tmp/xfk3yD_WGq - /build/samtools-1.16.1/test/dat/test_input_1_a.bam + /build/samtools-1.16.1/samtools merge -s 1 -O sam -b /tmp/fs2QL3qQos - /build/samtools-1.16.1/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2793,11 +2836,11 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/K12zu0h1CL/merge.tag.1.bam /tmp/K12zu0h1CL/merge.tag.2.bam + /build/samtools-1.16.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/8XFqOIQ9QB/merge.tag.1.bam /tmp/8XFqOIQ9QB/merge.tag.2.bam .. ok test_merge: - /build/samtools-1.16.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/K12zu0h1CL/merge.tag.3.bam /tmp/K12zu0h1CL/merge.tag.4.bam + /build/samtools-1.16.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/8XFqOIQ9QB/merge.tag.3.bam /tmp/8XFqOIQ9QB/merge.tag.4.bam .. ok test_merge: @@ -2805,7 +2848,7 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge --no-PG -O SAM -L /build/samtools-1.16.1/test/merge/merge.bed - /tmp/K12zu0h1CL/merge.bed.1.bam /tmp/K12zu0h1CL/merge.bed.2.bam + /build/samtools-1.16.1/samtools merge --no-PG -O SAM -L /build/samtools-1.16.1/test/merge/merge.bed - /tmp/8XFqOIQ9QB/merge.bed.1.bam /tmp/8XFqOIQ9QB/merge.bed.2.bam .. ok test_merge: @@ -2821,7 +2864,7 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/IN85hegwuN - /build/samtools-1.16.1/test/dat/test_input_1_a.bam + /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/EzqekvVRy4 - /build/samtools-1.16.1/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2845,11 +2888,11 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/K12zu0h1CL/merge.tag.1.bam /tmp/K12zu0h1CL/merge.tag.2.bam + /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/8XFqOIQ9QB/merge.tag.1.bam /tmp/8XFqOIQ9QB/merge.tag.2.bam .. ok test_merge: - /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/K12zu0h1CL/merge.tag.3.bam /tmp/K12zu0h1CL/merge.tag.4.bam + /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/8XFqOIQ9QB/merge.tag.3.bam /tmp/8XFqOIQ9QB/merge.tag.4.bam .. ok test_merge: @@ -2857,7 +2900,7 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -@ 2 --no-PG -O SAM -L /build/samtools-1.16.1/test/merge/merge.bed - /tmp/K12zu0h1CL/merge.bed.1.bam /tmp/K12zu0h1CL/merge.bed.2.bam + /build/samtools-1.16.1/samtools merge -@ 2 --no-PG -O SAM -L /build/samtools-1.16.1/test/merge/merge.bed - /tmp/8XFqOIQ9QB/merge.bed.1.bam /tmp/8XFqOIQ9QB/merge.bed.2.bam .. ok test_merge: @@ -2865,15 +2908,15 @@ .. ok test_sort: - /build/samtools-1.16.1/samtools sort /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/K12zu0h1CL/sortout + /build/samtools-1.16.1/samtools sort /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sortout .. ok test_sort: - /build/samtools-1.16.1/samtools sort -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/K12zu0h1CL/sortout.bam + /build/samtools-1.16.1/samtools sort -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sortout.bam .. ok test_sort: - /build/samtools-1.16.1/samtools sort -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/K12zu0h1CL/sorttmp + /build/samtools-1.16.1/samtools sort -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sorttmp .. ok test_sort: @@ -2905,15 +2948,15 @@ .. ok test_sort: - /build/samtools-1.16.1/samtools sort -@ 2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/K12zu0h1CL/sortout + /build/samtools-1.16.1/samtools sort -@ 2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sortout .. ok test_sort: - /build/samtools-1.16.1/samtools sort -@ 2 -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/K12zu0h1CL/sortout.bam + /build/samtools-1.16.1/samtools sort -@ 2 -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sortout.bam .. ok test_sort: - /build/samtools-1.16.1/samtools sort -@ 2 -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/K12zu0h1CL/sorttmp + /build/samtools-1.16.1/samtools sort -@ 2 -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sorttmp .. ok test_sort: @@ -3409,15 +3452,15 @@ .. ok test_large_positions: - /build/samtools-1.16.1/samtools view -h --no-PG /tmp/K12zu0h1CL/longref.sam.gz + /build/samtools-1.16.1/samtools view -h --no-PG /tmp/8XFqOIQ9QB/longref.sam.gz .. ok test_large_positions: - /build/samtools-1.16.1/samtools view -h --no-PG /tmp/K12zu0h1CL/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 + /build/samtools-1.16.1/samtools view -h --no-PG /tmp/8XFqOIQ9QB/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: - /build/samtools-1.16.1/samtools view -h --no-PG -L /build/samtools-1.16.1/test/large_pos/test.bed /tmp/K12zu0h1CL/longref.sam.gz + /build/samtools-1.16.1/samtools view -h --no-PG -L /build/samtools-1.16.1/test/large_pos/test.bed /tmp/8XFqOIQ9QB/longref.sam.gz .. ok test_large_positions: @@ -3437,7 +3480,7 @@ .. ok test_large_positions: - /build/samtools-1.16.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/K12zu0h1CL/longref.sam.gz + /build/samtools-1.16.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/8XFqOIQ9QB/longref.sam.gz .. ok test_large_positions: @@ -3567,7 +3610,7 @@ Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/samtools-1.16.1' - rm -fr -- /tmp/dh-xdg-rundir-a2n7MPUd + rm -fr -- /tmp/dh-xdg-rundir-6FcyVAKo make[1]: Leaving directory '/build/samtools-1.16.1' create-stamp debian/debhelper-build-stamp dh_prep @@ -3579,7 +3622,7 @@ dh_auto_install -- \ prefix=/usr install -m0755 -d /build/samtools-1.16.1/debian/tmp - make -j3 install DESTDIR=/build/samtools-1.16.1/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr + make -j4 install DESTDIR=/build/samtools-1.16.1/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/samtools-1.16.1' mkdir -p -m 755 /build/samtools-1.16.1/debian/tmp/usr/bin /build/samtools-1.16.1/debian/tmp/usr/bin /build/samtools-1.16.1/debian/tmp/usr/share/man/man1 install -p samtools /build/samtools-1.16.1/debian/tmp/usr/bin @@ -3634,14 +3677,14 @@ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/samtools-1.16.1' dh_installchangelogs NEWS - install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test - install -p -m0644 debian/.debhelper/generated/samtools-test/dh_installchangelogs.dch.trimmed 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 -m0755 -d debian/samtools/usr/share/doc/samtools install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed 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 -m0755 -d debian/samtools-test/usr/share/doc/samtools-test + install -p -m0644 debian/.debhelper/generated/samtools-test/dh_installchangelogs.dch.trimmed 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 make[1]: Leaving directory '/build/samtools-1.16.1' dh_installexamples install -m0755 -d debian/samtools/usr/share/doc/samtools/examples @@ -3663,14 +3706,10 @@ 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-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-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.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 - 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-consensus.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 debian/samtools/usr/share/man/man1/samtools-faidx.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reference.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-samples.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-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.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 - mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 - mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-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-reference.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-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/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-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 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-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 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-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 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 @@ -3679,7 +3718,7 @@ 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-reference.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-samples.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 + chmod 0644 -- 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/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 @@ -3691,10 +3730,22 @@ mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/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-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 + mv debian/samtools/usr/share/man/man1/samtools-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 + 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-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.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 + mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 + mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-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-reference.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-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.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 - 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-consensus.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 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 @@ -3703,13 +3754,7 @@ mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.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-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.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 - mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-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-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.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 + chmod 0644 -- 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 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 dh_lintian install -m0755 -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools @@ -3725,26 +3770,26 @@ Using 1664531159 as canonical time Normalizing debian/samtools-test/usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz using File::StripNondeterminism::handlers::gzip dh_compress - cd debian/samtools cd debian/samtools-test - chmod a-x usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/README 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-consensus.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-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.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-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.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/README 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-consensus.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-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.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-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.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 + cd debian/samtools chmod a-x usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian 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/README 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-consensus.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-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.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-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.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/README 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-consensus.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-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.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-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.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 cd '/build/samtools-1.16.1' cd '/build/samtools-1.16.1' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms - 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 ! -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/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools/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 f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -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-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-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a @@ -3754,41 +3799,41 @@ objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35/b7d9e605225c7d471050eea7e9e90aa8dc9fb3.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35/b7d9e605225c7d471050eea7e9e90aa8dc9fb3.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/35/b7d9e605225c7d471050eea7e9e90aa8dc9fb3.debug debian/samtools/usr/bin/samtools - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed/83258f6ad143594b7b4d3baa2cc70919dbe539.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed/83258f6ad143594b7b4d3baa2cc70919dbe539.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed/83258f6ad143594b7b4d3baa2cc70919dbe539.debug debian/samtools/usr/bin/wgsim - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/91e5484c9355d90d02970995a6164e308ed888.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/91e5484c9355d90d02970995a6164e308ed888.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/30/91e5484c9355d90d02970995a6164e308ed888.debug debian/samtools/usr/bin/ace2sam - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bb - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bb/9b32252da618b6afd8e35576bc3483a19dee0e.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bb/9b32252da618b6afd8e35576bc3483a19dee0e.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/bb/9b32252da618b6afd8e35576bc3483a19dee0e.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9/0c9f8b18516ddadeb3fae409c686dd15349b85.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9/0c9f8b18516ddadeb3fae409c686dd15349b85.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/b9/0c9f8b18516ddadeb3fae409c686dd15349b85.debug debian/samtools/usr/bin/maq2sam-long - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce/b85fae99f451f6138c77d223a1567d2e57a3d7.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce/b85fae99f451f6138c77d223a1567d2e57a3d7.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/ce/b85fae99f451f6138c77d223a1567d2e57a3d7.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a/43f12265461daabff57ae0cf66c1ea1e4a55cb.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a/43f12265461daabff57ae0cf66c1ea1e4a55cb.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/1a/43f12265461daabff57ae0cf66c1ea1e4a55cb.debug debian/samtools/usr/bin/md5fa + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/91e5484c9355d90d02970995a6164e308ed888.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/91e5484c9355d90d02970995a6164e308ed888.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/30/91e5484c9355d90d02970995a6164e308ed888.debug debian/samtools/usr/bin/ace2sam + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce/b85fae99f451f6138c77d223a1567d2e57a3d7.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce/b85fae99f451f6138c77d223a1567d2e57a3d7.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/ce/b85fae99f451f6138c77d223a1567d2e57a3d7.debug debian/samtools/usr/bin/maq2sam-short + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bb + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bb/9b32252da618b6afd8e35576bc3483a19dee0e.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bb/9b32252da618b6afd8e35576bc3483a19dee0e.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/bb/9b32252da618b6afd8e35576bc3483a19dee0e.debug debian/samtools/usr/bin/md5sum-lite + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed/83258f6ad143594b7b4d3baa2cc70919dbe539.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed/83258f6ad143594b7b4d3baa2cc70919dbe539.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed/83258f6ad143594b7b4d3baa2cc70919dbe539.debug debian/samtools/usr/bin/wgsim + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35/b7d9e605225c7d471050eea7e9e90aa8dc9fb3.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35/b7d9e605225c7d471050eea7e9e90aa8dc9fb3.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/35/b7d9e605225c7d471050eea7e9e90aa8dc9fb3.debug debian/samtools/usr/bin/samtools install -m0755 -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 @@ -3800,7 +3845,7 @@ rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN - dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa + dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools dh_installdeb install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN @@ -3814,11 +3859,11 @@ echo misc:Depends= >> debian/samtools-test.substvars echo misc:Pre-Depends= >> debian/samtools-test.substvars dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -Pdebian/samtools-test +dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined + chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools -dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined - chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums @@ -3834,9 +3879,9 @@ dh_builddeb dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools .. +dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.16.1-1_armhf.deb'. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools' in '../samtools_1.16.1-1_armhf.deb'. -dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.16.1-1_armhf.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.16.1-1_all.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.16.1-1_armhf.buildinfo dpkg-genchanges --build=binary -O../samtools_1.16.1-1_armhf.changes @@ -3846,12 +3891,14 @@ 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/30201/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30201/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/9163 and its subdirectories -I: Current time: Mon May 22 22:03:17 -12 2023 -I: pbuilder-time-stamp: 1684836197 +I: removing directory /srv/workspace/pbuilder/30201 and its subdirectories +I: Current time: Wed May 24 00:25:41 +14 2023 +I: pbuilder-time-stamp: 1684837541