Diff of the two buildlogs: -- --- b1/build.log 2024-04-25 14:13:34.435717761 +0000 +++ b2/build.log 2024-04-25 14:25:17.573749812 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 25 02:03:12 -12 2024 -I: pbuilder-time-stamp: 1714053792 +I: Current time: Fri Apr 26 04:14:05 +14 2024 +I: pbuilder-time-stamp: 1714054445 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying reproducible.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/32695/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13756/tmp/hooks/D01_modify_environment starting +debug: Running on virt32z. +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 Apr 25 14:14 /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/13756/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13756/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - 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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + 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=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='033eeb130bdc4d44ba353c8fc2ca393b' - 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='32695' - PS1='# ' - PS2='> ' + INVOCATION_ID=ed08d9c25ab5411885c1ae73ef39a725 + 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=13756 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.G8G0lBNx/pbuilderrc_ykEy --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.G8G0lBNx/b1 --logfile b1/build.log samtools_1.19.2-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - 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.G8G0lBNx/pbuilderrc_j9gO --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.G8G0lBNx/b2 --logfile b2/build.log samtools_1.19.2-1.dsc' + SUDO_GID=110 + SUDO_UID=103 + 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 virt64b 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 23 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/32695/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 25 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/13756/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -86,7 +118,7 @@ Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19638 files and directories currently installed.) +(Reading database ... 19468 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -125,11 +157,11 @@ pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: - autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} + autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: - bzip2-doc ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget -0 packages upgraded, 57 newly installed, 0 to remove and 0 not upgraded. -Need to get 25.4 MB of archives. After unpacking 91.7 MB will be used. + bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget +0 packages upgraded, 63 newly installed, 0 to remove and 0 not upgraded. +Need to get 25.9 MB of archives. After unpacking 93.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] @@ -165,33 +197,39 @@ Get: 32 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libbz2-dev armhf 1.0.8-5.1 [28.3 kB] -Get: 35 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4+b1 [18.2 kB] -Get: 36 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4+b1 [50.1 kB] -Get: 37 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5+b3 [158 kB] -Get: 38 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.59.0-1 [62.0 kB] -Get: 39 http://deb.debian.org/debian trixie/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB] -Get: 40 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] -Get: 41 http://deb.debian.org/debian trixie/main armhf libssh2-1 armhf 1.11.0-4 [197 kB] -Get: 42 http://deb.debian.org/debian trixie/main armhf libcurl3-gnutls armhf 8.5.0-2 [378 kB] -Get: 43 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.5.0-2 [490 kB] -Get: 44 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] -Get: 45 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.20-1 [44.0 kB] -Get: 46 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] -Get: 47 http://deb.debian.org/debian trixie/main armhf libhts3 armhf 1.19+ds-1 [394 kB] -Get: 48 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] -Get: 49 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] -Get: 50 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.19+ds-1 [1598 kB] -Get: 51 http://deb.debian.org/debian trixie/main armhf libio-pty-perl armhf 1:1.20-1 [33.7 kB] -Get: 52 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.4+20240414-1 [81.8 kB] -Get: 53 http://deb.debian.org/debian trixie/main armhf libncurses-dev armhf 6.4+20240414-1 [309 kB] -Get: 54 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-1+b2 [31.9 kB] -Get: 55 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-1+b2 [28.9 kB] -Get: 56 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] -Get: 57 http://deb.debian.org/debian trixie/main armhf tabix armhf 1.19+ds-1 [409 kB] -Fetched 25.4 MB in 1s (37.5 MB/s) +Get: 35 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.0-2+b1 [19.3 kB] +Get: 36 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.20.1-5+b1 [30.4 kB] +Get: 37 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.20.1-5+b1 [75.4 kB] +Get: 38 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] +Get: 39 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.20.1-5+b1 [289 kB] +Get: 40 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.20.1-5+b1 [112 kB] +Get: 41 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4+b1 [18.2 kB] +Get: 42 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4+b1 [50.1 kB] +Get: 43 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5+b3 [158 kB] +Get: 44 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.59.0-1 [62.0 kB] +Get: 45 http://deb.debian.org/debian trixie/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB] +Get: 46 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] +Get: 47 http://deb.debian.org/debian trixie/main armhf libssh2-1 armhf 1.11.0-4 [197 kB] +Get: 48 http://deb.debian.org/debian trixie/main armhf libcurl3-gnutls armhf 8.5.0-2 [378 kB] +Get: 49 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.5.0-2 [490 kB] +Get: 50 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] +Get: 51 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.20-1 [44.0 kB] +Get: 52 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] +Get: 53 http://deb.debian.org/debian trixie/main armhf libhts3 armhf 1.19+ds-1 [394 kB] +Get: 54 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] +Get: 55 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] +Get: 56 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.19+ds-1 [1598 kB] +Get: 57 http://deb.debian.org/debian trixie/main armhf libio-pty-perl armhf 1:1.20-1 [33.7 kB] +Get: 58 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.4+20240414-1 [81.8 kB] +Get: 59 http://deb.debian.org/debian trixie/main armhf libncurses-dev armhf 6.4+20240414-1 [309 kB] +Get: 60 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-1+b2 [31.9 kB] +Get: 61 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-1+b2 [28.9 kB] +Get: 62 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] +Get: 63 http://deb.debian.org/debian trixie/main armhf tabix armhf 1.19+ds-1 [409 kB] +Fetched 25.9 MB in 1s (25.0 MB/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 ... 19638 files and directories currently installed.) +(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 ... 19468 files and directories currently installed.) Preparing to unpack .../00-autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package sensible-utils. @@ -293,77 +331,96 @@ Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../33-libbz2-dev_1.0.8-5.1_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-5.1) ... +Selecting previously unselected package libcom-err2:armhf. +Preparing to unpack .../34-libcom-err2_1.47.0-2+b1_armhf.deb ... +Unpacking libcom-err2:armhf (1.47.0-2+b1) ... +Selecting previously unselected package libkrb5support0:armhf. +Preparing to unpack .../35-libkrb5support0_1.20.1-5+b1_armhf.deb ... +Unpacking libkrb5support0:armhf (1.20.1-5+b1) ... +Selecting previously unselected package libk5crypto3:armhf. +Preparing to unpack .../36-libk5crypto3_1.20.1-5+b1_armhf.deb ... +Unpacking libk5crypto3:armhf (1.20.1-5+b1) ... +Selecting previously unselected package libkeyutils1:armhf. +Preparing to unpack .../37-libkeyutils1_1.6.3-3_armhf.deb ... +Unpacking libkeyutils1:armhf (1.6.3-3) ... +Selecting previously unselected package libkrb5-3:armhf. +Preparing to unpack .../38-libkrb5-3_1.20.1-5+b1_armhf.deb ... +Unpacking libkrb5-3:armhf (1.20.1-5+b1) ... +Selecting previously unselected package libgssapi-krb5-2:armhf. +Preparing to unpack .../39-libgssapi-krb5-2_1.20.1-5+b1_armhf.deb ... +Unpacking libgssapi-krb5-2:armhf (1.20.1-5+b1) ... Selecting previously unselected package libsasl2-modules-db:armhf. -Preparing to unpack .../34-libsasl2-modules-db_2.1.28+dfsg1-4+b1_armhf.deb ... +Preparing to unpack .../40-libsasl2-modules-db_2.1.28+dfsg1-4+b1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libsasl2-2:armhf. -Preparing to unpack .../35-libsasl2-2_2.1.28+dfsg1-4+b1_armhf.deb ... +Preparing to unpack .../41-libsasl2-2_2.1.28+dfsg1-4+b1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libldap-2.5-0:armhf. -Preparing to unpack .../36-libldap-2.5-0_2.5.13+dfsg-5+b3_armhf.deb ... +Preparing to unpack .../42-libldap-2.5-0_2.5.13+dfsg-5+b3_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5+b3) ... Selecting previously unselected package libnghttp2-14:armhf. -Preparing to unpack .../37-libnghttp2-14_1.59.0-1_armhf.deb ... +Preparing to unpack .../43-libnghttp2-14_1.59.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.59.0-1) ... Selecting previously unselected package libpsl5:armhf. -Preparing to unpack .../38-libpsl5_0.21.2-1+b1_armhf.deb ... +Preparing to unpack .../44-libpsl5_0.21.2-1+b1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1+b1) ... Selecting previously unselected package librtmp1:armhf. -Preparing to unpack .../39-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... +Preparing to unpack .../45-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. -Preparing to unpack .../40-libssh2-1_1.11.0-4_armhf.deb ... +Preparing to unpack .../46-libssh2-1_1.11.0-4_armhf.deb ... Unpacking libssh2-1:armhf (1.11.0-4) ... Selecting previously unselected package libcurl3-gnutls:armhf. -Preparing to unpack .../41-libcurl3-gnutls_8.5.0-2_armhf.deb ... +Preparing to unpack .../47-libcurl3-gnutls_8.5.0-2_armhf.deb ... Unpacking libcurl3-gnutls:armhf (8.5.0-2) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. -Preparing to unpack .../42-libcurl4-gnutls-dev_8.5.0-2_armhf.deb ... +Preparing to unpack .../48-libcurl4-gnutls-dev_8.5.0-2_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (8.5.0-2) ... Selecting previously unselected package libdeflate0:armhf. -Preparing to unpack .../43-libdeflate0_1.20-1_armhf.deb ... +Preparing to unpack .../49-libdeflate0_1.20-1_armhf.deb ... Unpacking libdeflate0:armhf (1.20-1) ... Selecting previously unselected package libdeflate-dev:armhf. -Preparing to unpack .../44-libdeflate-dev_1.20-1_armhf.deb ... +Preparing to unpack .../50-libdeflate-dev_1.20-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.20-1) ... Selecting previously unselected package libhtscodecs2:armhf. -Preparing to unpack .../45-libhtscodecs2_1.6.0-1+b1_armhf.deb ... +Preparing to unpack .../51-libhtscodecs2_1.6.0-1+b1_armhf.deb ... Unpacking libhtscodecs2:armhf (1.6.0-1+b1) ... Selecting previously unselected package libhts3:armhf. -Preparing to unpack .../46-libhts3_1.19+ds-1_armhf.deb ... +Preparing to unpack .../52-libhts3_1.19+ds-1_armhf.deb ... Unpacking libhts3:armhf (1.19+ds-1) ... Selecting previously unselected package liblzma-dev:armhf. -Preparing to unpack .../47-liblzma-dev_5.6.1+really5.4.5-1_armhf.deb ... +Preparing to unpack .../53-liblzma-dev_5.6.1+really5.4.5-1_armhf.deb ... Unpacking liblzma-dev:armhf (5.6.1+really5.4.5-1) ... Selecting previously unselected package zlib1g-dev:armhf. -Preparing to unpack .../48-zlib1g-dev_1%3a1.3.dfsg-3+b1_armhf.deb ... +Preparing to unpack .../54-zlib1g-dev_1%3a1.3.dfsg-3+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Selecting previously unselected package libhts-dev:armhf. -Preparing to unpack .../49-libhts-dev_1.19+ds-1_armhf.deb ... +Preparing to unpack .../55-libhts-dev_1.19+ds-1_armhf.deb ... Unpacking libhts-dev:armhf (1.19+ds-1) ... Selecting previously unselected package libio-pty-perl. -Preparing to unpack .../50-libio-pty-perl_1%3a1.20-1_armhf.deb ... +Preparing to unpack .../56-libio-pty-perl_1%3a1.20-1_armhf.deb ... Unpacking libio-pty-perl (1:1.20-1) ... Selecting previously unselected package libncurses6:armhf. -Preparing to unpack .../51-libncurses6_6.4+20240414-1_armhf.deb ... +Preparing to unpack .../57-libncurses6_6.4+20240414-1_armhf.deb ... Unpacking libncurses6:armhf (6.4+20240414-1) ... Selecting previously unselected package libncurses-dev:armhf. -Preparing to unpack .../52-libncurses-dev_6.4+20240414-1_armhf.deb ... +Preparing to unpack .../58-libncurses-dev_6.4+20240414-1_armhf.deb ... Unpacking libncurses-dev:armhf (6.4+20240414-1) ... Selecting previously unselected package libpkgconf3:armhf. -Preparing to unpack .../53-libpkgconf3_1.8.1-1+b2_armhf.deb ... +Preparing to unpack .../59-libpkgconf3_1.8.1-1+b2_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-1+b2) ... Selecting previously unselected package pkgconf-bin. -Preparing to unpack .../54-pkgconf-bin_1.8.1-1+b2_armhf.deb ... +Preparing to unpack .../60-pkgconf-bin_1.8.1-1+b2_armhf.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:armhf. -Preparing to unpack .../55-pkgconf_1.8.1-1+b2_armhf.deb ... +Preparing to unpack .../61-pkgconf_1.8.1-1+b2_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-1+b2) ... Selecting previously unselected package tabix. -Preparing to unpack .../56-tabix_1.19+ds-1_armhf.deb ... +Preparing to unpack .../62-tabix_1.19+ds-1_armhf.deb ... Unpacking tabix (1.19+ds-1) ... Setting up libhtscodecs2:armhf (1.6.0-1+b1) ... Setting up libpipeline1:armhf (1.5.7-2) ... +Setting up libkeyutils1:armhf (1.6.3-3) ... Setting up libpsl5:armhf (0.21.2-1+b1) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... @@ -378,7 +435,9 @@ Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up autoconf-archive (20220903-3) ... +Setting up libcom-err2:armhf (1.47.0-2+b1) ... Setting up file (1:5.45-2+b1) ... +Setting up libkrb5support0:armhf (1.20.1-5+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:armhf (1.8.1-1+b2) ... @@ -387,6 +446,7 @@ Setting up libncurses6:armhf (6.4+20240414-1) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... +Setting up libk5crypto3:armhf (1.20.1-5+b1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:armhf (5.6.1+really5.4.5-1) ... @@ -395,6 +455,7 @@ Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libssh2-1:armhf (1.11.0-4) ... +Setting up libkrb5-3:armhf (1.20.1-5+b1) ... Setting up libdeflate-dev:armhf (1.20-1) ... Setting up tabix (1.19+ds-1) ... Setting up libelf1:armhf (0.190-1+b1) ... @@ -410,6 +471,7 @@ Setting up pkgconf:armhf (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... +Setting up libgssapi-krb5-2:armhf (1.20.1-5+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... @@ -431,7 +493,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/samtools-1.19.2/ && 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_1.19.2-1_source.changes +I: user script /srv/workspace/pbuilder/13756/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/13756/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/samtools-1.19.2/ && 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_1.19.2-1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.19.2-1 dpkg-buildpackage: info: source distribution unstable @@ -446,7 +512,7 @@ rm -f config.mk touch config.mk dh_auto_clean -- - make -j3 distclean + make -j4 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.19.2' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai @@ -534,15 +600,15 @@ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" - make -j3 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" + make -j4 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.19.2' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 @@ -561,8 +627,8 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -573,17 +639,17 @@ echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h sed -i -e 's@/build/reproducible-path/samtools-1.19.2@«BUILDPATH»@g' version.h +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 @@ -596,9 +662,9 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c @@ -612,9 +678,9 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c @@ -622,8 +688,8 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -632,8 +698,8 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -670,8 +736,8 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -688,22 +754,22 @@ 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 reset.o cram_size.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_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/reproducible-path/samtools-1.19.2' make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' 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/reproducible-path/samtools-1.19.2' test/split/test_count_rg test/split/test_expand_format_string @@ -742,75 +808,75 @@ /build/reproducible-path/samtools-1.19.2/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok -/usr/bin/bgzip -c -b 65272 -s 5 /tmp/XT5zqzfyuV/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/OXDiIs1BGi/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/XT5zqzfyuV/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/OXDiIs1BGi/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/XT5zqzfyuV/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/OXDiIs1BGi/bgzip.dat.gz .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/OXDiIs1BGi/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/OXDiIs1BGi/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/OXDiIs1BGi/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/OXDiIs1BGi/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/OXDiIs1BGi/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/OXDiIs1BGi/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/OXDiIs1BGi/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/OXDiIs1BGi/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq 3:11-13 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/OXDiIs1BGi/fqidx.fq 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq.gz 3:11-13 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/OXDiIs1BGi/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq 2:998-1003 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/OXDiIs1BGi/fqidx.fq 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq.gz 2:998-1003 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/OXDiIs1BGi/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq 1:100-104 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/OXDiIs1BGi/fqidx.fq 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq.gz 1:100-104 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/OXDiIs1BGi/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq 1:99998-100007 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/OXDiIs1BGi/fqidx.fq 1:99998-100007 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq.gz 1:99998-100007 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/OXDiIs1BGi/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -820,7 +886,7 @@ .. ok test_dict: - /build/reproducible-path/samtools-1.19.2/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/XT5zqzfyuV/dict.fa.gz + /build/reproducible-path/samtools-1.19.2/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/OXDiIs1BGi/dict.fa.gz .. ok test_dict: @@ -836,11 +902,11 @@ .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view /tmp/XT5zqzfyuV/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.19.2/samtools view /tmp/OXDiIs1BGi/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view /tmp/XT5zqzfyuV/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.19.2/samtools view /tmp/OXDiIs1BGi/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -848,19 +914,19 @@ .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b.bam.bai ref2 + /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/OXDiIs1BGi/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/OXDiIs1BGi/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai /tmp/XT5zqzfyuV/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.19.2/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai /tmp/OXDiIs1BGi/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b_opt.bam.bai ref2 + /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/OXDiIs1BGi/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -876,23 +942,23 @@ .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam /tmp/XT5zqzfyuV/auto_indexed.csi && cat /tmp/XT5zqzfyuV/auto_indexed.csi + /build/reproducible-path/samtools-1.19.2/samtools index -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam /tmp/OXDiIs1BGi/auto_indexed.csi && cat /tmp/OXDiIs1BGi/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.cram /tmp/XT5zqzfyuV/auto_indexed.crai && cat /tmp/XT5zqzfyuV/auto_indexed.crai + /build/reproducible-path/samtools-1.19.2/samtools index /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.cram /tmp/OXDiIs1BGi/auto_indexed.crai && cat /tmp/OXDiIs1BGi/auto_indexed.crai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.sam /tmp/XT5zqzfyuV/auto_indexed.csi && cat /tmp/XT5zqzfyuV/auto_indexed.csi + /build/reproducible-path/samtools-1.19.2/samtools index -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.sam /tmp/OXDiIs1BGi/auto_indexed.csi && cat /tmp/OXDiIs1BGi/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/XT5zqzfyuV/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/OXDiIs1BGi/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/XT5zqzfyuV/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/OXDiIs1BGi/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -900,19 +966,19 @@ .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b.bam.bai ref2 + /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/OXDiIs1BGi/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/OXDiIs1BGi/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai /tmp/XT5zqzfyuV/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai /tmp/OXDiIs1BGi/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b_opt.bam.bai ref2 + /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/OXDiIs1BGi/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -928,39 +994,39 @@ .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam /tmp/XT5zqzfyuV/auto_indexed.csi && cat /tmp/XT5zqzfyuV/auto_indexed.csi + /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam /tmp/OXDiIs1BGi/auto_indexed.csi && cat /tmp/OXDiIs1BGi/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.cram /tmp/XT5zqzfyuV/auto_indexed.crai && cat /tmp/XT5zqzfyuV/auto_indexed.crai + /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.cram /tmp/OXDiIs1BGi/auto_indexed.crai && cat /tmp/OXDiIs1BGi/auto_indexed.crai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.sam /tmp/XT5zqzfyuV/auto_indexed.csi && cat /tmp/XT5zqzfyuV/auto_indexed.csi + /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.sam /tmp/OXDiIs1BGi/auto_indexed.csi && cat /tmp/OXDiIs1BGi/auto_indexed.csi .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/XT5zqzfyuV/mpileup.bam.list -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/OXDiIs1BGi/mpileup.bam.list -f /tmp/OXDiIs1BGi/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/XT5zqzfyuV/mpileup.cram.list -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/OXDiIs1BGi/mpileup.cram.list -f /tmp/OXDiIs1BGi/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/XT5zqzfyuV/mpileup.bam.urllist -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/OXDiIs1BGi/mpileup.bam.urllist -f /tmp/OXDiIs1BGi/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/XT5zqzfyuV/mpileup.cram.urllist -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/OXDiIs1BGi/mpileup.cram.urllist -f /tmp/OXDiIs1BGi/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:1050-1060 /tmp/XT5zqzfyuV/mpileup.1.bam | grep -v mpileup + /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/OXDiIs1BGi/mpileup.ref.fa.gz -r17:1050-1060 /tmp/OXDiIs1BGi/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:1050-1060 /tmp/XT5zqzfyuV/mpileup.1.cram | grep -v mpileup + /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/OXDiIs1BGi/mpileup.ref.fa.gz -r17:1050-1060 /tmp/OXDiIs1BGi/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: @@ -1248,53 +1314,53 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/XT5zqzfyuV/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/OXDiIs1BGi/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/XT5zqzfyuV/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/OXDiIs1BGi/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/XT5zqzfyuV/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/OXDiIs1BGi/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/XT5zqzfyuV/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/OXDiIs1BGi/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/XT5zqzfyuV/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/OXDiIs1BGi/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/XT5zqzfyuV/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/OXDiIs1BGi/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/OXDiIs1BGi/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/OXDiIs1BGi/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/OXDiIs1BGi/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/OXDiIs1BGi/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/OXDiIs1BGi/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/OXDiIs1BGi/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/OXDiIs1BGi/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/OXDiIs1BGi/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/OXDiIs1BGi/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/OXDiIs1BGi/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/OXDiIs1BGi/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/OXDiIs1BGi/view.001.fogn (CRAM input).. ok - 67: Filter -N /tmp/XT5zqzfyuV/view.001.forn (SAM input) .. ok + 67: Filter -N /tmp/OXDiIs1BGi/view.001.forn (SAM input) .. ok - 68: Count -N /tmp/XT5zqzfyuV/view.001.forn (SAM input) .. ok + 68: Count -N /tmp/OXDiIs1BGi/view.001.forn (SAM input) .. ok - 69: Filter -N /tmp/XT5zqzfyuV/view.001.forn (BAM input) .. ok + 69: Filter -N /tmp/OXDiIs1BGi/view.001.forn (BAM input) .. ok - 70: Count -N /tmp/XT5zqzfyuV/view.001.forn (BAM input) .. ok + 70: Count -N /tmp/OXDiIs1BGi/view.001.forn (BAM input) .. ok - 71: Filter -N /tmp/XT5zqzfyuV/view.001.forn (CRAM input) .. ok + 71: Filter -N /tmp/OXDiIs1BGi/view.001.forn (CRAM input) .. ok - 72: Count -N /tmp/XT5zqzfyuV/view.001.forn (CRAM input) .. ok + 72: Count -N /tmp/OXDiIs1BGi/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok @@ -1320,53 +1386,53 @@ 84: Count -d BC:TGCA (CRAM input) .. ok - 85: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc (SAM input) .. ok + 85: Filter -D BC:/tmp/OXDiIs1BGi/view.001.fobc (SAM input) .. ok - 86: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc (SAM input) .. ok + 86: Count -D BC:/tmp/OXDiIs1BGi/view.001.fobc (SAM input) .. ok - 87: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc (BAM input) .. ok + 87: Filter -D BC:/tmp/OXDiIs1BGi/view.001.fobc (BAM input) .. ok - 88: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc (BAM input) .. ok + 88: Count -D BC:/tmp/OXDiIs1BGi/view.001.fobc (BAM input) .. ok - 89: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input) .. ok + 89: Filter -D BC:/tmp/OXDiIs1BGi/view.001.fobc (CRAM input) .. ok - 90: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input) .. ok + 90: Count -D BC:/tmp/OXDiIs1BGi/view.001.fobc (CRAM input) .. ok - 91: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (SAM input).. ok + 91: Filter -D BC:/tmp/OXDiIs1BGi/view.001.fobc -d BC:TGCA (SAM input).. ok - 92: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (SAM input).. ok + 92: Count -D BC:/tmp/OXDiIs1BGi/view.001.fobc -d BC:TGCA (SAM input).. ok - 93: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (BAM input).. ok + 93: Filter -D BC:/tmp/OXDiIs1BGi/view.001.fobc -d BC:TGCA (BAM input).. ok - 94: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (BAM input).. ok + 94: Count -D BC:/tmp/OXDiIs1BGi/view.001.fobc -d BC:TGCA (BAM input).. ok - 95: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (CRAM input).. ok + 95: Filter -D BC:/tmp/OXDiIs1BGi/view.001.fobc -d BC:TGCA (CRAM input).. ok - 96: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (CRAM input).. ok + 96: Count -D BC:/tmp/OXDiIs1BGi/view.001.fobc -d BC:TGCA (CRAM input).. ok - 97: Filter -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (SAM input).. ok + 97: Filter -d BC:TGCA -D BC:/tmp/OXDiIs1BGi/view.001.fobc (SAM input).. ok - 98: Count -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (SAM input).. ok + 98: Count -d BC:TGCA -D BC:/tmp/OXDiIs1BGi/view.001.fobc (SAM input).. ok - 99: Filter -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (BAM input).. ok + 99: Filter -d BC:TGCA -D BC:/tmp/OXDiIs1BGi/view.001.fobc (BAM input).. ok - 100: Count -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (BAM input).. ok + 100: Count -d BC:TGCA -D BC:/tmp/OXDiIs1BGi/view.001.fobc (BAM input).. ok - 101: Filter -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input).. ok + 101: Filter -d BC:TGCA -D BC:/tmp/OXDiIs1BGi/view.001.fobc (CRAM input).. ok - 102: Count -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input).. ok + 102: Count -d BC:TGCA -D BC:/tmp/OXDiIs1BGi/view.001.fobc (CRAM input).. ok - 103: Filter -D RG:/tmp/XT5zqzfyuV/view.001.fogn (SAM input) .. ok + 103: Filter -D RG:/tmp/OXDiIs1BGi/view.001.fogn (SAM input) .. ok - 104: Count -D RG:/tmp/XT5zqzfyuV/view.001.fogn (SAM input) .. ok + 104: Count -D RG:/tmp/OXDiIs1BGi/view.001.fogn (SAM input) .. ok - 105: Filter -D RG:/tmp/XT5zqzfyuV/view.001.fogn (BAM input) .. ok + 105: Filter -D RG:/tmp/OXDiIs1BGi/view.001.fogn (BAM input) .. ok - 106: Count -D RG:/tmp/XT5zqzfyuV/view.001.fogn (BAM input) .. ok + 106: Count -D RG:/tmp/OXDiIs1BGi/view.001.fogn (BAM input) .. ok - 107: Filter -D RG:/tmp/XT5zqzfyuV/view.001.fogn (CRAM input).. ok + 107: Filter -D RG:/tmp/OXDiIs1BGi/view.001.fogn (CRAM input).. ok - 108: Count -D RG:/tmp/XT5zqzfyuV/view.001.fogn (CRAM input) .. ok + 108: Count -D RG:/tmp/OXDiIs1BGi/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok @@ -1382,126 +1448,126 @@ 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test115.sam -h -d TGCA /tmp/XT5zqzfyuV/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/OXDiIs1BGi/view.test115.sam -h -d TGCA /tmp/OXDiIs1BGi/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/XT5zqzfyuV/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/OXDiIs1BGi/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test117.sam -h -d TGCA /tmp/XT5zqzfyuV/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/OXDiIs1BGi/view.test117.sam -h -d TGCA /tmp/OXDiIs1BGi/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/XT5zqzfyuV/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/OXDiIs1BGi/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test119.sam -h -d TGCA /tmp/XT5zqzfyuV/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/OXDiIs1BGi/view.test119.sam -h -d TGCA /tmp/OXDiIs1BGi/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/XT5zqzfyuV/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/OXDiIs1BGi/view.test006.cram --no-PG .. expected failure - 121: Filter -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" + 121: Filter -D BClong:/tmp/OXDiIs1BGi/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OXDiIs1BGi/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test121.sam -h -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/OXDiIs1BGi/view.test121.sam -h -D BClong:/tmp/OXDiIs1BGi/view.001.fobc /tmp/OXDiIs1BGi/view.001.sam --no-PG .. expected failure - 122: Count -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" + 122: Count -D BClong:/tmp/OXDiIs1BGi/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OXDiIs1BGi/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/OXDiIs1BGi/view.001.fobc /tmp/OXDiIs1BGi/view.001.sam --no-PG .. expected failure - 123: Filter -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" + 123: Filter -D BClong:/tmp/OXDiIs1BGi/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OXDiIs1BGi/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test123.sam -h -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/OXDiIs1BGi/view.test123.sam -h -D BClong:/tmp/OXDiIs1BGi/view.001.fobc /tmp/OXDiIs1BGi/view.test001.bam --no-PG .. expected failure - 124: Count -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" + 124: Count -D BClong:/tmp/OXDiIs1BGi/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OXDiIs1BGi/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/OXDiIs1BGi/view.001.fobc /tmp/OXDiIs1BGi/view.test001.bam --no-PG .. expected failure - 125: Filter -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" + 125: Filter -D BClong:/tmp/OXDiIs1BGi/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OXDiIs1BGi/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test125.sam -h -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/OXDiIs1BGi/view.test125.sam -h -D BClong:/tmp/OXDiIs1BGi/view.001.fobc /tmp/OXDiIs1BGi/view.test006.cram --no-PG .. expected failure - 126: Count -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" + 126: Count -D BClong:/tmp/OXDiIs1BGi/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OXDiIs1BGi/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/OXDiIs1BGi/view.001.fobc /tmp/OXDiIs1BGi/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/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/OXDiIs1BGi/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/OXDiIs1BGi/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/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/OXDiIs1BGi/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/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/OXDiIs1BGi/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/OXDiIs1BGi/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/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/OXDiIs1BGi/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/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/OXDiIs1BGi/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/OXDiIs1BGi/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/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/OXDiIs1BGi/view.test006.cram --no-PG .. expected failure @@ -2383,7 +2449,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.19.2/samtools fastq -N -s /tmp/XT5zqzfyuV/bam2fq.discard.s.fq -0 /tmp/XT5zqzfyuV/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam + /build/reproducible-path/samtools-1.19.2/samtools fastq -N -s /tmp/OXDiIs1BGi/bam2fq.discard.s.fq -0 /tmp/OXDiIs1BGi/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2512,7 +2578,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -s /tmp/XT5zqzfyuV/bam2fq.discard.s.fq -0 /tmp/XT5zqzfyuV/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam + /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -s /tmp/OXDiIs1BGi/bam2fq.discard.s.fq -0 /tmp/OXDiIs1BGi/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2717,7 +2783,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -O sam -b /tmp/EscCUgVokG - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -O sam -b /tmp/8R8BtbEtwb - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2741,11 +2807,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/XT5zqzfyuV/merge.tag.1.bam /tmp/XT5zqzfyuV/merge.tag.2.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/OXDiIs1BGi/merge.tag.1.bam /tmp/OXDiIs1BGi/merge.tag.2.bam .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/XT5zqzfyuV/merge.tag.3.bam /tmp/XT5zqzfyuV/merge.tag.4.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/OXDiIs1BGi/merge.tag.3.bam /tmp/OXDiIs1BGi/merge.tag.4.bam .. ok test_merge: @@ -2753,7 +2819,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.19.2/test/merge/merge.bed - /tmp/XT5zqzfyuV/merge.bed.1.bam /tmp/XT5zqzfyuV/merge.bed.2.bam + /build/reproducible-path/samtools-1.19.2/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.19.2/test/merge/merge.bed - /tmp/OXDiIs1BGi/merge.bed.1.bam /tmp/OXDiIs1BGi/merge.bed.2.bam .. ok test_merge: @@ -2769,7 +2835,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -O sam -b /tmp/g6yeMwTvYd - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -O sam -b /tmp/JKtLl54mb6 - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2793,11 +2859,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/XT5zqzfyuV/merge.tag.1.bam /tmp/XT5zqzfyuV/merge.tag.2.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/OXDiIs1BGi/merge.tag.1.bam /tmp/OXDiIs1BGi/merge.tag.2.bam .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/XT5zqzfyuV/merge.tag.3.bam /tmp/XT5zqzfyuV/merge.tag.4.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/OXDiIs1BGi/merge.tag.3.bam /tmp/OXDiIs1BGi/merge.tag.4.bam .. ok test_merge: @@ -2805,7 +2871,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.19.2/test/merge/merge.bed - /tmp/XT5zqzfyuV/merge.bed.1.bam /tmp/XT5zqzfyuV/merge.bed.2.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.19.2/test/merge/merge.bed - /tmp/OXDiIs1BGi/merge.bed.1.bam /tmp/OXDiIs1BGi/merge.bed.2.bam .. ok test_merge: @@ -2813,15 +2879,15 @@ .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sortout + /build/reproducible-path/samtools-1.19.2/samtools sort /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/OXDiIs1BGi/sortout .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort -f /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sortout.bam + /build/reproducible-path/samtools-1.19.2/samtools sort -f /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/OXDiIs1BGi/sortout.bam .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort -o /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sorttmp + /build/reproducible-path/samtools-1.19.2/samtools sort -o /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/OXDiIs1BGi/sorttmp .. ok test_sort: @@ -2869,15 +2935,15 @@ .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sortout + /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/OXDiIs1BGi/sortout .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sortout.bam + /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/OXDiIs1BGi/sortout.bam .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sorttmp + /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/OXDiIs1BGi/sorttmp .. ok test_sort: @@ -3449,15 +3515,15 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/XT5zqzfyuV/longref.sam.gz + /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/OXDiIs1BGi/longref.sam.gz .. ok test_large_positions: - /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/XT5zqzfyuV/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 + /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/OXDiIs1BGi/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: - /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.19.2/test/large_pos/test.bed /tmp/XT5zqzfyuV/longref.sam.gz + /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.19.2/test/large_pos/test.bed /tmp/OXDiIs1BGi/longref.sam.gz .. ok test_large_positions: @@ -3477,7 +3543,7 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.19.2/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/XT5zqzfyuV/longref.sam.gz + /build/reproducible-path/samtools-1.19.2/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/OXDiIs1BGi/longref.sam.gz .. ok test_large_positions: @@ -3696,7 +3762,7 @@ Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/reproducible-path/samtools-1.19.2' - rm -fr -- /tmp/dh-xdg-rundir-twqXnAxc + rm -fr -- /tmp/dh-xdg-rundir-1RFYJ9Ff make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' create-stamp debian/debhelper-build-stamp dh_prep @@ -3708,7 +3774,7 @@ dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.19.2/debian/tmp - make -j3 install DESTDIR=/build/reproducible-path/samtools-1.19.2/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr + make -j4 install DESTDIR=/build/reproducible-path/samtools-1.19.2/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.19.2' mkdir -p -m 755 /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin @@ -3766,12 +3832,12 @@ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' dh_installchangelogs NEWS.md - 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 NEWS.md 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 NEWS.md 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 NEWS.md debian/samtools-test/usr/share/doc/samtools-test/changelog make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' dh_installexamples install -m0755 -d debian/samtools/usr/share/doc/samtools/examples @@ -3793,12 +3859,34 @@ dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 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-cram-size.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-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 debian/samtools/usr/share/man/man1/samtools-reference.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.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-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 - mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 - mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.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-cram-size.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-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 + man-recode --to-code UTF-8 --suffix .dh-new 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 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-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.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 + mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 + mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 + mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 + mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 + mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 + mv debian/samtools/usr/share/man/man1/samtools-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-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.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-cram-size.1 + mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 + mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 + mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 + mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 + mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 + mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 + mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 + mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 + mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 + 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 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.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 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 @@ -3809,14 +3897,7 @@ 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-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.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-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 - mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 - mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 - mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 - mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 - 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 + chmod 0644 -- 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-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 @@ -3825,23 +3906,10 @@ 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 - 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 debian/samtools/usr/share/man/man1/samtools-reference.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 - mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 - mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 - mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 - mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 - mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 - mv debian/samtools/usr/share/man/man1/samtools-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-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 - mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 - mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 - mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 - mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 - 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-cram-size.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-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 + mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 + mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-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 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-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.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 @@ -3857,12 +3925,12 @@ Using 1708190561 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-test/changelog usr/share/doc/samtools-test/changelog.Debian + cd debian/samtools chmod a-x 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-cram-size.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-reset.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-test/changelog usr/share/doc/samtools-test/changelog.Debian gzip -9nf 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-cram-size.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-reset.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 + chmod a-x usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian + gzip -9nf usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian cd '/build/reproducible-path/samtools-1.19.2' cd '/build/reproducible-path/samtools-1.19.2' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz @@ -3873,10 +3941,10 @@ find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a @@ -3886,11 +3954,16 @@ 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/27 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/c17f69af515d044389d55224240178adca8372.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/c17f69af515d044389d55224240178adca8372.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/27/c17f69af515d044389d55224240178adca8372.debug debian/samtools/usr/bin/ace2sam + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/050730da5a56161fc0875af0a7ee36066276a2.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/050730da5a56161fc0875af0a7ee36066276a2.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/7e/050730da5a56161fc0875af0a7ee36066276a2.debug debian/samtools/usr/bin/maq2sam-long + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f5 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f5/f0232c54a3841e3f0d4a336ab6487e7e7d8db1.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f5/f0232c54a3841e3f0d4a336ab6487e7e7d8db1.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/f5/f0232c54a3841e3f0d4a336ab6487e7e7d8db1.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a5 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a5/da0f40f9ca98123002e817b9fb23512c465f63.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a5/da0f40f9ca98123002e817b9fb23512c465f63.debug @@ -3901,11 +3974,6 @@ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2e/dc4bebc01192dacffb25dcd542d6d58b990321.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/2e/dc4bebc01192dacffb25dcd542d6d58b990321.debug debian/samtools/usr/bin/md5sum-lite - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f5 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f5/f0232c54a3841e3f0d4a336ab6487e7e7d8db1.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f5/f0232c54a3841e3f0d4a336ab6487e7e7d8db1.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/f5/f0232c54a3841e3f0d4a336ab6487e7e7d8db1.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d9 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d9/7959d416b8184687911ecc73aab26c0f5bc693.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d9/7959d416b8184687911ecc73aab26c0f5bc693.debug @@ -3916,11 +3984,11 @@ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7b/736da9116a0005ad855ada6fc58cd2cd3fb0e7.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/7b/736da9116a0005ad855ada6fc58cd2cd3fb0e7.debug debian/samtools/usr/bin/wgsim - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/050730da5a56161fc0875af0a7ee36066276a2.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/050730da5a56161fc0875af0a7ee36066276a2.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/7e/050730da5a56161fc0875af0a7ee36066276a2.debug debian/samtools/usr/bin/maq2sam-long + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/c17f69af515d044389d55224240178adca8372.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/c17f69af515d044389d55224240178adca8372.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/27/c17f69af515d044389d55224240178adca8372.debug debian/samtools/usr/bin/ace2sam 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 @@ -3932,7 +4000,7 @@ rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN - dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long + dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam dh_installdeb install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN @@ -3964,12 +4032,12 @@ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb + dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/samtools-test .. - dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. -dpkg-deb: building package 'samtools' in '../samtools_1.19.2-1_armhf.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.19.2-1_armhf.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.19.2-1_all.deb'. +dpkg-deb: building package 'samtools' in '../samtools_1.19.2-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.19.2-1_armhf.buildinfo dpkg-genchanges --build=binary -O../samtools_1.19.2-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3978,12 +4046,14 @@ 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/13756/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13756/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/32695 and its subdirectories -I: Current time: Thu Apr 25 02:13:28 -12 2024 -I: pbuilder-time-stamp: 1714054408 +I: removing directory /srv/workspace/pbuilder/13756 and its subdirectories +I: Current time: Fri Apr 26 04:25:12 +14 2024 +I: pbuilder-time-stamp: 1714055112