I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 27 14:26:41 +14 2024 I: pbuilder-time-stamp: 1714177601 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [seqprep_1.3.2-9.dsc] I: copying [./seqprep_1.3.2.orig.tar.gz] I: copying [./seqprep_1.3.2-9.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Mar 14 19:39:56 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./seqprep_1.3.2-9.dsc: no acceptable signature found dpkg-source: info: extracting seqprep in seqprep-1.3.2 dpkg-source: info: unpacking seqprep_1.3.2.orig.tar.gz dpkg-source: info: unpacking seqprep_1.3.2-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_unused_variable_errors.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying replace-float-with-double.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying fix-declarations.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/18744/tmp/hooks/D01_modify_environment starting debug: Running on virt64c. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 27 00:27 /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/18744/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/18744/tmp/hooks/D02_print_environment starting I: set 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=35b5e71f80b34a6aad676e3d613de636 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=18744 PS4='+ ' 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.neUB6M6k/pbuilderrc_iL2w --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.neUB6M6k/b2 --logfile b2/build.log seqprep_1.3.2-9.dsc' SUDO_GID=113 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 25 11:27 /bin -> usr/bin I: user script /srv/workspace/pbuilder/18744/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), python3, zlib1g-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 ... 19467 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: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... 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} automake{a} autopoint{a} autotools-dev{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} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1{a} libnsl2{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtirpc-common{a} libtirpc3{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 25.4 MB of archives. After unpacking 92.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.8-1 [802 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.8-1 [1707 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.6-1 [26.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.20.1-5+b1 [30.4 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.0-2.4 [19.5 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.20.1-5+b1 [75.4 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 12 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.20.1-5+b1 [289 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.20.1-5+b1 [112 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libtirpc3 armhf 1.3.4+ds-1 [70.0 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libnsl2 armhf 1.3.0-3 [33.7 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-4 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libreadline8 armhf 8.2-3+b1 [144 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.8-1 [1709 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.8-1 [597 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.6-1 [9224 B] Get: 22 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.6-1 [26.2 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 45 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3.1 [904 kB] Fetched 25.4 MB in 1s (37.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19467 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.8-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_armhf.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:armhf (3.11.8-1) ... Setting up libexpat1:armhf (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-1) ... Selecting previously unselected package python3-minimal. (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 ... 19783 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.11.6-1_armhf.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../04-libkrb5support0_1.20.1-5+b1_armhf.deb ... Unpacking libkrb5support0:armhf (1.20.1-5+b1) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../05-libcom-err2_1.47.0-2.4_armhf.deb ... Unpacking libcom-err2:armhf (1.47.0-2.4) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../06-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 .../07-libkeyutils1_1.6.3-3_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-3) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../08-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 .../09-libgssapi-krb5-2_1.20.1-5+b1_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.20.1-5+b1) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3:armhf. Preparing to unpack .../11-libtirpc3_1.3.4+ds-1_armhf.deb ... Unpacking libtirpc3:armhf (1.3.4+ds-1) ... Selecting previously unselected package libnsl2:armhf. Preparing to unpack .../12-libnsl2_1.3.0-3_armhf.deb ... Unpacking libnsl2:armhf (1.3.0-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../14-libreadline8_8.2-3+b1_armhf.deb ... Unpacking libreadline8:armhf (8.2-3+b1) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../15-libpython3.11-stdlib_3.11.8-1_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../16-python3.11_3.11.8-1_armhf.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../17-libpython3-stdlib_3.11.6-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... Selecting previously unselected package python3. (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 ... 20836 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.6-1_armhf.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../03-libmagic1_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../09-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 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Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:armhf (1.47.0-2.4) ... Setting up file (1:5.45-2+b1) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up libkrb5support0:armhf (1.20.1-5+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Apr 27 00:27:49 UTC 2024. Universal Time is now: Sat Apr 27 00:27:49 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up libk5crypto3:armhf (1.20.1-5+b1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:armhf (1.20.1-5+b1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libreadline8:armhf (8.2-3+b1) ... 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 groff-base (1.23.0-3) ... Setting up libtirpc3:armhf (1.3.4+ds-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:armhf (1.3.0-3) ... Setting up libpython3.11-stdlib:armhf (3.11.8-1) ... Setting up debhelper (13.15.3) ... Setting up libpython3-stdlib:armhf (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up python3 (3.11.6-1) ... Processing triggers for libc-bin (2.37-18) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/18744/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/18744/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/seqprep-1.3.2/ && 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 > ../seqprep_1.3.2-9_source.changes dpkg-buildpackage: info: source package seqprep dpkg-buildpackage: info: source version 1.3.2-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/build/reproducible-path/seqprep-1.3.2' rm -f SeqPrep.o utils.o stdaln.o SeqPrep make[1]: Leaving directory '/build/reproducible-path/seqprep-1.3.2' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/seqprep-1.3.2' dh_clean rm -f seqprep rm -f README.html make[1]: Leaving directory '/build/reproducible-path/seqprep-1.3.2' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/seqprep-1.3.2' dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/seqprep-1.3.2' cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/seqprep-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu90 -c -Wall -O0 -g -std=c99 SeqPrep.c -o SeqPrep.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/seqprep-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu90 -c -Wall -O0 -g -std=c99 utils.c -o utils.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/seqprep-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu90 -c -Wall -O0 -g -std=c99 stdaln.c -o stdaln.o cc SeqPrep.o utils.o stdaln.o -Wl,-z,relro -Wl,-z,now -lz -lm -o SeqPrep make[2]: Leaving directory '/build/reproducible-path/seqprep-1.3.2' cp SeqPrep seqprep mv /build/reproducible-path/seqprep-1.3.2/debian/README.html /build/reproducible-path/seqprep-1.3.2 make[1]: Leaving directory '/build/reproducible-path/seqprep-1.3.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/seqprep-1.3.2' # This checks that the tests run and produce byte-identical results. cd Test && mkdir -p out info && \ bash -xc 'gzcat(){ zcat "$@" ; } ; . RUNTEST.sh' + . RUNTEST.sh ++ ../SeqPrep -6 -f ./data/multiplex_bad_contam_1.fq.gz -r ./data/multiplex_bad_contam_2.fq.gz -A GATCGGAAGAGCACACGTCT -B AGATCGGAAGAGCGTCGT -1 ./out/pe_bad_contam_merged_1.fastq.gz -2 ./out/pe_bad_contam_merged_2.fastq.gz -s ./out/pe_bad_contam_merged_s.fastq.gz -E ./info/alignments_merged.txt.gz fastq record not beginning with @ fastq record not beginning with @ Pairs Processed: 0 Pairs Merged: 14314 Pairs With Adapters: 4091 Pairs Discarded: 2228 CPU Time Used (Minutes): 0.539640 ++ ../SeqPrep -6 -f ./data/multiplex_bad_contam_1.fq.gz -r ./data/multiplex_bad_contam_2.fq.gz -A GATCGGAAGAGCACACGTCT -B AGATCGGAAGAGCGTCGT -1 ./out/pe_bad_contam_trimmed_1.fastq.gz -2 ./out/pe_bad_contam_trimmed_2.fastq.gz -E ./info/alignments_trimmed.txt.gz fastq record not beginning with @ fastq record not beginning with @ Pairs Processed: 0 Pairs Merged: 0 Pairs With Adapters: 4091 Pairs Discarded: 2228 CPU Time Used (Minutes): 0.515292 ++ prog=gzcat ++ python3 seqlens.py ++ gzcat ./out/pe_bad_contam_trimmed_1.fastq.gz ++ zcat ./out/pe_bad_contam_trimmed_1.fastq.gz ++ python3 seqlens.py ++ gzcat ./out/pe_bad_contam_trimmed_2.fastq.gz ++ zcat ./out/pe_bad_contam_trimmed_2.fastq.gz ++ python3 seqlens.py ++ gzcat ./out/pe_bad_contam_merged_1.fastq.gz ++ zcat ./out/pe_bad_contam_merged_1.fastq.gz ++ python3 seqlens.py ++ gzcat ./out/pe_bad_contam_merged_2.fastq.gz ++ zcat ./out/pe_bad_contam_merged_2.fastq.gz ++ python3 seqlens.py ++ gzcat ./out/pe_bad_contam_merged_s.fastq.gz ++ zcat ./out/pe_bad_contam_merged_s.fastq.gz [ `cat Test/info/pe_*.txt | md5sum | cut -b -10` = 8bc8e0787e ] # remove output dirs right after testing to make sure the files # will not be included in the data package rm -rf Test/info Test/out make[1]: Leaving directory '/build/reproducible-path/seqprep-1.3.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j4 install DESTDIR=/build/reproducible-path/seqprep-1.3.2/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/seqprep-1.3.2' cp SeqPrep /build/reproducible-path/seqprep-1.3.2/debian/.debhelper/generated/_source/home/bin make[1]: Leaving directory '/build/reproducible-path/seqprep-1.3.2' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/seqprep-1.3.2' dh_install sed -i 's#../SeqPrep#/usr/bin/seqprep#' /build/reproducible-path/seqprep-1.3.2/debian/seqprep-data/usr/share/doc/seqprep/examples/RUNTEST.sh make[1]: Leaving directory '/build/reproducible-path/seqprep-1.3.2' dh_install -Nseqprep-data dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'seqprep' in '../seqprep_1.3.2-9_armhf.deb'. dpkg-deb: building package 'seqprep-dbgsym' in '../seqprep-dbgsym_1.3.2-9_armhf.deb'. dpkg-deb: building package 'seqprep-data' in '../seqprep-data_1.3.2-9_all.deb'. dpkg-genbuildinfo --build=binary -O../seqprep_1.3.2-9_armhf.buildinfo dpkg-genchanges --build=binary -O../seqprep_1.3.2-9_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/18744/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/18744/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/18744 and its subdirectories I: Current time: Sat Apr 27 14:30:20 +14 2024 I: pbuilder-time-stamp: 1714177820