I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 1 08:51:27 +14 2025 I: pbuilder-time-stamp: 1748717487 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 [srst2_0.2.0-11.dsc] I: copying [./srst2_0.2.0.orig.tar.gz] I: copying [./srst2_0.2.0-11.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 18 20:18:47 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./srst2_0.2.0-11.dsc: no acceptable signature found dpkg-source: info: extracting srst2 in srst2-0.2.0 dpkg-source: info: unpacking srst2_0.2.0.orig.tar.gz dpkg-source: info: unpacking srst2_0.2.0-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying check_command_line_arguments.patch dpkg-source: info: applying add_usr_bin_python_to_scripts.patch dpkg-source: info: applying fix_test.patch dpkg-source: info: applying fix_grep_call.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying biopython-1.78.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1990592/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 31 18:51 /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/1990592/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1990592/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]="aarch64-unknown-linux-gnu") 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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=53450a615ccc4cbfb2bf3bf47c7359fc LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1990592 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.EqPI4MnK/pbuilderrc_b5Ej --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.EqPI4MnK/b2 --logfile b2/build.log srst2_0.2.0-11.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 26 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1990592/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: arm64 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), dh-sequence-python3, python3, python3-setuptools, markdown, dos2unix, python3-scipy, bowtie2, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19940 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on markdown; however: Package markdown is not installed. pbuilder-satisfydepends-dummy depends on dos2unix; however: Package dos2unix is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} bowtie2{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dos2unix{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack3{a} liblbfgsb0{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} markdown{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-decorator{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-scipy{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-pil wget 0 packages upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 56.4 MB of archives. After unpacking 274 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: samtools but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libssl3 [3.1.5-1 (now)] Install the following packages: 2) libbrotli1 [1.1.0-2+b3 (testing)] 3) libcurl3t64-gnutls [8.7.1-3 (testing)] 4) libdeflate0 [1.20-1 (testing)] 5) libhts3 [1.19+ds-1 (testing)] 6) libhtscodecs2 [1.6.0-1+b1 (testing)] 7) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 8) libncurses6 [6.4+20240414-1 (testing)] 9) libnghttp2-14 [1.59.0-1 (testing)] 10) libpsl5t64 [0.21.2-1.1 (testing)] 11) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 12) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 13) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 14) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 15) libssl3t64 [3.2.1-3 (testing)] 16) samtools [1.19.2-1 (testing)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bowtie2{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dos2unix{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhts3{a} libhtscodecs2{a} libicu72{a} liblapack3{a} liblbfgsb0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libssl3t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} markdown{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-decorator{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-scipy{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages will be REMOVED: libssl3{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-pil wget 0 packages upgraded, 77 newly installed, 1 to remove and 0 not upgraded. Need to get 61.5 MB of archives. After unpacking 282 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libssl3t64 arm64 3.2.1-3 [2537 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.8-1 [811 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.8-1 [1848 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.6-1 [26.2 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1781 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.8-1 [597 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.6-1 [9224 B] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.6-1 [26.2 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.2-1 [800 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.2-1 [1983 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 bowtie2 arm64 2.5.3-1 [1339 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 40 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240422 [107 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 dos2unix arm64 7.5.1-1 [509 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4+b1 [20.2 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4+b1 [55.5 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5+b3 [172 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.59.0-1 [70.2 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libhts3 arm64 1.19+ds-1 [412 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.4+20240414-1 [95.6 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.2-1 [1872 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 markdown all 1.0.1-12 [17.7 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.2-1 [653 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.24.2-2 [4122 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.11.4-6 [17.5 MB] Get: 77 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.19.2-1 [617 kB] Fetched 61.5 MB in 1s (71.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19940 files and directories currently installed.) Removing libssl3:arm64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:arm64. (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 ... 19927 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_arm64.deb ... Unpacking libssl3t64:arm64 (3.2.1-3) ... Setting up libssl3t64:arm64 (3.2.1-3) ... Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19942 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_arm64.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... Setting up libexpat1:arm64 (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 ... 20258 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_arm64.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_arm64.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (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 ... 21252 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.6-1_arm64.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../01-libpython3.12-minimal_3.12.2-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../02-python3.12-minimal_3.12.2-1_arm64.deb ... Unpacking python3.12-minimal (3.12.2-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../05-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-3+b1_arm64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../11-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-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 .../17-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package bowtie2. Preparing to unpack .../18-bowtie2_2.5.3-1_arm64.deb ... Unpacking bowtie2 (2.5.3-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../19-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../20-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../21-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../22-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 .../23-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 .../24-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../25-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../26-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../28-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../29-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../32-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../33-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../34-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../35-python3-lib2to3_3.12.3-1_all.deb ... Unpacking python3-lib2to3 (3.12.3-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../36-python3-distutils_3.12.3-1_all.deb ... Unpacking python3-distutils (3.12.3-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../37-python3-setuptools_68.1.2-2_all.deb ... Unpacking python3-setuptools (68.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../38-dh-python_6.20240422_all.deb ... Unpacking dh-python (6.20240422) ... Selecting previously unselected package dos2unix. Preparing to unpack .../39-dos2unix_7.5.1-1_arm64.deb ... Unpacking dos2unix (7.5.1-1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../40-libblas3_3.12.0-3_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../41-libbrotli1_1.1.0-2+b3_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../42-libsasl2-modules-db_2.1.28+dfsg1-4+b1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../43-libsasl2-2_2.1.28+dfsg1-4+b1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../44-libldap-2.5-0_2.5.13+dfsg-5+b3_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5+b3) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../45-libnghttp2-14_1.59.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.59.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../46-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../47-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../48-libssh2-1t64_1.11.0-4.1+b2_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../49-libcurl3t64-gnutls_8.7.1-3_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.7.1-3) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../50-libdeflate0_1.20-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.20-1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../51-libgfortran5_14-20240330-1_arm64.deb ... Unpacking libgfortran5:arm64 (14-20240330-1) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../52-libhtscodecs2_1.6.0-1+b1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.0-1+b1) ... Selecting previously unselected package libhts3:arm64. Preparing to unpack .../53-libhts3_1.19+ds-1_arm64.deb ... Unpacking libhts3:arm64 (1.19+ds-1) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../54-liblapack3_3.12.0-3_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-3) ... Selecting previously unselected package liblbfgsb0:arm64. Preparing to unpack .../55-liblbfgsb0_3.0+dfsg.4-1+b1_arm64.deb ... Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../56-libncurses6_6.4+20240414-1_arm64.deb ... Unpacking libncurses6:arm64 (6.4+20240414-1) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../57-libpython3.12-stdlib_3.12.2-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.2-1) ... Selecting previously unselected package markdown. Preparing to unpack .../58-markdown_1.0.1-12_all.deb ... Unpacking markdown (1.0.1-12) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../59-python3-decorator_5.1.1-5_all.deb ... Unpacking python3-decorator (5.1.1-5) ... Selecting previously unselected package python3.12. Preparing to unpack .../60-python3.12_3.12.2-1_arm64.deb ... Unpacking python3.12 (3.12.2-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../61-python3-numpy_1%3a1.24.2-2_arm64.deb ... Unpacking python3-numpy (1:1.24.2-2) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../62-python3-scipy_1.11.4-6_arm64.deb ... Unpacking python3-scipy (1.11.4-6) ... Selecting previously unselected package samtools. Preparing to unpack .../63-samtools_1.19.2-1_arm64.deb ... Unpacking samtools (1.19.2-1) ... Setting up libhtscodecs2:arm64 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libpython3.12-minimal:arm64 (3.12.2-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.59.0-1) ... Setting up libmagic1:arm64 (1:5.45-2+b1) ... Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sat May 31 18:52:21 UTC 2025. Universal Time is now: Sat May 31 18:52:21 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:arm64 (6.4+20240414-1) ... Setting up autopoint (0.21-14) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-4+b1) ... Setting up libgfortran5:arm64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up dos2unix (7.5.1-1) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up markdown (1.0.1-12) ... 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 python3.12-minimal (3.12.2-1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ... Setting up libpython3.12-stdlib:arm64 (3.12.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... Setting up python3.12 (3.12.2-1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-3) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:arm64 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up libhts3:arm64 (1.19+ds-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up samtools (1.19.2-1) ... Setting up bowtie2 (2.5.3-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-setuptools (68.1.2-2) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up dh-python (6.20240422) ... Setting up python3-scipy (1.11.4-6) ... 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/1990592/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1990592/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/srst2-0.2.0/ && 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 > ../srst2_0.2.0-11_source.changes dpkg-buildpackage: info: source package srst2 dpkg-buildpackage: info: source version 0.2.0-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.11 setup.py clean 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.11 setup.py config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build markdown README.md > README.html markdown database_clustering/README.md > database_clustering_README.html make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' cd tests && python3 test_slurm_srst2.py && python3 test_srst2.py ........... ---------------------------------------------------------------------- Ran 11 tests in 0.059s OK ................. ---------------------------------------------------------------------- Ran 17 tests in 0.057s OK make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/srst2/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/srst2-0.2.0/debian/srst2 /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_install mv debian/srst2/usr/lib/*/dist-packages/srst2/* debian/srst2/usr/share/srst2 rm -rf debian/*/usr/bin/*.py debian/srst2/usr/lib/*/dist-packages/ # fix line endings to make sure Python3 interpreter will be found find debian/*/usr/share -name "VFDB*" -exec dos2unix \{\} \; dos2unix: converting file debian/srst2/usr/share/srst2/database_clustering/VFDBgenus.py to Unix format... dos2unix: converting file debian/srst2/usr/share/srst2/database_clustering/VFDB_cdhit_to_csv.py to Unix format... sed -i '1s:^#!/usr/local.*python[.0-9]*$:#!/usr/bin/python3:' debian/srst2/usr/share/srst2/qsub_srst2.py find debian -name __pycache__ -type d | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_installdocs sed -i "s?sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__).*scripts.*?sys.path.append(os.path.abspath('/usr/share/srst2'))?" debian/srst2/usr/share/doc/srst2/tests/*.py make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_fixperms chmod +x debian/srst2/usr/share/srst2/database_clustering/get_genus_vfdb.sh chmod +x debian/srst2/usr/share/srst2/database_clustering/get_all_vfdb.sh chmod -x debian/srst2/usr/share/srst2/database_clustering/align_plot_tree_min3.py for py in `find debian -name "*.py"` ; do \ if head -n 1 $py | grep -q '^#! */usr/bin/.*python' ; then chmod +x $py ; fi ; \ done make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'srst2' in '../srst2_0.2.0-11_arm64.deb'. dpkg-genbuildinfo --build=binary -O../srst2_0.2.0-11_arm64.buildinfo dpkg-genchanges --build=binary -O../srst2_0.2.0-11_arm64.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/1990592/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1990592/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/1990592 and its subdirectories I: Current time: Sun Jun 1 08:53:33 +14 2025 I: pbuilder-time-stamp: 1748717614