I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 8 13:57:02 +14 2025 I: pbuilder-time-stamp: 1749340622 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 [kallisto_0.48.0+dfsg-4.dsc] I: copying [./kallisto_0.48.0+dfsg.orig.tar.xz] I: copying [./kallisto_0.48.0+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Apr 12 06:31:55 2023 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 ./kallisto_0.48.0+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting kallisto in kallisto-0.48.0+dfsg dpkg-source: info: unpacking kallisto_0.48.0+dfsg.orig.tar.xz dpkg-source: info: unpacking kallisto_0.48.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_htslib.patch dpkg-source: info: applying spelling dpkg-source: info: applying htslib1.3 dpkg-source: info: applying gcc11.patch dpkg-source: info: applying disable-failing-bustools-test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4041099/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 Jun 7 23:57 /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/4041099/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4041099/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=951d53014b7d4c7592defd15a5080c8b 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=4041099 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.bnw0FpdR/pbuilderrc_zrny --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.bnw0FpdR/b2 --logfile b2/build.log kallisto_0.48.0+dfsg-4.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 Jun 7 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4041099/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), catch2, cmake, libhdf5-dev, libhts-dev, snakemake dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19735 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 catch2; however: Package catch2 is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on snakemake; however: Package snakemake 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} ca-certificates{a} catch2{a} cmake{a} cmake-data{a} coinor-cbc{a} coinor-libcbc3.1{a} coinor-libcgl1{a} coinor-libclp1{a} coinor-libcoinutils3v5{a} coinor-libosi1v5{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-glyphicons-halflings{a} gettext{a} gettext-base{a} gir1.2-girepository-2.0{a} gir1.2-glib-2.0{a} git{a} git-man{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} liberror-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgirepository-1.0-1{a} libglib2.0-0t64{a} libgssapi-krb5-2{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-bootstrap{a} libjs-jquery{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsodium23{a} libssh2-1t64{a} libssl-dev{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} python3{a} python3-adal{a} python3-aiohttp{a} python3-aiosignal{a} python3-async-timeout{a} python3-attr{a} python3-avro{a} python3-azure{a} python3-azure-storage{a} python3-bcrypt{a} python3-blinker{a} python3-boto3{a} python3-botocore{a} python3-certifi{a} python3-cffi-backend{a} python3-chardet{a} python3-charset-normalizer{a} python3-colorama{a} python3-configargparse{a} python3-connection-pool{a} python3-cryptography{a} python3-dateutil{a} python3-datrie{a} python3-decorator{a} python3-distutils{a} python3-docutils{a} python3-dpath{a} python3-fastjsonschema{a} python3-frozenlist{a} python3-gi{a} python3-git{a} python3-gitdb{a} python3-hatch-vcs{a} python3-hatchling{a} python3-humanfriendly{a} python3-idna{a} python3-isodate{a} python3-jinja2{a} python3-jmespath{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-core{a} python3-jwt{a} python3-lib2to3{a} python3-markupsafe{a} python3-marshmallow{a} python3-minimal{a} python3-msal{a} python3-msal-extensions{a} python3-msrest{a} python3-msrestazure{a} python3-multidict{a} python3-nacl{a} python3-nbformat{a} python3-oauthlib{a} python3-packaging{a} python3-paramiko{a} python3-pathspec{a} python3-pkg-resources{a} python3-plac{a} python3-platformdirs{a} python3-pluggy{a} python3-portalocker{a} python3-psutil{a} python3-pulp{a} python3-py{a} python3-pyparsing{a} python3-ratelimiter{a} python3-referencing{a} python3-requests{a} python3-requests-oauthlib{a} python3-retry{a} python3-roman{a} python3-rpds-py{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3-s3transfer{a} python3-setuptools{a} python3-setuptools-scm{a} python3-six{a} python3-smart-open{a} python3-smmap{a} python3-stopit{a} python3-strictyaml{a} python3-tabulate{a} python3-throttler{a} python3-toposort{a} python3-tqdm{a} python3-traitlets{a} python3-trove-classifiers{a} python3-typing-extensions{a} python3-urllib3{a} python3-websocket{a} python3-wrapt{a} python3-yaml{a} python3-yarl{a} python3-yte{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} snakemake{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl cwltool graphicsmagick-imagemagick-compat imagemagick imagemagick-6.q16 javascript-common krb5-locales less libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx openssh-client psmisc publicsuffix python3-aiodns python3-babel python3-biopython python3-dropbox python3-flask python3-ftputil python3-invoke python3-irodsclient python3-json-pointer python3-kubernetes python3-pil python3-pygments python3-rfc3987 python3-tz python3-uritemplate python3-webcolors python3-yappi shared-mime-info wget xdg-user-dirs 0 packages upgraded, 214 newly installed, 0 to remove and 0 not upgraded. Need to get 99.6 MB of archives. After unpacking 1083 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-4 [869 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 openssl arm64 3.2.1-3 [1324 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 catch2 arm64 3.4.0-1 [551 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libarchive13t64 arm64 3.7.2-2 [321 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 43 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.7.1-3 [412 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 librhash0 arm64 1.4.3-3+b1 [127 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libuv1t64 arm64 1.48.0-1.1 [142 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 cmake-data all 3.29.2-2 [2167 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 cmake arm64 3.29.2-2 [9059 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 coinor-libcoinutils3v5 arm64 2.11.4+repack1-4 [383 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 coinor-libosi1v5 arm64 0.108.10+ds-1 [236 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 coinor-libclp1 arm64 1.17.9+ds-1 [721 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 coinor-libcgl1 arm64 0.60.8+ds-1 [342 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 coinor-libcbc3.1 arm64 2.10.11+ds1-2 [602 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 coinor-cbc arm64 2.10.11+ds1-2 [16.1 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 74 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.78.4-7 [1364 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 gir1.2-glib-2.0 arm64 1.78.1-15 [163 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libgirepository-1.0-1 arm64 1.78.1-15 [104 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 gir1.2-girepository-2.0 arm64 1.78.1-15 [36.1 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 liberror-perl all 0.17029-2 [29.0 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 git-man all 1:2.43.0-1 [2112 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 git arm64 1:2.43.0-1+b1 [8234 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 hdf5-helpers arm64 1.10.10+repack-3+b1 [23.5 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libaec0 arm64 1.1.3-1 [22.1 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libsz2 arm64 1.1.3-1 [7664 B] Get: 94 http://deb.debian.org/debian trixie/main arm64 libaec-dev arm64 1.1.3-1 [19.7 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.7.1-3 [523 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libhdf5-103-1 arm64 1.10.10+repack-3+b1 [1036 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libhdf5-cpp-103-1 arm64 1.10.10+repack-3+b1 [119 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libhdf5-fortran-102 arm64 1.10.10+repack-3+b1 [87.9 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-100 arm64 1.10.10+repack-3+b1 [59.9 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-fortran-100 arm64 1.10.10+repack-3+b1 [38.5 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-cpp-100 arm64 1.10.10+repack-3+b1 [21.1 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3 [292 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libjpeg-dev arm64 1:2.1.5-3 [71.9 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.2.1-3 [3089 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libhdf5-dev arm64 1.10.10+repack-3+b1 [2691 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.19+ds-1.1+b1 [413 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.19+ds-1.1+b1 [1604 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libsodium23 arm64 1.0.18-1+b1 [118 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 python3-cffi-backend arm64 1.16.0-2+b2 [109 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 python3-cryptography arm64 42.0.5-2 [1050 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 python3-six all 1.16.0-6 [16.3 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.10.0-1 [66.2 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 python3-jwt all 2.7.0-1 [29.7 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2023.11.17-1 [155 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.6-2 [37.0 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 1.26.18-2 [116 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-adal all 1.2.7-3 [32.2 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 python3-multidict arm64 6.0.4-1.1 [43.2 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 python3-yarl arm64 1.9.4-1 [92.8 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 python3-async-timeout all 4.0.3-1 [7660 B] Get: 136 http://deb.debian.org/debian trixie/main arm64 python3-frozenlist arm64 1.4.0-1+b1 [53.8 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 python3-aiosignal all 1.3.1-1 [6016 B] Get: 138 http://deb.debian.org/debian trixie/main arm64 python3-attr all 23.2.0-2 [65.5 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 python3-aiohttp arm64 3.9.1-1 [341 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 python3-avro all 1.11.1+dfsg-2 [70.5 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 python3-isodate all 0.6.1-2 [24.9 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 python3-blinker all 1.8.1-1 [13.1 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 python3-oauthlib all 3.2.2-1 [95.4 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 python3-requests-oauthlib all 1.3.1-1 [21.1 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 python3-msrest all 0.6.21-4 [47.7 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 python3-msrestazure all 0.6.4-3 [26.5 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 python3-azure-storage all 20230705+git-1 [285 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.0-1 [45.5 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 python3-pathspec all 0.12.1-1 [28.1 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 python3-trove-classifiers all 2024.1.31-1 [9968 B] Get: 153 http://deb.debian.org/debian trixie/main arm64 python3-hatchling all 1.24.2-1 [53.2 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 python3-setuptools-scm all 8.0.4-2 [39.5 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 python3-hatch-vcs all 0.4.0-1 [8336 B] Get: 159 http://deb.debian.org/debian trixie/main arm64 python3-rpds-py arm64 0.12.0-3 [241 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 python3-referencing all 0.31.0-1 [22.2 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 python3-jsonschema-specifications all 2023.12.1-1 [8976 B] Get: 162 http://deb.debian.org/debian trixie/main arm64 python3-jsonschema all 4.19.2-2 [71.2 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 python3-marshmallow all 3.20.1-1.1 [67.4 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 python3-msal all 1.28.0-1 [88.7 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 python3-portalocker all 2.2.1-1 [18.5 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 python3-gi arm64 3.48.2-1 [267 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 python3-msal-extensions all 1.1.0-1 [17.1 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 python3-ruamel.yaml.clib arm64 0.2.8+ds-1 [156 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 python3-ruamel.yaml all 0.18.6+ds-3 [145 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 python3-strictyaml all 1.6.1-3 [92.9 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-tqdm all 4.66.2-3 [90.7 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-websocket all 1.7.0-1 [45.0 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-yaml arm64 6.0.1-2 [153 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-azure all 20230705+git-1 [13.7 MB] Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-bcrypt arm64 3.2.2-1 [28.5 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-jmespath all 1.0.1-1 [21.1 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-botocore all 1.34.46+repack-1 [6464 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-s3transfer all 0.10.1-1 [55.6 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-boto3 all 1.34.46+dfsg-1 [269 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-configargparse all 1.7-1 [31.3 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-connection-pool all 0.0.3-2 [5584 B] Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-datrie arm64 0.8.2-4+b2 [144 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 python3-roman all 3.3-3 [9880 B] Get: 185 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 python3-dpath all 2.1.6-2 [19.7 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 python3-fastjsonschema all 2.19.1-1 [21.3 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 python3-smmap all 6.0.0-1 [20.1 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 python3-gitdb all 4.0.11-1 [45.5 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-git all 3.1.37-3 [137 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 python3-humanfriendly all 10.0-5 [85.4 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1 [14.6 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-platformdirs all 4.2.1-1 [16.0 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-traitlets all 5.5.0-2 [90.7 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 python3-jupyter-core all 5.3.2-1 [31.5 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 python3-nacl arm64 1.5.0-4 [53.6 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 python3-paramiko all 2.12.0-2 [133 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 python3-plac all 1.4.1-1 [64.0 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 python3-psutil arm64 5.9.8-2 [225 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 203 http://deb.debian.org/debian trixie/main arm64 python3-pulp all 2.7.0+dfsg-3 [72.3 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 python3-py all 1.11.0-2 [88.7 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 python3-ratelimiter arm64 1.2.0.post0-4 [5740 B] Get: 206 http://deb.debian.org/debian trixie/main arm64 python3-retry all 0.9.2-2 [7020 B] Get: 207 http://deb.debian.org/debian trixie/main arm64 python3-smart-open all 5.2.1-6 [87.9 kB] Get: 208 http://deb.debian.org/debian trixie/main arm64 python3-stopit all 1.1.2-2 [12.6 kB] Get: 209 http://deb.debian.org/debian trixie/main arm64 python3-tabulate all 0.8.10-1 [38.8 kB] Get: 210 http://deb.debian.org/debian trixie/main arm64 python3-throttler all 1.2.2-2 [7072 B] Get: 211 http://deb.debian.org/debian trixie/main arm64 python3-toposort all 1.10-1 [7544 B] Get: 212 http://deb.debian.org/debian trixie/main arm64 python3-wrapt arm64 1.15.0-2+b1 [48.3 kB] Get: 213 http://deb.debian.org/debian trixie/main arm64 python3-yte all 1.5.4-1 [13.6 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 snakemake all 7.32.4-3 [318 kB] Fetched 99.6 MB in 1s (88.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19735 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... 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_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20051 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.deb ... Unpacking python3-minimal (3.11.8-1) ... 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_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... 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 ... 21043 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... 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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 catch2 (3.4.0-1) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libsodium23:arm64 (1.0.18-1+b1) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up hdf5-helpers (1.10.10+repack-3+b1) ... Setting up libdatrie1:arm64 (0.2.13-3) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1+b1) ... Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libuv1t64:arm64 (1.48.0-1.1) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.61.0-1+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 libcom-err2:arm64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libaec0:arm64 (1.1.3-1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libkrb5support0:arm64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jun 7 23:58:14 UTC 2025. Universal Time is now: Sat Jun 7 23:58:14 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17029-2) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.78.4-7) ... No schema files found: doing nothing. 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 libjpeg62-turbo:arm64 (1:2.1.5-3) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-3) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libproc2-0:arm64 (2:4.0.4-4) ... Setting up libssl-dev:arm64 (3.2.1-3) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:arm64 (1.9.5-6+b2) ... Setting up gir1.2-glib-2.0:arm64 (1.78.1-15) ... Setting up libk5crypto3:arm64 (1.20.1-6+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:arm64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:arm64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up librhash0:arm64 (1.4.3-3+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up libsub-override-perl (0.10-1) ... Setting up git-man (1:2.43.0-1) ... Setting up libgirepository-1.0-1:arm64 (1.78.1-15) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.29.2-2) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.2.1-3) ... Setting up libdeflate-dev:arm64 (1.20-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up libsz2:arm64 (1.1.3-1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... 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 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 libaec-dev:arm64 (1.1.3-1) ... Setting up libjpeg-dev:arm64 (1:2.1.5-3) ... Setting up libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up coinor-libcoinutils3v5:arm64 (2.11.4+repack1-4) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up gir1.2-girepository-2.0:arm64 (1.78.1-15) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up coinor-libosi1v5:arm64 (0.108.10+ds-1) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libarchive13t64:arm64 (3.7.2-2) ... Setting up libcurl4t64:arm64 (8.7.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-3) ... Setting up libcurl4-gnutls-dev:arm64 (8.7.1-3) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up coinor-libclp1:arm64 (1.17.9+ds-1) ... Setting up git (1:2.43.0-1+b1) ... Setting up libhdf5-103-1:arm64 (1.10.10+repack-3+b1) ... Setting up libhdf5-cpp-103-1:arm64 (1.10.10+repack-3+b1) ... Setting up cmake (3.29.2-2) ... Setting up libhts3t64:arm64 (1.19+ds-1.1+b1) ... Setting up coinor-libcgl1:arm64 (0.60.8+ds-1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up libhts-dev:arm64 (1.19+ds-1.1+b1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up python3-plac (1.4.1-1) ... Setting up python3-platformdirs (4.2.1-1) ... Setting up python3-psutil (5.9.8-2) ... Setting up python3-multidict (6.0.4-1.1) ... Setting up python3-frozenlist (1.4.0-1+b1) ... Setting up python3-aiosignal (1.3.1-1) ... 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Setting up libhdf5-dev (1.10.10+repack-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3-retry (0.9.2-2) ... Setting up python3-ruamel.yaml (0.18.6+ds-3) ... Setting up python3-adal (1.2.7-3) ... Setting up python3-stopit (1.1.2-2) ... Setting up python3-hatchling (1.24.2-1) ... Setting up python3-jupyter-core (5.3.2-1) ... Setting up python3-nacl (1.5.0-4) ... Setting up python3-hatch-vcs (0.4.0-1) ... Setting up python3-referencing (0.31.0-1) ... Setting up python3-pulp (2.7.0+dfsg-3) ... Setting up python3-msal (1.28.0-1) ... Setting up python3-msal-extensions (1.1.0-1) ... Setting up python3-strictyaml (1.6.1-3) ... Setting up python3-oauthlib (3.2.2-1) ... Setting up python3-botocore (1.34.46+repack-1) ... Setting up python3-paramiko (2.12.0-2) ... Setting up python3-jsonschema-specifications (2023.12.1-1) ... Setting up python3-requests-oauthlib (1.3.1-1) ... Setting up python3-s3transfer (0.10.1-1) ... Setting up python3-msrest (0.6.21-4) ... Setting up python3-jsonschema (4.19.2-2) ... Setting up python3-boto3 (1.34.46+dfsg-1) ... Setting up python3-msrestazure (0.6.4-3) ... Setting up python3-nbformat (5.9.1-1) ... Setting up python3-azure-storage (20230705+git-1) ... Setting up python3-azure (20230705+git-1) ... Setting up python3-smart-open (5.2.1-6) ... Processing triggers for libc-bin (2.37-19) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up snakemake (7.32.4-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/4041099/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/4041099/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/kallisto-0.48.0+dfsg/ && 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 > ../kallisto_0.48.0+dfsg-4_source.changes dpkg-buildpackage: info: source package kallisto dpkg-buildpackage: info: source version 0.48.0+dfsg-4 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 dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg' dh_auto_configure -- -DDEBIAN_BUILD=1 -DLINK=shared -DBUILD_FUNCTESTING=1 cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DDEBIAN_BUILD=1 -DLINK=shared -DBUILD_FUNCTESTING=1 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done shared build -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3") Functional testing enabled. -- Configuring done (2.1s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg' dh_auto_build cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory 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-o CMakeFiles/kallisto_core.dir/Merge.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/Merge.cpp [ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -MF CMakeFiles/kallisto_core.dir/MinCollector.cpp.o.d -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/MinCollector.cpp [ 52%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -MF CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o.d -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/PlaintextWriter.cpp [ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -MF CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o.d -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/ProcessReads.cpp [ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -MF CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o.d -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/PseudoBam.cpp [ 66%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/common.cpp.o -MF CMakeFiles/kallisto_core.dir/common.cpp.o.d -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/common.cpp [ 71%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o -MF CMakeFiles/kallisto_core.dir/h5utils.cpp.o.d -o CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/h5utils.cpp [ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/hash.cpp.o -MF CMakeFiles/kallisto_core.dir/hash.cpp.o.d -o CMakeFiles/kallisto_core.dir/hash.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/hash.cpp [ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/main.cpp.o -MF CMakeFiles/kallisto_core.dir/main.cpp.o.d -o CMakeFiles/kallisto_core.dir/main.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/main.cpp [ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/weights.cpp.o -MF CMakeFiles/kallisto_core.dir/weights.cpp.o.d -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/weights.cpp [ 90%] Linking CXX static library libkallisto_core.a cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/kallisto_core.dir/cmake_clean_target.cmake cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kallisto_core.dir/link.txt --verbose=1 /usr/bin/ar qc libkallisto_core.a CMakeFiles/kallisto_core.dir/BUSData.cpp.o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o CMakeFiles/kallisto_core.dir/Kmer.cpp.o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o CMakeFiles/kallisto_core.dir/Merge.cpp.o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o CMakeFiles/kallisto_core.dir/common.cpp.o CMakeFiles/kallisto_core.dir/h5utils.cpp.o CMakeFiles/kallisto_core.dir/hash.cpp.o CMakeFiles/kallisto_core.dir/main.cpp.o CMakeFiles/kallisto_core.dir/weights.cpp.o /usr/bin/ranlib libkallisto_core.a make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' [ 90%] Built target kallisto_core make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend make[3]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kallisto-0.48.0+dfsg /build/reproducible-path/kallisto-0.48.0+dfsg/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/kallisto.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build make[3]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' [ 95%] Building CXX object src/CMakeFiles/kallisto.dir/main.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/main.cpp.o -MF CMakeFiles/kallisto.dir/main.cpp.o.d -o CMakeFiles/kallisto.dir/main.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/main.cpp [100%] Linking CXX executable kallisto cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kallisto.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/kallisto.dir/main.cpp.o -o kallisto libkallisto_core.a -lpthread -lhts libkallisto_core.a -lz -lrt make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' [100%] Built target kallisto make[2]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg' dh_auto_test cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 make[2]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 test make[3]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles 21 make -f CMakeFiles/Makefile2 CMakeFiles/test.dir/all make[4]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend make[5]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kallisto-0.48.0+dfsg /build/reproducible-path/kallisto-0.48.0+dfsg/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build make[5]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make[5]: Nothing to be done for 'src/CMakeFiles/kallisto_core.dir/build'. make[5]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' [ 90%] Built target kallisto_core make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend make[5]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kallisto-0.48.0+dfsg /build/reproducible-path/kallisto-0.48.0+dfsg/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/kallisto.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build make[5]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make[5]: Nothing to be done for 'src/CMakeFiles/kallisto.dir/build'. make[5]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' [100%] Built target kallisto make -f CMakeFiles/test.dir/build.make CMakeFiles/test.dir/depend make[5]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kallisto-0.48.0+dfsg /build/reproducible-path/kallisto-0.48.0+dfsg /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles/test.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/test.dir/build.make CMakeFiles/test.dir/build make[5]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' /bin/bash ./func_tests/runtests.sh [INDEX] ./src/kallisto index -i ./func_tests/basic7.idx -k 7 ./func_tests/simple.fasta ^[OK] ./src/kallisto inspect ./func_tests/basic7.idx 2>&1|head -4 ^[Output OK] ./src/kallisto index -i ./func_tests/basic9.idx -k 9 ./func_tests/simple.fasta ^[OK] ./src/kallisto inspect ./func_tests/basic9.idx 2>&1|head -4 ^[Output OK] ./src/kallisto index -i ./func_tests/nonATCG.idx -k 5 ./func_tests/nonATCG.fasta ^[OK] ./src/kallisto inspect ./func_tests/nonATCG.idx 2>&1|head -4 ^[Output OK] ./src/kallisto index -i ./func_tests/polyA.idx -k 5 ./func_tests/polyA.fasta ^[OK] ./src/kallisto inspect ./func_tests/polyA.idx 2>&1|head -4 ^[Output OK] ./src/kallisto index -i ./func_tests/basic_fail.idx -k 10 ./func_tests/simple.fasta ^[OK - Exited non-zero as expected] ./src/kallisto index -i ./func_tests/duplicates_fail.idx -k 11 ./func_tests/duplicates.fasta ^[OK - Exited non-zero as expected] ./src/kallisto index -i ./func_tests/duplicates.idx -k 11 --make-unique ./func_tests/duplicates.fasta ^[OK] ./src/kallisto inspect ./func_tests/duplicates.idx 2>&1|head -4 ^[Output OK] ./src/kallisto quant -o ./func_tests/quantbasic -i ./func_tests/basic7.idx --single -l 5 -s 2 ./func_tests/small.fastq.gz ^[OK] cat ./func_tests/quantbasic/abundance.tsv ^[Output OK] ./src/kallisto quant -o ./func_tests/quantnonATCG -i ./func_tests/nonATCG.idx --single -l 5 -s 2 ./func_tests/small.fastq.gz ^[OK] cat ./func_tests/quantnonATCG/abundance.tsv ^[Output OK] ./src/kallisto quant -o ./func_tests/quantpolyA -i ./func_tests/polyA.idx --single -l 5 -s 2 ./func_tests/small.fastq.gz ^[OK] cat ./func_tests/quantpolyA/abundance.tsv ^[Output OK] ./src/kallisto quant -o ./func_tests/quantduplicates -i ./func_tests/duplicates.idx --single -l 5 -s 2 ./func_tests/small.fastq.gz ^[OK] cat ./func_tests/quantduplicates/abundance.tsv ^[Output OK] ./src/kallisto quant -o ./func_tests/quantbasicfr -i ./func_tests/basic7.idx --single --fr-stranded -l 5 -s 2 ./func_tests/small.fastq.gz ^[OK] cat ./func_tests/quantbasicfr/abundance.tsv ^[Output OK] ./src/kallisto quant -o ./func_tests/quantbasicrf -i ./func_tests/basic7.idx --single --rf-stranded -l 5 -s 2 ./func_tests/small.fastq.gz ^[OK] cat ./func_tests/quantbasicrf/abundance.tsv ^[Output OK] ./src/kallisto quant -o ./func_tests/quantbasicpaired -i ./func_tests/basic7.idx ./func_tests/simple_pair1.fastq.gz ./func_tests/simple_pair2.fastq.gz ^[OK] cat ./func_tests/quantbasicpaired/abundance.tsv ^[Output OK] ./src/kallisto quant -o ./func_tests/quantbasicpairedfr -i ./func_tests/basic7.idx --fr-stranded ./func_tests/simple_pair1.fastq.gz ./func_tests/simple_pair2.fastq.gz ^[OK] cat ./func_tests/quantbasicpairedfr/abundance.tsv ^[Output OK] ./src/kallisto quant -o ./func_tests/quantbasicpairedrf -i ./func_tests/basic7.idx --rf-stranded ./func_tests/simple_pair1.fastq.gz ./func_tests/simple_pair2.fastq.gz ^[OK] cat ./func_tests/quantbasicpairedrf/abundance.tsv ^[Output OK] ./src/kallisto quant -o ./func_tests/quantbasicpairedmultfr -i ./func_tests/basic7.idx --fr-stranded ./func_tests/simple_pair1.fastq.gz ./func_tests/simple_pair2.fastq.gz ./func_tests/simple_pair2.fastq.gz ./func_tests/simple_pair1.fastq.gz ^[OK] cat ./func_tests/quantbasicpairedmultfr/abundance.tsv ^[Output OK] ./src/kallisto quant -o ./func_tests/quantlarge -t 12 -i ./func_tests/basic7.idx --single -l 5 -s 2 ./func_tests/large.fastq.gz ./func_tests/large.fastq.gz ./func_tests/large.fastq.gz ./func_tests/large.fastq.gz ./func_tests/large.fastq.gz ^[OK] cat ./func_tests/quantlarge/abundance.tsv ^[Output OK] Not testing with bustools as tests fail with bustools make[5]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' [100%] Built target test make[4]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' cd test && PATH=$(find ../obj-* -name src):/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path HOME=$(mktemp --directory) snakemake --cores 1 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Job stats: job count -------------- ------- all 1 index 1 kallisto_bus 1 kallisto_quant 1 total 4 Select jobs to execute... [Sun Jun 8 14:03:13 2025] rule index: input: transcripts.fasta.gz output: transcripts.kidx jobid: 2 reason: Missing output files: transcripts.kidx resources: tmpdir=/tmp [build] loading fasta file transcripts.fasta.gz [build] k-mer length: 31 [build] counting k-mers ... done. [build] building target de Bruijn graph ... done [build] creating equivalence classes ... done [build] target de Bruijn graph has 27 contigs and contains 22118 k-mers [Sun Jun 8 14:03:13 2025] Finished job 2. 1 of 4 steps (25%) done Select jobs to execute... [Sun Jun 8 14:03:14 2025] rule kallisto_quant: input: reads_1.fastq.gz, reads_2.fastq.gz, transcripts.kidx output: quant_out/abundance.tsv, quant_out/run_info.json jobid: 1 reason: Missing output files: quant_out/abundance.tsv; Input files updated by another job: transcripts.kidx resources: tmpdir=/tmp [quant] fragment length distribution will be estimated from the data Warning: kallisto was not compiled with HDF5 support so no bootstrapping will be performed. Run quant with --plaintext option or recompile with HDF5 support to obtain bootstrap estimates. [index] k-mer length: 31 [index] number of targets: 14 [index] number of k-mers: 22,118 [index] number of equivalence classes: 20 Warning: 13 transcripts were defined in GTF file, but not in the index [quant] running in paired-end mode [quant] will process pair 1: reads_1.fastq.gz reads_2.fastq.gz [quant] finding pseudoalignments for the reads ... done [quant] processed 10,000 reads, 9,413 reads pseudoaligned [quant] estimated average fragment length: 178.02 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 52 rounds [ bam] writing pseudoalignments to BAM format .. done [ bam] sorting BAM files .. done [ bam] indexing BAM file .. done [Sun Jun 8 14:03:17 2025] Finished job 1. 2 of 4 steps (50%) done Select jobs to execute... [Sun Jun 8 14:03:17 2025] rule kallisto_bus: input: sc_reads_1.fastq.gz, sc_reads_2.fastq.gz, transcripts.kidx output: bus_out/matrix.ec, bus_out/transcripts.txt, bus_out/output.bus, bus_out/run_info.json jobid: 3 reason: Missing output files: bus_out/output.bus; Input files updated by another job: transcripts.kidx resources: tmpdir=/tmp [bus] Note: Strand option was not specified; setting it to --fr-stranded for specified technology [index] k-mer length: 31 [index] number of targets: 14 [index] number of k-mers: 22,118 [index] number of equivalence classes: 20 [quant] will process sample 1: sc_reads_1.fastq.gz sc_reads_2.fastq.gz [quant] finding pseudoalignments for the reads ... done [quant] processed 10,000 reads, 4,808 reads pseudoaligned [Sun Jun 8 14:03:18 2025] Finished job 3. 3 of 4 steps (75%) done Select jobs to execute... [Sun Jun 8 14:03:18 2025] localrule all: input: quant_out/abundance.tsv, bus_out/output.bus jobid: 0 reason: Input files updated by another job: bus_out/output.bus, quant_out/abundance.tsv resources: tmpdir=/tmp [Sun Jun 8 14:03:18 2025] Finished job 0. 4 of 4 steps (100%) done Complete log: .snakemake/log/2025-06-08T140312.745256.snakemake.log rm -rf test/.snakemake test/bus_out test/quant_out/run_info.json test/transcripts.kidx.gz make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/kallisto-0.48.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/kallisto-0.48.0+dfsg/debian/tmp/usr/bin/kallisto make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' dh_install dh_installdocs dh_installchangelogs 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 'kallisto' in '../kallisto_0.48.0+dfsg-4_arm64.deb'. dpkg-deb: building package 'kallisto-examples' in '../kallisto-examples_0.48.0+dfsg-4_all.deb'. dpkg-deb: building package 'kallisto-dbgsym' in '../kallisto-dbgsym_0.48.0+dfsg-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../kallisto_0.48.0+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../kallisto_0.48.0+dfsg-4_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/4041099/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4041099/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/4041099 and its subdirectories I: Current time: Sun Jun 8 14:03:31 +14 2025 I: pbuilder-time-stamp: 1749341011