I: pbuilder: network access will be disabled during build I: Current time: Sat Mar 8 16:25:25 +14 2025 I: pbuilder-time-stamp: 1741400725 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 dpkg-source: warning: cannot verify inline signature for ./kallisto_0.48.0+dfsg-4.dsc: unsupported subcommand 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/3047210/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-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 Mar 8 02:25 /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/3047210/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3047210/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(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=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=aec4365e4b014f44a62c81bdca962465 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=3047210 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.bKcWwIrh/pbuilderrc_0pkx --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bKcWwIrh/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 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3047210/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 ... 19897 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} comerr-dev{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} git{a} git-man{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcatch2-dev{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} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-bootstrap{a} libjs-jquery{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack3{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libxml2{a} libyaml-0-2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-attr{a} python3-autocommand{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-configargparse{a} python3-connection-pool{a} python3-datrie{a} python3-decorator{a} python3-docutils{a} python3-dpath{a} python3-fastjsonschema{a} python3-git{a} python3-gitdb{a} python3-humanfriendly{a} python3-idna{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-core{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-nbformat{a} python3-packaging{a} python3-pkg-resources{a} python3-plac{a} python3-platformdirs{a} python3-psutil{a} python3-pulp{a} python3-py{a} python3-pyparsing{a} python3-ratelimiter{a} python3-referencing{a} python3-requests{a} python3-retry{a} python3-roman{a} python3-rpds-py{a} python3-smart-open{a} python3-smmap{a} python3-stopit{a} python3-tabulate{a} python3-throttler{a} python3-toposort{a} python3-traitlets{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-wrapt{a} python3-yaml{a} python3-yte{a} python3.13{a} python3.13-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: bzip2-doc curl cwltool graphicsmagick-imagemagick-compat imagemagick imagemagick-7.q16 javascript-common krb5-locales less libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx openssh-client psmisc publicsuffix python3-azure-storage python3-babel python3-biopython python3-boto3 python3-botocore python3-dropbox python3-flask python3-fqdn python3-ftputil python3-irodsclient python3-isoduration python3-json-pointer python3-kubernetes python3-paramiko python3-pil python3-pygments python3-rfc3339-validator python3-rfc3986-validator python3-rfc3987 python3-tz python3-uritemplate python3-webcolors python3-yappi python3-zstandard wget 0 packages upgraded, 208 newly installed, 0 to remove and 0 not upgraded. Need to get 87.8 MB of archives. After unpacking 354 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.2-2 [27.1 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 12.0.0 [28.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.2-2 [10.1 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.2-2 [28.1 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.4.1-1 [1390 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libcatch2-dev arm64 3.7.1-0.5 [588 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 catch2 all 3.7.1-0.5 [5144 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.6-1 [2268 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 46 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.12.1-3 [339 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.6-1 [9912 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-17 [361 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 coinor-libcoinutils3v5 arm64 2.11.11+ds-5 [397 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 coinor-libosi1v5 arm64 0.108.10+ds-2 [247 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 coinor-libclp1 arm64 1.17.10+ds-1 [751 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 coinor-libcgl1 arm64 0.60.9+ds-1 [359 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 coinor-libcbc3.1 arm64 2.10.12+ds-1 [615 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 coinor-cbc arm64 2.10.12+ds-1 [16.3 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 82 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.11.0-1 [121 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.11.0-1 [28.2 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.12.1-3 [336 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 liberror-perl all 0.17030-1 [26.9 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 git-man all 1:2.47.2-0.1 [2205 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 git arm64 1:2.47.2-0.1 [8756 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 hdf5-helpers arm64 1.14.5+repack-3 [26.6 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-4 [56.9 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-4 [41.0 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-4 [41.0 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-4 [53.1 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-4 [126 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 105 http://deb.debian.org/debian unstable/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.9-2 [452 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.9-2 [452 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10.1-1 [1325 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.9-2 [1419 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-4 [15.9 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.8.0-1 [89.4 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.11.0-1 [33.9 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.11.0-1 [174 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.4.1-1 [3232 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.12.1-3 [465 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.23-1+b1 [51.4 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libhdf5-cpp-310 arm64 1.14.5+repack-3 [121 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libhdf5-fortran-310 arm64 1.14.5+repack-3 [110 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-fortran-310 arm64 1.14.5+repack-3 [42.1 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-cpp-310 arm64 1.14.5+repack-3 [24.4 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3.1 [293 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libjpeg-dev arm64 1:2.1.5-3.1 [72.0 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libhdf5-dev arm64 1.14.5+repack-3 [3225 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.21+ds-1 [426 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.4-1 [319 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.21+ds-1 [1658 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 python3-attr all 25.1.0-1 [68.7 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 158 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.1-1+b1 [119 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 python3-configargparse all 1.7-2 [31.4 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 python3-connection-pool all 0.0.3-2 [5584 B] Get: 162 http://deb.debian.org/debian unstable/main arm64 python3-datrie arm64 0.8.2-5+b2 [111 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 python3-roman all 5.0-1 [10.6 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 python3-dpath all 2.2.0-1 [19.9 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 python3-fastjsonschema all 2.21.1-1 [22.4 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 python3-smmap all 6.0.0-1 [20.1 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 python3-gitdb all 4.0.11-1 [45.5 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 python3-git all 3.1.37-3 [137 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 python3-humanfriendly all 10.0-6 [85.6 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.10-1 [42.0 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 178 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b4 [14.1 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-rpds-py arm64 0.21.0-2+b1 [226 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 python3-referencing all 0.35.1-2 [23.5 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-plac all 1.4.3-2 [65.7 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 python3-psutil arm64 5.9.8-2+b1 [226 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 python3-pulp all 2.7.0+dfsg-4 [72.4 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 python3-py all 1.11.0-4 [88.8 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 python3-ratelimiter arm64 1.2.0.post0-4 [5740 B] Get: 197 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 python3-retry all 0.9.2-3 [7088 B] Get: 200 http://deb.debian.org/debian unstable/main arm64 python3-wrapt arm64 1.15.0-4+b1 [42.7 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 python3-smart-open all 7.1.0-1 [98.7 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 python3-stopit all 1.1.2-3 [12.8 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 python3-throttler all 1.2.2-2 [7072 B] Get: 205 http://deb.debian.org/debian unstable/main arm64 python3-toposort all 1.10-2 [7336 B] Get: 206 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.2-1+b2 [122 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 python3-yte all 1.5.4-1 [13.6 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 snakemake all 7.32.4-7 [318 kB] Fetched 87.8 MB in 1s (143 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-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 ... 19897 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... 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 ... 20231 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.2-2_arm64.deb ... Unpacking python3-minimal (3.13.2-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_12.0.0_all.deb ... Unpacking media-types (12.0.0) ... 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_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.7-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_arm64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.2-2_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.2-2) ... Setting up python3-minimal (3.13.2-2) ... 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 ... 21241 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.2-2_arm64.deb ... Unpacking python3 (3.13.2-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-7_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-7_arm64.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.4.1-1_arm64.deb ... Unpacking openssl (3.4.1-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. 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Setting up bsdextrautils (2.40.4-5) ... Setting up hdf5-helpers (1.14.5+repack-3) ... Setting up libdatrie1:arm64 (0.2.13-3+b1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-2) ... Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libuv1t64:arm64 (1.50.0-2) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up libdeflate0:arm64 (1.23-1+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:arm64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libaec0:arm64 (1.1.3-1+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-4) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Mar 8 02:26:28 UTC 2025. Universal Time is now: Sat Mar 8 02:26:28 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17030-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.1-2) ... 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 libunbound8:arm64 (1.22.0-1+b1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-3.1) ... Setting up libjsoncpp26:arm64 (1.9.6-3) ... Setting up libproc2-0:arm64 (2:4.0.4-7) ... Setting up comerr-dev:arm64 (2.1-1.47.2-1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libssl-dev:arm64 (3.4.1-1) ... Setting up autopoint (0.23.1-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-4) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:arm64 (14.2.0-17) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.8.0-1) ... Setting up libnghttp3-dev:arm64 (1.8.0-1) ... Setting up liblzma-dev:arm64 (5.6.4-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-7) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up git-man (1:2.47.2-0.1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.11.0-1) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.6-1) ... Setting up librhash1:arm64 (1.4.5-1) ... Setting up libkrb5-3:arm64 (1.21.3-4) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libtasn1-6-dev:arm64 (4.20.0-2) ... Setting up openssl (3.4.1-1) ... Setting up libcatch2-dev (3.7.1-0.5) ... Setting up libdeflate-dev:arm64 (1.23-1+b1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up libldap2:arm64 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b7) ... Setting up libsz2:arm64 (1.1.3-1+b1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up catch2 (3.7.1-0.5) ... Setting up liblapack3:arm64 (3.12.1-2) ... 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 (0.23.1-1) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:arm64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libaec-dev:arm64 (1.1.3-1+b1) ... Setting up libjpeg-dev:arm64 (1:2.1.5-3.1) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libngtcp2-dev:arm64 (1.11.0-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up coinor-libcoinutils3v5:arm64 (2.11.11+ds-5) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libldap-dev:arm64 (2.6.9+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-4) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.7-2+b1) ... Setting up coinor-libosi1v5:arm64 (0.108.10+ds-2) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libarchive13t64:arm64 (3.7.4-1.1) ... Setting up libpython3.13-stdlib:arm64 (3.13.2-1) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up libpython3-stdlib:arm64 (3.13.2-2) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:arm64 (3.8.9-2) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.2-2) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b4) ... Setting up python3-plac (1.4.3-2) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-psutil (5.9.8-2+b1) ... Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up python3-ratelimiter (1.2.0.post0-4) ... Setting up python3-roman (5.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up libgnutls-dane0t64:arm64 (3.8.9-2) ... Setting up python3-humanfriendly (10.0-6) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:arm64 (1.21.3-4) ... Setting up coinor-libclp1:arm64 (1.17.10+ds-1) ... Setting up python3-dpath (2.2.0-1) ... Setting up python3-connection-pool (0.0.3-2) ... Setting up python3-idna (3.10-1) ... Setting up python3-wrapt (1.15.0-4+b1) ... Setting up python3-throttler (1.2.2-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-rpds-py (0.21.0-2+b1) ... Setting up python3-fastjsonschema (2.21.1-1) ... Setting up python3-traitlets (5.14.3+really5.14.3-1) ... Setting up coinor-libcgl1:arm64 (0.60.9+ds-1) ... Setting up python3-datrie:arm64 (0.8.2-5+b2) ... Setting up python3-smmap (6.0.0-1) ... Setting up python3-jupyter-core (5.7.2-5) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.11.0-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-4) ... Setting up python3-toposort (1.10-2) ... Setting up libgnutls28-dev:arm64 (3.8.9-2) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-configargparse (1.7-2) ... Setting up python3-attr (25.1.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-smart-open (7.1.0-1) ... Setting up python3-py (1.11.0-4) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up libcurl4t64:arm64 (8.12.1-3) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3047210/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3047210/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 PKG_CONFIG=/usr/bin/pkg-config 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 < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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 "1.3.1") Functional testing enabled. -- Configuring done (2.0s) -- 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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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 -Wl,--dependency-file=CMakeFiles/kallisto.dir/link.d 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... [Sat Mar 8 16:28:34 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 [Sat Mar 8 16:28:34 2025] Finished job 2. 1 of 4 steps (25%) done Select jobs to execute... [Sat Mar 8 16:28:34 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 [Sat Mar 8 16:28:34 2025] Finished job 3. 2 of 4 steps (50%) done Select jobs to execute... [Sat Mar 8 16:28:34 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 [Sat Mar 8 16:28:36 2025] Finished job 1. 3 of 4 steps (75%) done Select jobs to execute... [Sat Mar 8 16:28:36 2025] localrule all: input: quant_out/abundance.tsv, bus_out/output.bus jobid: 0 reason: Input files updated by another job: quant_out/abundance.tsv, bus_out/output.bus resources: tmpdir=/tmp [Sat Mar 8 16:28:36 2025] Finished job 0. 4 of 4 steps (100%) done Complete log: .snakemake/log/2025-03-08T162834.373887.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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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-dbgsym' in '../kallisto-dbgsym_0.48.0+dfsg-4_arm64.deb'. dpkg-deb: building package 'kallisto-examples' in '../kallisto-examples_0.48.0+dfsg-4_all.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/3047210/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3047210/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/3047210 and its subdirectories I: Current time: Sat Mar 8 16:28:44 +14 2025 I: pbuilder-time-stamp: 1741400924