I: pbuilder: network access will be disabled during build I: Current time: Mon May 18 06:33:43 -12 2026 I: pbuilder-time-stamp: 1779129223 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 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/1546781/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c9d4cfbb420a40d3be416f60c463dde9' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1546781' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.M3LzdQAW/pbuilderrc_tIuo --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.M3LzdQAW/b1 --logfile b1/build.log kallisto_0.48.0+dfsg-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1546781/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: amd64 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 ... 19842 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} 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, 207 newly installed, 0 to remove and 0 not upgraded. Need to get 83.5 MB of archives. After unpacking 316 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-3 [861 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-3 [2212 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-2 [260 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-3 [1952 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-3 [746 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-2 [28.1 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.5.0-1 [1491 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-4 [94.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libcatch2-dev amd64 3.7.1-0.5 [613 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 catch2 all 3.7.1-0.5 [5144 B] Get: 37 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.6-2 [2268 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 45 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.13.0-1 [381 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-2 [12.0 MB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 coinor-libcoinutils3v5 amd64 2.11.11+ds-5 [460 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 coinor-libosi1v5 amd64 0.108.10+ds-2 [293 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 coinor-libclp1 amd64 1.17.10+ds-1 [883 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 coinor-libcgl1 amd64 0.60.9+ds-1 [426 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 coinor-libcbc3.1 amd64 2.10.12+ds-1 [714 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 coinor-cbc amd64 2.10.12+ds-1 [16.2 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.2-1+b1 [56.0 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 81 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.13.0-1 [374 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 liberror-perl all 0.17030-1 [26.9 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 git-man all 1:2.47.2-0.1 [2205 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 git amd64 1:2.47.2-0.1 [8788 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 104 http://deb.debian.org/debian trixie/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.6.9+dfsg-2 [311 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.5.0-1 [2949 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.13.0-1 [492 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3.1 [292 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3.1 [72.0 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 python3-configargparse all 1.7-2 [31.4 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-connection-pool all 0.0.3-2 [5584 B] Get: 161 http://deb.debian.org/debian trixie/main amd64 python3-datrie amd64 0.8.2-5+b2 [129 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 python3-roman all 5.0-1 [10.6 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 python3-dpath all 2.2.0-1 [19.9 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 python3-fastjsonschema all 2.21.1-1 [22.4 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 python3-smmap all 6.0.0-1 [20.1 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 python3-gitdb all 4.0.12-1 [45.8 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 python3-git all 3.1.44-1 [147 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 python3-humanfriendly all 10.0-6 [85.6 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.0-1 [90.1 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 177 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 python3-rpds-py amd64 0.21.0-2+b1 [257 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 python3-referencing all 0.36.2-1 [23.7 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 183 http://deb.debian.org/debian trixie/main amd64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.7-1 [16.6 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 python3-plac all 1.4.3-2 [65.7 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 python3-pulp all 2.7.0+dfsg-4 [72.4 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 python3-py all 1.11.0-4 [88.8 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 python3-ratelimiter amd64 1.2.0.post0-4 [5740 B] Get: 196 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-2 [114 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 python3-retry all 0.9.2-3 [7088 B] Get: 199 http://deb.debian.org/debian trixie/main amd64 python3-wrapt amd64 1.15.0-4+b1 [43.6 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 python3-smart-open all 7.1.0-1 [98.7 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 python3-stopit all 1.1.2-3 [12.8 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 python3-throttler all 1.2.2-2 [7072 B] Get: 204 http://deb.debian.org/debian trixie/main amd64 python3-toposort all 1.10-2 [7336 B] Get: 205 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 python3-yte all 1.5.4-1 [13.6 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 snakemake all 7.32.4-7 [318 kB] Fetched 83.5 MB in 10s (8382 kB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (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 ... 19842 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-3_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-3_amd64.deb ... Unpacking python3.13-minimal (3.13.2-3) ... Setting up libpython3.13-minimal:amd64 (3.13.2-3) ... Setting up libexpat1:amd64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.2-3) ... 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 ... 20176 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.2-2_amd64.deb ... Unpacking python3-minimal (3.13.2-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-2_all.deb ... Unpacking tzdata (2025b-2) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.7-1_amd64.deb ... Unpacking libffi8:amd64 (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:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-3_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-3_amd64.deb ... Unpacking python3.13 (3.13.2-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.2-2_amd64.deb ... Unpacking libpython3-stdlib:amd64 (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 ... 21187 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.2-2_amd64.deb ... Unpacking python3 (3.13.2-2) ... Selecting previously unselected package sgml-base. 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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17030-1) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunbound8:amd64 (1.22.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-3.1) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up comerr-dev:amd64 (2.1-1.47.2-1+b1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libssl-dev:amd64 (3.5.0-1) ... Setting up autopoint (0.23.1-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-7) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up git-man (1:2.47.2-0.1) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.6-2) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up openssl (3.5.0-1) ... Setting up libcatch2-dev (3.7.1-0.5) ... Setting up libdeflate-dev:amd64 (1.23-1+b1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libldap2:amd64 (2.6.9+dfsg-2) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libsz2:amd64 (1.1.3-1+b1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... 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:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libaec-dev:amd64 (1.1.3-1+b1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3.1) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up coinor-libcoinutils3v5:amd64 (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:amd64 (2.6.9+dfsg-2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-2) ... Setting up coinor-libosi1v5:amd64 (0.108.10+ds-2) ... Setting up libreadline8t64:amd64 (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:amd64 (3.7.4-1.1) ... 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Setting up python3-git (3.1.44-1) ... Setting up python3-stopit (1.1.2-3) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up libhdf5-hl-cpp-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:amd64 (1.14.5+repack-3) ... Setting up python3-pulp (2.7.0+dfsg-4) ... /usr/lib/python3/dist-packages/pulp/apis/xpress_api.py:325: SyntaxWarning: invalid escape sequence '\ ' otherwise be interpreted by the Tcl shell: \ $ " [ Setting up libcurl4-gnutls-dev:amd64 (8.13.0-1) ... Setting up python3-jsonschema (4.19.2-6) ... Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libhts-dev:amd64 (1.21+ds-1) ... Setting up python3-nbformat (5.9.1-1) ... Processing triggers for libc-bin (2.41-6) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up snakemake (7.32.4-7) ... Processing triggers for ca-certificates (20241223) ... 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: Running cd /build/reproducible-path/kallisto-0.48.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 amd64 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-x86_64-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/x86_64-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/x86_64-linux-gnu/libz.so (found version "1.3.1") Functional testing enabled. -- Configuring done (0.7s) -- 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-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg' dh_auto_build cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend make[3]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build make[3]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' [ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o [ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o [ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o [ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o [ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o [ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o [ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o [ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o [ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 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CMakeFiles/kallisto_core.dir/BUSTools.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/BUSTools.cpp cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -MF CMakeFiles/kallisto_core.dir/GeneModel.cpp.o.d -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/GeneModel.cpp cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 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-c /build/reproducible-path/kallisto-0.48.0+dfsg/src/KmerIndex.cpp cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -MF CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o.d -o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/KmerIterator.cpp cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSData.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/BUSData.cpp [ 71%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Merge.cpp.o -MF CMakeFiles/kallisto_core.dir/Merge.cpp.o.d -o CMakeFiles/kallisto_core.dir/Merge.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/Merge.cpp cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 [ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/Bootstrap.cpp cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 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/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 [ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 [ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 [ 90%] Linking CXX static library libkallisto_core.a cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-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-x86_64-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-x86_64-linux-gnu' cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/kallisto.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu' [ 95%] Building CXX object src/CMakeFiles/kallisto.dir/main.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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-x86_64-linux-gnu' [100%] Built target kallisto make[2]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[2]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-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-x86_64-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-x86_64-linux-gnu' cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-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-x86_64-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-x86_64-linux-gnu' cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/kallisto.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-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-x86_64-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-x86_64-linux-gnu' cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles/test.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu' [100%] Built target test make[4]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' cd test && PATH=$(find ../obj-* -name src):/usr/sbin:/usr/bin:/sbin:/bin:/usr/games HOME=$(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... [Mon May 18 06:35:36 2026] 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 [Mon May 18 06:35:36 2026] Finished job 2. 1 of 4 steps (25%) done Select jobs to execute... [Mon May 18 06:35:36 2026] 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 [Mon May 18 06:35:36 2026] Finished job 3. 2 of 4 steps (50%) done Select jobs to execute... [Mon May 18 06:35:36 2026] 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 [Mon May 18 06:35:38 2026] Finished job 1. 3 of 4 steps (75%) done Select jobs to execute... [Mon May 18 06:35:38 2026] 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 [Mon May 18 06:35:39 2026] Finished job 0. 4 of 4 steps (100%) done Complete log: .snakemake/log/2026-05-18T063536.025305.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-x86_64-linux-gnu && make -j42 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-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-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-dbgsym' in '../kallisto-dbgsym_0.48.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'kallisto' in '../kallisto_0.48.0+dfsg-4_amd64.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_amd64.buildinfo dpkg-genchanges --build=binary -O../kallisto_0.48.0+dfsg-4_amd64.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: 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/1546781 and its subdirectories I: Current time: Mon May 18 06:35:48 -12 2026 I: pbuilder-time-stamp: 1779129348