Tue Mar 11 18:02:57 UTC 2025 I: starting to build kallisto/trixie/amd64 on jenkins on '2025-03-11 18:02' Tue Mar 11 18:02:57 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/47497/console.log Tue Mar 11 18:02:57 UTC 2025 I: Downloading source for trixie/kallisto=0.48.0+dfsg-4 --2025-03-11 18:02:57-- http://deb.debian.org/debian/pool/main/k/kallisto/kallisto_0.48.0%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2287 (2.2K) [text/prs.lines.tag] Saving to: ‘kallisto_0.48.0+dfsg-4.dsc’ 0K .. 100% 285M=0s 2025-03-11 18:02:57 (285 MB/s) - ‘kallisto_0.48.0+dfsg-4.dsc’ saved [2287/2287] Tue Mar 11 18:02:57 UTC 2025 I: kallisto_0.48.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: kallisto Binary: kallisto, kallisto-examples Architecture: any-amd64 arm64 mips64el ppc64el s390x alpha hppa ia64 ppc64 riscv64 sparc64 all Version: 0.48.0+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://pachterlab.github.io/kallisto Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/kallisto Vcs-Git: https://salsa.debian.org/med-team/kallisto.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), catch2, cmake, libhdf5-dev, libhts-dev, snakemake Package-List: kallisto deb science optional arch=any-amd64,arm64,mips64el,ppc64el,s390x,alpha,hppa,ia64,ppc64,riscv64,sparc64 kallisto-examples deb science optional arch=all Checksums-Sha1: 50c8a540a62ab57f31aaf7deabf3687f296b6d7c 1085076 kallisto_0.48.0+dfsg.orig.tar.xz 5f317432603d010f34dd9935d6cc43f18e4a4394 7116 kallisto_0.48.0+dfsg-4.debian.tar.xz Checksums-Sha256: 304a7b7fbfa4f49b60543d476f1e1ad7b3ea3d2b53510bd6ba6bdc812e69215c 1085076 kallisto_0.48.0+dfsg.orig.tar.xz f0fa8ca0d2bb8ce6210e2c7725547397adc0e8520e3703889289524308e9b298 7116 kallisto_0.48.0+dfsg-4.debian.tar.xz Files: fcce4ec57b434469d66837f75030998e 1085076 kallisto_0.48.0+dfsg.orig.tar.xz 8e5675599154f7503ab32dff51b39063 7116 kallisto_0.48.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmQ2UFsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGlcw/9HajFHsPPPJvnV2cBeOdFZcjAc/6ETr5c ECFrVV/XR+Ga6mLmazkLIkL2O99k6DWeg2bGncC/yBuHRxl9jgmuLj04h+YRJjdF PAW4QLbLDF5i+j2ZC6EZLAE0HsVnJhcgLtHDc9KFse4Dwn/UULgIOt690GGBUWOP IsOpKx11iYLd35goUYTyDmqsC9b4I2Og8UB2zY2N/9phWNTXQQTxccgXccEjaYqz MQK6PvuPysbEu5sdr4m0ZWdZEewnrqpxjFRW/S6b2hh0n+wuMIszuxUwsevHQfTV fFAq3RWMdNEFN/Ta8nUSktfuB8+2hTkZ5N/uo8r4M+S6pI0j77y85d5VhIXFd4nK 8wY2K6rH8fly+n8H1BpebMjNwywwNGGaNW92o28kDvrRzGnTOK22h73vABdy7W1X ftvpV/Rm+CpZ6lahUO+/b9d6EXtzO55NF1Hn7pBmRWqf15O/P0Y9SwxxLANgq04n QDGDHrA6pd3no3v2Cfn1fgFEBywlo9bBuGvJipg8Hw8JxiiOzUYxC3h+ahXBuQdX jjkZE8ADZK3o4EupMQAdxXCVD0P5SCLJ6hNjSl9LEhzTN7SdrIICxIi8AG1SX2m1 c30qIZthgaU4p4VgNDKRjTuTkGmvlcXvkkx4tUU/u3cPBQvu94wszUjlyjH9xigy 0xDniwpf1Vw= =7BIM -----END PGP SIGNATURE----- Tue Mar 11 18:02:57 UTC 2025 I: Checking whether the package is not for us Tue Mar 11 18:02:57 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Tue Mar 11 18:02:57 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Tue Mar 11 18:08:14 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 13 12:25:56 -12 2026 I: pbuilder-time-stamp: 1776126356 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/2223227/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='28da34f217584f76866226501679f576' 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='2223227' 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.RtMUpntC/pbuilderrc_fNDt --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.RtMUpntC/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/2223227/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 ... 19800 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 92.6 MB of archives. After unpacking 352 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-1 [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 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 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 3.13.2-1 [1979 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-1 [10.0 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-1 [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 3.4.1-1 [1427 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 2.40.4-5 [92.4 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 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [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 3.31.6-1 [2268 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 46 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-1 [12.0 MB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 coinor-libcoinutils3v5 amd64 2.11.11+ds-5 [460 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 coinor-libosi1v5 amd64 0.108.10+ds-2 [293 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 coinor-libclp1 amd64 1.17.10+ds-1 [883 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 coinor-libcgl1 amd64 0.60.9+ds-1 [426 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 coinor-libcbc3.1 amd64 2.10.12+ds-1 [714 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 coinor-cbc amd64 2.10.12+ds-1 [16.2 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 82 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 liberror-perl all 0.17030-1 [26.9 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 git-man all 1:2.47.2-0.1 [2205 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 git amd64 1:2.47.2-0.1 [8788 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 105 http://deb.debian.org/debian trixie/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3.1 [292 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3.1 [72.0 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-attr all 25.1.0-1 [68.7 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-configargparse all 1.7-2 [31.4 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 python3-connection-pool all 0.0.3-2 [5584 B] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-datrie amd64 0.8.2-5+b2 [129 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 python3-roman all 5.0-1 [10.6 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 python3-dpath all 2.2.0-1 [19.9 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 python3-fastjsonschema all 2.21.1-1 [22.4 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 python3-smmap all 6.0.0-1 [20.1 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 python3-gitdb all 4.0.11-1 [45.5 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 python3-git all 3.1.37-3 [137 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 python3-humanfriendly all 10.0-6 [85.6 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 178 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 python3-rpds-py amd64 0.21.0-2+b1 [257 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 python3-referencing all 0.35.1-2 [23.5 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 184 http://deb.debian.org/debian trixie/main amd64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 python3-plac all 1.4.3-2 [65.7 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 python3-pulp all 2.7.0+dfsg-4 [72.4 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 python3-py all 1.11.0-4 [88.8 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 python3-ratelimiter amd64 1.2.0.post0-4 [5740 B] Get: 197 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 python3-retry all 0.9.2-3 [7088 B] Get: 200 http://deb.debian.org/debian trixie/main amd64 python3-wrapt amd64 1.15.0-4+b1 [43.6 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 python3-smart-open all 7.1.0-1 [98.7 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 python3-stopit all 1.1.2-3 [12.8 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 python3-throttler all 1.2.2-2 [7072 B] Get: 205 http://deb.debian.org/debian trixie/main amd64 python3-toposort all 1.10-2 [7336 B] Get: 206 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 python3-yte all 1.5.4-1 [13.6 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 snakemake all 7.32.4-7 [318 kB] Fetched 92.6 MB in 9s (10.1 MB/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 ... 19800 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... 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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 (5.0s) -- 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-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 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'/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' [ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o [ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.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/BUSTools.cpp.o -MF 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 [ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o [ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o cd 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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/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 [ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.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/KmerIndex.cpp.o -MF CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o.d -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/KmerIndex.cpp [ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.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/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/hash.cpp.o [ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o [ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o [ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o [ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o [ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o [ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o [ 85%] 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/Kmer.cpp.o -MF CMakeFiles/kallisto_core.dir/Kmer.cpp.o.d -o CMakeFiles/kallisto_core.dir/Kmer.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/Kmer.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/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 [ 71%] 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/ProcessReads.cpp.o -MF CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o.d -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/ProcessReads.cpp 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/PseudoBam.cpp.o -MF CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o.d -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/PseudoBam.cpp 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/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 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 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 [ 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 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/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 Apr 13 12:30:46 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 Apr 13 12:30:46 2026] Finished job 2. 1 of 4 steps (25%) done Select jobs to execute... [Mon Apr 13 12:30:46 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 Apr 13 12:30:47 2026] Finished job 3. 2 of 4 steps (50%) done Select jobs to execute... [Mon Apr 13 12:30:47 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 Apr 13 12:30:50 2026] Finished job 1. 3 of 4 steps (75%) done Select jobs to execute... [Mon Apr 13 12:30:50 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 Apr 13 12:30:50 2026] Finished job 0. 4 of 4 steps (100%) done Complete log: .snakemake/log/2026-04-13T123045.935864.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' in '../kallisto_0.48.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'kallisto-dbgsym' in '../kallisto-dbgsym_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/2223227 and its subdirectories I: Current time: Mon Apr 13 12:31:10 -12 2026 I: pbuilder-time-stamp: 1776126670 Tue Mar 11 18:08:15 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Tue Mar 11 18:08:15 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Tue Mar 11 18:11:08 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Tue Mar 11 18:11:08 UTC 2025 I: kallisto_0.48.0+dfsg-4_amd64.changes: Format: 1.8 Date: Wed, 12 Apr 2023 07:44:19 +0200 Source: kallisto Binary: kallisto kallisto-dbgsym kallisto-examples Architecture: amd64 all Version: 0.48.0+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: kallisto - near-optimal RNA-Seq quantification kallisto-examples - near-optimal RNA-Seq quantification (example data) Closes: 1004053 Changes: kallisto (0.48.0+dfsg-4) unstable; urgency=medium . [ Vagrant Cascadian ] * Remove quant_out/run_info.json to enable reproducible-builds Closes: #1004053 Checksums-Sha1: 1b55b2707762899004c693410004112192e662eb 4164744 kallisto-dbgsym_0.48.0+dfsg-4_amd64.deb b70efb23544483e68433ba9d3c761d23eca22562 1302500 kallisto-examples_0.48.0+dfsg-4_all.deb 6b45fc80631f2ed79f771360a14b36e7ac4d0cf2 10982 kallisto_0.48.0+dfsg-4_amd64.buildinfo 25cfe180e8a62b3d64658356fa69b85b5017a8b1 301408 kallisto_0.48.0+dfsg-4_amd64.deb Checksums-Sha256: 45c14695ff50f9a32227e155c3b81037b573aa690674da5a9560c5c56e4fadf4 4164744 kallisto-dbgsym_0.48.0+dfsg-4_amd64.deb 4612681995bfa92ff9c7a31fa9651da33a3b49aa7ae6f96f6af9f1769fb4a4b8 1302500 kallisto-examples_0.48.0+dfsg-4_all.deb 08aae79ac69534ad28bf191439f77be1bce96c912244958abfd3703136e0ca0b 10982 kallisto_0.48.0+dfsg-4_amd64.buildinfo 0e003e47d0952d64db107dbb8d6cbe53cbfc44fe940175158e7d60ccd8651368 301408 kallisto_0.48.0+dfsg-4_amd64.deb Files: 994542cc9c9689f9678b031289294bd3 4164744 debug optional kallisto-dbgsym_0.48.0+dfsg-4_amd64.deb 59f632b001ef290f2f1c91d977c5ec1a 1302500 science optional kallisto-examples_0.48.0+dfsg-4_all.deb 6ae539eda8a6151dc674f5a63093c500 10982 science optional kallisto_0.48.0+dfsg-4_amd64.buildinfo 1bfae4ae32024c859af9d34e694221cf 301408 science optional kallisto_0.48.0+dfsg-4_amd64.deb Tue Mar 11 18:11:09 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_4-47497.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.RtMUpntC/kallisto_0.48.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.RtMUpntC/kallisto_0.48.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.RtMUpntC/kallisto_0.48.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.RtMUpntC/b1/kallisto_0.48.0+dfsg-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.RtMUpntC/b2/kallisto_0.48.0+dfsg-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 219ms CPU time consumed: 219ms Tue Mar 11 18:11:10 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Tue Mar 11 18:11:10 UTC 2025 I: kallisto from trixie built successfully and reproducibly on amd64. Tue Mar 11 18:11:11 UTC 2025 I: Submitting .buildinfo files to external archives: Tue Mar 11 18:11:11 UTC 2025 I: Submitting 12K b1/kallisto_0.48.0+dfsg-4_amd64.buildinfo.asc Tue Mar 11 18:11:12 UTC 2025 I: Submitting 12K b2/kallisto_0.48.0+dfsg-4_amd64.buildinfo.asc Tue Mar 11 18:11:12 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Mar 11 18:11:12 UTC 2025 I: Done submitting .buildinfo files. Tue Mar 11 18:11:12 UTC 2025 I: Removing signed kallisto_0.48.0+dfsg-4_amd64.buildinfo.asc files: removed './b1/kallisto_0.48.0+dfsg-4_amd64.buildinfo.asc' removed './b2/kallisto_0.48.0+dfsg-4_amd64.buildinfo.asc'