Sun Jan 26 07:48:53 UTC 2025 I: starting to build kallisto/trixie/arm64 on jenkins on '2025-01-26 07:48'
Sun Jan 26 07:48:53 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_1/57421/console.log
Sun Jan 26 07:48:53 UTC 2025 I: Downloading source for trixie/kallisto=0.48.0+dfsg-4
--2025-01-26 07:48:53-- 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% 327M=0s
2025-01-26 07:48:53 (327 MB/s) - ‘kallisto_0.48.0+dfsg-4.dsc’ saved [2287/2287]
Sun Jan 26 07:48:53 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 <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
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 <!nocheck>
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:
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5f317432603d010f34dd9935d6cc43f18e4a4394 7116 kallisto_0.48.0+dfsg-4.debian.tar.xz
Checksums-Sha256:
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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
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Sun Jan 26 07:48:53 UTC 2025 I: Checking whether the package is not for us
Sun Jan 26 07:48:53 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net.
Sun Jan 26 07:48:53 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net.
Sun Jan 26 07:50:38 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Feb 28 02:11:54 -12 2026
I: pbuilder-time-stamp: 1772287914
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/804997/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='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='9c392287ac7044059ea59beed3bd72e2'
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='804997'
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.Q6nwQWb1/pbuilderrc_f4An --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.Q6nwQWb1/b1 --logfile b1/build.log kallisto_0.48.0+dfsg-4.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/804997/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19970 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} libnsl2{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-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} libtirpc-common{a} libtirpc3t64{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} python3.12{a} python3.12-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, 211 newly installed, 0 to remove and 0 not upgraded.
Need to get 87.1 MB of archives. After unpacking 355 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.8-5 [810 kB]
Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.8-5 [1934 kB]
Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.8-1 [26.9 kB]
Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB]
Get: 8 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB]
Get: 9 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB]
Get: 10 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB]
Get: 11 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB]
Get: 12 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B]
Get: 13 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB]
Get: 14 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB]
Get: 15 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 16 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB]
Get: 18 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB]
Get: 19 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB]
Get: 20 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.8-5 [1904 kB]
Get: 21 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.8-5 [677 kB]
Get: 22 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.8-1 [9788 B]
Get: 23 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.8-1 [27.9 kB]
Get: 24 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB]
Get: 25 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB]
Get: 26 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-6 [872 kB]
Get: 27 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 28 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB]
Get: 29 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB]
Get: 30 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 31 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 32 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 33 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB]
Get: 34 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 35 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 36 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB]
Get: 37 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 38 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 39 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 40 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB]
Get: 41 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 42 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 43 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB]
Get: 44 http://deb.debian.org/debian trixie/main arm64 libcatch2-dev arm64 3.7.1-0.4 [588 kB]
Get: 45 http://deb.debian.org/debian trixie/main arm64 catch2 all 3.7.1-0.4 [5052 B]
Get: 46 http://deb.debian.org/debian trixie/main arm64 cmake-data all 3.31.4-2 [2267 kB]
Get: 47 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 48 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 49 http://deb.debian.org/debian trixie/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB]
Get: 50 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB]
Get: 51 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 52 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB]
Get: 53 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB]
Get: 54 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB]
Get: 55 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB]
Get: 56 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB]
Get: 57 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB]
Get: 58 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB]
Get: 59 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB]
Get: 60 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB]
Get: 61 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB]
Get: 62 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB]
Get: 63 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.11.1-1+b1 [324 kB]
Get: 64 http://deb.debian.org/debian trixie/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB]
Get: 65 http://deb.debian.org/debian trixie/main arm64 librhash1 arm64 1.4.5-1 [129 kB]
Get: 66 http://deb.debian.org/debian trixie/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB]
Get: 67 http://deb.debian.org/debian trixie/main arm64 cmake arm64 3.31.4-2 [9898 kB]
Get: 68 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB]
Get: 69 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB]
Get: 70 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB]
Get: 71 http://deb.debian.org/debian trixie/main arm64 coinor-libcoinutils3v5 arm64 2.11.11+ds-2 [397 kB]
Get: 72 http://deb.debian.org/debian trixie/main arm64 coinor-libosi1v5 arm64 0.108.10+ds-1+b1 [248 kB]
Get: 73 http://deb.debian.org/debian trixie/main arm64 coinor-libclp1 arm64 1.17.10+ds-1 [751 kB]
Get: 74 http://deb.debian.org/debian trixie/main arm64 coinor-libcgl1 arm64 0.60.9+ds-1 [359 kB]
Get: 75 http://deb.debian.org/debian trixie/main arm64 coinor-libcbc3.1 arm64 2.10.12+ds-1 [615 kB]
Get: 76 http://deb.debian.org/debian trixie/main arm64 coinor-cbc arm64 2.10.12+ds-1 [16.3 kB]
Get: 77 http://deb.debian.org/debian trixie/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB]
Get: 78 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB]
Get: 79 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB]
Get: 80 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 81 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 82 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 83 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 84 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 85 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 86 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB]
Get: 87 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 88 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 89 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB]
Get: 90 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB]
Get: 91 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 92 http://deb.debian.org/debian trixie/main arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB]
Get: 93 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB]
Get: 94 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB]
Get: 95 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB]
Get: 96 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.1-1+b1 [331 kB]
Get: 97 http://deb.debian.org/debian trixie/main arm64 liberror-perl all 0.17029-2 [29.0 kB]
Get: 98 http://deb.debian.org/debian trixie/main arm64 git-man all 1:2.45.2-1 [2158 kB]
Get: 99 http://deb.debian.org/debian trixie/main arm64 git arm64 1:2.45.2-1 [8513 kB]
Get: 100 http://deb.debian.org/debian trixie/main arm64 hdf5-helpers arm64 1.14.5+repack-3 [26.6 kB]
Get: 101 http://deb.debian.org/debian trixie/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB]
Get: 102 http://deb.debian.org/debian trixie/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB]
Get: 103 http://deb.debian.org/debian trixie/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB]
Get: 104 http://deb.debian.org/debian trixie/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB]
Get: 105 http://deb.debian.org/debian trixie/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB]
Get: 106 http://deb.debian.org/debian trixie/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB]
Get: 107 http://deb.debian.org/debian trixie/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B]
Get: 108 http://deb.debian.org/debian trixie/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB]
Get: 109 http://deb.debian.org/debian trixie/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB]
Get: 110 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB]
Get: 111 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB]
Get: 112 http://deb.debian.org/debian trixie/main arm64 libunbound8 arm64 1.22.0-1 [553 kB]
Get: 113 http://deb.debian.org/debian trixie/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB]
Get: 114 http://deb.debian.org/debian trixie/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB]
Get: 115 http://deb.debian.org/debian trixie/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB]
Get: 116 http://deb.debian.org/debian trixie/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB]
Get: 117 http://deb.debian.org/debian trixie/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB]
Get: 118 http://deb.debian.org/debian trixie/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB]
Get: 119 http://deb.debian.org/debian trixie/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB]
Get: 120 http://deb.debian.org/debian trixie/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB]
Get: 121 http://deb.debian.org/debian trixie/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB]
Get: 122 http://deb.debian.org/debian trixie/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB]
Get: 123 http://deb.debian.org/debian trixie/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB]
Get: 124 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get: 125 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get: 126 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Get: 127 http://deb.debian.org/debian trixie/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB]
Get: 128 http://deb.debian.org/debian trixie/main arm64 libnghttp3-dev arm64 1.6.0-2 [86.5 kB]
Get: 129 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.9.1-1 [23.0 kB]
Get: 130 http://deb.debian.org/debian trixie/main arm64 libngtcp2-dev arm64 1.9.1-1 [162 kB]
Get: 131 http://deb.debian.org/debian trixie/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB]
Get: 132 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get: 133 http://deb.debian.org/debian trixie/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB]
Get: 134 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.4.0-2 [3234 kB]
Get: 135 http://deb.debian.org/debian trixie/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB]
Get: 136 http://deb.debian.org/debian trixie/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB]
Get: 137 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.11.1-1+b1 [461 kB]
Get: 138 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB]
Get: 139 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB]
Get: 140 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.23-1+b1 [51.4 kB]
Get: 141 http://deb.debian.org/debian trixie/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB]
Get: 142 http://deb.debian.org/debian trixie/main arm64 libhdf5-cpp-310 arm64 1.14.5+repack-3 [121 kB]
Get: 143 http://deb.debian.org/debian trixie/main arm64 libhdf5-fortran-310 arm64 1.14.5+repack-3 [110 kB]
Get: 144 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB]
Get: 145 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-fortran-310 arm64 1.14.5+repack-3 [42.1 kB]
Get: 146 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-cpp-310 arm64 1.14.5+repack-3 [24.4 kB]
Get: 147 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB]
Get: 148 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB]
Get: 149 http://deb.debian.org/debian trixie/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB]
Get: 150 http://deb.debian.org/debian trixie/main arm64 libhdf5-dev arm64 1.14.5+repack-3 [3225 kB]
Get: 151 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB]
Get: 152 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB]
Get: 153 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB]
Get: 154 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB]
Get: 155 http://deb.debian.org/debian trixie/main arm64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB]
Get: 156 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 157 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB]
Get: 158 http://deb.debian.org/debian trixie/main arm64 python3-attr all 24.3.0-1 [68.8 kB]
Get: 159 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 160 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.12.14+ds-1 [9624 B]
Get: 161 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 162 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB]
Get: 163 http://deb.debian.org/debian trixie/main arm64 python3-configargparse all 1.7-2 [31.4 kB]
Get: 164 http://deb.debian.org/debian trixie/main arm64 python3-connection-pool all 0.0.3-2 [5584 B]
Get: 165 http://deb.debian.org/debian trixie/main arm64 python3-datrie arm64 0.8.2-5+b1 [145 kB]
Get: 166 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get: 167 http://deb.debian.org/debian trixie/main arm64 python3-roman all 4.2-1 [10.4 kB]
Get: 168 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 169 http://deb.debian.org/debian trixie/main arm64 python3-dpath all 2.2.0-1 [19.9 kB]
Get: 170 http://deb.debian.org/debian trixie/main arm64 python3-fastjsonschema all 2.21.1-1 [22.4 kB]
Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-smmap all 6.0.0-1 [20.1 kB]
Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-gitdb all 4.0.11-1 [45.5 kB]
Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-git all 3.1.37-3 [137 kB]
Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-humanfriendly all 10.0-6 [85.6 kB]
Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB]
Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB]
Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.3-2 [120 kB]
Get: 184 http://deb.debian.org/debian trixie/main arm64 python3-rpds-py arm64 0.21.0-2 [259 kB]
Get: 185 http://deb.debian.org/debian trixie/main arm64 python3-referencing all 0.35.1-2 [23.5 kB]
Get: 186 http://deb.debian.org/debian trixie/main arm64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B]
Get: 187 http://deb.debian.org/debian trixie/main arm64 python3-jsonschema all 4.19.2-6 [71.4 kB]
Get: 188 http://deb.debian.org/debian trixie/main arm64 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get: 189 http://deb.debian.org/debian trixie/main arm64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB]
Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-jupyter-core all 5.7.2-5 [35.3 kB]
Get: 191 http://deb.debian.org/debian trixie/main arm64 python3-nbformat all 5.9.1-1 [45.1 kB]
Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB]
Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-plac all 1.4.3-2 [65.7 kB]
Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-psutil arm64 5.9.8-2+b1 [226 kB]
Get: 196 http://deb.debian.org/debian trixie/main arm64 python3-pyparsing all 3.1.2-1 [146 kB]
Get: 197 http://deb.debian.org/debian trixie/main arm64 python3-pulp all 2.7.0+dfsg-4 [72.4 kB]
Get: 198 http://deb.debian.org/debian trixie/main arm64 python3-py all 1.11.0-2 [88.7 kB]
Get: 199 http://deb.debian.org/debian trixie/main arm64 python3-ratelimiter arm64 1.2.0.post0-4 [5740 B]
Get: 200 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.3.0-1 [114 kB]
Get: 201 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get: 202 http://deb.debian.org/debian trixie/main arm64 python3-retry all 0.9.2-3 [7088 B]
Get: 203 http://deb.debian.org/debian trixie/main arm64 python3-wrapt arm64 1.15.0-4 [42.6 kB]
Get: 204 http://deb.debian.org/debian trixie/main arm64 python3-smart-open all 7.1.0-1 [98.7 kB]
Get: 205 http://deb.debian.org/debian trixie/main arm64 python3-stopit all 1.1.2-3 [12.8 kB]
Get: 206 http://deb.debian.org/debian trixie/main arm64 python3-tabulate all 0.9.0-1 [45.9 kB]
Get: 207 http://deb.debian.org/debian trixie/main arm64 python3-throttler all 1.2.2-2 [7072 B]
Get: 208 http://deb.debian.org/debian trixie/main arm64 python3-toposort all 1.10-2 [7336 B]
Get: 209 http://deb.debian.org/debian trixie/main arm64 python3-yaml arm64 6.0.2-1+b1 [148 kB]
Get: 210 http://deb.debian.org/debian trixie/main arm64 python3-yte all 1.5.4-1 [13.6 kB]
Get: 211 http://deb.debian.org/debian trixie/main arm64 snakemake all 7.32.4-6 [318 kB]
Fetched 87.1 MB in 1s (114 MB/s)
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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 <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
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dh_update_autotools_config
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make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg'
dh_auto_configure -- -DDEBIAN_BUILD=1 -DLINK=shared -DBUILD_FUNCTESTING=1
cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DDEBIAN_BUILD=1 -DLINK=shared -DBUILD_FUNCTESTING=1 ..
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is GNU 14.2.0
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shared build
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Functional testing enabled.
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dh_auto_build
cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1
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cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/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
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/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-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/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-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -MF CMakeFiles/kallisto_core.dir/H5Writer.cpp.o.d -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/H5Writer.cpp
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/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
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/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-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/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
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/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-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/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
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cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -MF CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o.d -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/PlaintextWriter.cpp
[ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -MF CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o.d -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/ProcessReads.cpp
[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -MF CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o.d -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/PseudoBam.cpp
[ 66%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/common.cpp.o -MF CMakeFiles/kallisto_core.dir/common.cpp.o.d -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/common.cpp
[ 71%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o
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[ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o
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[ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o
[ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/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-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/weights.cpp.o -MF CMakeFiles/kallisto_core.dir/weights.cpp.o.d -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/weights.cpp
[ 90%] Linking CXX static library libkallisto_core.a
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/kallisto_core.dir/cmake_clean_target.cmake
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kallisto_core.dir/link.txt --verbose=1
/usr/bin/ar qc libkallisto_core.a CMakeFiles/kallisto_core.dir/BUSData.cpp.o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o CMakeFiles/kallisto_core.dir/Kmer.cpp.o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o CMakeFiles/kallisto_core.dir/Merge.cpp.o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o CMakeFiles/kallisto_core.dir/common.cpp.o CMakeFiles/kallisto_core.dir/h5utils.cpp.o CMakeFiles/kallisto_core.dir/hash.cpp.o CMakeFiles/kallisto_core.dir/main.cpp.o CMakeFiles/kallisto_core.dir/weights.cpp.o
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[ 95%] Building CXX object src/CMakeFiles/kallisto.dir/main.cpp.o
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/main.cpp.o -MF CMakeFiles/kallisto.dir/main.cpp.o.d -o CMakeFiles/kallisto.dir/main.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/main.cpp
[100%] Linking CXX executable kallisto
cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kallisto.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/kallisto.dir/link.d CMakeFiles/kallisto.dir/main.cpp.o -o kallisto libkallisto_core.a -lpthread -lhts libkallisto_core.a -lz -lrt
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[100%] Built target kallisto
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dh_auto_test
cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12
make[2]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu'
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cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kallisto-0.48.0+dfsg /build/reproducible-path/kallisto-0.48.0+dfsg/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake "--color="
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[ 90%] Built target kallisto_core
make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend
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cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kallisto-0.48.0+dfsg /build/reproducible-path/kallisto-0.48.0+dfsg/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/kallisto.dir/DependInfo.cmake "--color="
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[100%] Built target kallisto
make -f CMakeFiles/test.dir/build.make CMakeFiles/test.dir/depend
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cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kallisto-0.48.0+dfsg /build/reproducible-path/kallisto-0.48.0+dfsg /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles/test.dir/DependInfo.cmake "--color="
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make[5]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu'
/bin/bash ./func_tests/runtests.sh
[INDEX]
./src/kallisto index -i ./func_tests/basic7.idx -k 7 ./func_tests/simple.fasta
^[OK]
./src/kallisto inspect ./func_tests/basic7.idx 2>&1|head -4
^[Output OK]
./src/kallisto index -i ./func_tests/basic9.idx -k 9 ./func_tests/simple.fasta
^[OK]
./src/kallisto inspect ./func_tests/basic9.idx 2>&1|head -4
^[Output OK]
./src/kallisto index -i ./func_tests/nonATCG.idx -k 5 ./func_tests/nonATCG.fasta
^[OK]
./src/kallisto inspect ./func_tests/nonATCG.idx 2>&1|head -4
^[Output OK]
./src/kallisto index -i ./func_tests/polyA.idx -k 5 ./func_tests/polyA.fasta
^[OK]
./src/kallisto inspect ./func_tests/polyA.idx 2>&1|head -4
^[Output OK]
./src/kallisto index -i ./func_tests/basic_fail.idx -k 10 ./func_tests/simple.fasta
^[OK - Exited non-zero as expected]
./src/kallisto index -i ./func_tests/duplicates_fail.idx -k 11 ./func_tests/duplicates.fasta
^[OK - Exited non-zero as expected]
./src/kallisto index -i ./func_tests/duplicates.idx -k 11 --make-unique ./func_tests/duplicates.fasta
^[OK]
./src/kallisto inspect ./func_tests/duplicates.idx 2>&1|head -4
^[Output OK]
./src/kallisto quant -o ./func_tests/quantbasic -i ./func_tests/basic7.idx --single -l 5 -s 2 ./func_tests/small.fastq.gz
^[OK]
cat ./func_tests/quantbasic/abundance.tsv
^[Output OK]
./src/kallisto quant -o ./func_tests/quantnonATCG -i ./func_tests/nonATCG.idx --single -l 5 -s 2 ./func_tests/small.fastq.gz
^[OK]
cat ./func_tests/quantnonATCG/abundance.tsv
^[Output OK]
./src/kallisto quant -o ./func_tests/quantpolyA -i ./func_tests/polyA.idx --single -l 5 -s 2 ./func_tests/small.fastq.gz
^[OK]
cat ./func_tests/quantpolyA/abundance.tsv
^[Output OK]
./src/kallisto quant -o ./func_tests/quantduplicates -i ./func_tests/duplicates.idx --single -l 5 -s 2 ./func_tests/small.fastq.gz
^[OK]
cat ./func_tests/quantduplicates/abundance.tsv
^[Output OK]
./src/kallisto quant -o ./func_tests/quantbasicfr -i ./func_tests/basic7.idx --single --fr-stranded -l 5 -s 2 ./func_tests/small.fastq.gz
^[OK]
cat ./func_tests/quantbasicfr/abundance.tsv
^[Output OK]
./src/kallisto quant -o ./func_tests/quantbasicrf -i ./func_tests/basic7.idx --single --rf-stranded -l 5 -s 2 ./func_tests/small.fastq.gz
^[OK]
cat ./func_tests/quantbasicrf/abundance.tsv
^[Output OK]
./src/kallisto quant -o ./func_tests/quantbasicpaired -i ./func_tests/basic7.idx ./func_tests/simple_pair1.fastq.gz ./func_tests/simple_pair2.fastq.gz
^[OK]
cat ./func_tests/quantbasicpaired/abundance.tsv
^[Output OK]
./src/kallisto quant -o ./func_tests/quantbasicpairedfr -i ./func_tests/basic7.idx --fr-stranded ./func_tests/simple_pair1.fastq.gz ./func_tests/simple_pair2.fastq.gz
^[OK]
cat ./func_tests/quantbasicpairedfr/abundance.tsv
^[Output OK]
./src/kallisto quant -o ./func_tests/quantbasicpairedrf -i ./func_tests/basic7.idx --rf-stranded ./func_tests/simple_pair1.fastq.gz ./func_tests/simple_pair2.fastq.gz
^[OK]
cat ./func_tests/quantbasicpairedrf/abundance.tsv
^[Output OK]
./src/kallisto quant -o ./func_tests/quantbasicpairedmultfr -i ./func_tests/basic7.idx --fr-stranded ./func_tests/simple_pair1.fastq.gz ./func_tests/simple_pair2.fastq.gz ./func_tests/simple_pair2.fastq.gz ./func_tests/simple_pair1.fastq.gz
^[OK]
cat ./func_tests/quantbasicpairedmultfr/abundance.tsv
^[Output OK]
./src/kallisto quant -o ./func_tests/quantlarge -t 12 -i ./func_tests/basic7.idx --single -l 5 -s 2 ./func_tests/large.fastq.gz ./func_tests/large.fastq.gz ./func_tests/large.fastq.gz ./func_tests/large.fastq.gz ./func_tests/large.fastq.gz
^[OK]
cat ./func_tests/quantlarge/abundance.tsv
^[Output OK]
Not testing with bustools as tests fail with bustools
make[5]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu'
[100%] Built target test
make[4]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0
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make[2]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu'
cd test && PATH=$(find ../obj-* -name src):/usr/sbin:/usr/bin:/sbin:/bin:/usr/games HOME=$(mktemp --directory) snakemake --cores 1
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count
-------------- -------
all 1
index 1
kallisto_bus 1
kallisto_quant 1
total 4
Select jobs to execute...
[Sat Feb 28 02:13:26 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
[Sat Feb 28 02:13:26 2026]
Finished job 2.
1 of 4 steps (25%) done
Select jobs to execute...
[Sat Feb 28 02:13:26 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
[Sat Feb 28 02:13:28 2026]
Finished job 1.
2 of 4 steps (50%) done
Select jobs to execute...
[Sat Feb 28 02:13:28 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
[Sat Feb 28 02:13:28 2026]
Finished job 3.
3 of 4 steps (75%) done
Select jobs to execute...
[Sat Feb 28 02:13:28 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
[Sat Feb 28 02:13:28 2026]
Finished job 0.
4 of 4 steps (100%) done
Complete log: .snakemake/log/2026-02-28T021326.500374.snakemake.log
rm -rf test/.snakemake test/bus_out test/quant_out/run_info.json test/transcripts.kidx.gz
make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/kallisto-0.48.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/reproducible-path/kallisto-0.48.0+dfsg/debian/tmp/usr/bin/kallisto
make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu'
dh_install
dh_installdocs
dh_installchangelogs
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'kallisto' in '../kallisto_0.48.0+dfsg-4_arm64.deb'.
dpkg-deb: building package 'kallisto-dbgsym' in '../kallisto-dbgsym_0.48.0+dfsg-4_arm64.deb'.
dpkg-deb: building package 'kallisto-examples' in '../kallisto-examples_0.48.0+dfsg-4_all.deb'.
dpkg-genbuildinfo --build=binary -O../kallisto_0.48.0+dfsg-4_arm64.buildinfo
dpkg-genchanges --build=binary -O../kallisto_0.48.0+dfsg-4_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: 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/804997 and its subdirectories
I: Current time: Sat Feb 28 02:13:36 -12 2026
I: pbuilder-time-stamp: 1772288016
Sun Jan 26 07:50:39 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net.
Sun Jan 26 07:50:39 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net.
Sun Jan 26 07:56:20 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net.
Sun Jan 26 07:56:21 UTC 2025 I: kallisto_0.48.0+dfsg-4_arm64.changes:
Format: 1.8
Date: Wed, 12 Apr 2023 07:44:19 +0200
Source: kallisto
Binary: kallisto kallisto-dbgsym kallisto-examples
Architecture: arm64 all
Version: 0.48.0+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
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:
2aa9be04e5150bdda605e574aef3d9720f83bbcd 3991432 kallisto-dbgsym_0.48.0+dfsg-4_arm64.deb
b70efb23544483e68433ba9d3c761d23eca22562 1302500 kallisto-examples_0.48.0+dfsg-4_all.deb
620bb78a785e5e7d9e6111a79b233c4a141dfcfa 11193 kallisto_0.48.0+dfsg-4_arm64.buildinfo
f06168ee16bbb8c6a1697846f536ad30f251df69 256332 kallisto_0.48.0+dfsg-4_arm64.deb
Checksums-Sha256:
a011d661df4705e8b656a88e900865c04f0a8767d2d678ba04503b2575779e47 3991432 kallisto-dbgsym_0.48.0+dfsg-4_arm64.deb
4612681995bfa92ff9c7a31fa9651da33a3b49aa7ae6f96f6af9f1769fb4a4b8 1302500 kallisto-examples_0.48.0+dfsg-4_all.deb
77a71ea734a1036e0ab359e67a5c07fccc6f59be748b4621a8bd518fa126774d 11193 kallisto_0.48.0+dfsg-4_arm64.buildinfo
85a5437024fd9e51e8e6b718ea526b1d4889435e7fefcf56ec435e04313016f2 256332 kallisto_0.48.0+dfsg-4_arm64.deb
Files:
912a8487b5be06909d02f2a8fbcea1ac 3991432 debug optional kallisto-dbgsym_0.48.0+dfsg-4_arm64.deb
59f632b001ef290f2f1c91d977c5ec1a 1302500 science optional kallisto-examples_0.48.0+dfsg-4_all.deb
96a341c4770b8fa5a0edb202442f19b9 11193 science optional kallisto_0.48.0+dfsg-4_arm64.buildinfo
4f31b1053fa1893b6643a6895d4951df 256332 science optional kallisto_0.48.0+dfsg-4_arm64.deb
Sun Jan 26 07:56:22 UTC 2025 I: diffoscope 286 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_1-57421.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Q6nwQWb1/kallisto_0.48.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Q6nwQWb1/kallisto_0.48.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Q6nwQWb1/kallisto_0.48.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Q6nwQWb1/b1/kallisto_0.48.0+dfsg-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Q6nwQWb1/b2/kallisto_0.48.0+dfsg-4_arm64.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: 0.004s)
0.004s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 240ms
CPU time consumed: 238ms
Sun Jan 26 07:56:23 UTC 2025 I: diffoscope 286 found no differences in the changes files, and a .buildinfo file also exists.
Sun Jan 26 07:56:23 UTC 2025 I: kallisto from trixie built successfully and reproducibly on arm64.
Sun Jan 26 07:56:24 UTC 2025 I: Submitting .buildinfo files to external archives:
Sun Jan 26 07:56:24 UTC 2025 I: Submitting 12K b1/kallisto_0.48.0+dfsg-4_arm64.buildinfo.asc
Sun Jan 26 07:56:25 UTC 2025 I: Submitting 12K b2/kallisto_0.48.0+dfsg-4_arm64.buildinfo.asc
Sun Jan 26 07:56:26 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Jan 26 07:56:26 UTC 2025 I: Done submitting .buildinfo files.
Sun Jan 26 07:56:26 UTC 2025 I: Removing signed kallisto_0.48.0+dfsg-4_arm64.buildinfo.asc files:
removed './b1/kallisto_0.48.0+dfsg-4_arm64.buildinfo.asc'
removed './b2/kallisto_0.48.0+dfsg-4_arm64.buildinfo.asc'