Wed Dec 11 11:49:00 UTC 2024 I: starting to build mapdamage/trixie/arm64 on jenkins on '2024-12-11 11:48' Wed Dec 11 11:49:00 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_17/67746/console.log Wed Dec 11 11:49:00 UTC 2024 I: Downloading source for trixie/mapdamage=2.2.2+dfsg-1 --2024-12-11 11:49:01-- http://deb.debian.org/debian/pool/main/m/mapdamage/mapdamage_2.2.2%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2396 (2.3K) [text/prs.lines.tag] Saving to: ‘mapdamage_2.2.2+dfsg-1.dsc’ 0K .. 100% 389M=0s 2024-12-11 11:49:01 (389 MB/s) - ‘mapdamage_2.2.2+dfsg-1.dsc’ saved [2396/2396] Wed Dec 11 11:49:01 UTC 2024 I: mapdamage_2.2.2+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mapdamage Binary: mapdamage Architecture: all Version: 2.2.2+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://ginolhac.github.io/mapDamage/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/mapdamage Vcs-Git: https://salsa.debian.org/med-team/mapdamage.git Testsuite: autopkgtest Testsuite-Triggers: gfortran, r-cran-runit Build-Depends: debhelper-compat (= 13), python3, dh-python, python3-setuptools, python3-pysam , seqtk , r-base-core , r-cran-gam , r-cran-ggplot2 , r-cran-inline Package-List: mapdamage deb science optional arch=all Checksums-Sha1: 174ba18693f2e4d160f3033fa0afc56432768350 36208 mapdamage_2.2.2+dfsg.orig.tar.xz 9723e135bf2a567898b017ef64a6a6b136306915 7824 mapdamage_2.2.2+dfsg-1.debian.tar.xz Checksums-Sha256: 6fb12f1401138dabebc637ffa11131f511113f63a8eda50e0e62e977552ef896 36208 mapdamage_2.2.2+dfsg.orig.tar.xz d894df2bf45f691b5798d6ffdaa6c635620a389e5f73a8c73666882ca45fd82b 7824 mapdamage_2.2.2+dfsg-1.debian.tar.xz Files: 9c7daa5b50ad1f6c67482a0ad5083a18 36208 mapdamage_2.2.2+dfsg.orig.tar.xz 7813a454144adcbb0b01cfdd618cb47c 7824 mapdamage_2.2.2+dfsg-1.debian.tar.xz Dgit: 3b3215985c9af2593201a549aefba15b22f276b0 debian archive/debian/2.2.2+dfsg-1 https://git.dgit.debian.org/mapdamage -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbLYHwUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoFCQ/9E/h+zSa46/V/7oupwQo00gockhXv FrOg47pSrloYnR1KeQEsv8j+PwHI9yFY2LpsOR8eJ2rOLTGinKkEgfT8M+sIPVJR NrxKjLuWZvo/tBzJZWiloiBtnifJbF58lMAnmkD/yH24hReHYMU1lx/lroUZh/M2 FyCvXH1HEV0p2SGGOVh2E5XC2KxNo45eZXa7ZeMQqys4lnbSsYqnwjcn1N3YwdbI o7uXj5s/EfgK/aFMtBevE7ZVFecvfIytYXOBHAExCV2/Lz5V7zp1vvWKfCufCZtF GvKyf51m4L2RLtrBKCY3p4cjMunaj/XB1pRL33EiTuQjL044JdRGKgUTva4ATMx7 OmFqjwjEMpLNcVIvsvLmoQ0rT1GDbGpD/8TaZOep36+qRUMUg1Rd6T6+0Vp6qs7a qjdOajKaPN5Qys49qHnlImrXpnlGrXZraVFqYSTF90k64vGNhrLkCtETJn3VuFGC iVEsFpxx+A/Dt1EUnI9CYr3dk2QsP56QTz6KtTurfd90X33gi8m7ysUypjkbLudU 5MipYb3CwHHf0O0AltniOMa2zlh0+fnHD09OoAcwFWkFFVwvpTpzM8AwOhWQa2ko Oj0xUuvoy/QEk3sBIUdUIBMIyXAyRBs0ZjNcr24S+Q5NyS9eRwEbzDigaDoHccEp /gjxlYqZg79Ic4k= =wYp6 -----END PGP SIGNATURE----- Wed Dec 11 11:49:01 UTC 2024 I: Checking whether the package is not for us Wed Dec 11 11:49:01 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Wed Dec 11 11:49:01 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Wed Dec 11 11:50:01 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 13 06:12:02 -12 2026 I: pbuilder-time-stamp: 1768327922 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 [mapdamage_2.2.2+dfsg-1.dsc] I: copying [./mapdamage_2.2.2+dfsg.orig.tar.xz] I: copying [./mapdamage_2.2.2+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 25 16:49:00 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mapdamage_2.2.2+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting mapdamage in mapdamage-2.2.2+dfsg dpkg-source: info: unpacking mapdamage_2.2.2+dfsg.orig.tar.xz dpkg-source: info: unpacking mapdamage_2.2.2+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_seqtk.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/801310/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='2556edd145be470086203305fea1ef69' 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='801310' 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.t5nOD47e/pbuilderrc_dtfi --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.t5nOD47e/b1 --logfile b1/build.log mapdamage_2.2.2+dfsg-1.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 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/801310/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), python3, dh-python, python3-setuptools, python3-pysam, seqtk, r-base-core, r-cran-gam, r-cran-ggplot2, r-cran-inline dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20083 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 python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on seqtk; however: Package seqtk is not installed. pbuilder-satisfydepends-dummy depends on r-base-core; however: Package r-base-core is not installed. pbuilder-satisfydepends-dummy depends on r-cran-gam; however: Package r-cran-gam is not installed. pbuilder-satisfydepends-dummy depends on r-cran-ggplot2; however: Package r-cran-ggplot2 is not installed. pbuilder-satisfydepends-dummy depends on r-cran-inline; however: Package r-cran-inline 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} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libxt6t64{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-codetools{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-foreach{a} r-cran-gam{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gtable{a} r-cran-inline{a} r-cran-isoband{a} r-cran-iterators{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} readline-common{a} sensible-utils{a} seqtk{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix r-base-dev r-cran-bit64 r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dichromat r-cran-digest r-cran-dplyr r-cran-formattable r-cran-fs r-cran-generics r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-interp r-cran-jpeg r-cran-kernlab r-cran-kernsmooth r-cran-knitr r-cran-lintr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-multcomp r-cran-mvtnorm r-cran-pkgdown r-cran-png r-cran-processx r-cran-profvis r-cran-ps r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-shiny r-cran-shinyjs r-cran-stringi r-cran-svglite r-cran-testthat r-cran-tidyverse r-cran-unitizer r-cran-usethis r-cran-vcd r-cran-vdiffr r-cran-viridis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 170 newly installed, 0 to remove and 0 not upgraded. Need to get 110 MB of archives. After unpacking 309 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.8-1 [808 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 3.12.8-1 [1930 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.6-1 [26.7 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-4 [256 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2~rc1-2 [23.7 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 12 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.8-1 [1905 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.8-1 [677 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-6 [1130 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-12 [91.4 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0045 [45.2 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 63 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20241024 [109 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-1.1+b1 [463 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 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 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.55.0+ds-3 [212 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.55.0+ds-3 [52.1 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.55.0+ds-3 [33.4 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libpaper1 arm64 1.1.29+b2 [13.0 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libpaper-utils arm64 1.1.29+b2 [9128 B] Get: 123 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b2 [51.6 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b2 [17.1 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b1 [173 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b3 [3903 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 zip arm64 3.0-14+b1 [227 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 r-base-core arm64 4.4.2-1 [28.0 MB] Get: 137 http://deb.debian.org/debian trixie/main arm64 r-cran-cli arm64 3.6.3-1 [1340 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1713 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 r-cran-fansi arm64 1.0.5-1+b1 [626 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 r-cran-farver arm64 2.1.2-1+b1 [1397 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 r-cran-iterators all 1.0.14-1 [337 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 r-cran-foreach all 1.5.2-1 [122 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 r-cran-gam arm64 1.22-5-1 [387 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 r-cran-glue arm64 1.8.0-1 [165 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 r-cran-rlang arm64 1.1.4-1+b1 [1708 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 r-cran-isoband arm64 0.2.7-1+b1 [1614 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 r-cran-mass arm64 7.3-61-1+b1 [1112 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 r-cran-lattice arm64 0.22-6-1+b1 [1417 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 r-cran-nlme arm64 3.1.166-1 [2326 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 r-cran-matrix arm64 1.7-1-1 [4023 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 r-cran-mgcv arm64 1.9-1-1+b1 [3218 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 r-cran-scales all 1.3.0-1 [677 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 r-cran-magrittr arm64 2.0.3-1+b1 [203 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 r-cran-utf8 arm64 1.2.4-1+b1 [133 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 r-cran-vctrs arm64 0.6.5-1+b1 [1378 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 r-cran-tibble arm64 3.2.1+dfsg-2+b1 [425 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 r-cran-inline all 0.3.20-1 [132 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 seqtk arm64 1.4-2+b1 [33.0 kB] Fetched 110 MB in 1s (189 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20083 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-1_arm64.deb ... Unpacking python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-minimal:arm64 (3.12.8-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20403 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-1_arm64.deb ... Unpacking python3.12 (3.12.8-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21466 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... 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Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b1) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libhts3t64:arm64 (1.20+ds-2) ... Setting up libpangoft2-1.0-0:arm64 (1.55.0+ds-3) ... Setting up libpangocairo-1.0-0:arm64 (1.55.0+ds-3) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-1) ... Setting up python3.12 (3.12.8-1) ... Setting up debhelper (13.20) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-6-1+b1) ... Setting up r-cran-nlme (3.1.166-1) ... Setting up r-cran-farver (2.1.2-1+b1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-magrittr (2.0.3-1+b1) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up r-cran-codetools (0.2-20-1) ... 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Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-pysam (0.22.1+ds-2+b3) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/mapdamage-2.2.2+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 > ../mapdamage_2.2.2+dfsg-1_source.changes dpkg-buildpackage: info: source package mapdamage dpkg-buildpackage: info: source version 2.2.2+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mapdamage-2.2.2+dfsg' dh_auto_clean I: pybuild base:311: python3.12 setup.py clean 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -f mapdamage/_version.py rm -f mapdamage/tests/results/Fragmisincorporation_plot.pdf mapdamage/tests/results/Fragmisincorporation_plot.pdf mapdamage/tests/results/Length_plot.pdf mapdamage/tests/results/Length_plot.pdf rm -f mapdamage/tests/fake1.fasta.fai mapdamage/tests/results/3pGtoA_freq.txt mapdamage/tests/results/5pCtoT_freq.txt mapdamage/tests/results/Runtime_log.txt mapdamage/tests/results/dnacomp.txt mapdamage/tests/results/lgdistribution.txt mapdamage/tests/results/misincorporation.txt mapdamage/tests/test.rescaled.sam make[1]: Leaving directory '/build/reproducible-path/mapdamage-2.2.2+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/mapdamage-2.2.2+dfsg' cd mapdamage && \ PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/build/reproducible-path/mapdamage-2.2.2+dfsg/bin \ PYTHONPATH=/build/reproducible-path/mapdamage-2.2.2+dfsg/.pybuild/cpython3_3.12/build \ python3 mp_test.py Started with the command: /build/reproducible-path/mapdamage-2.2.2+dfsg/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats additional tests/results/Length_plot.pdf generated Successful run Missing the following R libraries 'Rcpp' and 'RcppGSL' The Bayesian estimation has been disabled Reading from 'tests/test.bam' Writing results to 'tests/results/' pdf tests/results/Fragmisincorporation_plot.pdf generated .. ---------------------------------------------------------------------- Ran 2 tests in 2.805s OK make[1]: Leaving directory '/build/reproducible-path/mapdamage-2.2.2+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/mapdamage/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/mapdamage-2.2.2+dfsg/debian/mapdamage dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/mapdamage-2.2.2+dfsg' dh_python3 --no-ext-rename make[1]: Leaving directory '/build/reproducible-path/mapdamage-2.2.2+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/mapdamage-2.2.2+dfsg' dh_fixperms find debian -name checkLibraries.R -exec chmod +x \{\} \; find debian -name runGeneral.R -exec chmod +x \{\} \; make[1]: Leaving directory '/build/reproducible-path/mapdamage-2.2.2+dfsg' dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'mapdamage' in '../mapdamage_2.2.2+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../mapdamage_2.2.2+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../mapdamage_2.2.2+dfsg-1_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: including full 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/801310 and its subdirectories I: Current time: Tue Jan 13 06:13:00 -12 2026 I: pbuilder-time-stamp: 1768327980 Wed Dec 11 11:50:02 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Wed Dec 11 11:50:02 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Wed Dec 11 11:51:10 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Wed Dec 11 11:51:11 UTC 2024 I: mapdamage_2.2.2+dfsg-1_arm64.changes: Format: 1.8 Date: Sun, 25 Aug 2024 18:37:56 +0200 Source: mapdamage Binary: mapdamage Architecture: all Version: 2.2.2+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: mapdamage - tracking and quantifying damage patterns in ancient DNA sequences Changes: mapdamage (2.2.2+dfsg-1) unstable; urgency=medium . * New upstream version 2.2.2+dfsg * use_debian_packaged_seqtk.patch: unfuzz. * d/control: add myself to uploaders. * d/control: declare compliance to standards version 4.7.0. * use_debian_packaged_seqtk.patch: declare forwarding not-needed. Checksums-Sha1: 9f17503ad0cb7c166f03c857f71da19e63667e4f 42136 mapdamage_2.2.2+dfsg-1_all.deb f6989a6cb63fcc66b0b18ee5aaea2604d444b084 9215 mapdamage_2.2.2+dfsg-1_arm64.buildinfo Checksums-Sha256: 6df9312cf37e55cc255268766117d9bbb1eb25b72624c11455056ed9beb50b57 42136 mapdamage_2.2.2+dfsg-1_all.deb 45a69e338c1e92c51d0f7ff20e5c9edcbb2f9bd3abb60e93f58f64c5c0e066b1 9215 mapdamage_2.2.2+dfsg-1_arm64.buildinfo Files: ab47b0e4c159c5e39be76de9af28bddf 42136 science optional mapdamage_2.2.2+dfsg-1_all.deb a01ae27933872a01ce9d8d73bf1e0d5d 9215 science optional mapdamage_2.2.2+dfsg-1_arm64.buildinfo Wed Dec 11 11:51:12 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_17-67746.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.t5nOD47e/mapdamage_2.2.2+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.t5nOD47e/mapdamage_2.2.2+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.t5nOD47e/mapdamage_2.2.2+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.t5nOD47e/b1/mapdamage_2.2.2+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.t5nOD47e/b2/mapdamage_2.2.2+dfsg-1_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 abc.DotChangesFile ## main (total time: 0.350s) 0.350s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.015s) 0.015s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 667ms CPU time consumed: 664ms Wed Dec 11 11:51:13 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Wed Dec 11 11:51:13 UTC 2024 I: mapdamage from trixie built successfully and reproducibly on arm64. Wed Dec 11 11:51:14 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Dec 11 11:51:14 UTC 2024 I: Submitting 12K b1/mapdamage_2.2.2+dfsg-1_arm64.buildinfo.asc Wed Dec 11 11:51:15 UTC 2024 I: Submitting 12K b2/mapdamage_2.2.2+dfsg-1_arm64.buildinfo.asc Wed Dec 11 11:51:16 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Dec 11 11:51:16 UTC 2024 I: Done submitting .buildinfo files. Wed Dec 11 11:51:16 UTC 2024 I: Removing signed mapdamage_2.2.2+dfsg-1_arm64.buildinfo.asc files: removed './b1/mapdamage_2.2.2+dfsg-1_arm64.buildinfo.asc' removed './b2/mapdamage_2.2.2+dfsg-1_arm64.buildinfo.asc'