I: pbuilder: network access will be disabled during build
I: Current time: Thu Jan 23 01:45:33 +14 2025
I: pbuilder-time-stamp: 1737546333
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 [r-bioc-deseq2_1.46.0+dfsg-2.dsc]
I: copying [./r-bioc-deseq2_1.46.0+dfsg.orig.tar.xz]
I: copying [./r-bioc-deseq2_1.46.0+dfsg-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./r-bioc-deseq2_1.46.0+dfsg-2.dsc: unsupported subcommand
dpkg-source: info: extracting r-bioc-deseq2 in r-bioc-deseq2-1.46.0+dfsg
dpkg-source: info: unpacking r-bioc-deseq2_1.46.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking r-bioc-deseq2_1.46.0+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_autopkgtest.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1244240/tmp/hooks/D01_modify_environment starting
debug: Running on ionos1-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Jan 22 11:45 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/1244240/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/1244240/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
  BASH_VERSION='5.2.37(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=amd64
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
  DIRSTACK=()
  DISTRIBUTION=trixie
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=x86_64
  HOST_ARCH=amd64
  IFS=' 	
  '
  INVOCATION_ID=0e1359cdc37d49599dd05508e73eff99
  LANG=C
  LANGUAGE=et_EE:et
  LC_ALL=C
  MACHTYPE=x86_64-pc-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=1244240
  PS4='+ '
  PWD=/
  SHELL=/bin/bash
  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
  SHLVL=3
  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6MIHKxPB/pbuilderrc_sqH1 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6MIHKxPB/b2 --logfile b2/build.log r-bioc-deseq2_1.46.0+dfsg-2.dsc'
  SUDO_GID=110
  SUDO_UID=105
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://46.16.76.132:3128
I: uname -a
  Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1244240/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <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), dh-r, r-base-dev, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomicranges, r-bioc-summarizedexperiment, r-bioc-biocgenerics, r-bioc-biobase, r-bioc-biocparallel, r-cran-matrixstats, r-cran-locfit, r-cran-ggplot2 (>= 3.4.0), r-cran-rcpp, r-bioc-matrixgenerics, r-cran-rcpparmadillo, architecture-is-64-bit
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19856 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 dh-r; however:
  Package dh-r is not installed.
 pbuilder-satisfydepends-dummy depends on r-base-dev; however:
  Package r-base-dev is not installed.
 pbuilder-satisfydepends-dummy depends on r-bioc-s4vectors; however:
  Package r-bioc-s4vectors is not installed.
 pbuilder-satisfydepends-dummy depends on r-bioc-iranges; however:
  Package r-bioc-iranges is not installed.
 pbuilder-satisfydepends-dummy depends on r-bioc-genomicranges; however:
  Package r-bioc-genomicranges is not installed.
 pbuilder-satisfydepends-dummy depends on r-bioc-summarizedexperiment; however:
  Package r-bioc-summarizedexperiment is not installed.
 pbuilder-satisfydepends-dummy depends on r-bioc-biocgenerics; however:
  Package r-bioc-biocgenerics is not installed.
 pbuilder-satisfydepends-dummy depends on r-bioc-biobase; however:
  Package r-bioc-biobase is not installed.
 pbuilder-satisfydepends-dummy depends on r-bioc-biocparallel; however:
  Package r-bioc-biocparallel is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-matrixstats; however:
  Package r-cran-matrixstats is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-locfit; however:
  Package r-cran-locfit is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-ggplot2 (>= 3.4.0); however:
  Package r-cran-ggplot2 is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-rcpp; however:
  Package r-cran-rcpp is not installed.
 pbuilder-satisfydepends-dummy depends on r-bioc-matrixgenerics; however:
  Package r-bioc-matrixgenerics is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-rcpparmadillo; however:
  Package r-cran-rcpparmadillo is not installed.
 pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however:
  Package architecture-is-64-bit 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:
  architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} dctrl-tools{a} debhelper{a} dh-autoreconf{a} dh-r{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} gfortran{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} icu-devtools{a} intltool-debian{a} libalgorithm-c3-perl{a} libarchive-zip-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libclass-c3-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclone-perl{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-optlist-perl{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libeval-closure-perl{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran-14-dev{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhttp-date-perl{a} libhttp-message-perl{a} libice6{a} libicu-dev{a} libicu72{a} libidn2-0{a} libio-html-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap2{a} liblerc4{a} liblwp-mediatypes-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmodule-implementation-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoose-perl{a} libmro-compat-perl{a} libnamespace-clean-perl{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libparams-classify-perl{a} libparams-util-perl{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libswitch-perl{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc-dev{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} liburi-perl{a} libvariable-magic-perl{a} libwebp7{a} libwww-curl-perl{a} libwww-curl-simple-perl{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} libxmuu1{a} libxrender1{a} libxss1{a} libxt6t64{a} littler{a} m4{a} man-db{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} r-base-core{a} r-base-dev{a} r-bioc-biobase{a} r-bioc-biocgenerics{a} r-bioc-biocparallel{a} r-bioc-delayedarray{a} r-bioc-genomeinfodb{a} r-bioc-genomeinfodbdata{a} r-bioc-genomicranges{a} r-bioc-iranges{a} r-bioc-matrixgenerics{a} r-bioc-s4arrays{a} r-bioc-s4vectors{a} r-bioc-sparsearray{a} r-bioc-summarizedexperiment{a} r-bioc-ucsc.utils{a} r-bioc-xvector{a} r-bioc-zlibbioc{a} r-cran-abind{a} r-cran-askpass{a} r-cran-bh{a} r-cran-cli{a} r-cran-codetools{a} r-cran-colorspace{a} r-cran-cpp11{a} r-cran-crayon{a} r-cran-curl{a} r-cran-fansi{a} r-cran-farver{a} r-cran-formatr{a} r-cran-futile.logger{a} r-cran-futile.options{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gtable{a} r-cran-httr{a} r-cran-isoband{a} r-cran-jsonlite{a} r-cran-labeling{a} r-cran-lambda.r{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-locfit{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-matrixstats{a} r-cran-mgcv{a} r-cran-mime{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-openssl{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rcpparmadillo{a} r-cran-rlang{a} r-cran-scales{a} r-cran-snow{a} r-cran-sys{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} tzdata{a} ucf{a} unzip{a} x11-common{a} xauth{a} xdg-utils{a} zip{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  bzip2-doc cme curl devscripts git-buildpackage krb5-locales libarchive-cpio-perl libclass-c3-xs-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libio-compress-brotli-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix r-cran-base64enc r-cran-bench r-cran-bit64 r-cran-brio r-cran-callr r-cran-covr r-cran-data.table r-cran-dbi r-cran-decor r-cran-desc r-cran-diagrammer 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-httpuv r-cran-jpeg r-cran-kernlab r-cran-kernsmooth r-cran-knitr r-cran-later r-cran-lintr r-cran-lobstr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-markdown r-cran-microbenchmark r-cran-mockery r-cran-multcomp r-cran-mvtnorm r-cran-nanotime r-cran-palmerpenguins r-cran-pkgdown r-cran-png r-cran-processx r-cran-profvis r-cran-progress r-cran-ps r-cran-quantreg r-cran-r.devices r-cran-r.rsp r-cran-ragg r-cran-readr 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-sodium r-cran-spelling r-cran-stringi r-cran-survival r-cran-svglite r-cran-testit r-cran-testthat r-cran-tidyverse r-cran-unitizer r-cran-units r-cran-usethis r-cran-vcd r-cran-vdiffr r-cran-viridis r-cran-waldo r-cran-webutils 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, 266 newly installed, 0 to remove and 0 not upgraded.
Need to get 189 MB of archives. After unpacking 610 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-6 [257 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.0-2 [1422 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-4 [200 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B]
Get: 18 http://deb.debian.org/debian trixie/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 19 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0048 [42.0 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 architecture-properties amd64 0.2.3 [2184 B]
Get: 21 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 22 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-4 [723 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.23 [90.6 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-2 [539 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 33 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 34 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 37 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-4 [1600 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 41 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.23 [919 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 libpaper2 amd64 2.2.5-0.3 [16.3 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 2.2.5-0.3 [16.1 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get: 52 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 53 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 54 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB]
Get: 55 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 61 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 65 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB]
Get: 67 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB]
Get: 68 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 69 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB]
Get: 70 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 71 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB]
Get: 72 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB]
Get: 73 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 74 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB]
Get: 75 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB]
Get: 76 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 77 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 78 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 79 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB]
Get: 80 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 81 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB]
Get: 82 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB]
Get: 83 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 84 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 85 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.1-1+b1 [352 kB]
Get: 86 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 87 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.4-2 [1502 kB]
Get: 88 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB]
Get: 89 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-12 [836 kB]
Get: 90 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB]
Get: 91 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB]
Get: 92 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get: 93 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get: 94 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB]
Get: 95 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get: 96 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB]
Get: 97 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB]
Get: 98 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB]
Get: 99 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB]
Get: 100 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB]
Get: 101 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 102 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB]
Get: 103 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get: 104 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get: 105 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get: 106 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get: 107 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get: 108 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 109 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB]
Get: 110 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB]
Get: 111 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.2 [216 kB]
Get: 112 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB]
Get: 113 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB]
Get: 114 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB]
Get: 115 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB]
Get: 116 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB]
Get: 117 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB]
Get: 118 http://deb.debian.org/debian trixie/main amd64 libgfortran-14-dev amd64 14.2.0-12 [881 kB]
Get: 119 http://deb.debian.org/debian trixie/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-12 [11.7 MB]
Get: 120 http://deb.debian.org/debian trixie/main amd64 gfortran-14 amd64 14.2.0-12 [13.4 kB]
Get: 121 http://deb.debian.org/debian trixie/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1 [1284 B]
Get: 122 http://deb.debian.org/debian trixie/main amd64 gfortran amd64 4:14.2.0-1 [1436 B]
Get: 123 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-4 [161 kB]
Get: 124 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-4 [4991 kB]
Get: 125 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB]
Get: 126 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB]
Get: 127 http://deb.debian.org/debian trixie/main amd64 libreadline-dev amd64 8.2-6 [153 kB]
Get: 128 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB]
Get: 129 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB]
Get: 130 http://deb.debian.org/debian trixie/main amd64 libpcre2-16-0 amd64 10.44-5 [260 kB]
Get: 131 http://deb.debian.org/debian trixie/main amd64 libpcre2-32-0 amd64 10.44-5 [248 kB]
Get: 132 http://deb.debian.org/debian trixie/main amd64 libpcre2-posix3 amd64 10.44-5 [60.4 kB]
Get: 133 http://deb.debian.org/debian trixie/main amd64 libpcre2-dev amd64 10.44-5 [790 kB]
Get: 134 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 135 http://deb.debian.org/debian trixie/main amd64 libpng-dev amd64 1.6.44-3 [366 kB]
Get: 136 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get: 137 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB]
Get: 138 http://deb.debian.org/debian trixie/main amd64 icu-devtools amd64 72.1-6 [210 kB]
Get: 139 http://deb.debian.org/debian trixie/main amd64 libicu-dev amd64 72.1-6 [10.4 MB]
Get: 140 http://deb.debian.org/debian trixie/main amd64 libxmuu1 amd64 2:1.1.3-3+b4 [21.9 kB]
Get: 141 http://deb.debian.org/debian trixie/main amd64 xauth amd64 1:1.1.2-1.1 [35.9 kB]
Get: 142 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 143 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 144 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 145 http://deb.debian.org/debian trixie/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3+b1 [190 kB]
Get: 146 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB]
Get: 147 http://deb.debian.org/debian trixie/main amd64 r-base-dev all 4.4.2-1 [4516 B]
Get: 148 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 149 http://deb.debian.org/debian trixie/main amd64 libswitch-perl all 2.17-3 [20.3 kB]
Get: 150 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB]
Get: 151 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get: 152 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get: 153 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get: 154 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get: 155 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get: 156 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.30-1 [105 kB]
Get: 157 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB]
Get: 158 http://deb.debian.org/debian trixie/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB]
Get: 159 http://deb.debian.org/debian trixie/main amd64 libsub-install-perl all 0.929-1 [10.5 kB]
Get: 160 http://deb.debian.org/debian trixie/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB]
Get: 161 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB]
Get: 162 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB]
Get: 163 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB]
Get: 164 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB]
Get: 165 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get: 166 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB]
Get: 167 http://deb.debian.org/debian trixie/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB]
Get: 168 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB]
Get: 169 http://deb.debian.org/debian trixie/main amd64 libclass-load-perl all 0.25-2 [15.3 kB]
Get: 170 http://deb.debian.org/debian trixie/main amd64 libclass-load-xs-perl amd64 0.10-2+b4 [14.2 kB]
Get: 171 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get: 172 http://deb.debian.org/debian trixie/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B]
Get: 173 http://deb.debian.org/debian trixie/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB]
Get: 174 http://deb.debian.org/debian trixie/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB]
Get: 175 http://deb.debian.org/debian trixie/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB]
Get: 176 http://deb.debian.org/debian trixie/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B]
Get: 177 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get: 178 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB]
Get: 179 http://deb.debian.org/debian trixie/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB]
Get: 180 http://deb.debian.org/debian trixie/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB]
Get: 181 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B]
Get: 182 http://deb.debian.org/debian trixie/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB]
Get: 183 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b4 [20.9 kB]
Get: 184 http://deb.debian.org/debian trixie/main amd64 libmoose-perl amd64 2.2207-1+b3 [766 kB]
Get: 185 http://deb.debian.org/debian trixie/main amd64 libvariable-magic-perl amd64 0.64-1+b1 [44.9 kB]
Get: 186 http://deb.debian.org/debian trixie/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB]
Get: 187 http://deb.debian.org/debian trixie/main amd64 libsub-identify-perl amd64 0.14-3+b3 [11.3 kB]
Get: 188 http://deb.debian.org/debian trixie/main amd64 libsub-name-perl amd64 0.28-1 [12.2 kB]
Get: 189 http://deb.debian.org/debian trixie/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB]
Get: 190 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB]
Get: 191 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB]
Get: 192 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB]
Get: 193 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.1-1+b1 [360 kB]
Get: 194 http://deb.debian.org/debian trixie/main amd64 libwww-curl-perl amd64 4.17-11 [57.9 kB]
Get: 195 http://deb.debian.org/debian trixie/main amd64 libwww-curl-simple-perl all 0.100191-3 [12.6 kB]
Get: 196 http://deb.debian.org/debian trixie/main amd64 dh-r all 20241218 [42.5 kB]
Get: 197 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB]
Get: 198 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B]
Get: 199 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB]
Get: 200 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-2 [16.0 kB]
Get: 201 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.52.0-2 [627 kB]
Get: 202 http://deb.debian.org/debian trixie/main amd64 r-bioc-biobase amd64 2.66.0-2 [2316 kB]
Get: 203 http://deb.debian.org/debian trixie/main amd64 r-cran-formatr all 1.14-2 [152 kB]
Get: 204 http://deb.debian.org/debian trixie/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB]
Get: 205 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB]
Get: 206 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB]
Get: 207 http://deb.debian.org/debian trixie/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB]
Get: 208 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB]
Get: 209 http://deb.debian.org/debian trixie/main amd64 r-cran-bh all 1.84.0-1 [5912 B]
Get: 210 http://deb.debian.org/debian trixie/main amd64 r-cran-cpp11 all 0.5.0-1 [213 kB]
Get: 211 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocparallel amd64 1.40.0-2 [1326 kB]
Get: 212 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB]
Get: 213 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB]
Get: 214 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixstats amd64 1.4.1-1 [510 kB]
Get: 215 http://deb.debian.org/debian trixie/main amd64 r-bioc-matrixgenerics all 1.18.1-1 [449 kB]
Get: 216 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2061 kB]
Get: 217 http://deb.debian.org/debian trixie/main amd64 r-bioc-iranges amd64 2.40.1-2 [2309 kB]
Get: 218 http://deb.debian.org/debian trixie/main amd64 r-cran-abind all 1.4-8-1 [68.1 kB]
Get: 219 http://deb.debian.org/debian trixie/main amd64 r-cran-crayon all 1.5.2-1 [165 kB]
Get: 220 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [702 kB]
Get: 221 http://deb.debian.org/debian trixie/main amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [9968 B]
Get: 222 http://deb.debian.org/debian trixie/main amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
Get: 223 http://deb.debian.org/debian trixie/main amd64 r-bioc-sparsearray amd64 1.6.0+dfsg-2 [1372 kB]
Get: 224 http://deb.debian.org/debian trixie/main amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2076 kB]
Get: 225 http://deb.debian.org/debian trixie/main amd64 r-cran-curl amd64 5.2.3+dfsg-1 [178 kB]
Get: 226 http://deb.debian.org/debian trixie/main amd64 r-cran-jsonlite amd64 1.8.9+dfsg-1 [445 kB]
Get: 227 http://deb.debian.org/debian trixie/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB]
Get: 228 http://deb.debian.org/debian trixie/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB]
Get: 229 http://deb.debian.org/debian trixie/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB]
Get: 230 http://deb.debian.org/debian trixie/main amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [401 kB]
Get: 231 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB]
Get: 232 http://deb.debian.org/debian trixie/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
Get: 233 http://deb.debian.org/debian trixie/main amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.3 kB]
Get: 234 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
Get: 235 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodb all 1.42.1+dfsg-2 [3844 kB]
Get: 236 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2092 kB]
Get: 237 http://deb.debian.org/debian trixie/main amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1116 kB]
Get: 238 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB]
Get: 239 http://deb.debian.org/debian trixie/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB]
Get: 240 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB]
Get: 241 http://deb.debian.org/debian trixie/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB]
Get: 242 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB]
Get: 243 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB]
Get: 244 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
Get: 245 http://deb.debian.org/debian trixie/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB]
Get: 246 http://deb.debian.org/debian trixie/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB]
Get: 247 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-64-1 [1113 kB]
Get: 248 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB]
Get: 249 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB]
Get: 250 http://deb.debian.org/debian trixie/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB]
Get: 251 http://deb.debian.org/debian trixie/main amd64 r-cran-munsell all 0.5.1-1 [237 kB]
Get: 252 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB]
Get: 253 http://deb.debian.org/debian trixie/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB]
Get: 254 http://deb.debian.org/debian trixie/main amd64 r-cran-scales all 1.3.0-1 [677 kB]
Get: 255 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB]
Get: 256 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB]
Get: 257 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB]
Get: 258 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
Get: 259 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB]
Get: 260 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB]
Get: 261 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB]
Get: 262 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB]
Get: 263 http://deb.debian.org/debian trixie/main amd64 r-cran-locfit amd64 1.5-9.10-1 [515 kB]
Get: 264 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB]
Get: 265 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.14-1 [2080 kB]
Get: 266 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpparmadillo amd64 14.2.2-1-1 [864 kB]
Fetched 189 MB in 11s (16.6 MB/s)
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update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ...
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Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1) ...
Setting up gfortran (4:14.2.0-1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libcairo2:amd64 (1.18.2-2) ...
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Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ...
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Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ...
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Setting up libmodule-implementation-perl (0.09-2) ...
Setting up libpackage-stash-perl (0.40-1) ...
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Setting up libwww-curl-perl:amd64 (4.17-11) ...
Setting up debhelper (13.23) ...
Setting up libmodule-runtime-conflicts-perl (0.003-2) ...
Setting up libclass-load-perl (0.25-2) ...
Setting up r-base-core (4.4.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-crayon (1.5.2-1) ...
Setting up r-cran-labeling (0.4.3-1) ...
Setting up r-cran-futile.options (1.0.1-3) ...
Setting up r-cran-lattice (0.22-6-1) ...
Setting up r-cran-nlme (3.1.166-1) ...
Setting up r-cran-farver (2.1.2-1) ...
Setting up r-cran-formatr (1.14-2) ...
Setting up libpackage-deprecationmanager-perl (0.18-1) ...
Setting up r-cran-viridislite (0.4.2-2) ...
Setting up r-cran-locfit (1.5-9.10-1) ...
Setting up libdevel-overloadinfo-perl (0.007-1) ...
Setting up libclass-load-xs-perl (0.10-2+b4) ...
Setting up r-cran-r6 (2.5.1-1) ...
Setting up r-cran-pkgkitten (0.2.4-1) ...
Setting up libb-hooks-endofscope-perl (0.28-1) ...
Setting up r-cran-magrittr (2.0.3-1) ...
Setting up r-bioc-genomeinfodbdata (1.2.13-2) ...
Setting up r-cran-littler (0.3.20-2) ...
Setting up r-cran-bh (1.84.0-1) ...
Setting up r-cran-rcpp (1.0.14-1) ...
Setting up r-cran-curl (5.2.3+dfsg-1) ...
Setting up r-cran-codetools (0.2-20-1) ...
Setting up r-bioc-biocgenerics (0.52.0-2) ...
Setting up r-cran-rlang (1.1.4-1) ...
Setting up r-cran-matrixstats (1.4.1-1) ...
Setting up r-base-dev (4.4.2-1) ...
Setting up littler (0.3.20-2) ...
Setting up r-bioc-matrixgenerics (1.18.1-1) ...
Setting up r-cran-sys (3.4.3-1) ...
Setting up r-cran-withr (3.0.2+dfsg-1) ...
Setting up r-cran-mime (0.12-2) ...
Setting up libmoose-perl:amd64 (2.2207-1+b3) ...
Setting up r-cran-abind (1.4-8-1) ...
Setting up r-cran-lambda.r (1.2.4-2) ...
Setting up r-cran-fansi (1.0.5-1) ...
Setting up r-cran-mass (7.3-64-1) ...
Setting up r-cran-snow (1:0.4.4-2) ...
Setting up r-cran-glue (1.8.0-1) ...
Setting up r-cran-cli (3.6.3-1) ...
Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
Setting up r-cran-askpass (1.2.1-1) ...
Setting up r-bioc-biobase (2.66.0-2) ...
Setting up r-cran-jsonlite (1.8.9+dfsg-1) ...
Setting up r-cran-pkgconfig (2.0.3-2) ...
Setting up r-cran-utf8 (1.2.4-1) ...
Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
Setting up r-cran-cpp11 (0.5.0-1) ...
Setting up r-cran-rcolorbrewer (1.1-3-1) ...
Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
Setting up r-cran-isoband (0.2.7-1) ...
Setting up r-cran-futile.logger (1.4.3-4) ...
Setting up libnamespace-clean-perl (0.27-2) ...
Setting up r-cran-gtable (0.3.6+dfsg-1) ...
Setting up r-cran-matrix (1.7-1-1) ...
Setting up r-cran-mgcv (1.9-1-1) ...
Setting up r-cran-rcpparmadillo (14.2.2-1-1) ...
Setting up r-bioc-iranges (2.40.1-2) ...
Setting up r-cran-vctrs (0.6.5-1) ...
Setting up r-cran-pillar (1.10.1+dfsg-1) ...
Setting up r-cran-openssl (2.2.0+dfsg-1) ...
Setting up r-bioc-s4arrays (1.6.0+dfsg-2) ...
Setting up r-bioc-biocparallel (1.40.0-2) ...
Setting up libwww-curl-simple-perl (0.100191-3) ...
Setting up r-cran-munsell (0.5.1-1) ...
Setting up r-cran-tibble (3.2.1+dfsg-2) ...
Setting up r-cran-httr (1.4.7+dfsg-1) ...
Setting up r-cran-scales (1.3.0-1) ...
Setting up r-bioc-xvector (0.46.0-2) ...
Setting up dh-r (20241218) ...
Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
Setting up r-bioc-sparsearray (1.6.0+dfsg-2) ...
Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
Setting up r-bioc-genomeinfodb (1.42.1+dfsg-2) ...
Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ...
Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ...
Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
Processing triggers for libc-bin (2.40-5) ...
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/1244240/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/1244240/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/r-bioc-deseq2-1.46.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../r-bioc-deseq2_1.46.0+dfsg-2_source.changes
dpkg-buildpackage: info: source package r-bioc-deseq2
dpkg-buildpackage: info: source version 1.46.0+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --buildsystem R
   dh_auto_clean -O--buildsystem=R
   dh_autoreconf_clean -O--buildsystem=R
   dh_clean -O--buildsystem=R
 debian/rules binary
dh binary --buildsystem R
   dh_update_autotools_config -O--buildsystem=R
   dh_autoreconf -O--buildsystem=R
   dh_auto_configure -O--buildsystem=R
   dh_auto_build -O--buildsystem=R
   dh_auto_test -O--buildsystem=R
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=R
   dh_prep -O--buildsystem=R
   dh_auto_install --destdir=debian/r-bioc-deseq2/ -O--buildsystem=R
I: R Package: DESeq2 Version: 1.46.0
I: Building using R version 4.4.2-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 13 Jan 2025 08:57:33 +0100
	mkdir -p /build/reproducible-path/r-bioc-deseq2-1.46.0\+dfsg/debian/r-bioc-deseq2/usr/lib/R/site-library
	R CMD INSTALL -l /build/reproducible-path/r-bioc-deseq2-1.46.0\+dfsg/debian/r-bioc-deseq2/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 08:57:33 +0100'"
* installing *source* package 'DESeq2' ...
file 'inst/doc/DESeq2.html' is missing
files 'tests/testthat/test_design_matrix.R', 'tests/testthat/test_dispersions.R', 'tests/testthat/test_lfcShrink.R', 'tests/testthat/test_parallel.R' have the wrong MD5 checksums
** using staged installation
** libs
using C++ compiler: 'g++ (Debian 14.2.0-12) 14.2.0'
make[1]: Entering directory '/build/reproducible-path/r-bioc-deseq2-1.46.0+dfsg/src'
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/RcppArmadillo/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c DESeq2.cpp -o DESeq2.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/RcppArmadillo/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o DESeq2.so DESeq2.o RcppExports.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/build/reproducible-path/r-bioc-deseq2-1.46.0+dfsg/src'
make[1]: Entering directory '/build/reproducible-path/r-bioc-deseq2-1.46.0+dfsg/src'
make[1]: Leaving directory '/build/reproducible-path/r-bioc-deseq2-1.46.0+dfsg/src'
installing to /build/reproducible-path/r-bioc-deseq2-1.46.0+dfsg/debian/r-bioc-deseq2/usr/lib/R/site-library/00LOCK-r-bioc-deseq2-1.46.0+dfsg/00new/DESeq2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DESeq2)
I: Using r-bioc-s4vectors for Depends:S4Vectors (>= 0.23.18)
I: Using r-bioc-iranges for Depends:IRanges
I: Using r-bioc-genomicranges for Depends:GenomicRanges
I: Using r-bioc-summarizedexperiment for Depends:SummarizedExperiment (>= 1.1.6)
I: Using r-cran-testthat for Suggests:testthat
I: Using r-cran-knitr for Suggests:knitr
I: Using r-cran-rmarkdown for Suggests:rmarkdown
W: Cannot find a debian package for Suggests:vsn
I: Using r-cran-pheatmap for Suggests:pheatmap
I: Using r-cran-rcolorbrewer by changing version to  for Suggests:RColorBrewer
W: Cannot find a debian package for Suggests:apeglm
W: Cannot find a debian package for Suggests:ashr
I: Using r-bioc-tximport for Suggests:tximport
I: Using r-bioc-tximeta for Suggests:tximeta
I: Using r-bioc-tximportdata for Suggests:tximportData
I: Using r-cran-readr for Suggests:readr
I: Using r-cran-pbapply for Suggests:pbapply
W: Cannot find a debian package for Suggests:airway
W: Cannot find a debian package for Suggests:pasilla (>= 0.2.10)
I: Using r-bioc-glmgampoi for Suggests:glmGamPoi
I: Using r-cran-biocmanager for Suggests:BiocManager
I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.7.5)
I: Using r-bioc-biobase for Imports:Biobase
I: Using r-bioc-biocparallel for Imports:BiocParallel
I: Using r-cran-matrixstats for Imports:matrixStats
I: Using r-cran-locfit for Imports:locfit
I: Using r-cran-ggplot2 for Imports:ggplot2 (>= 3.4.0)
I: Using r-cran-rcpp for Imports:Rcpp (>= 0.11.0)
I: Using r-bioc-matrixgenerics for Imports:MatrixGenerics
I: Using r-cran-rcpp for LinkingTo:Rcpp
I: Using r-cran-rcpparmadillo for LinkingTo:RcppArmadillo
I: BioConductor API version: r-api-bioc-3.20
I: Use r-bioc-deseq2 as Debian binary package for variables substitution
   dh_installdocs -O--buildsystem=R
   dh_installchangelogs -O--buildsystem=R
   dh_installsystemduser -O--buildsystem=R
   dh_perl -O--buildsystem=R
   dh_link -O--buildsystem=R
   dh_strip_nondeterminism -O--buildsystem=R
   dh_compress -O--buildsystem=R
   dh_fixperms -O--buildsystem=R
   dh_missing -O--buildsystem=R
   dh_dwz -a -O--buildsystem=R
   dh_strip -a -O--buildsystem=R
   dh_makeshlibs -a -O--buildsystem=R
   dh_shlibdeps -a -O--buildsystem=R
   dh_installdeb -O--buildsystem=R
   dh_gencontrol -O--buildsystem=R
   dh_md5sums -O--buildsystem=R
   dh_builddeb -O--buildsystem=R
dpkg-deb: building package 'r-bioc-deseq2' in '../r-bioc-deseq2_1.46.0+dfsg-2_amd64.deb'.
dpkg-deb: building package 'r-bioc-deseq2-dbgsym' in '../r-bioc-deseq2-dbgsym_1.46.0+dfsg-2_amd64.deb'.
 dpkg-genbuildinfo --build=binary -O../r-bioc-deseq2_1.46.0+dfsg-2_amd64.buildinfo
 dpkg-genchanges --build=binary -O../r-bioc-deseq2_1.46.0+dfsg-2_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/1244240/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/1244240/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/1244240 and its subdirectories
I: Current time: Thu Jan 23 01:56:28 +14 2025
I: pbuilder-time-stamp: 1737546988