I: pbuilder: network access will be disabled during build I: Current time: Thu May 29 21:21:37 +14 2025 I: pbuilder-time-stamp: 1748503297 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-genomicfeatures_1.54.3+dfsg-1.dsc] I: copying [./r-bioc-genomicfeatures_1.54.3+dfsg.orig.tar.xz] I: copying [./r-bioc-genomicfeatures_1.54.3+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Feb 5 09:32:46 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./r-bioc-genomicfeatures_1.54.3+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting r-bioc-genomicfeatures in r-bioc-genomicfeatures-1.54.3+dfsg dpkg-source: info: unpacking r-bioc-genomicfeatures_1.54.3+dfsg.orig.tar.xz dpkg-source: info: unpacking r-bioc-genomicfeatures_1.54.3+dfsg-1.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/2250423/tmp/hooks/D01_modify_environment starting debug: Running on infom02-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 May 29 07:21 /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/2250423/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2250423/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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(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=12 ' 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=00619949071244188901456710b19990 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=2250423 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.ox6y54oh/pbuilderrc_R87N --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.ox6y54oh/b2 --logfile b2/build.log r-bioc-genomicfeatures_1.54.3+dfsg-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 24 13:34 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2250423/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-biocgenerics, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomeinfodb (>= 1.35.8), r-bioc-genomicranges, r-bioc-annotationdbi, r-cran-dbi, r-cran-rsqlite, r-cran-rcurl, r-bioc-xvector, r-bioc-biostrings, r-bioc-biocio, r-bioc-rtracklayer (>= 1.51.5), r-bioc-biomart (>= 2.58.2), r-bioc-biobase, r-cran-knitr, r-cran-markdown, r-bioc-biocstyle dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19892 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-biocgenerics; however: Package r-bioc-biocgenerics 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-genomeinfodb (>= 1.35.8); however: Package r-bioc-genomeinfodb 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-annotationdbi; however: Package r-bioc-annotationdbi is not installed. pbuilder-satisfydepends-dummy depends on r-cran-dbi; however: Package r-cran-dbi is not installed. pbuilder-satisfydepends-dummy depends on r-cran-rsqlite; however: Package r-cran-rsqlite is not installed. pbuilder-satisfydepends-dummy depends on r-cran-rcurl; however: Package r-cran-rcurl is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-xvector; however: Package r-bioc-xvector is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biostrings; however: Package r-bioc-biostrings is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biocio; however: Package r-bioc-biocio is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-rtracklayer (>= 1.51.5); however: Package r-bioc-rtracklayer is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biomart (>= 2.58.2); however: Package r-bioc-biomart 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-cran-knitr; however: Package r-cran-knitr is not installed. pbuilder-satisfydepends-dummy depends on r-cran-markdown; however: Package r-cran-markdown is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biocstyle; however: Package r-bioc-biocstyle 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.0 MB of archives. After unpacking 73.3 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: dh-r but it is not installable Depends: r-base-dev but it is not installable Depends: r-bioc-biocgenerics but it is not installable Depends: r-bioc-s4vectors but it is not installable Depends: r-bioc-iranges but it is not installable Depends: r-bioc-genomeinfodb (>= 1.35.8) but it is not installable Depends: r-bioc-genomicranges but it is not installable Depends: r-bioc-annotationdbi but it is not installable Depends: r-cran-dbi but it is not installable Depends: r-cran-rsqlite but it is not installable Depends: r-cran-rcurl but it is not installable Depends: r-bioc-xvector but it is not installable Depends: r-bioc-biostrings but it is not installable Depends: r-bioc-biocio but it is not installable Depends: r-bioc-rtracklayer (>= 1.51.5) but it is not installable Depends: r-bioc-biomart (>= 2.58.2) but it is not installable Depends: r-bioc-biobase but it is not installable Depends: r-cran-knitr but it is not installable Depends: r-cran-markdown but it is not installable Depends: r-bioc-biocstyle but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libgnutls30 [3.8.3-1 (now)] 2) libhogweed6 [3.9.1-2+b1 (now)] 3) libnettle8 [3.9.1-2+b1 (now)] 4) libssl3 [3.1.5-1 (now)] Install the following packages: 5) ca-certificates [20240203 (testing)] 6) dctrl-tools [2.24-3+b1 (testing)] 7) dh-r [20231212 (testing)] 8) fontconfig [2.15.0-1.1 (testing)] 9) fontconfig-config [2.15.0-1.1 (testing)] 10) fonts-font-awesome [5.0.10+really4.7.0~dfsg-4.1 (testing)] 11) fonts-glyphicons-halflings [1.009~3.4.1+dfsg-3 (testing)] 12) fonts-lmodern [2.005-1 (testing)] 13) fonts-mathjax [2.7.9+dfsg-1 (testing)] 14) fonts-urw-base35 [20200910-8 (testing)] 15) gfortran [4:13.2.0-7 (testing)] 16) gfortran-13 [13.2.0-23 (testing)] 17) gfortran-13-x86-64-linux-gnu [13.2.0-23 (testing)] 18) gfortran-x86-64-linux-gnu [4:13.2.0-7 (testing)] 19) icu-devtools [72.1-4+b1 (testing)] 20) javascript-common [11+nmu1 (testing)] 21) libalgorithm-c3-perl [0.11-2 (testing)] 22) libatlas-base-dev [3.10.3-14 (testing)] 23) libatlas3-base [3.10.3-14 (testing)] 24) libb-hooks-endofscope-perl [0.28-1 (testing)] 25) libb-hooks-op-check-perl [0.22-2+b2 (testing)] 26) libbibtex-parser-perl [1.04+dfsg-1 (testing)] 27) libboost-dev [1.83.0.2+b2 (testing)] 28) libboost1.83-dev [1.83.0-2+b2 (testing)] 29) libbrotli1 [1.1.0-2+b3 (testing)] 30) libbsd0 [0.12.2-1 (testing)] 31) libbz2-dev [1.0.8-5.1 (testing)] 32) libcairo2 [1.18.0-1+b1 (testing)] 33) libclass-c3-perl [0.35-2 (testing)] 34) libclass-load-perl [0.25-2 (testing)] 35) libclass-load-xs-perl [0.10-2+b2 (testing)] 36) libclone-perl [0.46-1+b1 (testing)] 37) libcurl3t64-gnutls [8.7.1-3 (testing)] 38) libcurl4t64 [8.7.1-3 (testing)] 39) libdata-optlist-perl [0.114-1 (testing)] 40) libdatrie1 [0.2.13-3 (testing)] 41) libdeflate0 [1.20-1 (testing)] 42) libdevel-callchecker-perl [0.008-2+b1 (testing)] 43) libdevel-globaldestruction-perl [0.14-4 (testing)] 44) libdevel-overloadinfo-perl [0.007-1 (testing)] 45) libdevel-stacktrace-perl [2.0500-1 (testing)] 46) libdist-checkconflicts-perl [0.11-2 (testing)] 47) libdynaloader-functions-perl [0.003-3 (testing)] 48) libencode-locale-perl [1.05-3 (testing)] 49) libeval-closure-perl [0.14-3 (testing)] 50) libexpat1 [2.6.2-1 (testing)] 51) libfile-which-perl [1.27-2 (testing)] 52) libfontconfig1 [2.15.0-1.1 (testing)] 53) libfontenc1 [1:1.1.8-1 (testing)] 54) libfreetype6 [2.13.2+dfsg-1+b4 (testing)] 55) libfribidi0 [1.0.13-3+b1 (testing)] 56) libgfortran-13-dev [13.2.0-23 (testing)] 57) libgfortran5 [14-20240330-1 (testing)] 58) libglib2.0-0 [2.78.4-1 (testing)] 59) libgnutls30t64 [3.8.5-2 (testing)] 60) libgraphite2-3 [1.3.14-2 (testing)] 61) libharfbuzz0b [8.3.0-2 (testing)] 62) libhogweed6t64 [3.9.1-2.2 (testing)] 63) libhttp-date-perl [6.06-1 (testing)] 64) libhttp-message-perl [6.45-1 (testing)] 65) libice6 [2:1.0.10-1 (testing)] 66) libicu-dev [72.1-4+b1 (testing)] 67) libio-html-perl [1.004-3 (testing)] 68) libio-string-perl [1.08-4 (testing)] 69) libjbig0 [2.1-6.1+b1 (testing)] 70) libjpeg62-turbo [1:2.1.5-2+b2 (testing)] 71) libjpeg62-turbo-dev [1:2.1.5-2+b2 (testing)] 72) libjs-bootstrap [3.4.1+dfsg-3 (testing)] 73) libjs-bootstrap4 [4.6.1+dfsg1-4 (testing)] 74) libjs-d3 [3.5.17-4 (testing)] 75) libjs-es5-shim [4.6.7-2 (testing)] 76) libjs-highlight.js [9.18.5+dfsg1-2 (testing)] 77) libjs-jquery [3.6.1+dfsg+~3.5.14-1 (testing)] 78) libjs-jquery-datatables [1.11.5+dfsg-2 (testing)] 79) libjs-jquery-selectize.js [0.12.6+dfsg-1.1 (testing)] 80) libjs-jquery-ui [1.13.2+dfsg-1 (testing)] 81) libjs-json [0~20221030+~1.0.8-1 (testing)] 82) libjs-lunr [2.3.9~dfsg-2 (testing)] 83) libjs-mathjax [2.7.9+dfsg-1 (testing)] 84) libjs-microplugin.js [0.0.3+dfsg-1.1 (testing)] 85) libjs-modernizr [2.6.2+ds1-5 (testing)] 86) libjs-popper.js [1.16.1+ds-6 (testing)] 87) libjs-prettify [2015.12.04+dfsg-1.1 (testing)] 88) libjs-sifter.js [0.6.0+dfsg-3 (testing)] 89) libjs-twitter-bootstrap-datepicker [1.3.1+dfsg1-4.1 (testing)] 90) libkpathsea6 [2023.20230311.66589-9 (testing)] 91) liblatex-tounicode-perl [0.54-2 (testing)] 92) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 93) liblerc4 [4.0.0+ds-4+b1 (testing)] 94) liblua5.4-0 [5.4.6-3+b1 (testing)] 95) liblwp-mediatypes-perl [6.04-2 (testing)] 96) liblzma-dev [5.6.1+really5.4.5-1 (testing)] 97) libmodule-implementation-perl [0.09-2 (testing)] 98) libmodule-runtime-conflicts-perl [0.003-2 (testing)] 99) libmodule-runtime-perl [0.016-2 (testing)] 100) libmoose-perl [2.2207-1 (testing)] 101) libmro-compat-perl [0.15-2 (testing)] 102) libnamespace-clean-perl [0.27-2 (testing)] 103) libncurses-dev [6.4+20240414-1 (testing)] 104) libncurses6 [6.4+20240414-1 (testing)] 105) libnettle8t64 [3.9.1-2.2 (testing)] 106) libnghttp2-14 [1.59.0-1 (testing)] 107) libpackage-deprecationmanager-perl [0.18-1 (testing)] 108) libpackage-stash-perl [0.40-1 (testing)] 109) libpackage-stash-xs-perl [0.30-1+b2 (testing)] 110) libpango-1.0-0 [1.52.0+ds-1 (testing)] 111) libpangocairo-1.0-0 [1.52.0+ds-1 (testing)] 112) libpangoft2-1.0-0 [1.52.0+ds-1 (testing)] 113) libpaper-utils [1.1.29 (testing)] 114) libpaper1 [1.1.29 (testing)] 115) libparams-classify-perl [0.015-2+b2 (testing)] 116) libparams-util-perl [1.102-2+b2 (testing)] 117) libpcre2-16-0 [10.42-4+b1 (testing)] 118) libpcre2-32-0 [10.42-4+b1 (testing)] 119) libpcre2-dev [10.42-4+b1 (testing)] 120) libpcre2-posix3 [10.42-4+b1 (testing)] 121) libpixman-1-0 [0.42.2-1+b1 (testing)] 122) libpkgconf3 [1.8.1-1+b2 (testing)] 123) libpng-dev [1.6.43-5 (testing)] 124) libpng16-16t64 [1.6.43-5 (testing)] 125) libpotrace0 [1.16-2+b1 (testing)] 126) libpsl5t64 [0.21.2-1.1 (testing)] 127) libptexenc1 [2023.20230311.66589-9 (testing)] 128) libreadline-dev [8.2-4 (testing)] 129) libreadline8t64 [8.2-4 (testing)] 130) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 131) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 132) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 133) libsharpyuv0 [1.3.2-0.4+b1 (testing)] 134) libsm6 [2:1.2.3-1 (testing)] 135) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 136) libssl3t64 [3.2.1-3 (testing)] 137) libsub-exporter-perl [0.990-1 (testing)] 138) libsub-exporter-progressive-perl [0.001013-3 (testing)] 139) libsub-identify-perl [0.14-3+b1 (testing)] 140) libsub-install-perl [0.929-1 (testing)] 141) libsub-name-perl [0.27-1+b1 (testing)] 142) libswitch-perl [2.17-3 (testing)] 143) libsynctex2 [2023.20230311.66589-9 (testing)] 144) libtcl8.6 [8.6.14+dfsg-1 (testing)] 145) libteckit0 [2.5.12+ds1-1 (testing)] 146) libtexlua53-5 [2023.20230311.66589-9 (testing)] 147) libthai-data [0.1.29-2 (testing)] 148) libthai0 [0.1.29-2 (testing)] 149) libtiff6 [4.5.1+git230720-4 (testing)] 150) libtimedate-perl [2.3300-2 (testing)] 151) libtk8.6 [8.6.14-1 (testing)] 152) libtry-tiny-perl [0.31-2 (testing)] 153) liburi-perl [5.28-1 (testing)] 154) libuv1 [1.48.0-1 (testing)] 155) libvariable-magic-perl [0.63-1+b2 (testing)] 156) libwebp7 [1.3.2-0.4+b1 (testing)] 157) libwww-curl-perl [4.17-10+b1 (testing)] 158) libwww-curl-simple-perl [0.100191-3 (testing)] 159) libx11-6 [2:1.8.7-1 (testing)] 160) libx11-data [2:1.8.7-1 (testing)] 161) libxau6 [1:1.0.9-1 (testing)] 162) libxaw7 [2:1.0.14-1 (testing)] 163) libxcb-render0 [1.15-1 (testing)] 164) libxcb-shm0 [1.15-1 (testing)] 165) libxcb1 [1.15-1 (testing)] 166) libxdmcp6 [1:1.1.2-3 (testing)] 167) libxext6 [2:1.3.4-1+b1 (testing)] 168) libxft2 [2.3.6-1+b1 (testing)] 169) libxi6 [2:1.8.1-1 (testing)] 170) libxmu6 [2:1.1.3-3 (testing)] 171) libxmuu1 [2:1.1.3-3 (testing)] 172) libxpm4 [1:3.5.17-1 (testing)] 173) libxrender1 [1:0.9.10-1.1 (testing)] 174) libxss1 [1:1.2.3-1 (testing)] 175) libxt6 [1:1.2.1-1.1 (testing)] 176) libyaml-0-2 [0.2.5-1 (testing)] 177) libzzip-0-13t64 [0.13.72+dfsg.1-1.2+b1 (testing)] 178) node-bootstrap-sass [3.4.3-2 (testing)] 179) node-html5shiv [3.7.3+dfsg-5 (testing)] 180) node-normalize.css [8.0.1-5 (testing)] 181) openssl [3.2.1-3 (testing)] 182) pandoc [3.1.3+ds-2 (testing)] 183) pandoc-data [3.1.3-1 (testing)] 184) pkgconf [1.8.1-1+b2 (testing)] 185) pkgconf-bin [1.8.1-1+b2 (testing)] 186) r-base-core [4.3.2-1 (testing)] 187) r-base-dev [4.3.2-1 (testing)] 188) r-bioc-annotationdbi [1.64.1-1 (testing)] 189) r-bioc-biobase [2.62.0-1 (testing)] 190) r-bioc-biocfilecache [2.10.1+dfsg-1 (testing)] 191) r-bioc-biocgenerics [0.48.1-2 (testing)] 192) r-bioc-biocio [1.12.0+dfsg-1 (testing)] 193) r-bioc-biocparallel [1.36.0-1 (testing)] 194) r-bioc-biocstyle [2.30.0+dfsg-1 (testing)] 195) r-bioc-biomart [2.58.2+dfsg-1 (testing)] 196) r-bioc-biostrings [2.70.3+dfsg-1 (testing)] 197) r-bioc-delayedarray [0.28.0+dfsg-1 (testing)] 198) r-bioc-genomeinfodb [1.38.6+dfsg-1 (testing)] 199) r-bioc-genomeinfodbdata [1.2.11-2 (testing)] 200) r-bioc-genomicalignments [1.38.2-1 (testing)] 201) r-bioc-genomicranges [1.54.1+dfsg-1 (testing)] 202) r-bioc-iranges [2.36.0-1 (testing)] 203) r-bioc-keggrest [1.42.0+dfsg-1 (testing)] 204) r-bioc-matrixgenerics [1.14.0-1 (testing)] 205) r-bioc-rhtslib [2.4.1+dfsg-3 (testing)] 206) r-bioc-rsamtools [2.18.0+dfsg-1+b1 (testing)] 207) r-bioc-rtracklayer [1.62.0-1 (testing)] 208) r-bioc-s4arrays [1.2.0+dfsg-1 (testing)] 209) r-bioc-s4vectors [0.40.2+dfsg-1 (testing)] 210) r-bioc-sparsearray [1.2.4+dfsg-1 (testing)] 211) r-bioc-summarizedexperiment [1.32.0+dfsg-1 (testing)] 212) r-bioc-xvector [0.42.0-1 (testing)] 213) r-bioc-zlibbioc [1.48.0+dfsg-1 (testing)] 214) r-cran-abind [1.4-5-2 (testing)] 215) r-cran-askpass [1.2.0-1 (testing)] 216) r-cran-base64enc [0.1-3-3 (testing)] 217) r-cran-bh [1.84.0-1 (testing)] 218) r-cran-biocmanager [1.30.22+dfsg-2 (testing)] 219) r-cran-bit [4.0.5-1 (testing)] 220) r-cran-bit64 [4.0.5-1 (testing)] 221) r-cran-bitops [1.0-7-1 (testing)] 222) r-cran-blob [1.2.4-1 (testing)] 223) r-cran-bookdown [0.37+dfsg-1 (testing)] 224) r-cran-bslib [0.6.1+dfsg-1 (testing)] 225) r-cran-cachem [1.0.8-1 (testing)] 226) r-cran-cli [3.6.2-1 (testing)] 227) r-cran-codetools [0.2-19-1 (testing)] 228) r-cran-commonmark [1.9.1-1 (testing)] 229) r-cran-cpp11 [0.4.7-1 (testing)] 230) r-cran-crayon [1.5.2-1 (testing)] 231) r-cran-curl [5.2.0+dfsg-1+b1 (testing)] 232) r-cran-dbi [1.2.2-1 (testing)] 233) r-cran-dbplyr [2.4.0+dfsg-1 (testing)] 234) r-cran-digest [0.6.34-1 (testing)] 235) r-cran-dplyr [1.1.4-1 (testing)] 236) r-cran-ellipsis [0.3.2-2 (testing)] 237) r-cran-evaluate [0.23-1 (testing)] 238) r-cran-fansi [1.0.5-1 (testing)] 239) r-cran-fastmap [1.1.1-1 (testing)] 240) r-cran-filelock [1.0.3-1 (testing)] 241) r-cran-fontawesome [0.5.2-1 (testing)] 242) r-cran-formatr [1.14-2 (testing)] 243) r-cran-fs [1.6.3+dfsg-1 (testing)] 244) r-cran-futile.logger [1.4.3-4 (testing)] 245) r-cran-futile.options [1.0.1-3 (testing)] 246) r-cran-generics [0.1.3-1 (testing)] 247) r-cran-glue [1.7.0-1 (testing)] 248) r-cran-highr [0.10+dfsg-2 (testing)] 249) r-cran-hms [1.1.3-1 (testing)] 250) r-cran-htmltools [0.5.7-1 (testing)] 251) r-cran-httpuv [1.6.14+dfsg-1 (testing)] 252) r-cran-httr [1.4.7+dfsg-1 (testing)] 253) r-cran-jquerylib [0.1.4+dfsg-4 (testing)] 254) r-cran-jsonlite [1.8.8+dfsg-1 (testing)] 255) r-cran-knitr [1.46+dfsg-1 (testing)] 256) r-cran-lambda.r [1.2.4-2 (testing)] 257) r-cran-later [1.3.2+dfsg-1 (testing)] 258) r-cran-lattice [0.22-5-1 (testing)] 259) r-cran-lifecycle [1.0.4+dfsg-1 (testing)] 260) r-cran-littler [0.3.19-1 (testing)] 261) r-cran-magrittr [2.0.3-1 (testing)] 262) r-cran-markdown [1.12+dfsg-2 (testing)] 263) r-cran-matrix [1.6-5-1 (testing)] 264) r-cran-matrixstats [1.2.0-1 (testing)] 265) r-cran-memoise [2.0.1-1 (testing)] 266) r-cran-mime [0.12-2 (testing)] 267) r-cran-openssl [2.1.1+dfsg-2+b1 (testing)] 268) r-cran-pillar [1.9.0+dfsg-1 (testing)] 269) r-cran-pkgconfig [2.0.3-2 (testing)] 270) r-cran-pkgkitten [0.2.3-1 (testing)] 271) r-cran-plogr [0.2.0-3 (testing)] 272) r-cran-png [0.1-8-1+b1 (testing)] 273) r-cran-prettyunits [1.2.0-1 (testing)] 274) r-cran-progress [1.2.3-1 (testing)] 275) r-cran-promises [1.2.1+dfsg-1 (testing)] 276) r-cran-purrr [1.0.2-1 (testing)] 277) r-cran-r6 [2.5.1-1 (testing)] 278) r-cran-rappdirs [0.3.3-1 (testing)] 279) r-cran-rcpp [1.0.12-1 (testing)] 280) r-cran-rcurl [1.98-1.14+dfsg-1+b1 (testing)] 281) r-cran-restfulr [0.0.15-1 (testing)] 282) r-cran-rjson [0.2.21-1 (testing)] 283) r-cran-rlang [1.1.3-1 (testing)] 284) r-cran-rmarkdown [2.25+dfsg-3 (testing)] 285) r-cran-rsqlite [2.3.4-1 (testing)] 286) r-cran-sass [0.4.8+dfsg-1 (testing)] 287) r-cran-shiny [1.8.0+dfsg-1 (testing)] 288) r-cran-snow [1:0.4.4-2 (testing)] 289) r-cran-sourcetools [0.1.7-1-1 (testing)] 290) r-cran-stringi [1.8.3-1 (testing)] 291) r-cran-stringr [1.5.1-1 (testing)] 292) r-cran-sys [3.4.2-1 (testing)] 293) r-cran-tibble [3.2.1+dfsg-2 (testing)] 294) r-cran-tidyr [1.3.1-1 (testing)] 295) r-cran-tidyselect [1.2.0+dfsg-1 (testing)] 296) r-cran-tinytex [0.49-1 (testing)] 297) r-cran-utf8 [1.2.4-1 (testing)] 298) r-cran-vctrs [0.6.5-1 (testing)] 299) r-cran-withr [3.0.0+dfsg-1 (testing)] 300) r-cran-xfun [0.43+dfsg-1 (testing)] 301) r-cran-xml [3.99-0.16.1-1 (testing)] 302) r-cran-xml2 [1.3.6-1 (testing)] 303) r-cran-xtable [1:1.8-4-2 (testing)] 304) r-cran-yaml [2.3.8-1 (testing)] 305) readline-common [8.2-4 (testing)] 306) t1utils [1.41-4 (testing)] 307) tex-common [6.18 (testing)] 308) texlive-base [2023.20240207-1 (testing)] 309) texlive-bibtex-extra [2023.20240207-1 (testing)] 310) texlive-binaries [2023.20230311.66589-9 (testing)] 311) texlive-latex-base [2023.20240207-1 (testing)] 312) tzdata [2024a-3 (testing)] 313) ucf [3.0043+nmu1 (testing)] 314) unzip [6.0-28 (testing)] 315) x11-common [1:7.7+23 (testing)] 316) xauth [1:1.1.2-1 (testing)] 317) xdg-utils [1.1.3-4.1 (testing)] 318) xfonts-encodings [1:1.0.4-2.2 (testing)] 319) xfonts-utils [1:7.7+6 (testing)] 320) zip [3.0-13 (testing)] 321) zlib1g-dev [1:1.3.dfsg-3+b1 (testing)] The following NEW packages will be installed: 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-font-awesome{a} fonts-glyphicons-halflings{a} fonts-lmodern{a} fonts-mathjax{a} fonts-urw-base35{a} gettext{a} gettext-base{a} gfortran{a} gfortran-13{a} gfortran-13-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} icu-devtools{a} intltool-debian{a} javascript-common{a} libalgorithm-c3-perl{a} libarchive-zip-perl{a} libatlas-base-dev{a} libatlas3-base{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libbibtex-parser-perl{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo2{a} libclass-c3-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclone-perl{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-optlist-perl{a} libdatrie1{a} libdebhelper-perl{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} libelf1{a} libencode-locale-perl{a} libeval-closure-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran-13-dev{a} libgfortran5{a} libglib2.0-0{a} libgnutls30t64{a} libgraphite2-3{a} libharfbuzz0b{a} libhogweed6t64{a} libhttp-date-perl{a} libhttp-message-perl{a} libice6{a} libicu-dev{a} libicu72{a} libio-html-perl{a} libio-string-perl{a} libjbig0{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-bootstrap{a} libjs-bootstrap4{a} libjs-d3{a} libjs-es5-shim{a} libjs-highlight.js{a} libjs-jquery{a} libjs-jquery-datatables{a} libjs-jquery-selectize.js{a} libjs-jquery-ui{a} libjs-json{a} libjs-lunr{a} libjs-mathjax{a} libjs-microplugin.js{a} libjs-modernizr{a} libjs-popper.js{a} libjs-prettify{a} libjs-sifter.js{a} libjs-twitter-bootstrap-datepicker{a} libkpathsea6{a} liblatex-tounicode-perl{a} libldap-2.5-0{a} liblerc4{a} liblua5.4-0{a} liblwp-mediatypes-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{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} libnettle8t64{a} libnghttp2-14{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} libpaper1{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} libpotrace0{a} libpsl5t64{a} libptexenc1{a} libreadline-dev{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libssl3t64{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libsub-override-perl{a} libswitch-perl{a} libsynctex2{a} libtcl8.6{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libuv1{a} libvariable-magic-perl{a} libwebp7{a} libwww-curl-perl{a} libwww-curl-simple-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxi6{a} libxml2{a} libxmu6{a} libxmuu1{a} libxpm4{a} libxrender1{a} libxss1{a} libxt6{a} libyaml-0-2{a} libzzip-0-13t64{a} m4{a} man-db{a} node-bootstrap-sass{a} node-html5shiv{a} node-normalize.css{a} openssl{a} pandoc{a} pandoc-data{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} r-base-core{a} r-base-dev{a} r-bioc-annotationdbi{a} r-bioc-biobase{a} r-bioc-biocfilecache{a} r-bioc-biocgenerics{a} r-bioc-biocio{a} r-bioc-biocparallel{a} r-bioc-biocstyle{a} r-bioc-biomart{a} r-bioc-biostrings{a} r-bioc-delayedarray{a} r-bioc-genomeinfodb{a} r-bioc-genomeinfodbdata{a} r-bioc-genomicalignments{a} r-bioc-genomicranges{a} r-bioc-iranges{a} r-bioc-keggrest{a} r-bioc-matrixgenerics{a} r-bioc-rhtslib{a} r-bioc-rsamtools{a} r-bioc-rtracklayer{a} r-bioc-s4arrays{a} r-bioc-s4vectors{a} r-bioc-sparsearray{a} r-bioc-summarizedexperiment{a} r-bioc-xvector{a} r-bioc-zlibbioc{a} r-cran-abind{a} r-cran-askpass{a} r-cran-base64enc{a} r-cran-bh{a} r-cran-biocmanager{a} r-cran-bit{a} r-cran-bit64{a} r-cran-bitops{a} r-cran-blob{a} r-cran-bookdown{a} r-cran-bslib{a} r-cran-cachem{a} r-cran-cli{a} r-cran-codetools{a} r-cran-commonmark{a} r-cran-cpp11{a} r-cran-crayon{a} r-cran-curl{a} r-cran-dbi{a} r-cran-dbplyr{a} r-cran-digest{a} r-cran-dplyr{a} r-cran-ellipsis{a} r-cran-evaluate{a} r-cran-fansi{a} r-cran-fastmap{a} r-cran-filelock{a} r-cran-fontawesome{a} r-cran-formatr{a} r-cran-fs{a} r-cran-futile.logger{a} r-cran-futile.options{a} r-cran-generics{a} r-cran-glue{a} r-cran-highr{a} r-cran-hms{a} r-cran-htmltools{a} r-cran-httpuv{a} r-cran-httr{a} r-cran-jquerylib{a} r-cran-jsonlite{a} r-cran-knitr{a} r-cran-lambda.r{a} r-cran-later{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-markdown{a} r-cran-matrix{a} r-cran-matrixstats{a} r-cran-memoise{a} r-cran-mime{a} r-cran-openssl{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plogr{a} r-cran-png{a} r-cran-prettyunits{a} r-cran-progress{a} r-cran-promises{a} r-cran-purrr{a} r-cran-r6{a} r-cran-rappdirs{a} r-cran-rcpp{a} r-cran-rcurl{a} r-cran-restfulr{a} r-cran-rjson{a} r-cran-rlang{a} r-cran-rmarkdown{a} r-cran-rsqlite{a} r-cran-sass{a} r-cran-shiny{a} r-cran-snow{a} r-cran-sourcetools{a} r-cran-stringi{a} r-cran-stringr{a} r-cran-sys{a} r-cran-tibble{a} r-cran-tidyr{a} r-cran-tidyselect{a} r-cran-tinytex{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-withr{a} r-cran-xfun{a} r-cran-xml{a} r-cran-xml2{a} r-cran-xtable{a} r-cran-yaml{a} readline-common{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-bibtex-extra{a} texlive-binaries{a} texlive-latex-base{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xauth{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} zip{a} zlib1g-dev{a} The following packages will be REMOVED: libgnutls30{a} libhogweed6{a} libnettle8{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc cme curl devscripts dvisvgm git-buildpackage 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 lmodern lynx node-highlight.js node-jquery publicsuffix r-bioc-biocversion r-cran-bench r-cran-brio r-cran-broom r-cran-cairo r-cran-callr r-cran-covr r-cran-data.table r-cran-dbitest r-cran-decor r-cran-desc r-cran-downlit r-cran-dygraphs r-cran-formattable r-cran-future r-cran-gert r-cran-ggplot2 r-cran-gh r-cran-gridsvg r-cran-htmlwidgets r-cran-jpeg r-cran-lintr r-cran-lobstr r-cran-lubridate r-cran-magick r-cran-miniui r-cran-mockery r-cran-mockr r-cran-pkgdown r-cran-pkgload r-cran-processx r-cran-ps r-cran-r.devices r-cran-r.rsp r-cran-ragg r-cran-readr r-cran-remotes r-cran-renv r-cran-reticulate r-cran-rgl r-cran-rmysql r-cran-rpostgresql r-cran-rprojroot r-cran-rsconnect r-cran-rstudioapi r-cran-rsvg r-cran-runit r-cran-rvest r-cran-scales r-cran-sf r-cran-sodium r-cran-spelling r-cran-survival r-cran-svglite r-cran-testit r-cran-testthat r-cran-thematic r-cran-tidyverse r-cran-tikzdevice r-cran-tufte r-cran-unitizer r-cran-usethis r-cran-waldo r-cran-webshot r-cran-webutils r-cran-whoami r-cran-zeallot r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 347 newly installed, 4 to remove and 0 not upgraded. Need to get 391 MB of archives. After unpacking 1214 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libnettle8t64 amd64 3.9.1-2.2 [296 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libhogweed6t64 amd64 3.9.1-2.2 [328 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.5-2 [1437 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-2+b1 [314 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libmagic1 amd64 1:5.45-2+b1 [105 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-2+b1 [43.1 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3 [1180 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 33 http://deb.debian.org/debian trixie/main amd64 libelf1 amd64 0.190-1+b1 [176 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1 [109 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-13 [230 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get: 45 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libatlas3-base amd64 3.10.3-14 [3396 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 57 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-3 [441 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0 amd64 2.78.4-1 [1452 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2 [2213 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.52.0+ds-1 [216 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.52.0+ds-1 [48.0 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.52.0+ds-1 [35.0 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.3.2-1 [26.8 MB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libgfortran-13-dev amd64 13.2.0-23 [847 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-23 [10.7 MB] Get: 108 http://deb.debian.org/debian trixie/main amd64 gfortran-13 amd64 13.2.0-23 [11.2 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7 [1280 B] Get: 110 http://deb.debian.org/debian trixie/main amd64 gfortran amd64 4:13.2.0-7 [1440 B] Get: 111 http://deb.debian.org/debian trixie/main amd64 libatlas-base-dev amd64 3.10.3-14 [3626 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.4+20240414-1 [349 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libreadline-dev amd64 8.2-4 [152 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2+b2 [290 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libpcre2-32-0 amd64 10.42-4+b1 [234 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libpcre2-posix3 amd64 10.42-4+b1 [55.8 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libpcre2-dev amd64 10.42-4+b1 [755 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3+b1 [919 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libpng-dev amd64 1.6.43-5 [360 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libxmuu1 amd64 2:1.1.3-3 [23.9 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 xauth amd64 1:1.1.2-1 [36.0 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 r-base-dev all 4.3.2-1 [4504 B] Get: 132 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libswitch-perl all 2.17-3 [20.3 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b1 [13.8 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libparams-util-perl amd64 1.102-2+b2 [24.4 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b2 [10.7 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.008-2+b1 [15.1 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b2 [22.4 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libclass-load-xs-perl amd64 0.10-2+b2 [14.2 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 156 http://deb.debian.org/debian trixie/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 157 http://deb.debian.org/debian trixie/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 161 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 166 http://deb.debian.org/debian trixie/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b2 [20.2 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libmoose-perl amd64 2.2207-1 [765 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libvariable-magic-perl amd64 0.63-1+b2 [43.9 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libsub-identify-perl amd64 0.14-3+b1 [11.2 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libsub-name-perl amd64 0.27-1+b1 [12.5 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-3 [432 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libwww-curl-perl amd64 4.17-10+b1 [58.0 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libwww-curl-simple-perl all 0.100191-3 [12.6 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 dh-r all 20231212 [42.2 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 javascript-common all 11+nmu1 [6260 B] Get: 183 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 liblatex-tounicode-perl all 0.54-2 [29.1 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libbibtex-parser-perl all 1.04+dfsg-1 [17.6 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-2+b2 [10.6 MB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 188 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get: 198 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libjs-lunr all 2.3.9~dfsg-2 [76.6 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libjs-modernizr all 2.6.2+ds1-5 [47.1 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libkpathsea6 amd64 2023.20230311.66589-9 [154 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 liblua5.4-0 amd64 5.4.6-3+b1 [147 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libpotrace0 amd64 1.16-2+b1 [25.2 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libptexenc1 amd64 2023.20230311.66589-9 [47.0 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libsynctex2 amd64 2023.20230311.66589-9 [61.9 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libteckit0 amd64 2.5.12+ds1-1 [339 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libtexlua53-5 amd64 2023.20230311.66589-9 [113 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libuv1 amd64 1.48.0-1 [147 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3 [60.1 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1 [55.8 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libxaw7 amd64 2:1.0.14-1 [201 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2+b1 [56.2 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 pandoc-data all 3.1.3-1 [445 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 pandoc amd64 3.1.3+ds-2 [24.3 MB] Get: 225 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 r-bioc-biobase amd64 2.62.0-1 [2119 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4vectors amd64 0.40.2+dfsg-1 [2062 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 r-bioc-iranges amd64 2.36.0-1 [2258 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 r-cran-dbi all 1.2.2-1 [824 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.3-1 [1669 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 r-cran-fastmap amd64 1.1.1-1 [68.9 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 r-cran-cachem amd64 1.0.8-1 [72.0 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 r-cran-cpp11 all 0.4.7-1 [219 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 r-cran-rsqlite amd64 2.3.4-1 [1159 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 r-cran-curl amd64 5.2.0+dfsg-1+b1 [176 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [443 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 r-cran-sys amd64 3.4.2-1 [43.7 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 r-cran-askpass amd64 1.2.0-1 [24.0 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 r-cran-openssl amd64 2.1.1+dfsg-2+b1 [397 kB] Get: 251 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9344 B] Get: 255 http://deb.debian.org/debian trixie/main amd64 r-bioc-xvector amd64 0.42.0-1 [622 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 r-cran-bitops amd64 1.0-7-1 [30.2 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1+b1 [787 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodbdata all 1.2.11-2 [12.3 MB] Get: 259 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodb all 1.38.6+dfsg-1 [3848 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 r-bioc-biostrings amd64 2.70.3+dfsg-1 [13.7 MB] Get: 262 http://deb.debian.org/debian trixie/main amd64 r-bioc-keggrest all 1.42.0+dfsg-1 [188 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 r-bioc-annotationdbi all 1.64.1-1 [4705 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [219 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 r-cran-dplyr amd64 1.1.4-1 [1524 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 r-cran-purrr amd64 1.0.2-1 [507 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 r-cran-stringi amd64 1.8.3-1 [861 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 r-cran-dbplyr all 2.4.0+dfsg-1 [1188 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 r-cran-filelock amd64 1.0.3-1 [27.3 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocfilecache all 2.10.1+dfsg-1 [301 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocio all 1.12.0+dfsg-1 [214 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 r-cran-formatr all 1.14-2 [152 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get: 288 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocparallel amd64 1.36.0-1 [1337 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 r-cran-digest amd64 0.6.34-1 [192 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 r-cran-htmltools amd64 0.5.7-1 [374 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 r-cran-evaluate all 0.23-1 [90.6 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 r-cran-xfun amd64 0.43+dfsg-1 [471 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 r-cran-highr all 0.10+dfsg-2 [38.3 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 r-cran-yaml amd64 2.3.8-1 [106 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 r-cran-knitr all 1.46+dfsg-1 [907 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 r-cran-fs amd64 1.6.3+dfsg-1 [227 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 r-cran-sass amd64 0.4.8+dfsg-1 [959 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 r-cran-bslib all 0.6.1+dfsg-1 [5006 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 r-cran-fontawesome all 0.5.2-1 [1286 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 r-cran-tinytex all 0.49-1 [142 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.19-1 [99.8 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.12-1 [2071 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 r-cran-later amd64 1.3.2+dfsg-1 [118 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 r-cran-promises amd64 1.2.1+dfsg-1 [281 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 r-cran-httpuv amd64 1.6.14+dfsg-1 [492 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 r-cran-commonmark amd64 1.9.1-1 [119 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 r-cran-shiny all 1.8.0+dfsg-1 [2764 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 r-cran-rmarkdown all 2.25+dfsg-3 [1454 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 r-cran-bookdown all 0.37+dfsg-1 [1402 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 r-cran-biocmanager all 1.30.22+dfsg-2 [126 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 tex-common all 6.18 [32.5 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 texlive-binaries amd64 2023.20230311.66589-9 [8478 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 texlive-base all 2023.20240207-1 [22.0 MB] Get: 322 http://deb.debian.org/debian trixie/main amd64 texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 323 http://deb.debian.org/debian trixie/main amd64 texlive-bibtex-extra all 2023.20240207-1 [79.1 MB] Get: 324 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocstyle all 2.30.0+dfsg-1 [452 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 r-cran-xml amd64 3.99-0.16.1-1 [1751 kB] Get: 326 http://deb.debian.org/debian trixie/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get: 328 http://deb.debian.org/debian trixie/main amd64 r-cran-progress all 1.2.3-1 [93.0 kB] Get: 329 http://deb.debian.org/debian trixie/main amd64 r-cran-xml2 amd64 1.3.6-1 [320 kB] Get: 330 http://deb.debian.org/debian trixie/main amd64 r-bioc-biomart all 2.58.2+dfsg-1 [450 kB] Get: 331 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-5-1 [1394 kB] Get: 332 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.6-5-1 [3789 kB] Get: 333 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixstats amd64 1.2.0-1 [484 kB] Get: 334 http://deb.debian.org/debian trixie/main amd64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB] Get: 335 http://deb.debian.org/debian trixie/main amd64 r-cran-abind all 1.4-5-2 [64.6 kB] Get: 336 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4arrays amd64 1.2.0+dfsg-1 [504 kB] Get: 337 http://deb.debian.org/debian trixie/main amd64 r-bioc-sparsearray amd64 1.2.4+dfsg-1 [1196 kB] Get: 338 http://deb.debian.org/debian trixie/main amd64 r-bioc-delayedarray amd64 0.28.0+dfsg-1 [1794 kB] Get: 339 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicranges amd64 1.54.1+dfsg-1 [1827 kB] Get: 340 http://deb.debian.org/debian trixie/main amd64 r-bioc-summarizedexperiment all 1.32.0+dfsg-1 [1139 kB] Get: 341 http://deb.debian.org/debian trixie/main amd64 r-bioc-rhtslib amd64 2.4.1+dfsg-3 [1285 kB] Get: 342 http://deb.debian.org/debian trixie/main amd64 r-bioc-rsamtools amd64 2.18.0+dfsg-1+b1 [3584 kB] Get: 343 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicalignments amd64 1.38.2-1 [2144 kB] Get: 344 http://deb.debian.org/debian trixie/main amd64 r-cran-rjson amd64 0.2.21-1 [139 kB] Get: 345 http://deb.debian.org/debian trixie/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get: 346 http://deb.debian.org/debian trixie/main amd64 r-bioc-rtracklayer amd64 1.62.0-1 [5094 kB] Get: 347 http://deb.debian.org/debian trixie/main amd64 r-cran-markdown all 1.12+dfsg-2 [179 kB] Fetched 391 MB in 6s (62.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libnettle8:amd64: dependency problems, but removing anyway as you requested: libhogweed6:amd64 depends on libnettle8. libgnutls30:amd64 depends on libnettle8 (>= 3.9~). (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 ... 19892 files and directories currently installed.) Removing libnettle8:amd64 (3.9.1-2+b1) ... Selecting previously unselected package libnettle8t64:amd64. (Reading database ... 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Setting up libgnutls30t64:amd64 (3.8.5-2) ... dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: libkrb5-3:amd64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19893 files and directories currently installed.) Removing libssl3:amd64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:amd64. (Reading database ... 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Preparing to unpack .../086-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../087-libtcl8.6_8.6.14+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../088-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) ... 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Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu May 29 07:24:36 UTC 2025. Universal Time is now: Thu May 29 07:24:36 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libio-string-perl (1.08-4) ... Setting up zip (3.0-13) ... Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up libpackage-stash-xs-perl:amd64 (0.30-1+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:amd64 (10.42-4+b1) ... Setting up libpkgconf3:amd64 (1.8.1-1+b2) ... Setting up libuv1:amd64 (1.48.0-1) ... Setting up libalgorithm-c3-perl (0.11-2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libswitch-perl (2.17-3) ... Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2+b1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-2+b2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... 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Setting up libwebp7:amd64 (1.3.2-0.4+b1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Setting up libsub-name-perl:amd64 (0.27-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3+b1) ... Setting up libpcre2-posix3:amd64 (10.42-4+b1) ... Setting up libjs-highlight.js (9.18.5+dfsg1-2) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up fonts-lmodern (2.005-1) ... Setting up liblua5.4-0:amd64 (5.4.6-3+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libthai-data (0.1.29-2) ... Setting up libdevel-globaldestruction-perl (0.14-4) ... Setting up node-bootstrap-sass (3.4.3-2) ... Setting up libjs-prettify (2015.12.04+dfsg-1.1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libjs-bootstrap4 (4.6.1+dfsg1-4) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up pandoc-data (3.1.3-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libgfortran-13-dev:amd64 (13.2.0-23) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up node-normalize.css (8.0.1-5) ... Setting up libelf1:amd64 (0.190-1+b1) ... Setting up readline-common (8.2-4) ... Setting up libicu-dev:amd64 (72.1-4+b1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liburi-perl (5.28-1) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libsynctex2:amd64 (2023.20230311.66589-9) ... Setting up libbz2-dev:amd64 (1.0.8-5.1) ... Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... Setting up libpotrace0:amd64 (1.16-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libncurses-dev:amd64 (6.4+20240414-1) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libatlas3-base:amd64 (3.10.3-14) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libpcre2-dev:amd64 (10.42-4+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Setting up libpng-dev:amd64 (1.6.43-5) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libbibtex-parser-perl (1.04+dfsg-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2+b1) ... Setting up gfortran-13-x86-64-linux-gnu (13.2.0-23) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Setting up libatlas-base-dev:amd64 (3.10.3-14) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/atlas/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... Setting up pkgconf:amd64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libptexenc1:amd64 (2023.20230311.66589-9) ... Setting up pandoc (3.1.3+ds-2) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up gfortran-13 (13.2.0-23) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2) ... Setting up libmro-compat-perl (0.15-2) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libxmuu1:amd64 (2:1.1.3-3) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libeval-closure-perl (0.14-3) ... 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Setting up texlive-base (2023.20240207-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpangocairo-1.0-0:amd64 (1.52.0+ds-1) ... Setting up texlive-latex-base (2023.20240207-1) ... Setting up r-base-core (4.3.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-sourcetools (0.1.7-1-1) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.22-5-1) ... Setting up r-cran-formatr (1.14-2) ... Setting up r-cran-xml (3.99-0.16.1-1) ... Setting up r-cran-commonmark (1.9.1-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... 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Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... 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/2250423/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2250423/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/r-bioc-genomicfeatures-1.54.3+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-genomicfeatures_1.54.3+dfsg-1_source.changes dpkg-buildpackage: info: source package r-bioc-genomicfeatures dpkg-buildpackage: info: source version 1.54.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --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 debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/r-bioc-genomicfeatures-1.54.3+dfsg' cd inst/doc && \ Rscript -e "require(knitr); require(markdown); knit('GenomicFeatures.Rmd', 'GenomicFeatures.md'); markdownToHTML('GenomicFeatures.md', 'GenomicFeatures.html', options=c('use_xhtml', 'base64_images'));" && \ sed -i -e 's#https://mathjax\.rstudio.*/MathJax.js\(?config=TeX.*L"\)#file:///usr/share/javascript/mathjax/MathJax.js\1#' *.html Loading required package: knitr Warning message: package 'knitr' was built under R version 4.3.3 Loading required package: markdown Warning message: package 'markdown' was built under R version 4.3.3 processing file: GenomicFeatures.Rmd 1/54 2/54 [loadGenomicFeatures] 3/54 4/54 [loadDb] 5/54 6/54 [loadPackage] 7/54 8/54 [seqlevels] 9/54 10/54 [seqlevels2] 11/54 12/54 [seqlevels3] 13/54 14/54 [seqlevels4] 15/54 16/54 [selectExample] 17/54 18/54 [selectExercise] 19/54 20/54 [transcripts1] 21/54 22/54 [transcripts2] 23/54 24/54 [transcripts3] 25/54 26/54 [transcripts4] 27/54 28/54 [exonsExer1] 29/54 30/54 [transcriptsBy] 31/54 32/54 [exonsBy] 33/54 34/54 [internalID] 35/54 36/54 [introns-UTRs] 37/54 38/54 [extract] 39/54 40/54 [translate1] 41/54 42/54 [betterTranslation] 43/54 44/54 [supportedUCSCtables] 45/54 [makeTxDbFromUCSC] 46/54 47/54 [makeTxDbFromBiomart] 48/54 49/54 [saveDb-1] 50/54 51/54 [loadDb-1] 52/54 53/54 [SessionInfo] 54/54 output file: GenomicFeatures.md [1] "GenomicFeatures.md" make[1]: Leaving directory '/build/reproducible-path/r-bioc-genomicfeatures-1.54.3+dfsg' 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-genomicfeatures/ -O--buildsystem=R I: R Package: GenomicFeatures Version: 1.54.3 I: Building using R version 4.3.2-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Mon, 05 Feb 2024 10:01:08 +0100 mkdir -p /build/reproducible-path/r-bioc-genomicfeatures-1.54.3\+dfsg/debian/r-bioc-genomicfeatures/usr/lib/R/site-library R CMD INSTALL -l /build/reproducible-path/r-bioc-genomicfeatures-1.54.3\+dfsg/debian/r-bioc-genomicfeatures/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 05 Feb 2024 10:01:08 +0100'" * installing *source* package 'GenomicFeatures' ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicFeatures) W: Ignoring specified R dependency: R (>= 3.5.0) I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.1.0) I: Using r-bioc-s4vectors for Depends:S4Vectors (>= 0.17.29) I: Using r-bioc-iranges for Depends:IRanges (>= 2.13.23) I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.35.8) I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.31.17) I: Using r-bioc-annotationdbi for Depends:AnnotationDbi (>= 1.41.4) W: Cannot find a debian package for Suggests:RMariaDB W: Cannot find a debian package for Suggests:org.Mm.eg.db I: Using r-bioc-org.hs.eg.db for Suggests:org.Hs.eg.db I: Using r-bioc-bsgenome for Suggests:BSgenome W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17) W: Cannot find a debian package for Suggests:BSgenome.Celegans.UCSC.ce11 W: Cannot find a debian package for Suggests:BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17) W: Cannot find a debian package for Suggests:mirbase.db W: Cannot find a debian package for Suggests:FDb.UCSC.tRNAs W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg19.knownGene W: Cannot find a debian package for Suggests:TxDb.Celegans.UCSC.ce11.ensGene W: Cannot find a debian package for Suggests:TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1) W: Cannot find a debian package for Suggests:TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7) W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6) W: Cannot find a debian package for Suggests:SNPlocs.Hsapiens.dbSNP144.GRCh38 I: Using r-bioc-rsamtools for Suggests:Rsamtools W: Cannot find a debian package for Suggests:pasillaBamSubset (>= 0.0.5) I: Using r-bioc-genomicalignments for Suggests:GenomicAlignments (>= 1.15.7) I: Using r-bioc-ensembldb for Suggests:ensembldb I: Using r-bioc-annotationfilter for Suggests:AnnotationFilter I: Using r-cran-runit for Suggests:RUnit I: Using r-bioc-biocstyle for Suggests:BiocStyle I: Using r-cran-knitr for Suggests:knitr I: Using r-cran-markdown for Suggests:markdown I: Using r-cran-dbi for Imports:DBI I: Using r-cran-rsqlite for Imports:RSQLite (>= 2.0) I: Using r-cran-rcurl for Imports:RCurl I: Using r-bioc-xvector for Imports:XVector (>= 0.19.7) I: Using r-bioc-biostrings for Imports:Biostrings (>= 2.47.6) I: Using r-bioc-biocio for Imports:BiocIO I: Using r-bioc-rtracklayer for Imports:rtracklayer (>= 1.51.5) I: Using r-bioc-biomart for Imports:biomaRt (>= 2.58.2) I: Using r-bioc-biobase for Imports:Biobase (>= 2.15.1) I: BioConductor API version: r-api-bioc-3.18 I: Use r-bioc-genomicfeatures 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_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-genomicfeatures' in '../r-bioc-genomicfeatures_1.54.3+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../r-bioc-genomicfeatures_1.54.3+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../r-bioc-genomicfeatures_1.54.3+dfsg-1_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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2250423/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2250423/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/2250423 and its subdirectories I: Current time: Thu May 29 21:26:12 +14 2025 I: pbuilder-time-stamp: 1748503572