I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 21 01:24:48 +14 2023 I: pbuilder-time-stamp: 1681989888 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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: using eatmydata during job I: Copying source file I: copying [mapdamage_2.2.1+dfsg-3.dsc] I: copying [./mapdamage_2.2.1+dfsg.orig.tar.xz] I: copying [./mapdamage_2.2.1+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Nov 25 01:25:05 2022 +14 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 ./mapdamage_2.2.1+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting mapdamage in mapdamage-2.2.1+dfsg dpkg-source: info: unpacking mapdamage_2.2.1+dfsg.orig.tar.xz dpkg-source: info: unpacking mapdamage_2.2.1+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_seqtk.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/19764/tmp/hooks/D01_modify_environment starting debug: Running on ionos12-i386. 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 Apr 21 01:24 /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/19764/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/19764/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]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=9f68666d956a46fb804178eed66328eb LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-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=19764 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.kgx36WHU/pbuilderrc_7TLo --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kgx36WHU/b2 --logfile b2/build.log --extrapackages usrmerge mapdamage_2.2.1+dfsg-3.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-21-686-pae #1 SMP Debian 5.10.162-1 (2023-01-21) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Feb 13 10:21 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash -rwxr-xr-x 1 root root 137160 Sep 21 2022 date -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd -rwxr-xr-x 1 root root 108940 Sep 21 2022 df -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 34664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 10:21 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 3 06:31 run-parts -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Apr 21 01:24 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar -rwxr-xr-x 1 root root 13860 Nov 3 06:31 tempfile -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch -rwxr-xr-x 1 root root 34664 Sep 21 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/19764/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: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), python3, dh-python, python3-setuptools, python3-pysam, seqtk, r-base-core, r-cran-gam, r-cran-ggplot2, r-cran-inline dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19604 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on seqtk; however: Package seqtk is not installed. pbuilder-satisfydepends-dummy depends on r-base-core; however: Package r-base-core is not installed. pbuilder-satisfydepends-dummy depends on r-cran-gam; however: Package r-cran-gam is not installed. pbuilder-satisfydepends-dummy depends on r-cran-ggplot2; however: Package r-cran-ggplot2 is not installed. pbuilder-satisfydepends-dummy depends on r-cran-inline; however: Package r-cran-inline is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcurl3-gnutls{a} libcurl4{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhts3{a} libhtscodecs2{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsm6{a} libssh2-1{a} libsub-override-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libxt6{a} m4{a} man-db{a} media-types{a} openssl{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-codetools{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-foreach{a} r-cran-gam{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gtable{a} r-cran-inline{a} r-cran-isoband{a} r-cran-iterators{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} readline-common{a} sensible-utils{a} seqtk{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx publicsuffix r-base-dev r-cran-bit64 r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dplyr r-cran-formattable r-cran-generics r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-interp r-cran-knitr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-maptools r-cran-mockery r-cran-mockr r-cran-multcomp r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rsqlite r-cran-sf r-cran-stringi r-cran-svglite r-cran-testthat r-cran-vdiffr r-cran-waldo r-cran-xml2 r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 147 newly installed, 0 to remove and 0 not upgraded. Need to get 104 MB of archives. After unpacking 251 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 11 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.8-1 [1412 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 35 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.1+b3 [720 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-2 [131 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130 [104 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-4 [410 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 fontconfig i386 2.14.1-4 [450 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 libblas3 i386 3.11.0-2 [139 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 libpixman-1-0 i386 0.42.2-1 [548 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2 [292 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2 [782 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libcairo2 i386 1.16.0-7 [627 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-8 [412 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-8 [419 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 libdatrie1 i386 0.2.13-2+b1 [45.0 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 libfribidi0 i386 1.0.8-2.1 [65.6 kB] Get: 80 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB] Get: 82 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB] Get: 86 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB] Get: 87 http://deb.debian.org/debian bookworm/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 liblapack3 i386 3.11.0-2 [2092 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 libthai-data all 0.1.29-1 [176 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 libthai0 i386 0.1.29-1 [58.6 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 libpango-1.0-0 i386 1.50.12+ds-1 [220 kB] Get: 95 http://deb.debian.org/debian bookworm/main i386 libpangoft2-1.0-0 i386 1.50.12+ds-1 [50.5 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 libpangocairo-1.0-0 i386 1.50.12+ds-1 [35.4 kB] Get: 97 http://deb.debian.org/debian bookworm/main i386 libpaper1 i386 1.1.29 [12.7 kB] Get: 98 http://deb.debian.org/debian bookworm/main i386 libpaper-utils i386 1.1.29 [8972 B] Get: 99 http://deb.debian.org/debian bookworm/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 100 http://deb.debian.org/debian bookworm/main i386 libtcl8.6 i386 8.6.13+dfsg-2 [1095 kB] Get: 101 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.1 [293 kB] Get: 102 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-5 [332 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 libxft2 i386 2.3.6-1 [62.8 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 libxss1 i386 1:1.2.3-1 [18.1 kB] Get: 105 http://deb.debian.org/debian bookworm/main i386 libtk8.6 i386 8.6.13-2 [824 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 libxt6 i386 1:1.2.1-1.1 [192 kB] Get: 107 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 108 http://deb.debian.org/debian bookworm/main i386 python3-pysam i386 0.20.0+ds-3+b1 [1708 kB] Get: 109 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB] Get: 110 http://deb.debian.org/debian bookworm/main i386 zip i386 3.0-13 [236 kB] Get: 111 http://deb.debian.org/debian bookworm/main i386 unzip i386 6.0-28 [166 kB] Get: 112 http://deb.debian.org/debian bookworm/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 113 http://deb.debian.org/debian bookworm/main i386 r-base-core i386 4.2.2.20221110-2 [26.1 MB] Get: 114 http://deb.debian.org/debian bookworm/main i386 r-cran-cli i386 3.6.0-1 [1288 kB] Get: 115 http://deb.debian.org/debian bookworm/main i386 r-cran-codetools all 0.2-19-1 [90.9 kB] Get: 116 http://deb.debian.org/debian bookworm/main i386 r-cran-colorspace i386 2.1-0+dfsg-1 [1695 kB] Get: 117 http://deb.debian.org/debian bookworm/main i386 r-cran-fansi i386 1.0.4-1 [624 kB] Get: 118 http://deb.debian.org/debian bookworm/main i386 r-cran-farver i386 2.1.1-1 [1404 kB] Get: 119 http://deb.debian.org/debian bookworm/main i386 r-cran-iterators all 1.0.14-1 [337 kB] Get: 120 http://deb.debian.org/debian bookworm/main i386 r-cran-foreach all 1.5.2-1 [122 kB] Get: 121 http://deb.debian.org/debian bookworm/main i386 r-cran-gam i386 1.22-1-1 [305 kB] Get: 122 http://deb.debian.org/debian bookworm/main i386 r-cran-glue i386 1.6.2-1 [152 kB] Get: 123 http://deb.debian.org/debian bookworm/main i386 r-cran-gtable all 0.3.1+dfsg-1 [165 kB] Get: 124 http://deb.debian.org/debian bookworm/main i386 r-cran-isoband i386 0.2.7-1 [1617 kB] Get: 125 http://deb.debian.org/debian bookworm/main i386 r-cran-rlang i386 1.0.6-1 [1634 kB] Get: 126 http://deb.debian.org/debian bookworm/main i386 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get: 127 http://deb.debian.org/debian bookworm/main i386 r-cran-mass i386 7.3-58.2-1 [1123 kB] Get: 128 http://deb.debian.org/debian bookworm/main i386 r-cran-lattice i386 0.20-45-3 [1172 kB] Get: 129 http://deb.debian.org/debian bookworm/main i386 r-cran-nlme i386 3.1.162-1 [2250 kB] Get: 130 http://deb.debian.org/debian bookworm/main i386 r-cran-matrix i386 1.5-3-1 [3821 kB] Get: 131 http://deb.debian.org/debian bookworm/main i386 r-cran-mgcv i386 1.8-41-1 [3167 kB] Get: 132 http://deb.debian.org/debian bookworm/main i386 r-cran-labeling all 0.4.2-1 [62.7 kB] Get: 133 http://deb.debian.org/debian bookworm/main i386 r-cran-munsell all 0.5.0-2 [236 kB] Get: 134 http://deb.debian.org/debian bookworm/main i386 r-cran-r6 all 2.5.1-1 [105 kB] Get: 135 http://deb.debian.org/debian bookworm/main i386 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 136 http://deb.debian.org/debian bookworm/main i386 r-cran-viridislite all 0.4.1-1 [1299 kB] Get: 137 http://deb.debian.org/debian bookworm/main i386 r-cran-scales all 1.2.1-1 [614 kB] Get: 138 http://deb.debian.org/debian bookworm/main i386 r-cran-magrittr i386 2.0.3-1 [201 kB] Get: 139 http://deb.debian.org/debian bookworm/main i386 r-cran-utf8 i386 1.2.3-1 [135 kB] Get: 140 http://deb.debian.org/debian bookworm/main i386 r-cran-vctrs i386 0.5.2-1 [1388 kB] Get: 141 http://deb.debian.org/debian bookworm/main i386 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get: 142 http://deb.debian.org/debian bookworm/main i386 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 143 http://deb.debian.org/debian bookworm/main i386 r-cran-tibble i386 3.1.8+dfsg-1 [513 kB] Get: 144 http://deb.debian.org/debian bookworm/main i386 r-cran-withr all 2.5.0-1 [236 kB] Get: 145 http://deb.debian.org/debian bookworm/main i386 r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB] Get: 146 http://deb.debian.org/debian bookworm/main i386 r-cran-inline all 0.3.19-2 [129 kB] Get: 147 http://deb.debian.org/debian bookworm/main i386 seqtk i386 1.3-4 [33.6 kB] Fetched 104 MB in 3s (35.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19604 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.2-6) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_i386.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:i386 (3.11.2-6) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19920 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_i386.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../3-libreadline8_8.2-1.3_i386.deb ... Unpacking libreadline8:i386 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_i386.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20354 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_i386.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.8-1_i386.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../005-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../008-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../011-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package ucf. Preparing to unpack .../013-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../019-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../021-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../022-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../023-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../024-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../025-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../026-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../027-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../028-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../029-libxml2_2.9.14+dfsg-1.1+b3_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../030-gettext_0.21-12_i386.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../031-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../032-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../033-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../034-python3-lib2to3_3.11.2-2_all.deb ... Unpacking python3-lib2to3 (3.11.2-2) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../035-python3-distutils_3.11.2-2_all.deb ... Unpacking python3-distutils (3.11.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../036-dh-python_5.20230130_all.deb ... Unpacking dh-python (5.20230130) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../037-libbrotli1_1.0.9-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../038-libpng16-16_1.6.39-2_i386.deb ... Unpacking libpng16-16:i386 (1.6.39-2) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../039-libfreetype6_2.12.1+dfsg-4_i386.deb ... Unpacking libfreetype6:i386 (2.12.1+dfsg-4) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../040-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../041-fontconfig-config_2.14.1-4_i386.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:i386. Preparing to unpack .../042-libfontconfig1_2.14.1-4_i386.deb ... Unpacking libfontconfig1:i386 (2.14.1-4) ... Selecting previously unselected package fontconfig. Preparing to unpack .../043-fontconfig_2.14.1-4_i386.deb ... Unpacking fontconfig (2.14.1-4) ... Selecting previously unselected package libblas3:i386. Preparing to unpack .../044-libblas3_3.11.0-2_i386.deb ... Unpacking libblas3:i386 (3.11.0-2) ... 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Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:i386 (1.52.0-1) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up libdeflate0:i386 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libjbig0:i386 (2.1-6.1) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg-10) ... Setting up zip (3.0-13) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.11.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libjpeg62-turbo:i386 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libfribidi0:i386 (1.0.8-2.1) ... Setting up libpng16-16:i386 (1.6.39-2) ... Setting up libtcl8.6:i386 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libsasl2-2:i386 (2.1.28+dfsg-10) ... Setting up libgfortran5:i386 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:i386 (1.2.4-0.1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:i386 (4.5.0-5) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:i386 (1.10.0-3+b1) ... Setting up openssl (3.0.8-1) ... Setting up libbsd0:i386 (0.11.7-2) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:i386 (2.9.14+dfsg-1.1+b3) ... 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 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:i386 (2:1.0.10-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up liblapack3:i386 (3.11.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:i386 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libreadline8:i386 (8.2-1.3) ... Setting up libxcb-shm0:i386 (1.15-1) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:i386 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libfreetype6:i386 (2.12.1+dfsg-4) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libcurl4:i386 (7.88.1-8) ... Setting up libx11-6:i386 (2:1.8.4-2) ... Setting up libharfbuzz0b:i386 (6.0.0+dfsg-3) ... Setting up libfontconfig1:i386 (2.14.1-4) ... Setting up libsm6:i386 (2:1.2.3-1) ... Setting up libpaper1:i386 (1.1.29) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.2-6) ... Setting up libpango-1.0-0:i386 (1.50.12+ds-1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:i386 (7.88.1-8) ... Setting up libpaper-utils (1.1.29) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.16.0-7) ... Setting up libxt6:i386 (1:1.2.1-1.1) ... Setting up libxss1:i386 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:i386 (1.50.12+ds-1) ... Setting up libpangocairo-1.0-0:i386 (1.50.12+ds-1) ... Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:i386 (2.3.6-1) ... Setting up libhts3:i386 (1.16+ds-3) ... Setting up libtk8.6:i386 (8.6.13-2) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-gtable (0.3.1+dfsg-1) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.20-45-3) ... Setting up r-cran-nlme (3.1.162-1) ... Setting up r-cran-farver (2.1.1-1) ... Setting up r-cran-viridislite (0.4.1-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up r-cran-codetools (0.2-19-1) ... Setting up r-cran-inline (0.3.19-2) ... Setting up r-cran-rlang (1.0.6-1) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up r-cran-withr (2.5.0-1) ... Setting up r-cran-iterators (1.0.14-1) ... Setting up r-cran-foreach (1.5.2-1) ... Setting up r-cran-fansi (1.0.4-1) ... Setting up r-cran-mass (7.3-58.2-1) ... Setting up r-cran-glue (1.6.2-1) ... Setting up r-cran-gam (1.22-1-1) ... Setting up r-cran-cli (3.6.0-1) ... Setting up r-cran-lifecycle (1.0.3+dfsg-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.3-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-matrix (1.5-3-1) ... Setting up r-cran-mgcv (1.8-41-1) ... Setting up r-cran-vctrs (0.5.2-1) ... Setting up r-cran-pillar (1.8.1+dfsg-1) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-tibble (3.1.8+dfsg-1) ... Setting up r-cran-scales (1.2.1-1) ... Setting up r-cran-ggplot2 (3.4.1+dfsg-1) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... 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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/19764/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/19764/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/mapdamage-2.2.1+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 > ../mapdamage_2.2.1+dfsg-3_source.changes dpkg-buildpackage: info: source package mapdamage dpkg-buildpackage: info: source version 2.2.1+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/mapdamage-2.2.1+dfsg' dh_auto_clean I: pybuild base:240: python3.11 setup.py clean 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -f mapdamage/_version.py rm -f mapdamage/tests/results/Fragmisincorporation_plot.pdf mapdamage/tests/results/Fragmisincorporation_plot.pdf mapdamage/tests/results/Length_plot.pdf mapdamage/tests/results/Length_plot.pdf rm -f mapdamage/tests/fake1.fasta.fai mapdamage/tests/results/3pGtoA_freq.txt mapdamage/tests/results/5pCtoT_freq.txt mapdamage/tests/results/Runtime_log.txt mapdamage/tests/results/dnacomp.txt mapdamage/tests/results/lgdistribution.txt mapdamage/tests/results/misincorporation.txt mapdamage/tests/test.rescaled.sam make[1]: Leaving directory '/build/mapdamage-2.2.1+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build debian/rules override_dh_auto_test make[1]: Entering directory '/build/mapdamage-2.2.1+dfsg' cd mapdamage && \ PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path:/build/mapdamage-2.2.1+dfsg/bin \ PYTHONPATH=/build/mapdamage-2.2.1+dfsg/.pybuild/cpython3_3.11/build \ python3 mp_test.py Started with the command: /build/mapdamage-2.2.1+dfsg/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats [E::idx_find_and_load] Could not retrieve index file for 'tests/test.bam' Warning message: In (yaxis.at == 2) && (yaxis.at == ylabels.at) : 'length(x) = 2 > 1' in coercion to 'logical(1)' Warning message: In (yaxis.at == 2) && (yaxis.at == ylabels.at) : 'length(x) = 2 > 1' in coercion to 'logical(1)' additional tests/results/Length_plot.pdf generated Successful run Missing the following R libraries 'Rcpp' and 'RcppGSL' The Bayesian estimation has been disabled Reading from 'tests/test.bam' Writing results to 'tests/results/' pdf tests/results/Fragmisincorporation_plot.pdf generated .[E::idx_find_and_load] Could not retrieve index file for 'tests/test.bam' . ---------------------------------------------------------------------- Ran 2 tests in 4.585s OK make[1]: Leaving directory '/build/mapdamage-2.2.1+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/mapdamage/ -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/mapdamage-2.2.1+dfsg/debian/mapdamage dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/mapdamage-2.2.1+dfsg' dh_python3 --no-ext-rename make[1]: Leaving directory '/build/mapdamage-2.2.1+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/mapdamage-2.2.1+dfsg' dh_fixperms find debian -name checkLibraries.R -exec chmod +x \{\} \; find debian -name runGeneral.R -exec chmod +x \{\} \; make[1]: Leaving directory '/build/mapdamage-2.2.1+dfsg' dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'mapdamage' in '../mapdamage_2.2.1+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../mapdamage_2.2.1+dfsg-3_i386.buildinfo dpkg-genchanges --build=binary -O../mapdamage_2.2.1+dfsg-3_i386.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/19764/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/19764/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/19764 and its subdirectories I: Current time: Fri Apr 21 01:25:54 +14 2023 I: pbuilder-time-stamp: 1681989954