I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 17 00:11:59 +14 2024 I: pbuilder-time-stamp: 1713262319 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-makecdfenv_1.78.0-1.dsc] I: copying [./r-bioc-makecdfenv_1.78.0.orig.tar.gz] I: copying [./r-bioc-makecdfenv_1.78.0-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 30 09:45:36 2023 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-makecdfenv_1.78.0-1.dsc: no acceptable signature found dpkg-source: info: extracting r-bioc-makecdfenv in r-bioc-makecdfenv-1.78.0 dpkg-source: info: unpacking r-bioc-makecdfenv_1.78.0.orig.tar.gz dpkg-source: info: unpacking r-bioc-makecdfenv_1.78.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying delete_configure.patch dpkg-source: info: applying fix_cflags.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/26923/tmp/hooks/D01_modify_environment starting debug: Running on virt64z. 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 16 10:12 /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/26923/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/26923/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]="arm-unknown-linux-gnueabihf") 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=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=9f8fd9e56d624c64800f698aa9f64602 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=26923 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.PfrpiOSk/pbuilderrc_KFtQ --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.PfrpiOSk/b2 --logfile b2/build.log r-bioc-makecdfenv_1.78.0-1.dsc' SUDO_GID=110 SUDO_UID=103 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 14 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/26923/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: armhf 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-affyio, r-bioc-biobase, r-bioc-affy, r-bioc-zlibbioc dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19635 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-affyio; however: Package r-bioc-affyio is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biobase; however: Package r-bioc-biobase is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-affy; however: Package r-bioc-affy is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-zlibbioc; however: Package r-bioc-zlibbioc 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} dctrl-tools{a} debhelper{a} dh-autoreconf{a} dh-r{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gfortran{a} gfortran-13{a} gfortran-13-arm-linux-gnueabihf{a} gfortran-arm-linux-gnueabihf{a} groff-base{a} icu-devtools{a} intltool-debian{a} libalgorithm-c3-perl{a} libarchive-zip-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libblas-dev{a} libblas3{a} 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} libcurl3-gnutls{a} libcurl4{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} libfreetype6{a} libfribidi0{a} libgfortran-13-dev{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhttp-date-perl{a} libhttp-message-perl{a} libice6{a} libicu-dev{a} libicu72{a} libio-html-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} liblerc4{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} 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} libpng16-16{a} libpsl5{a} libreadline-dev{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1{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} libtcl8.6{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} libvariable-magic-perl{a} libwebp7{a} libwww-curl-perl{a} libwww-curl-simple-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxmuu1{a} libxrender1{a} libxss1{a} libxt6{a} m4{a} man-db{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} r-base-core{a} r-base-dev{a} r-bioc-affy{a} r-bioc-affyio{a} r-bioc-biobase{a} r-bioc-biocgenerics{a} r-bioc-preprocesscore{a} r-bioc-zlibbioc{a} r-cran-biocmanager{a} readline-common{a} sensible-utils{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xauth{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc cme curl devscripts git-buildpackage 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 lynx publicsuffix r-bioc-biocversion r-cran-curl r-cran-knitr r-cran-remotes r-cran-rmarkdown r-cran-testthat r-cran-withr r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 182 newly installed, 0 to remove and 0 not upgraded. Need to get 94.8 MB of archives. After unpacking 258 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-1 [255 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-3 [69.1 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.1.5-1 [1208 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf ucf all 3.0043+nmu1 [55.2 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf dctrl-tools armhf 2.24-3 [96.0 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 29 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf zip armhf 3.0-13 [218 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf unzip armhf 6.0-28 [152 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libpaper1 armhf 1.1.29 [11.9 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libpaper-utils armhf 1.1.29 [8400 B] Get: 41 http://deb.debian.org/debian trixie/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libblas3 armhf 3.12.0-3 [108 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.5.0-2+b2 [80.2 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libpng16-16 armhf 1.6.43-1 [262 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libfreetype6 armhf 2.13.2+dfsg-1+b1 [371 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf fontconfig-config armhf 2.15.0-1.1 [317 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libfontconfig1 armhf 2.15.0-1.1 [370 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libpixman-1-0 armhf 0.42.2-1+b1 [476 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libbsd0 armhf 0.12.2-1 [127 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.7-1 [328 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.7-1 [735 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libxcb-render0 armhf 1.15-1 [114 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libxcb-shm0 armhf 1.15-1 [106 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libcairo2 armhf 1.18.0-1+b1 [441 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4+b1 [18.2 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4+b1 [50.1 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5+b3 [158 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.59.0-1 [62.0 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libssh2-1 armhf 1.11.0-4 [197 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libcurl4 armhf 8.5.0-2 [383 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libglib2.0-0 armhf 2.78.4-1 [1281 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-2+b2 [143 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14-20240201-3 [263 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf liblapack3 armhf 3.12.0-3 [1803 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf fontconfig armhf 2.15.0-1.1 [461 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libfribidi0 armhf 1.0.13-3+b1 [69.4 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libgraphite2-3 armhf 1.3.14-2 [63.2 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libharfbuzz0b armhf 8.3.0-2 [2155 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libthai-data all 0.1.29-2 [168 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libdatrie1 armhf 0.2.13-3 [34.4 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libthai0 armhf 0.1.29-2 [45.8 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libpango-1.0-0 armhf 1.52.0+ds-1 [192 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libpangoft2-1.0-0 armhf 1.52.0+ds-1 [41.8 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libpangocairo-1.0-0 armhf 1.52.0+ds-1 [31.2 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libreadline8 armhf 8.2-3+b1 [144 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libtcl8.6 armhf 8.6.14+dfsg-1 [928 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libjbig0 armhf 2.1-6.1+b1 [27.3 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf liblerc4 armhf 4.0.0+ds-4+b1 [137 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libsharpyuv0 armhf 1.3.2-0.4 [105 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libwebp7 armhf 1.3.2-0.4 [261 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libtiff6 armhf 4.5.1+git230720-4 [301 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libxft2 armhf 2.3.6-1+b1 [46.4 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf x11-common all 1:7.7+23 [252 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libxss1 armhf 1:1.2.3-1 [17.2 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libtk8.6 armhf 8.6.14-1 [693 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libice6 armhf 2:1.0.10-1 [51.9 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libxt6 armhf 1:1.2.1-1.1 [157 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf r-base-core armhf 4.3.2-1 [26.4 MB] Get: 101 http://deb.debian.org/debian trixie/main armhf libgfortran-13-dev armhf 13.2.0-13 [306 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf gfortran-13-arm-linux-gnueabihf armhf 13.2.0-13 [8193 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf gfortran-13 armhf 13.2.0-13 [10.5 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf gfortran-arm-linux-gnueabihf armhf 4:13.2.0-7 [1288 B] Get: 105 http://deb.debian.org/debian trixie/main armhf gfortran armhf 4:13.2.0-7 [1432 B] Get: 106 http://deb.debian.org/debian trixie/main armhf libblas-dev armhf 3.12.0-3 [119 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf liblapack-dev armhf 3.12.0-3 [1903 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.4+20240113-1 [81.8 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libncurses-dev armhf 6.4+20240113-1 [309 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf libreadline-dev armhf 8.2-3+b1 [137 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2+b2 [260 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf libjpeg-dev armhf 1:2.1.5-2+b2 [72.1 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf libpcre2-16-0 armhf 10.42-4+b1 [212 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf libpcre2-32-0 armhf 10.42-4+b1 [203 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf libpcre2-posix3 armhf 10.42-4+b1 [55.3 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf libpcre2-dev armhf 10.42-4+b1 [668 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] Get: 118 http://deb.debian.org/debian trixie/main armhf libpng-dev armhf 1.6.43-1 [344 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf libbz2-dev armhf 1.0.8-5.1 [28.3 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf icu-devtools armhf 72.1-4+b1 [185 kB] Get: 122 http://deb.debian.org/debian trixie/main armhf libicu-dev armhf 72.1-4+b1 [10.1 MB] Get: 123 http://deb.debian.org/debian trixie/main armhf libxmuu1 armhf 2:1.1.3-3 [23.3 kB] Get: 124 http://deb.debian.org/debian trixie/main armhf xauth armhf 1:1.1.2-1 [33.2 kB] Get: 125 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-1+b2 [31.9 kB] Get: 126 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-1+b2 [28.9 kB] Get: 127 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] Get: 128 http://deb.debian.org/debian trixie/main armhf pkg-config armhf 1.8.1-1+b2 [14.0 kB] Get: 129 http://deb.debian.org/debian trixie/main armhf r-base-dev all 4.3.2-1 [4504 B] Get: 130 http://deb.debian.org/debian trixie/main armhf libfile-which-perl all 1.27-2 [15.1 kB] Get: 131 http://deb.debian.org/debian trixie/main armhf libswitch-perl all 2.17-3 [20.3 kB] Get: 132 http://deb.debian.org/debian trixie/main armhf libclone-perl armhf 0.46-1+b1 [13.2 kB] Get: 133 http://deb.debian.org/debian trixie/main armhf libencode-locale-perl all 1.05-3 [12.9 kB] Get: 134 http://deb.debian.org/debian trixie/main armhf libtimedate-perl all 2.3300-2 [39.3 kB] Get: 135 http://deb.debian.org/debian trixie/main armhf libhttp-date-perl all 6.06-1 [10.7 kB] Get: 136 http://deb.debian.org/debian trixie/main armhf libio-html-perl all 1.004-3 [16.2 kB] Get: 137 http://deb.debian.org/debian trixie/main armhf liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 138 http://deb.debian.org/debian trixie/main armhf liburi-perl all 5.28-1 [98.6 kB] Get: 139 http://deb.debian.org/debian trixie/main armhf libhttp-message-perl all 6.45-1 [82.0 kB] Get: 140 http://deb.debian.org/debian trixie/main armhf libparams-util-perl armhf 1.102-2+b2 [23.3 kB] Get: 141 http://deb.debian.org/debian trixie/main armhf libsub-install-perl all 0.929-1 [10.5 kB] Get: 142 http://deb.debian.org/debian trixie/main armhf libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 143 http://deb.debian.org/debian trixie/main armhf libb-hooks-op-check-perl armhf 0.22-2+b2 [10.3 kB] Get: 144 http://deb.debian.org/debian trixie/main armhf libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 145 http://deb.debian.org/debian trixie/main armhf libdevel-callchecker-perl armhf 0.008-2+b1 [14.9 kB] Get: 146 http://deb.debian.org/debian trixie/main armhf libparams-classify-perl armhf 0.015-2+b2 [21.3 kB] Get: 147 http://deb.debian.org/debian trixie/main armhf libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 148 http://deb.debian.org/debian trixie/main armhf libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 149 http://deb.debian.org/debian trixie/main armhf libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 150 http://deb.debian.org/debian trixie/main armhf libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 151 http://deb.debian.org/debian trixie/main armhf libclass-load-perl all 0.25-2 [15.3 kB] Get: 152 http://deb.debian.org/debian trixie/main armhf libclass-load-xs-perl armhf 0.10-2+b2 [13.8 kB] Get: 153 http://deb.debian.org/debian trixie/main armhf libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 154 http://deb.debian.org/debian trixie/main armhf libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 155 http://deb.debian.org/debian trixie/main armhf libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 156 http://deb.debian.org/debian trixie/main armhf libclass-c3-perl all 0.35-2 [21.0 kB] Get: 157 http://deb.debian.org/debian trixie/main armhf libmro-compat-perl all 0.15-2 [11.8 kB] Get: 158 http://deb.debian.org/debian trixie/main armhf libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 159 http://deb.debian.org/debian trixie/main armhf libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 160 http://deb.debian.org/debian trixie/main armhf libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 161 http://deb.debian.org/debian trixie/main armhf libeval-closure-perl all 0.14-3 [11.2 kB] Get: 162 http://deb.debian.org/debian trixie/main armhf libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 163 http://deb.debian.org/debian trixie/main armhf libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 164 http://deb.debian.org/debian trixie/main armhf libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 165 http://deb.debian.org/debian trixie/main armhf libpackage-stash-xs-perl armhf 0.30-1+b2 [18.4 kB] Get: 166 http://deb.debian.org/debian trixie/main armhf libmoose-perl armhf 2.2207-1 [764 kB] Get: 167 http://deb.debian.org/debian trixie/main armhf libvariable-magic-perl armhf 0.63-1+b2 [41.4 kB] Get: 168 http://deb.debian.org/debian trixie/main armhf libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 169 http://deb.debian.org/debian trixie/main armhf libsub-identify-perl armhf 0.14-3+b1 [10.8 kB] Get: 170 http://deb.debian.org/debian trixie/main armhf libsub-name-perl armhf 0.27-1+b1 [12.0 kB] Get: 171 http://deb.debian.org/debian trixie/main armhf libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 172 http://deb.debian.org/debian trixie/main armhf libcurl3-gnutls armhf 8.5.0-2 [378 kB] Get: 173 http://deb.debian.org/debian trixie/main armhf libwww-curl-perl armhf 4.17-10+b1 [56.2 kB] Get: 174 http://deb.debian.org/debian trixie/main armhf libwww-curl-simple-perl all 0.100191-3 [12.6 kB] Get: 175 http://deb.debian.org/debian trixie/main armhf dh-r all 20231212 [42.2 kB] Get: 176 http://deb.debian.org/debian trixie/main armhf r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get: 177 http://deb.debian.org/debian trixie/main armhf r-bioc-biobase armhf 2.62.0-1 [2118 kB] Get: 178 http://deb.debian.org/debian trixie/main armhf r-bioc-zlibbioc all 1.48.0+dfsg-1 [9344 B] Get: 179 http://deb.debian.org/debian trixie/main armhf r-bioc-affyio armhf 1.72.0-1 [78.6 kB] Get: 180 http://deb.debian.org/debian trixie/main armhf r-cran-biocmanager all 1.30.22+dfsg-2 [126 kB] Get: 181 http://deb.debian.org/debian trixie/main armhf r-bioc-preprocesscore armhf 1.64.0+ds-1 [134 kB] Get: 182 http://deb.debian.org/debian trixie/main armhf r-bioc-affy armhf 1.80.0-1 [1342 kB] Fetched 94.8 MB in 1s (73.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package tzdata. (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 ... 19635 files and directories currently installed.) Preparing to unpack .../000-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.1.5-1_armhf.deb ... Unpacking openssl (3.1.5-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../006-libmagic1_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../009-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../012-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package ucf. Preparing to unpack .../014-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 .../015-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../016-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../017-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../018-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 .../019-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../020-dctrl-tools_2.24-3_armhf.deb ... Unpacking dctrl-tools (2.24-3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../021-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../022-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../023-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../024-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 .../025-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../026-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 .../027-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../028-libelf1_0.190-1+b1_armhf.deb ... Unpacking libelf1:armhf (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../029-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../030-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../031-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../032-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../033-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 .../034-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../035-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package zip. Preparing to unpack .../036-zip_3.0-13_armhf.deb ... Unpacking zip (3.0-13) ... Selecting previously unselected package unzip. Preparing to unpack .../037-unzip_6.0-28_armhf.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package libpaper1:armhf. Preparing to unpack .../038-libpaper1_1.1.29_armhf.deb ... Unpacking libpaper1:armhf (1.1.29) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../039-libpaper-utils_1.1.29_armhf.deb ... Unpacking libpaper-utils (1.1.29) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../040-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../041-libblas3_3.12.0-3_armhf.deb ... Unpacking libblas3:armhf (3.12.0-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../042-libexpat1_2.5.0-2+b2_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-2+b2) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../043-libbrotli1_1.1.0-2+b3_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../044-libpng16-16_1.6.43-1_armhf.deb ... Unpacking libpng16-16:armhf (1.6.43-1) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../045-libfreetype6_2.13.2+dfsg-1+b1_armhf.deb ... Unpacking libfreetype6:armhf (2.13.2+dfsg-1+b1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../046-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../047-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../048-fontconfig-config_2.15.0-1.1_armhf.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../049-libfontconfig1_2.15.0-1.1_armhf.deb ... Unpacking libfontconfig1:armhf (2.15.0-1.1) ... Selecting previously unselected package libpixman-1-0:armhf. Preparing to unpack .../050-libpixman-1-0_0.42.2-1+b1_armhf.deb ... Unpacking libpixman-1-0:armhf (0.42.2-1+b1) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../051-libxau6_1%3a1.0.9-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1) ... Selecting previously unselected package libbsd0:armhf. 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Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... 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 libtry-tiny-perl (0.31-2) ... Setting up libnghttp2-14:armhf (1.59.0-1) ... Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up file (1:5.45-2+b1) ... Setting up libjbig0:armhf (2.1-6.1+b1) ... Setting up libpcre2-16-0:armhf (10.42-4+b1) ... Setting up libsub-install-perl (0.929-1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Apr 16 10:12:45 UTC 2024. Universal Time is now: Tue Apr 16 10:12:45 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-13) ... Setting up libpackage-stash-xs-perl:armhf (0.30-1+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:armhf (10.42-4+b1) ... Setting up libblas3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libpkgconf3:armhf (1.8.1-1+b2) ... Setting up libalgorithm-c3-perl (0.11-2) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-2+b2) ... Setting up libswitch-perl (2.17-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libjpeg62-turbo-dev:armhf (1:2.1.5-2+b2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:armhf (6.4+20240113-1) ... Setting up libfribidi0:armhf (1.0.13-3+b1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:armhf (1.6.43-1) ... 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Setting up libuchardet0:armhf (0.0.8-1+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 libssh2-1:armhf (1.11.0-4) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libgfortran-13-dev:armhf (13.2.0-13) ... Setting up openssl (3.1.5-1) ... Setting up libbsd0:armhf (0.12.2-1) ... Setting up libelf1:armhf (0.190-1+b1) ... Setting up readline-common (8.2-3) ... Setting up libicu-dev:armhf (72.1-4+b1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... 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 libblas-dev:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up dctrl-tools (2.24-3) ... Setting up libbz2-dev:armhf (1.0.8-5.1) ... 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 gfortran-13-arm-linux-gnueabihf (13.2.0-13) ... Setting up libice6:armhf (2:1.0.10-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up liblapack3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libncurses-dev:armhf (6.4+20240113-1) ... Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libpcre2-dev:armhf (10.42-4+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:armhf (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libreadline8:armhf (8.2-3+b1) ... Setting up libpng-dev:armhf (1.6.43-1) ... Setting up libjpeg-dev:armhf (1:2.1.5-2+b2) ... Setting up libxcb-shm0:armhf (1.15-1) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libreadline-dev:armhf (8.2-3+b1) ... Setting up libdevel-callchecker-perl:armhf (0.008-2+b1) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5+b3) ... Setting up gfortran-arm-linux-gnueabihf (4:13.2.0-7) ... Setting up pkgconf:armhf (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:armhf (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:armhf (2.13.2+dfsg-1+b1) ... Setting up gfortran-13 (13.2.0-13) ... Setting up liblapack-dev:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up libdata-optlist-perl (0.114-1) ... Setting up pkg-config:armhf (1.8.1-1+b2) ... 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 (1.23.0-3) ... Setting up libcurl4:armhf (8.5.0-2) ... Setting up libx11-6:armhf (2:1.8.7-1) ... Setting up libharfbuzz0b:armhf (8.3.0-2) ... Setting up libfontconfig1:armhf (2.15.0-1.1) ... Setting up libmro-compat-perl (0.15-2) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up libxmuu1:armhf (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) ... Setting up libpaper1:armhf (1.1.29) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxrender1:armhf (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libparams-classify-perl:armhf (0.015-2+b2) ... Setting up libpango-1.0-0:armhf (1.52.0+ds-1) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:armhf (8.5.0-2) ... Setting up libpaper-utils (1.1.29) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:13.2.0-7) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libcairo2:armhf (1.18.0-1+b1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up libxt6:armhf (1:1.2.1-1.1) ... Setting up xauth (1:1.1.2-1) ... Setting up libxss1:armhf (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:armhf (1.52.0+ds-1) ... Setting up libpangocairo-1.0-0:armhf (1.52.0+ds-1) ... Setting up libxft2:armhf (2.3.6-1+b1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libtk8.6:armhf (8.6.14-1) ... Setting up libwww-curl-perl:armhf (4.17-10+b1) ... Setting up debhelper (13.15.3) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up libclass-load-perl (0.25-2) ... Setting up r-base-core (4.3.2-1) ... Creating config file /etc/R/Renviron with new version Setting up libpackage-deprecationmanager-perl (0.18-1) ... Setting up libdevel-overloadinfo-perl (0.007-1) ... Setting up libclass-load-xs-perl (0.10-2+b2) ... Setting up libb-hooks-endofscope-perl (0.28-1) ... Setting up r-bioc-biocgenerics (0.48.1-2) ... Setting up r-base-dev (4.3.2-1) ... Setting up libmoose-perl:armhf (2.2207-1) ... Setting up r-cran-biocmanager (1.30.22+dfsg-2) ... Setting up r-bioc-zlibbioc (1.48.0+dfsg-1) ... Setting up r-bioc-biobase (2.62.0-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up r-bioc-preprocesscore (1.64.0+ds-1) ... Setting up r-bioc-affyio (1.72.0-1) ... Setting up libwww-curl-simple-perl (0.100191-3) ... Setting up r-bioc-affy (1.80.0-1) ... Setting up dh-r (20231212) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/26923/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/26923/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/r-bioc-makecdfenv-1.78.0/ && 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-makecdfenv_1.78.0-1_source.changes dpkg-buildpackage: info: source package r-bioc-makecdfenv dpkg-buildpackage: info: source version 1.78.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf 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 autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:27: warning: AC_OUTPUT should be used without arguments. configure.in:27: You should run autoupdate. dh_auto_configure -O--buildsystem=R dh_auto_build -O--buildsystem=R dh_auto_test -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=R dh_prep -O--buildsystem=R dh_auto_install --destdir=debian/r-bioc-makecdfenv/ -O--buildsystem=R I: R Package: makecdfenv Version: 1.78.0 I: Building using R version 4.3.2-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Thu, 30 Nov 2023 10:42:39 +0100 mkdir -p /build/reproducible-path/r-bioc-makecdfenv-1.78.0/debian/r-bioc-makecdfenv/usr/lib/R/site-library R CMD INSTALL -l /build/reproducible-path/r-bioc-makecdfenv-1.78.0/debian/r-bioc-makecdfenv/usr/lib/R/site-library --clean . "--built-timestamp='Thu, 30 Nov 2023 10:42:39 +0100'" * installing *source* package 'makecdfenv' ... ** using staged installation ./configure: line 1721: R_ZLIB: command not found configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: 'gcc (Debian 13.2.0-13) 13.2.0' make[1]: Entering directory '/build/reproducible-path/r-bioc-makecdfenv-1.78.0/src' gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdffile.c -o read_cdffile.o read_cdffile.c: In function 'openCDFfile': read_cdffile.c:340:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 340 | fgets(buffy, SIZE_LINE, affyFile->stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o makecdfenv.so read_cdffile.o -L/usr/lib/R/lib -lR make[1]: Leaving directory '/build/reproducible-path/r-bioc-makecdfenv-1.78.0/src' make[1]: Entering directory '/build/reproducible-path/r-bioc-makecdfenv-1.78.0/src' make[1]: Leaving directory '/build/reproducible-path/r-bioc-makecdfenv-1.78.0/src' installing to /build/reproducible-path/r-bioc-makecdfenv-1.78.0/debian/r-bioc-makecdfenv/usr/lib/R/site-library/00LOCK-r-bioc-makecdfenv-1.78.0/00new/makecdfenv/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (makecdfenv) W: Ignoring specified R dependency: R (>= 2.6.0) I: Using r-bioc-affyio for Depends:affyio I: Using r-bioc-biobase for Imports:Biobase I: Using r-bioc-affy for Imports:affy I: Using r-bioc-zlibbioc for Imports:zlibbioc I: BioConductor API version: r-api-bioc-3.18 I: Use r-bioc-makecdfenv as Debian binary package for variables substitution dh_installdocs -O--buildsystem=R dh_installchangelogs -O--buildsystem=R dh_installexamples -O--buildsystem=R dh_installsystemduser -O--buildsystem=R dh_perl -O--buildsystem=R dh_link -O--buildsystem=R dh_strip_nondeterminism -O--buildsystem=R dh_compress -O--buildsystem=R dh_fixperms -O--buildsystem=R dh_missing -O--buildsystem=R dh_dwz -a -O--buildsystem=R dh_strip -a -O--buildsystem=R dh_makeshlibs -a -O--buildsystem=R dh_shlibdeps -a -O--buildsystem=R dh_installdeb -O--buildsystem=R dh_gencontrol -O--buildsystem=R dh_md5sums -O--buildsystem=R dh_builddeb -O--buildsystem=R dpkg-deb: building package 'r-bioc-makecdfenv' in '../r-bioc-makecdfenv_1.78.0-1_armhf.deb'. dpkg-deb: building package 'r-bioc-makecdfenv-dbgsym' in '../r-bioc-makecdfenv-dbgsym_1.78.0-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../r-bioc-makecdfenv_1.78.0-1_armhf.buildinfo dpkg-genchanges --build=binary -O../r-bioc-makecdfenv_1.78.0-1_armhf.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/26923/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/26923/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/26923 and its subdirectories I: Current time: Wed Apr 17 00:13:23 +14 2024 I: pbuilder-time-stamp: 1713262403