Thu Aug 19 00:22:39 UTC 2021 I: starting to build r-bioc-shortread/bullseye/i386 on jenkins on '2021-08-19 00:22' Thu Aug 19 00:22:39 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_14/20913/console.log Thu Aug 19 00:22:39 UTC 2021 I: Downloading source for bullseye/r-bioc-shortread=1.48.0-2 --2021-08-19 00:22:40-- http://cdn-fastly.deb.debian.org/debian/pool/main/r/r-bioc-shortread/r-bioc-shortread_1.48.0-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2531 (2.5K) Saving to: ‘r-bioc-shortread_1.48.0-2.dsc’ 0K .. 100% 11.5M=0s 2021-08-19 00:22:40 (11.5 MB/s) - ‘r-bioc-shortread_1.48.0-2.dsc’ saved [2531/2531] Thu Aug 19 00:22:40 UTC 2021 I: r-bioc-shortread_1.48.0-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: r-bioc-shortread Binary: r-bioc-shortread Architecture: any Version: 1.48.0-2 Maintainer: Debian R Packages Maintainers Uploaders: Andreas Tille Homepage: https://bioconductor.org/packages/ShortRead/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-shortread Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-shortread.git Testsuite: autopkgtest, autopkgtest-pkg-r Testsuite-Triggers: r-cran-runit Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-biocgenerics (>= 0.23.3), r-bioc-biocparallel, r-bioc-biostrings (>= 2.47.6), r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6), r-bioc-biobase, r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.31.8), r-cran-hwriter, r-bioc-zlibbioc, r-cran-lattice, r-cran-latticeextra, r-bioc-xvector, r-bioc-rhtslib Package-List: r-bioc-shortread deb gnu-r optional arch=any Checksums-Sha1: 55dc67894bed2eca4b043ed354c3de3a341bf5e5 5184521 r-bioc-shortread_1.48.0.orig.tar.gz 42d4d8ba9a9cbdc943b1120e69751096cd967ed8 5548 r-bioc-shortread_1.48.0-2.debian.tar.xz Checksums-Sha256: 69badfa1ca5c075ff29adda33d6bd71a2b62433640dcea45ae15180347439570 5184521 r-bioc-shortread_1.48.0.orig.tar.gz 89c0c3a0ec617f41947b1920ca75190e764626ae6f11b1cfa688edf10018ca43 5548 r-bioc-shortread_1.48.0-2.debian.tar.xz Files: a1d99be87db91cbbcda1dcfead019d0f 5184521 r-bioc-shortread_1.48.0.orig.tar.gz 980e1f395b69c5f8cee3743c0921cdb4 5548 r-bioc-shortread_1.48.0-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmAf0PoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFl+g/+Lqiv9HLcaVJsJ6VATLuyZnyTv24MoU6Y 8iJMfzDA+FSfZes4dVehiqx/h7dftCtPJwKBMnGv2YBq2IHkHPftf9MLEZxOyskD PgXAmSwqVWp/hieYgl0wyZT66UWr+JRVwD32JHGQDowp0BikFYT471d98Q8otJbD pJG8b5raMSsf0TZrxkgIB7JeA6EvNTSHC4g73RgXiCJ+N6m2zAlQss0Uxv6fFX8C 0ceBCcWVo4301RAg3n3xsQTPkmQYSGvwa7owstO8T1vO3VrorF2cUh43+oDfxlWR VLA8Z0Djx+COXxUUh+gMf+xdHzY7Af41Uc71WKQERf8DZXFBJ0FTLtX1+/0ewgNX t0L2p/RkoLiJP16LO5NdRON6ipGxd5ynPMt5Gg2mxAgrPP54Ir+Xf8zc677OQdR/ H+9+T+xhjw5gFqq6Pf5nyBriTSMBmJe2NogTINlMkMEZSGdf9wamQ7YqpOuirIiW Dsv+xy1Fxp5PPXCJgxjMVg9lPKLAxyYTby7PfukkbJWmoBdgvnU9vUACmD6jId8a K1wyI6gqpnQR1UXVUUwmFtRAeFdhLcMXdnTaNKOxLL0Z0a8z4Xj910VT/5YUvrhA DdeDk/+YzMak3FZkna/75nKjBQzGORYWr51/BBBk64NzmDvBMfR+X90iRudDZfYh j3MLov9OUT4= =8QE/ -----END PGP SIGNATURE----- Thu Aug 19 00:22:40 UTC 2021 I: Checking whether the package is not for us Thu Aug 19 00:22:40 UTC 2021 I: Starting 1st build on remote node ionos6-i386.debian.net. Thu Aug 19 00:22:40 UTC 2021 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Thu Aug 19 00:24:10 UTC 2021 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 20 18:45:40 -12 2022 I: pbuilder-time-stamp: 1663742740 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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 [r-bioc-shortread_1.48.0-2.dsc] I: copying [./r-bioc-shortread_1.48.0.orig.tar.gz] I: copying [./r-bioc-shortread_1.48.0-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.vhuCakfw/trustedkeys.kbx': General error gpgv: Signature made Sat Feb 6 23:37:30 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./r-bioc-shortread_1.48.0-2.dsc dpkg-source: info: extracting r-bioc-shortread in r-bioc-shortread-1.48.0 dpkg-source: info: unpacking r-bioc-shortread_1.48.0.orig.tar.gz dpkg-source: info: unpacking r-bioc-shortread_1.48.0-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1874/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='20d2bf292b514a6986484e36044b8abd' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1874' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.ffVOaaiApN/pbuilderrc_tWKs --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ffVOaaiApN/b1 --logfile b1/build.log r-bioc-shortread_1.48.0-2.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos6-i386 5.10.0-8-amd64 #1 SMP Debian 5.10.46-4 (2021-08-03) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Aug 4 2021 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Jul 28 2021 more -rwsr-xr-x 1 root root 50720 Jul 28 2021 mount -rwxr-xr-x 1 root root 13856 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 17 03:48 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jul 28 2021 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jul 28 2021 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/1874/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), dh-r, r-base-dev, r-bioc-biocgenerics (>= 0.23.3), r-bioc-biocparallel, r-bioc-biostrings (>= 2.47.6), r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6), r-bioc-biobase, r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.31.8), r-cran-hwriter, r-bioc-zlibbioc, r-cran-lattice, r-cran-latticeextra, r-bioc-xvector, r-bioc-rhtslib dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-r; however: Package dh-r is not installed. pbuilder-satisfydepends-dummy depends on r-base-dev; however: Package r-base-dev is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biocgenerics (>= 0.23.3); however: Package r-bioc-biocgenerics is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biocparallel; however: Package r-bioc-biocparallel is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biostrings (>= 2.47.6); however: Package r-bioc-biostrings is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-rsamtools (>= 1.31.2); however: Package r-bioc-rsamtools is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomicalignments (>= 1.15.6); however: Package r-bioc-genomicalignments 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-s4vectors (>= 0.17.25); however: Package r-bioc-s4vectors is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-iranges (>= 2.13.12); however: Package r-bioc-iranges is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomeinfodb (>= 1.15.2); however: Package r-bioc-genomeinfodb is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomicranges (>= 1.31.8); however: Package r-bioc-genomicranges is not installed. pbuilder-satisfydepends-dummy depends on r-cran-hwriter; however: Package r-cran-hwriter is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-zlibbioc; however: Package r-bioc-zlibbioc is not installed. pbuilder-satisfydepends-dummy depends on r-cran-lattice; however: Package r-cran-lattice is not installed. pbuilder-satisfydepends-dummy depends on r-cran-latticeextra; however: Package r-cran-latticeextra is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-xvector; however: Package r-bioc-xvector is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-rhtslib; however: Package r-bioc-rhtslib 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} gettext{a} gettext-base{a} gfortran{a} gfortran-10{a} groff-base{a} icu-devtools{a} intltool-debian{a} libalgorithm-c3-perl{a} libarchive-zip-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo2{a} libclass-c3-perl{a} libclass-load-perl{a} libclass-load-xs-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-10-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} libicu67{a} libio-html-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} liblapack-dev{a} liblapack3{a} libldap-2.4-2{a} liblwp-mediatypes-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmd0{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} libncurses5-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} libpcre16-3{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix2{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpipeline1{a} libpixman-1-0{a} libpng-dev{a} libpng16-16{a} libpsl5{a} libreadline-dev{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{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} libtiff5{a} libtimedate-perl{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libvariable-magic-perl{a} libwebp6{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} po-debconf{a} r-base-core{a} r-base-dev{a} r-bioc-biobase{a} r-bioc-biocgenerics{a} r-bioc-biocparallel{a} r-bioc-biostrings{a} r-bioc-delayedarray{a} r-bioc-genomeinfodb{a} r-bioc-genomeinfodbdata{a} r-bioc-genomicalignments{a} r-bioc-genomicranges{a} r-bioc-iranges{a} r-bioc-matrixgenerics{a} r-bioc-rhtslib{a} r-bioc-rsamtools{a} r-bioc-s4vectors{a} r-bioc-summarizedexperiment{a} r-bioc-xvector{a} r-bioc-zlibbioc{a} r-cran-bh{a} r-cran-bitops{a} r-cran-crayon{a} r-cran-formatr{a} r-cran-futile.logger{a} r-cran-futile.options{a} r-cran-hwriter{a} r-cran-jpeg{a} r-cran-lambda.r{a} r-cran-lattice{a} r-cran-latticeextra{a} r-cran-matrix{a} r-cran-matrixstats{a} r-cran-png{a} r-cran-rcolorbrewer{a} r-cran-rcurl{a} r-cran-snow{a} readline-common{a} sensible-utils{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 libclone-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libx11-protocol-perl lynx publicsuffix r-bioc-annotate r-bioc-shortread r-cran-batchjobs r-cran-batchtools r-cran-codetools r-cran-digest r-cran-doparallel r-cran-mockery r-cran-rmpi r-cran-runit r-cran-survival r-cran-testit 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, 208 newly installed, 0 to remove and 0 not upgraded. Need to get 163 MB of archives. After unpacking 508 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8 [149 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 openssl i386 1.1.1k-1 [860 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 ca-certificates all 20210119 [158 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 ucf all 3.0043 [74.0 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 dctrl-tools i386 2.24-3 [105 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 zip i386 3.0-12 [240 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 unzip i386 6.0-26 [171 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libpaper1 i386 1.1.28+b1 [21.7 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libpaper-utils i386 1.1.28+b1 [18.6 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3 [147 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1 [429 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libfontconfig1 i386 2.13.1-4.2 [358 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libpixman-1-0 i386 0.40.0-1 [545 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.2-1 [311 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.2-1 [794 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libxcb-render0 i386 1.14-3 [112 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libxcb-shm0 i386 1.14-3 [102 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libcairo2 i386 1.16.0-5 [746 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libcurl4 i386 7.74.0-1.3+b1 [372 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3 [1960 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 fontconfig i386 2.13.1-4.2 [417 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libfribidi0 i386 1.0.8-2 [65.4 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libharfbuzz0b i386 2.7.4-1 [1490 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libthai-data all 0.1.28-3 [170 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libdatrie1 i386 0.2.13-1 [44.5 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libthai0 i386 0.1.28-3 [55.3 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libpango-1.0-0 i386 1.46.2-3 [197 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libpangoft2-1.0-0 i386 1.46.2-3 [65.1 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 libpangocairo-1.0-0 i386 1.46.2-3 [51.9 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libtcl8.6 i386 8.6.11+dfsg-1 [1082 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 libwebp6 i386 0.6.1-2.1 [269 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1 [305 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 libxft2 i386 2.3.2-2 [58.2 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 x11-common all 1:7.7+22 [252 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libxss1 i386 1:1.2.3-1 [18.1 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 libtk8.6 i386 8.6.11-2 [825 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 libxt6 i386 1:1.2.0-1 [195 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 r-base-core i386 4.0.4-1 [25.1 MB] Get: 99 http://deb.debian.org/debian bullseye/main i386 libgfortran-10-dev i386 10.2.1-6 [705 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 gfortran-10 i386 10.2.1-6 [9642 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 gfortran i386 4:10.2.1-1 [1436 B] Get: 102 http://deb.debian.org/debian bullseye/main i386 libblas-dev i386 3.9.0-3 [157 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 liblapack-dev i386 3.9.0-3 [3759 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 105 http://deb.debian.org/debian bullseye/main i386 libncurses-dev i386 6.2+20201114-2 [373 kB] Get: 106 http://deb.debian.org/debian bullseye/main i386 libncurses5-dev i386 6.2+20201114-2 [932 B] Get: 107 http://deb.debian.org/debian bullseye/main i386 libreadline-dev i386 8.1-1 [161 kB] Get: 108 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo-dev i386 1:2.0.6-4 [299 kB] Get: 109 http://deb.debian.org/debian bullseye/main i386 libjpeg-dev i386 1:2.0.6-4 [67.8 kB] Get: 110 http://deb.debian.org/debian bullseye/main i386 libpcre2-16-0 i386 10.36-2 [231 kB] Get: 111 http://deb.debian.org/debian bullseye/main i386 libpcre2-32-0 i386 10.36-2 [219 kB] Get: 112 http://deb.debian.org/debian bullseye/main i386 libpcre2-posix2 i386 10.36-2 [49.2 kB] Get: 113 http://deb.debian.org/debian bullseye/main i386 libpcre2-dev i386 10.36-2 [739 kB] Get: 114 http://deb.debian.org/debian bullseye/main i386 libpcre16-3 i386 2:8.39-13 [258 kB] Get: 115 http://deb.debian.org/debian bullseye/main i386 libpcre32-3 i386 2:8.39-13 [249 kB] Get: 116 http://deb.debian.org/debian bullseye/main i386 libpcrecpp0v5 i386 2:8.39-13 [153 kB] Get: 117 http://deb.debian.org/debian bullseye/main i386 libpcre3-dev i386 2:8.39-13 [656 kB] Get: 118 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 119 http://deb.debian.org/debian bullseye/main i386 libpng-dev i386 1.6.37-3 [307 kB] Get: 120 http://deb.debian.org/debian bullseye/main i386 libbz2-dev i386 1.0.8-4 [31.3 kB] Get: 121 http://deb.debian.org/debian bullseye/main i386 liblzma-dev i386 5.2.5-2 [240 kB] Get: 122 http://deb.debian.org/debian bullseye/main i386 icu-devtools i386 67.1-7 [209 kB] Get: 123 http://deb.debian.org/debian bullseye/main i386 libicu-dev i386 67.1-7 [9801 kB] Get: 124 http://deb.debian.org/debian bullseye/main i386 libxmuu1 i386 2:1.1.2-2+b3 [24.2 kB] Get: 125 http://deb.debian.org/debian bullseye/main i386 xauth i386 1:1.1-1 [41.2 kB] Get: 126 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB] Get: 127 http://deb.debian.org/debian bullseye/main i386 r-base-dev all 4.0.4-1 [4484 B] Get: 128 http://deb.debian.org/debian bullseye/main i386 libfile-which-perl all 1.23-1 [16.6 kB] Get: 129 http://deb.debian.org/debian bullseye/main i386 libswitch-perl all 2.17-2.1 [20.0 kB] Get: 130 http://deb.debian.org/debian bullseye/main i386 libencode-locale-perl all 1.05-1.1 [13.2 kB] Get: 131 http://deb.debian.org/debian bullseye/main i386 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 132 http://deb.debian.org/debian bullseye/main i386 libhttp-date-perl all 6.05-1 [10.4 kB] Get: 133 http://deb.debian.org/debian bullseye/main i386 libio-html-perl all 1.004-2 [16.1 kB] Get: 134 http://deb.debian.org/debian bullseye/main i386 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get: 135 http://deb.debian.org/debian bullseye/main i386 liburi-perl all 5.08-1 [90.6 kB] Get: 136 http://deb.debian.org/debian bullseye/main i386 libhttp-message-perl all 6.28-1 [79.6 kB] Get: 137 http://deb.debian.org/debian bullseye/main i386 libparams-util-perl i386 1.102-1+b1 [26.3 kB] Get: 138 http://deb.debian.org/debian bullseye/main i386 libsub-install-perl all 0.928-1.1 [10.8 kB] Get: 139 http://deb.debian.org/debian bullseye/main i386 libdata-optlist-perl all 0.110-1.1 [10.8 kB] Get: 140 http://deb.debian.org/debian bullseye/main i386 libb-hooks-op-check-perl i386 0.22-1+b3 [11.4 kB] Get: 141 http://deb.debian.org/debian bullseye/main i386 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get: 142 http://deb.debian.org/debian bullseye/main i386 libdevel-callchecker-perl i386 0.008-1+b2 [15.9 kB] Get: 143 http://deb.debian.org/debian bullseye/main i386 libparams-classify-perl i386 0.015-1+b3 [26.4 kB] Get: 144 http://deb.debian.org/debian bullseye/main i386 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 145 http://deb.debian.org/debian bullseye/main i386 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 146 http://deb.debian.org/debian bullseye/main i386 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get: 147 http://deb.debian.org/debian bullseye/main i386 libpackage-stash-perl all 0.39-1 [21.9 kB] Get: 148 http://deb.debian.org/debian bullseye/main i386 libclass-load-perl all 0.25-1 [16.1 kB] Get: 149 http://deb.debian.org/debian bullseye/main i386 libclass-load-xs-perl i386 0.10-1+b5 [14.7 kB] Get: 150 http://deb.debian.org/debian bullseye/main i386 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get: 151 http://deb.debian.org/debian bullseye/main i386 libdevel-globaldestruction-perl all 0.14-1.1 [8312 B] Get: 152 http://deb.debian.org/debian bullseye/main i386 libalgorithm-c3-perl all 0.11-1 [11.7 kB] Get: 153 http://deb.debian.org/debian bullseye/main i386 libclass-c3-perl all 0.35-1 [22.9 kB] Get: 154 http://deb.debian.org/debian bullseye/main i386 libmro-compat-perl all 0.13-1 [12.2 kB] Get: 155 http://deb.debian.org/debian bullseye/main i386 libsub-identify-perl i386 0.14-1+b3 [12.2 kB] Get: 156 http://deb.debian.org/debian bullseye/main i386 libdevel-overloadinfo-perl all 0.005-1 [7212 B] Get: 157 http://deb.debian.org/debian bullseye/main i386 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get: 158 http://deb.debian.org/debian bullseye/main i386 libsub-exporter-perl all 0.987-1 [47.2 kB] Get: 159 http://deb.debian.org/debian bullseye/main i386 libeval-closure-perl all 0.14-1 [11.5 kB] Get: 160 http://deb.debian.org/debian bullseye/main i386 libdist-checkconflicts-perl all 0.11-1.1 [10.2 kB] Get: 161 http://deb.debian.org/debian bullseye/main i386 libmodule-runtime-conflicts-perl all 0.003-1.1 [7156 B] Get: 162 http://deb.debian.org/debian bullseye/main i386 libsub-name-perl i386 0.26-1+b1 [14.1 kB] Get: 163 http://deb.debian.org/debian bullseye/main i386 libpackage-deprecationmanager-perl all 0.17-1.1 [16.6 kB] Get: 164 http://deb.debian.org/debian bullseye/main i386 libpackage-stash-xs-perl i386 0.29-1+b2 [21.2 kB] Get: 165 http://deb.debian.org/debian bullseye/main i386 libmoose-perl i386 2.2014-2 [804 kB] Get: 166 http://deb.debian.org/debian bullseye/main i386 libvariable-magic-perl i386 0.62-1+b3 [46.2 kB] Get: 167 http://deb.debian.org/debian bullseye/main i386 libb-hooks-endofscope-perl all 0.24-1.1 [18.9 kB] Get: 168 http://deb.debian.org/debian bullseye/main i386 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get: 169 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.3+b1 [368 kB] Get: 170 http://deb.debian.org/debian bullseye/main i386 libwww-curl-perl i386 4.17-7+b1 [63.5 kB] Get: 171 http://deb.debian.org/debian bullseye/main i386 libwww-curl-simple-perl all 0.100191-2 [12.5 kB] Get: 172 http://deb.debian.org/debian bullseye/main i386 dh-r all 20210303 [41.8 kB] Get: 173 http://deb.debian.org/debian bullseye/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get: 174 http://deb.debian.org/debian bullseye/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 175 http://deb.debian.org/debian bullseye/main i386 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get: 176 http://deb.debian.org/debian bullseye/main i386 r-bioc-biobase i386 2.50.0-1 [2230 kB] Get: 177 http://deb.debian.org/debian bullseye/main i386 r-cran-formatr all 1.7-2 [151 kB] Get: 178 http://deb.debian.org/debian bullseye/main i386 r-cran-lambda.r all 1.2.4-2 [118 kB] Get: 179 http://deb.debian.org/debian bullseye/main i386 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get: 180 http://deb.debian.org/debian bullseye/main i386 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get: 181 http://deb.debian.org/debian bullseye/main i386 r-cran-snow all 1:0.4.3-2 [109 kB] Get: 182 http://deb.debian.org/debian bullseye/main i386 r-cran-bh all 1.74.0-1 [5196 B] Get: 183 http://deb.debian.org/debian bullseye/main i386 r-bioc-biocparallel i386 1.24.1-1 [1142 kB] Get: 184 http://deb.debian.org/debian bullseye/main i386 r-bioc-s4vectors i386 0.28.1-1 [2034 kB] Get: 185 http://deb.debian.org/debian bullseye/main i386 r-bioc-iranges i386 2.24.1-1 [2176 kB] Get: 186 http://deb.debian.org/debian bullseye/main i386 r-bioc-zlibbioc all 1.36.0+dfsg-1 [8824 B] Get: 187 http://deb.debian.org/debian bullseye/main i386 r-bioc-xvector i386 0.30.0-1 [622 kB] Get: 188 http://deb.debian.org/debian bullseye/main i386 r-cran-crayon all 1.4.0-1 [143 kB] Get: 189 http://deb.debian.org/debian bullseye/main i386 r-bioc-biostrings i386 2.58.0-1 [14.2 MB] Get: 190 http://deb.debian.org/debian bullseye/main i386 r-cran-lattice i386 0.20-41-1+b1 [1162 kB] Get: 191 http://deb.debian.org/debian bullseye/main i386 r-cran-matrix i386 1.3-2-1 [3582 kB] Get: 192 http://deb.debian.org/debian bullseye/main i386 r-cran-matrixstats i386 0.58.0-3 [642 kB] Get: 193 http://deb.debian.org/debian bullseye/main i386 r-bioc-matrixgenerics all 1.2.1-4 [288 kB] Get: 194 http://deb.debian.org/debian bullseye/main i386 r-bioc-delayedarray i386 0.16.1+dfsg-1 [1800 kB] Get: 195 http://deb.debian.org/debian bullseye/main i386 r-cran-bitops i386 1.0-6-5 [23.8 kB] Get: 196 http://deb.debian.org/debian bullseye/main i386 r-cran-rcurl i386 1.98-1.2-1+b1 [761 kB] Get: 197 http://deb.debian.org/debian bullseye/main i386 r-bioc-genomeinfodbdata all 1.2.4-1 [10.7 MB] Get: 198 http://deb.debian.org/debian bullseye/main i386 r-bioc-genomeinfodb all 1.26.2-2 [3905 kB] Get: 199 http://deb.debian.org/debian bullseye/main i386 r-bioc-genomicranges i386 1.42.0+dfsg-1 [1856 kB] Get: 200 http://deb.debian.org/debian bullseye/main i386 r-bioc-summarizedexperiment all 1.20.0+dfsg-1 [1955 kB] Get: 201 http://deb.debian.org/debian bullseye/main i386 r-bioc-rhtslib i386 1.22.0+dfsg-1 [1057 kB] Get: 202 http://deb.debian.org/debian bullseye/main i386 r-bioc-rsamtools i386 2.6.0-1 [3690 kB] Get: 203 http://deb.debian.org/debian bullseye/main i386 r-bioc-genomicalignments i386 1.26.0-1 [2159 kB] Get: 204 http://deb.debian.org/debian bullseye/main i386 r-cran-hwriter all 1.3.2-4 [162 kB] Get: 205 http://deb.debian.org/debian bullseye/main i386 r-cran-jpeg i386 0.1-8.1-1+b1 [30.8 kB] Get: 206 http://deb.debian.org/debian bullseye/main i386 r-cran-png i386 0.1-7-4 [41.3 kB] Get: 207 http://deb.debian.org/debian bullseye/main i386 r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB] Get: 208 http://deb.debian.org/debian bullseye/main i386 r-cran-latticeextra all 0.6-29-3 [2192 kB] Fetched 163 MB in 2s (71.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-8_i386.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../001-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../003-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../005-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../006-libreadline8_8.1-1_i386.deb ... Unpacking libreadline8:i386 (8.1-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../007-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../008-openssl_1.1.1k-1_i386.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../009-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../010-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../011-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../012-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../013-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../014-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../015-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../021-dctrl-tools_2.24-3_i386.deb ... Unpacking dctrl-tools (2.24-3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../022-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../023-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../024-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../025-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 .../026-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../027-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../028-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../029-libelf1_0.183-1_i386.deb ... Unpacking libelf1:i386 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../030-dwz_0.13+20210201-1_i386.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:i386. Preparing to unpack .../031-libicu67_67.1-7_i386.deb ... Unpacking libicu67:i386 (67.1-7) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../032-libxml2_2.9.10+dfsg-6.7_i386.deb ... Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../033-gettext_0.21-4_i386.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../034-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../035-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../036-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package zip. Preparing to unpack .../037-zip_3.0-12_i386.deb ... Unpacking zip (3.0-12) ... Selecting previously unselected package unzip. Preparing to unpack .../038-unzip_6.0-26_i386.deb ... Unpacking unzip (6.0-26) ... Selecting previously unselected package libpaper1:i386. Preparing to unpack .../039-libpaper1_1.1.28+b1_i386.deb ... Unpacking libpaper1:i386 (1.1.28+b1) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../040-libpaper-utils_1.1.28+b1_i386.deb ... Unpacking libpaper-utils (1.1.28+b1) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../041-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package libblas3:i386. Preparing to unpack .../042-libblas3_3.9.0-3_i386.deb ... Unpacking libblas3:i386 (3.9.0-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../043-libexpat1_2.2.10-2_i386.deb ... Unpacking libexpat1:i386 (2.2.10-2) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../044-libbrotli1_1.0.9-2+b2_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../045-libpng16-16_1.6.37-3_i386.deb ... Unpacking libpng16-16:i386 (1.6.37-3) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../046-libfreetype6_2.10.4+dfsg-1_i386.deb ... Unpacking libfreetype6:i386 (2.10.4+dfsg-1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../047-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../048-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:i386. Preparing to unpack .../049-libfontconfig1_2.13.1-4.2_i386.deb ... Unpacking libfontconfig1:i386 (2.13.1-4.2) ... Selecting previously unselected package libpixman-1-0:i386. Preparing to unpack .../050-libpixman-1-0_0.40.0-1_i386.deb ... Unpacking libpixman-1-0:i386 (0.40.0-1) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../051-libxau6_1%3a1.0.9-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../052-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../053-libbsd0_0.11.3-1_i386.deb ... Unpacking libbsd0:i386 (0.11.3-1) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../054-libxdmcp6_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../055-libxcb1_1.14-3_i386.deb ... Unpacking libxcb1:i386 (1.14-3) ... Selecting previously unselected package libx11-data. Preparing to unpack .../056-libx11-data_2%3a1.7.2-1_all.deb ... Unpacking libx11-data (2:1.7.2-1) ... Selecting previously unselected package libx11-6:i386. Preparing to unpack .../057-libx11-6_2%3a1.7.2-1_i386.deb ... Unpacking libx11-6:i386 (2:1.7.2-1) ... Selecting previously unselected package libxcb-render0:i386. Preparing to unpack .../058-libxcb-render0_1.14-3_i386.deb ... Unpacking libxcb-render0:i386 (1.14-3) ... Selecting previously unselected package libxcb-shm0:i386. Preparing to unpack .../059-libxcb-shm0_1.14-3_i386.deb ... Unpacking libxcb-shm0:i386 (1.14-3) ... Selecting previously unselected package libxext6:i386. Preparing to unpack .../060-libxext6_2%3a1.3.3-1.1_i386.deb ... Unpacking libxext6:i386 (2:1.3.3-1.1) ... Selecting previously unselected package libxrender1:i386. Preparing to unpack .../061-libxrender1_1%3a0.9.10-1_i386.deb ... Unpacking libxrender1:i386 (1:0.9.10-1) ... Selecting previously unselected package libcairo2:i386. Preparing to unpack .../062-libcairo2_1.16.0-5_i386.deb ... Unpacking libcairo2:i386 (1.16.0-5) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../063-libsasl2-modules-db_2.1.27+dfsg-2.1_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... 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Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up libtiff5:i386 (4.2.0-1) ... Setting up openssl (1.1.1k-1) ... Setting up libbsd0:i386 (0.11.3-1) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libicu-dev:i386 (67.1-7) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... 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 (5.08-1) ... Setting up libblas-dev:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up dctrl-tools (2.24-3) ... Setting up libbz2-dev:i386 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up r-cran-bh (1.74.0-1) ... Setting up libice6:i386 (2:1.0.10-1) ... Setting up libhttp-date-perl (6.05-1) ... 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Setting up gfortran (4:10.2.1-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up dh-autoreconf (20) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libdist-checkconflicts-perl (0.11-1.1) ... Setting up libxt6:i386 (1:1.2.0-1) ... Setting up xauth (1:1.1-1) ... Setting up libxss1:i386 (1:1.2.3-1) ... Setting up libfontconfig1:i386 (2.13.1-4.2) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:i386 (2.3.2-2) ... Setting up libmodule-implementation-perl (0.09-1.1) ... Setting up libpackage-stash-perl (0.39-1) ... Setting up libtk8.6:i386 (8.6.11-2) ... Setting up libpango-1.0-0:i386 (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up libmodule-runtime-conflicts-perl (0.003-1.1) ... Setting up libcairo2:i386 (1.16.0-5) ... Setting up libclass-load-perl (0.25-1) ... 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Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-snow (1:0.4.3-2) ... Setting up r-cran-bitops (1.0-6-5) ... Setting up r-bioc-zlibbioc (1.36.0+dfsg-1) ... Setting up r-cran-png (0.1-7-4) ... Setting up r-bioc-biobase (2.50.0-1) ... Setting up r-cran-hwriter (1.3.2-4) ... Setting up r-cran-rcolorbrewer (1.1-2-3) ... Setting up r-bioc-s4vectors (0.28.1-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-matrix (1.3-2-1) ... Setting up r-bioc-iranges (2.24.1-1) ... Setting up dh-r (20210303) ... Setting up r-cran-rcurl (1.98-1.2-1+b1) ... Setting up r-bioc-delayedarray (0.16.1+dfsg-1) ... Setting up r-bioc-biocparallel (1.24.1-1) ... Setting up r-bioc-rhtslib (1.22.0+dfsg-1) ... Setting up r-cran-latticeextra (0.6-29-3) ... Setting up r-bioc-genomeinfodb (1.26.2-2) ... Setting up r-bioc-xvector (0.30.0-1) ... Setting up r-bioc-genomicranges (1.42.0+dfsg-1) ... Setting up r-bioc-biostrings (2.58.0-1) ... Setting up r-bioc-rsamtools (2.6.0-1) ... Setting up r-bioc-summarizedexperiment (1.20.0+dfsg-1) ... Setting up r-bioc-genomicalignments (1.26.0-1) ... Processing triggers for libc-bin (2.31-13) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/r-bioc-shortread-1.48.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../r-bioc-shortread_1.48.0-2_source.changes dpkg-buildpackage: info: source package r-bioc-shortread dpkg-buildpackage: info: source version 1.48.0-2 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 --buildsystem R dh_auto_clean -O--buildsystem=R dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules binary dh binary --buildsystem R dh_update_autotools_config -O--buildsystem=R dh_autoreconf -O--buildsystem=R dh_auto_configure -O--buildsystem=R dh_auto_build -O--buildsystem=R dh_auto_test -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=R dh_prep -O--buildsystem=R dh_auto_install -O--buildsystem=R I: R packages needed for DEP8: runit I: R Package: ShortRead Version: 1.48.0 I: Building using R version 4.0.4-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Sun, 07 Feb 2021 12:28:32 +0100 mkdir -p /build/r-bioc-shortread-1.48.0/debian/r-bioc-shortread/usr/lib/R/site-library R CMD INSTALL -l /build/r-bioc-shortread-1.48.0/debian/r-bioc-shortread/usr/lib/R/site-library --clean . "--built-timestamp='Sun, 07 Feb 2021 12:28:32 +0100'" * installing *source* package 'ShortRead' ... ** using staged installation checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of unsigned long... 4 configure: creating ./config.status config.status: creating src/Makevars ** libs make[1]: Entering directory '/build/r-bioc-shortread-1.48.0/src' gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_ShortRead.c -o R_init_ShortRead.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c alphabet.c -o alphabet.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c count.c -o count.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.c -o io.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_bowtie.c -o io_bowtie.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_soap.c -o io_soap.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readBfaToc.cc -o readBfaToc.o readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXP)': readBfaToc.cc:35:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 35 | (void) fread( seq_name, sizeof(char), name_len, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:36:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:37:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | (void) fread( &seq_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_maq_map.cc -o read_maq_map.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sampler.c -o sampler.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c trim.c -o trim.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4GyIYX/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xsnap.c -o xsnap.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-z,relro -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/usr/lib/R/lib -lR make[1]: Leaving directory '/build/r-bioc-shortread-1.48.0/src' make[1]: Entering directory '/build/r-bioc-shortread-1.48.0/src' make[1]: Leaving directory '/build/r-bioc-shortread-1.48.0/src' installing to /build/r-bioc-shortread-1.48.0/debian/r-bioc-shortread/usr/lib/R/site-library/00LOCK-r-bioc-shortread-1.48.0/00new/ShortRead/libs ** R ** inst ** byte-compile and prepare package for lazy loading code for methods in class "ShortReadFile" was not checked for suspicious field assignments (recommended package 'codetools' not available?) code for methods in class "FastqFileReader" was not checked for suspicious field assignments (recommended package 'codetools' not available?) code for methods in class "QAData" was not checked for suspicious field assignments (recommended package 'codetools' not available?) code for methods in class "Snapshot" was not checked for suspicious field assignments (recommended package 'codetools' not available?) code for methods in class "SpTrellis" was not checked for suspicious field assignments (recommended package 'codetools' not available?) code for methods in class "FastqSampler" was not checked for suspicious field assignments (recommended package 'codetools' not available?) code for methods in class "FastqStreamer" was not checked for suspicious field assignments (recommended package 'codetools' not available?) ** 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 (ShortRead) I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.23.3) I: Using r-bioc-biocparallel for Depends:BiocParallel I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.47.6) I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.31.2) I: Using r-bioc-genomicalignments for Depends:GenomicAlignments (>= 1.15.6) I: Using r-cran-runit for Recommends:runit I: Using r-bioc-biocstyle for Suggests:BiocStyle I: Using r-bioc-biomart for Suggests:biomaRt I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures W: Cannot find a debian package for Suggests:yeastNagalakshmi I: Using r-bioc-biobase for Imports:Biobase I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.17.25) I: Using r-bioc-iranges for Imports:IRanges (>= 2.13.12) I: Using r-bioc-genomeinfodb for Imports:GenomeInfoDb (>= 1.15.2) I: Using r-bioc-genomicranges for Imports:GenomicRanges (>= 1.31.8) I: Using r-cran-hwriter for Imports:hwriter I: Using r-bioc-zlibbioc for Imports:zlibbioc I: Using r-cran-lattice for Imports:lattice I: Using r-cran-latticeextra for Imports:latticeExtra I: Using r-bioc-s4vectors for LinkingTo:S4Vectors I: Using r-bioc-iranges for LinkingTo:IRanges I: Using r-bioc-xvector for LinkingTo:XVector I: Using r-bioc-biostrings for LinkingTo:Biostrings I: Using r-bioc-rhtslib for LinkingTo:Rhtslib I: Using r-bioc-zlibbioc for LinkingTo:zlibbioc I: BioConductor API version: r-api-bioc-3.12 I: Use r-bioc-shortread as Debian binary package for variables substitution dh_installdocs -O--buildsystem=R dh_installchangelogs -O--buildsystem=R dh_installsystemduser -O--buildsystem=R dh_perl -O--buildsystem=R dh_link -O--buildsystem=R dh_strip_nondeterminism -O--buildsystem=R dh_compress -O--buildsystem=R dh_fixperms -O--buildsystem=R dh_missing -O--buildsystem=R dh_dwz -a -O--buildsystem=R dh_strip -a -O--buildsystem=R dh_makeshlibs -a -O--buildsystem=R dh_shlibdeps -a -O--buildsystem=R dh_installdeb -O--buildsystem=R dh_gencontrol -O--buildsystem=R dh_md5sums -O--buildsystem=R dh_builddeb -O--buildsystem=R dpkg-deb: building package 'r-bioc-shortread' in '../r-bioc-shortread_1.48.0-2_i386.deb'. dpkg-deb: building package 'r-bioc-shortread-dbgsym' in '../r-bioc-shortread-dbgsym_1.48.0-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../r-bioc-shortread_1.48.0-2_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: 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/1874 and its subdirectories I: Current time: Tue Sep 20 18:47:09 -12 2022 I: pbuilder-time-stamp: 1663742829 Thu Aug 19 00:24:10 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Thu Aug 19 00:24:10 UTC 2021 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Thu Aug 19 00:45:43 UTC 2021 I: Deleting $TMPDIR on ionos12-i386.debian.net. Thu Aug 19 00:45:43 UTC 2021 I: r-bioc-shortread_1.48.0-2_i386.changes: Format: 1.8 Date: Sun, 07 Feb 2021 12:28:32 +0100 Source: r-bioc-shortread Binary: r-bioc-shortread r-bioc-shortread-dbgsym Architecture: i386 Version: 1.48.0-2 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers Changed-By: Andreas Tille Description: r-bioc-shortread - GNU R classes and methods for high-throughput short-read sequenci Closes: 980082 Changes: r-bioc-shortread (1.48.0-2) unstable; urgency=medium . * Exclude failing test on non-Intel architectures Closes: #980082 Checksums-Sha1: 47101a1ad8069b94e45641c857a7c78dc1a8b51b 132340 r-bioc-shortread-dbgsym_1.48.0-2_i386.deb db5582bc049e3a580378755ae86293c9eef3747e 10639 r-bioc-shortread_1.48.0-2_i386.buildinfo 031b956bd1fe978023dcbc1e029ad9a203357531 5072040 r-bioc-shortread_1.48.0-2_i386.deb Checksums-Sha256: 567e153935f8d661b85aa948d99eaed693e7bb8c080dc06631c1a1470a065139 132340 r-bioc-shortread-dbgsym_1.48.0-2_i386.deb e8a92f0984da824fbf02b31e115cd12a6e7566ab87f9a9071b4923c19cb21129 10639 r-bioc-shortread_1.48.0-2_i386.buildinfo d59286a7d29f703a6804711567a6a47bbeb69acd55b56cab264629c410b6f40a 5072040 r-bioc-shortread_1.48.0-2_i386.deb Files: 70346ded54e5dfe4080c2896fe5f5ad4 132340 debug optional r-bioc-shortread-dbgsym_1.48.0-2_i386.deb 950e0afa607356e9e2336fcbdc775b22 10639 gnu-r optional r-bioc-shortread_1.48.0-2_i386.buildinfo 56888998c0063492bf92e459efedcf93 5072040 gnu-r optional r-bioc-shortread_1.48.0-2_i386.deb Thu Aug 19 00:45:45 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.ffVOaaiApN/r-bioc-shortread_1.48.0-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.ffVOaaiApN/r-bioc-shortread_1.48.0-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.ffVOaaiApN/r-bioc-shortread_1.48.0-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.ffVOaaiApN/b1/r-bioc-shortread_1.48.0-2_i386.changes /srv/reproducible-results/rbuild-debian/tmp.ffVOaaiApN/b2/r-bioc-shortread_1.48.0-2_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.332s) 0.332s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.062s) 0.062s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Aug 19 00:45:46 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Thu Aug 19 00:45:46 UTC 2021 I: r-bioc-shortread from bullseye built successfully and reproducibly on i386. Thu Aug 19 00:45:48 UTC 2021 I: Submitting .buildinfo files to external archives: Thu Aug 19 00:45:48 UTC 2021 I: Submitting 12K b1/r-bioc-shortread_1.48.0-2_i386.buildinfo.asc Thu Aug 19 00:45:49 UTC 2021 I: Submitting 12K b2/r-bioc-shortread_1.48.0-2_i386.buildinfo.asc Thu Aug 19 00:45:50 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Aug 19 00:45:50 UTC 2021 I: Done submitting .buildinfo files. Thu Aug 19 00:45:50 UTC 2021 I: Removing signed r-bioc-shortread_1.48.0-2_i386.buildinfo.asc files: removed './b1/r-bioc-shortread_1.48.0-2_i386.buildinfo.asc' removed './b2/r-bioc-shortread_1.48.0-2_i386.buildinfo.asc'