RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux z13-001 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 16:30:42 UTC 2017 s390x Buildd toolchain package versions: launchpad-buildd_152 python-lpbuildd_152 sbuild_0.67.0-2ubuntu7.1 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 5 Oct 20:12:22 ntpdate[45732]: adjust time server 10.211.37.1 offset -0.000683 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=artful --arch=s390x PACKAGEBUILD-13546905 /home/buildd/filecache-default/c63540de4962374dad549ddd7685c5c502845718 Creating target for build PACKAGEBUILD-13546905 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=artful --arch=s390x PACKAGEBUILD-13546905 Starting target for build PACKAGEBUILD-13546905 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=artful --arch=s390x PACKAGEBUILD-13546905 'deb http://ftpmaster.internal/ubuntu artful main universe' 'deb http://ftpmaster.internal/ubuntu artful-security main universe' 'deb http://ftpmaster.internal/ubuntu artful-updates main universe' 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-13546905 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=artful --arch=s390x PACKAGEBUILD-13546905 Updating target for build PACKAGEBUILD-13546905 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main s390x Packages [1012 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [543 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe s390x Packages [7785 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4787 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main s390x Packages [41.8 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [23.1 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe s390x Packages [52.0 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [36.1 kB] Fetched 14.9 MB in 2s (5119 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt apt-transport-https binutils binutils-common binutils-s390x-linux-gnu build-essential cpp-7 g++-7 gcc-7 gcc-7-base libapt-pkg5.0 libatomic1 libbinutils libcc1-0 libcurl3-gnutls libgcc-7-dev libgcc1 libgomp1 libitm1 libpng16-16 libstdc++-7-dev libstdc++6 libsystemd0 libudev1 linux-libc-dev systemd systemd-sysv 27 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 27.4 MB of archives. After this operation, 116 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main s390x libgomp1 s390x 7.2.0-8ubuntu2 [70.1 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main s390x libitm1 s390x 7.2.0-8ubuntu2 [26.9 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main s390x gcc-7-base s390x 7.2.0-8ubuntu2 [17.9 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main s390x libgcc1 s390x 1:7.2.0-8ubuntu2 [25.2 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main s390x libatomic1 s390x 7.2.0-8ubuntu2 [8210 B] Get:6 http://ftpmaster.internal/ubuntu artful/main s390x cpp-7 s390x 7.2.0-8ubuntu2 [5173 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main s390x libcc1-0 s390x 7.2.0-8ubuntu2 [37.6 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main s390x g++-7 s390x 7.2.0-8ubuntu2 [5966 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main s390x gcc-7 s390x 7.2.0-8ubuntu2 [5836 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main s390x libgcc-7-dev s390x 7.2.0-8ubuntu2 [279 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main s390x libstdc++-7-dev s390x 7.2.0-8ubuntu2 [1447 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main s390x libstdc++6 s390x 7.2.0-8ubuntu2 [407 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main s390x libbinutils s390x 2.29.1-4ubuntu1 [304 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main s390x binutils s390x 2.29.1-4ubuntu1 [3274 B] Get:15 http://ftpmaster.internal/ubuntu artful/main s390x binutils-common s390x 2.29.1-4ubuntu1 [190 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main s390x binutils-s390x-linux-gnu s390x 2.29.1-4ubuntu1 [1698 kB] Get:17 http://ftpmaster.internal/ubuntu artful-proposed/main s390x libudev1 s390x 234-2ubuntu12 [48.4 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main s390x libapt-pkg5.0 s390x 1.5 [727 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main s390x apt s390x 1.5 [1089 kB] Get:20 http://ftpmaster.internal/ubuntu artful-proposed/main s390x systemd s390x 234-2ubuntu12 [2522 kB] Get:21 http://ftpmaster.internal/ubuntu artful-proposed/main s390x libsystemd0 s390x 234-2ubuntu12 [190 kB] Get:22 http://ftpmaster.internal/ubuntu artful-proposed/main s390x systemd-sysv s390x 234-2ubuntu12 [10.8 kB] Get:23 http://ftpmaster.internal/ubuntu artful-proposed/main s390x libcurl3-gnutls s390x 7.55.1-1ubuntu2 [177 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main s390x apt-transport-https s390x 1.5 [31.8 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main s390x libpng16-16 s390x 1.6.34-1 [171 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main s390x build-essential s390x 12.4ubuntu1 [4754 B] Get:27 http://ftpmaster.internal/ubuntu artful-proposed/main s390x linux-libc-dev s390x 4.13.0-15.16 [950 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.4 MB in 2s (12.0 MB/s) (Reading database ... 12436 files and directories currently installed.) Preparing to unpack .../libgomp1_7.2.0-8ubuntu2_s390x.deb ... Unpacking libgomp1:s390x (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Preparing to unpack .../libitm1_7.2.0-8ubuntu2_s390x.deb ... Unpacking libitm1:s390x (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Preparing to unpack .../gcc-7-base_7.2.0-8ubuntu2_s390x.deb ... Unpacking gcc-7-base:s390x (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Setting up gcc-7-base:s390x (7.2.0-8ubuntu2) ... (Reading database ... 12436 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a7.2.0-8ubuntu2_s390x.deb ... Unpacking libgcc1:s390x (1:7.2.0-8ubuntu2) over (1:7.2.0-6ubuntu1) ... Setting up libgcc1:s390x (1:7.2.0-8ubuntu2) ... (Reading database ... 12436 files and directories currently installed.) Preparing to unpack .../0-libatomic1_7.2.0-8ubuntu2_s390x.deb ... Unpacking libatomic1:s390x (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Preparing to unpack .../1-cpp-7_7.2.0-8ubuntu2_s390x.deb ... Unpacking cpp-7 (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Preparing to unpack .../2-libcc1-0_7.2.0-8ubuntu2_s390x.deb ... Unpacking libcc1-0:s390x (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Preparing to unpack .../3-g++-7_7.2.0-8ubuntu2_s390x.deb ... Unpacking g++-7 (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Preparing to unpack .../4-gcc-7_7.2.0-8ubuntu2_s390x.deb ... Unpacking gcc-7 (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Preparing to unpack .../5-libgcc-7-dev_7.2.0-8ubuntu2_s390x.deb ... Unpacking libgcc-7-dev:s390x (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Preparing to unpack .../6-libstdc++-7-dev_7.2.0-8ubuntu2_s390x.deb ... Unpacking libstdc++-7-dev:s390x (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Preparing to unpack .../7-libstdc++6_7.2.0-8ubuntu2_s390x.deb ... Unpacking libstdc++6:s390x (7.2.0-8ubuntu2) over (7.2.0-6ubuntu1) ... Setting up libstdc++6:s390x (7.2.0-8ubuntu2) ... (Reading database ... 12437 files and directories currently installed.) Preparing to unpack .../libbinutils_2.29.1-4ubuntu1_s390x.deb ... Unpacking libbinutils:s390x (2.29.1-4ubuntu1) over (2.29.1-1ubuntu1) ... Preparing to unpack .../binutils_2.29.1-4ubuntu1_s390x.deb ... Unpacking binutils (2.29.1-4ubuntu1) over (2.29.1-1ubuntu1) ... Preparing to unpack .../binutils-common_2.29.1-4ubuntu1_s390x.deb ... Unpacking binutils-common:s390x (2.29.1-4ubuntu1) over (2.29.1-1ubuntu1) ... Preparing to unpack .../binutils-s390x-linux-gnu_2.29.1-4ubuntu1_s390x.deb ... Unpacking binutils-s390x-linux-gnu (2.29.1-4ubuntu1) over (2.29.1-1ubuntu1) ... Preparing to unpack .../libudev1_234-2ubuntu12_s390x.deb ... Unpacking libudev1:s390x (234-2ubuntu12) over (234-2ubuntu10) ... Setting up libudev1:s390x (234-2ubuntu12) ... (Reading database ... 12437 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.5_s390x.deb ... Unpacking libapt-pkg5.0:s390x (1.5) over (1.5~rc4) ... Setting up libapt-pkg5.0:s390x (1.5) ... (Reading database ... 12437 files and directories currently installed.) Preparing to unpack .../apt/archives/apt_1.5_s390x.deb ... Unpacking apt (1.5) over (1.5~rc4) ... Setting up apt (1.5) ... (Reading database ... 12437 files and directories currently installed.) Preparing to unpack .../systemd_234-2ubuntu12_s390x.deb ... Unpacking systemd (234-2ubuntu12) over (234-2ubuntu10) ... Preparing to unpack .../libsystemd0_234-2ubuntu12_s390x.deb ... Unpacking libsystemd0:s390x (234-2ubuntu12) over (234-2ubuntu10) ... Setting up libsystemd0:s390x (234-2ubuntu12) ... Setting up systemd (234-2ubuntu12) ... Removing empty /etc/rc.local addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removed /etc/systemd/system/network-online.target.wants/systemd-networkd-wait-online.service. (Reading database ... 12437 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_234-2ubuntu12_s390x.deb ... Unpacking systemd-sysv (234-2ubuntu12) over (234-2ubuntu10) ... Preparing to unpack .../1-libcurl3-gnutls_7.55.1-1ubuntu2_s390x.deb ... Unpacking libcurl3-gnutls:s390x (7.55.1-1ubuntu2) over (7.55.1-1ubuntu1) ... Preparing to unpack .../2-apt-transport-https_1.5_s390x.deb ... Unpacking apt-transport-https (1.5) over (1.5~rc4) ... Preparing to unpack .../3-libpng16-16_1.6.34-1_s390x.deb ... Unpacking libpng16-16:s390x (1.6.34-1) over (1.6.32-2) ... Preparing to unpack .../4-build-essential_12.4ubuntu1_s390x.deb ... Unpacking build-essential (12.4ubuntu1) over (12.1ubuntu2) ... Preparing to unpack .../5-linux-libc-dev_4.13.0-15.16_s390x.deb ... Unpacking linux-libc-dev:s390x (4.13.0-15.16) over (4.13.0-11.12) ... Setting up libgomp1:s390x (7.2.0-8ubuntu2) ... Setting up libatomic1:s390x (7.2.0-8ubuntu2) ... Setting up libcc1-0:s390x (7.2.0-8ubuntu2) ... Setting up libpng16-16:s390x (1.6.34-1) ... Setting up build-essential (12.4ubuntu1) ... Setting up libcurl3-gnutls:s390x (7.55.1-1ubuntu2) ... Setting up systemd-sysv (234-2ubuntu12) ... Setting up linux-libc-dev:s390x (4.13.0-15.16) ... Setting up cpp-7 (7.2.0-8ubuntu2) ... Setting up binutils-common:s390x (2.29.1-4ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... Setting up libitm1:s390x (7.2.0-8ubuntu2) ... Setting up apt-transport-https (1.5) ... Setting up libbinutils:s390x (2.29.1-4ubuntu1) ... Setting up binutils-s390x-linux-gnu (2.29.1-4ubuntu1) ... Setting up libgcc-7-dev:s390x (7.2.0-8ubuntu2) ... Setting up libstdc++-7-dev:s390x (7.2.0-8ubuntu2) ... Setting up binutils (2.29.1-4ubuntu1) ... Setting up gcc-7 (7.2.0-8ubuntu2) ... Setting up g++-7 (7.2.0-8ubuntu2) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13546905 s390x artful-proposed -c chroot:build-PACKAGEBUILD-13546905 --arch=s390x --dist=artful-proposed --nolog r-bioc-variantannotation_1.22.3-1.dsc Initiating build PACKAGEBUILD-13546905 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 16:30:42 UTC 2017 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on z13-001.buildd +==============================================================================+ | r-bioc-variantannotation 1.22.3-1 (s390x) 05 Oct 2017 20:12 | +==============================================================================+ Package: r-bioc-variantannotation Version: 1.22.3-1 Source Version: 1.22.3-1 Distribution: artful-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/r-bioc-variantannotation-ZZujVT/r-bioc-variantannotation-1.22.3' with '<>' I: NOTICE: Log filtering will replace 'build/r-bioc-variantannotation-ZZujVT' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13546905/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- r-bioc-variantannotation_1.22.3-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-MaGZRH/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-MaGZRH/apt_archive ./ InRelease Get:2 copy:/<>/resolver-MaGZRH/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-MaGZRH/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-MaGZRH/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-MaGZRH/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-MaGZRH/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12437 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), dh-r, r-base-dev, r-bioc-bsgenome (>= 1.38.0), r-bioc-genomicfeatures (>= 1.27.4), r-bioc-summarizedexperiment (>= 1.5.3), r-bioc-rsamtools (>= 1.28.0) Filtered Build-Depends: debhelper (>= 10), dh-r, r-base-dev, r-bioc-bsgenome (>= 1.38.0), r-bioc-genomicfeatures (>= 1.27.4), r-bioc-summarizedexperiment (>= 1.5.3), r-bioc-rsamtools (>= 1.28.0) dpkg-deb: building package 'sbuild-build-depends-r-bioc-variantannotation-dummy' in '/<>/resolver-ALsJBF/apt_archive/sbuild-build-depends-r-bioc-variantannotation-dummy.deb'. Ign:1 copy:/<>/resolver-ALsJBF/apt_archive ./ InRelease Get:2 copy:/<>/resolver-ALsJBF/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-ALsJBF/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-ALsJBF/apt_archive ./ Sources [293 B] Get:5 copy:/<>/resolver-ALsJBF/apt_archive ./ Packages [609 B] Fetched 3021 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install r-bioc-variantannotation build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cdbs dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dh-translations file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-7 groff-base icu-devtools intltool intltool-debian libarchive-zip-perl libblas-dev libblas3 libbsd0 libbz2-dev libcairo2 libcroco3 libcurl3 libdatrie1 libencode-locale-perl libexpat1 libfile-listing-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran-7-dev libgfortran4 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu-dev libicu57 libio-html-perl libio-socket-ssl-perl libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev libmagic-mgc libmagic1 libncurses5-dev libnet-http-perl libnet-ssleay-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev libsigsegv2 libsm6 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6 libtool liburi-perl libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml2 libxmuu1 libxrender1 libxss1 libxt6 littler m4 man-db mime-support netbase perl-openssl-defaults pkg-config po-debconf python python-minimal python-pkg-resources python-scour python-six python2.7 python2.7-minimal r-base-core r-base-dev r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector r-cran-bitops r-cran-dbi r-cran-digest r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-lattice r-cran-littler r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-pkgkitten r-cran-rcpp r-cran-rcurl r-cran-rsqlite r-cran-snow r-cran-xml ucf unzip x11-common xauth xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation devscripts debtags dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-7-multilib gfortran-7-doc libgfortran4-dbg libcoarrays-dev groff liblapack-doc libdata-dump-perl icu-doc libcrypt-ssleay-perl liblzma-doc ncurses-doc readline-doc tcl8.6 tk8.6 libtool-doc gcj-jdk libauthen-ntlm-perl m4-doc less www-browser libmail-box-perl python-doc python-tk python-setuptools python-rsvg python-cairo python2.7-doc binfmt-support ess r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo r-bioc-go.db r-cran-runit r-bioc-graph r-cran-knitr r-cran-foreach r-cran-batchjobs r-cran-bbmisc r-cran-doparallel r-cran-rmpi r-bioc-shortread r-cran-codetools r-bioc-annotate r-bioc-affy r-bioc-biocinstaller r-bioc-genefilter r-bioc-deseq2 r-bioc-edger r-bioc-gviz r-bioc-variantannotation r-bioc-annotationhub r-bioc-limma r-cran-data.table r-cran-jsonlite r-cran-rmysql r-cran-testthat r-cran-getopt r-cran-base64enc r-cran-ggplot2 r-cran-inline r-cran-dbitest r-cran-rsprng r-cran-rlecuyer gvfs-bin Recommended packages: curl | wget | lynx-cur bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl libpng-tools libltdl-dev libhtml-form-perl libhttp-daemon-perl libmailtools-perl xml-core libmail-sendmail-perl r-recommended r-doc-html libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cdbs dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dh-translations file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-7 groff-base icu-devtools intltool intltool-debian libarchive-zip-perl libblas-dev libblas3 libbsd0 libbz2-dev libcairo2 libcroco3 libcurl3 libdatrie1 libencode-locale-perl libexpat1 libfile-listing-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran-7-dev libgfortran4 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu-dev libicu57 libio-html-perl libio-socket-ssl-perl libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev libmagic-mgc libmagic1 libncurses5-dev libnet-http-perl libnet-ssleay-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev libsigsegv2 libsm6 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6 libtool liburi-perl libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml2 libxmuu1 libxrender1 libxss1 libxt6 littler m4 man-db mime-support netbase perl-openssl-defaults pkg-config po-debconf python python-minimal python-pkg-resources python-scour python-six python2.7 python2.7-minimal r-base-core r-base-dev r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector r-cran-bitops r-cran-dbi r-cran-digest r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-lattice r-cran-littler r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-pkgkitten r-cran-rcpp r-cran-rcurl r-cran-rsqlite r-cran-snow r-cran-xml sbuild-build-depends-r-bioc-variantannotation-dummy ucf unzip x11-common xauth xdg-utils zip zlib1g-dev 0 upgraded, 177 newly installed, 1 to remove and 0 not upgraded. Need to get 151 MB of archives. After this operation, 414 MB of additional disk space will be used. Get:1 copy:/<>/resolver-ALsJBF/apt_archive ./ sbuild-build-depends-r-bioc-variantannotation-dummy 0.invalid.0 [870 B] Get:2 http://ftpmaster.internal/ubuntu artful/main s390x groff-base s390x 1.22.3-9 [1174 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main s390x libbsd0 s390x 0.8.6-1 [40.7 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main s390x bsdmainutils s390x 9.0.12+nmu1ubuntu1 [179 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main s390x libpipeline1 s390x 1.4.2-1 [24.3 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main s390x man-db s390x 2.7.6.1-2 [887 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main s390x fonts-dejavu-core all 2.37-1 [1041 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main s390x ucf all 3.0036 [52.9 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main s390x fontconfig-config all 2.11.94-0ubuntu2 [49.9 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main s390x libexpat1 s390x 2.2.3-1 [66.7 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main s390x libfreetype6 s390x 2.8-0.2ubuntu2 [313 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main s390x libfontconfig1 s390x 2.11.94-0ubuntu2 [127 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main s390x fontconfig s390x 2.11.94-0ubuntu2 [178 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main s390x libjpeg-turbo8 s390x 1.5.2-0ubuntu3 [100 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main s390x libpython2.7-minimal s390x 2.7.14-2ubuntu2 [338 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main s390x python2.7-minimal s390x 2.7.14-2ubuntu2 [1167 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main s390x python-minimal s390x 2.7.14-2ubuntu1 [28.1 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main s390x mime-support all 3.60ubuntu1 [30.1 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main s390x libpython2.7-stdlib s390x 2.7.14-2ubuntu2 [1849 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main s390x python2.7 s390x 2.7.14-2ubuntu2 [233 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main s390x libpython-stdlib s390x 2.7.14-2ubuntu1 [7576 B] Get:22 http://ftpmaster.internal/ubuntu artful/main s390x python s390x 2.7.14-2ubuntu1 [140 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main s390x libmagic-mgc s390x 1:5.32-1 [185 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main s390x libmagic1 s390x 1:5.32-1 [66.9 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main s390x file s390x 1:5.32-1 [21.8 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main s390x netbase all 5.4 [12.7 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main s390x gettext-base s390x 0.19.8.1-4ubuntu1 [47.7 kB] Get:28 http://ftpmaster.internal/ubuntu artful-proposed/main s390x libglib2.0-0 s390x 2.54.1-1ubuntu1 [1075 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main s390x libicu57 s390x 57.1-6 [7484 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main s390x libxau6 s390x 1:1.0.8-1 [7420 B] Get:31 http://ftpmaster.internal/ubuntu artful/main s390x libxdmcp6 s390x 1:1.1.2-3 [10.7 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main s390x libxcb1 s390x 1.11.1-1ubuntu1 [38.8 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main s390x libx11-data all 2:1.6.4-3 [114 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main s390x libx11-6 s390x 2:1.6.4-3 [546 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main s390x libxext6 s390x 2:1.3.3-1 [27.8 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main s390x libxml2 s390x 2.9.4+dfsg1-3.1 [594 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main s390x libxmuu1 s390x 2:1.1.2-2 [9762 B] Get:38 http://ftpmaster.internal/ubuntu artful/main s390x xauth s390x 1:1.0.9-1ubuntu2 [22.9 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main s390x libsigsegv2 s390x 2.11-1 [12.6 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main s390x m4 s390x 1.4.18-1 [195 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main s390x autoconf all 2.69-11 [322 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main s390x autotools-dev all 20161112.1 [39.5 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main s390x automake all 1:1.15-6ubuntu1 [509 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main s390x autopoint all 0.19.8.1-4ubuntu1 [412 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main s390x libtool all 2.4.6-2 [194 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main s390x dh-autoreconf all 14 [15.5 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main s390x libarchive-zip-perl all 1.59-1 [84.0 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main s390x libfile-stripnondeterminism-perl all 0.038-1 [13.3 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main s390x libtimedate-perl all 2.3000-2 [37.5 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main s390x dh-strip-nondeterminism all 0.038-1 [5026 B] Get:51 http://ftpmaster.internal/ubuntu artful/main s390x libcroco3 s390x 0.6.12-1 [74.7 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main s390x gettext s390x 0.19.8.1-4ubuntu1 [1048 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main s390x intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main s390x po-debconf all 1.0.20 [232 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main s390x debhelper all 10.7.2ubuntu2 [877 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main s390x liburi-perl all 1.72-1 [76.6 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main s390x libencode-locale-perl all 1.05-1 [12.3 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main s390x libhttp-date-perl all 6.02-1 [10.4 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main s390x libfile-listing-perl all 6.04-1 [9774 B] Get:60 http://ftpmaster.internal/ubuntu artful/main s390x libhtml-tagset-perl all 3.20-3 [12.1 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main s390x libhtml-parser-perl s390x 3.72-3build1 [85.1 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main s390x libhtml-tree-perl all 5.03-2 [197 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main s390x libio-html-perl all 1.001-1 [14.9 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main s390x liblwp-mediatypes-perl all 6.02-1 [21.7 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main s390x libhttp-message-perl all 6.11-1 [74.3 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main s390x libhttp-cookies-perl all 6.01-1 [17.2 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main s390x libhttp-negotiate-perl all 6.00-2 [13.4 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main s390x perl-openssl-defaults s390x 3 [6816 B] Get:69 http://ftpmaster.internal/ubuntu artful/main s390x libnet-ssleay-perl s390x 1.80-1build1 [254 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main s390x libio-socket-ssl-perl all 2.050-1 [168 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main s390x libnet-http-perl all 6.16-1 [22.6 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main s390x liblwp-protocol-https-perl all 6.07-2 [8284 B] Get:73 http://ftpmaster.internal/ubuntu artful/main s390x libwww-robotrules-perl all 6.01-1 [14.1 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main s390x libwww-perl all 6.15-2 [135 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main s390x libxml-parser-perl s390x 2.44-2build3 [197 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main s390x intltool all 0.51.0-4 [44.3 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main s390x dh-translations all 131 [22.3 kB] Get:78 http://ftpmaster.internal/ubuntu artful-proposed/main s390x python-six all 1.11.0-1 [11.1 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main s390x python-pkg-resources all 36.2.7-2 [128 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main s390x python-scour all 0.32-2 [42.8 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main s390x cdbs all 0.4.151ubuntu2 [45.4 kB] Get:82 http://ftpmaster.internal/ubuntu artful/main s390x dctrl-tools s390x 2.24-2build1 [58.7 kB] Get:83 http://ftpmaster.internal/ubuntu artful/main s390x zip s390x 3.0-11build1 [157 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main s390x unzip s390x 6.0-21ubuntu1 [156 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main s390x libpaper1 s390x 1.1.24+nmu5ubuntu1 [13.5 kB] Get:86 http://ftpmaster.internal/ubuntu artful/main s390x libpaper-utils s390x 1.1.24+nmu5ubuntu1 [8182 B] Get:87 http://ftpmaster.internal/ubuntu artful/main s390x xdg-utils all 1.1.1-1ubuntu2 [59.6 kB] Get:88 http://ftpmaster.internal/ubuntu artful/main s390x libblas3 s390x 3.7.1-3ubuntu2 [119 kB] Get:89 http://ftpmaster.internal/ubuntu artful/main s390x libpixman-1-0 s390x 0.34.0-1 [136 kB] Get:90 http://ftpmaster.internal/ubuntu artful/main s390x libxcb-render0 s390x 1.11.1-1ubuntu1 [11.4 kB] Get:91 http://ftpmaster.internal/ubuntu artful/main s390x libxcb-shm0 s390x 1.11.1-1ubuntu1 [5488 B] Get:92 http://ftpmaster.internal/ubuntu artful/main s390x libxrender1 s390x 1:0.9.10-1 [17.8 kB] Get:93 http://ftpmaster.internal/ubuntu artful/main s390x libcairo2 s390x 1.14.10-1ubuntu1 [512 kB] Get:94 http://ftpmaster.internal/ubuntu artful-proposed/main s390x libcurl3 s390x 7.55.1-1ubuntu2 [179 kB] Get:95 http://ftpmaster.internal/ubuntu artful/main s390x libjpeg8 s390x 8c-2ubuntu8 [2142 B] Get:96 http://ftpmaster.internal/ubuntu artful/main s390x libgfortran4 s390x 7.2.0-8ubuntu2 [276 kB] Get:97 http://ftpmaster.internal/ubuntu artful/main s390x liblapack3 s390x 3.7.1-3ubuntu2 [1631 kB] Get:98 http://ftpmaster.internal/ubuntu artful/main s390x libthai-data all 0.1.26-3 [132 kB] Get:99 http://ftpmaster.internal/ubuntu artful/main s390x libdatrie1 s390x 0.2.10-5 [17.4 kB] Get:100 http://ftpmaster.internal/ubuntu artful/main s390x libthai0 s390x 0.1.26-3 [17.8 kB] Get:101 http://ftpmaster.internal/ubuntu artful/main s390x libpango-1.0-0 s390x 1.40.12-1 [148 kB] Get:102 http://ftpmaster.internal/ubuntu artful/main s390x libgraphite2-3 s390x 1.3.10-2 [71.2 kB] Get:103 http://ftpmaster.internal/ubuntu artful/main s390x libharfbuzz0b s390x 1.4.2-1 [200 kB] Get:104 http://ftpmaster.internal/ubuntu artful/main s390x libpangoft2-1.0-0 s390x 1.40.12-1 [31.7 kB] Get:105 http://ftpmaster.internal/ubuntu artful/main s390x libpangocairo-1.0-0 s390x 1.40.12-1 [19.2 kB] Get:106 http://ftpmaster.internal/ubuntu artful/main s390x libtcl8.6 s390x 8.6.7+dfsg-1 [816 kB] Get:107 http://ftpmaster.internal/ubuntu artful/main s390x libjbig0 s390x 2.1-3.1 [26.6 kB] Get:108 http://ftpmaster.internal/ubuntu artful/main s390x libtiff5 s390x 4.0.8-5 [140 kB] Get:109 http://ftpmaster.internal/ubuntu artful/main s390x libxft2 s390x 2.3.2-1 [36.7 kB] Get:110 http://ftpmaster.internal/ubuntu artful/main s390x x11-common all 1:7.7+19ubuntu2 [22.2 kB] Get:111 http://ftpmaster.internal/ubuntu artful/main s390x libxss1 s390x 1:1.2.2-1 [7602 B] Get:112 http://ftpmaster.internal/ubuntu artful-proposed/main s390x libtk8.6 s390x 8.6.7-1ubuntu1 [651 kB] Get:113 http://ftpmaster.internal/ubuntu artful/main s390x libice6 s390x 2:1.0.9-2 [36.9 kB] Get:114 http://ftpmaster.internal/ubuntu artful/main s390x libsm6 s390x 2:1.2.2-1 [15.3 kB] Get:115 http://ftpmaster.internal/ubuntu artful/main s390x libxt6 s390x 1:1.1.5-1 [147 kB] Get:116 http://ftpmaster.internal/ubuntu artful/universe s390x r-base-core s390x 3.4.2-1 [22.9 MB] Get:117 http://ftpmaster.internal/ubuntu artful/main s390x libgfortran-7-dev s390x 7.2.0-8ubuntu2 [320 kB] Get:118 http://ftpmaster.internal/ubuntu artful/main s390x gfortran-7 s390x 7.2.0-8ubuntu2 [5508 kB] Get:119 http://ftpmaster.internal/ubuntu artful/main s390x gfortran s390x 4:7.2.0-1ubuntu1 [1278 B] Get:120 http://ftpmaster.internal/ubuntu artful/main s390x libblas-dev s390x 3.7.1-3ubuntu2 [121 kB] Get:121 http://ftpmaster.internal/ubuntu artful/main s390x liblapack-dev s390x 3.7.1-3ubuntu2 [1626 kB] Get:122 http://ftpmaster.internal/ubuntu artful/main s390x libtinfo-dev s390x 6.0+20160625-1ubuntu1 [80.1 kB] Get:123 http://ftpmaster.internal/ubuntu artful/main s390x libncurses5-dev s390x 6.0+20160625-1ubuntu1 [171 kB] Get:124 http://ftpmaster.internal/ubuntu artful/main s390x libreadline-dev s390x 7.0-0ubuntu2 [132 kB] Get:125 http://ftpmaster.internal/ubuntu artful/main s390x libjpeg-turbo8-dev s390x 1.5.2-0ubuntu3 [231 kB] Get:126 http://ftpmaster.internal/ubuntu artful/main s390x libjpeg8-dev s390x 8c-2ubuntu8 [1612 B] Get:127 http://ftpmaster.internal/ubuntu artful/main s390x libjpeg-dev s390x 8c-2ubuntu8 [1612 B] Get:128 http://ftpmaster.internal/ubuntu artful/main s390x libpcre16-3 s390x 2:8.39-4 [79.2 kB] Get:129 http://ftpmaster.internal/ubuntu artful/main s390x libpcre32-3 s390x 2:8.39-4 [73.8 kB] Get:130 http://ftpmaster.internal/ubuntu artful/main s390x libpcrecpp0v5 s390x 2:8.39-4 [14.4 kB] Get:131 http://ftpmaster.internal/ubuntu artful/main s390x libpcre3-dev s390x 2:8.39-4 [374 kB] Get:132 http://ftpmaster.internal/ubuntu artful/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-0ubuntu2 [173 kB] Get:133 http://ftpmaster.internal/ubuntu artful/main s390x libpng-dev s390x 1.6.34-1 [173 kB] Get:134 http://ftpmaster.internal/ubuntu artful/main s390x libbz2-dev s390x 1.0.6-8.1 [30.4 kB] Get:135 http://ftpmaster.internal/ubuntu artful/main s390x liblzma-dev s390x 5.2.2-1.3 [145 kB] Get:136 http://ftpmaster.internal/ubuntu artful/main s390x icu-devtools s390x 57.1-6 [164 kB] Get:137 http://ftpmaster.internal/ubuntu artful/main s390x libicu-dev s390x 57.1-6 [16.9 MB] Get:138 http://ftpmaster.internal/ubuntu artful/main s390x pkg-config s390x 0.29.1-0ubuntu2 [44.0 kB] Get:139 http://ftpmaster.internal/ubuntu artful/universe s390x r-base-dev all 3.4.2-1 [4452 B] Get:140 http://ftpmaster.internal/ubuntu artful/universe s390x dh-r all 20161219 [8828 B] Get:141 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-littler s390x 0.3.2-1 [53.9 kB] Get:142 http://ftpmaster.internal/ubuntu artful/universe s390x littler all 0.3.2-1 [2740 B] Get:143 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-biocgenerics all 0.22.0-1build1 [562 kB] Get:144 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-biobase s390x 2.36.2-1build1 [2026 kB] Get:145 http://ftpmaster.internal/ubuntu artful-proposed/universe s390x r-bioc-s4vectors s390x 0.14.3-1ubuntu1 [1166 kB] Get:146 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-iranges s390x 2.10.2-1ubuntu1 [1447 kB] Get:147 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-dbi s390x 0.7-1build1 [662 kB] Get:148 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-digest s390x 0.6.12-1build1 [104 kB] Get:149 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-memoise all 1.0.0-1build1 [24.8 kB] Get:150 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-pkgkitten all 0.1.4-1build1 [18.1 kB] Get:151 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-rcpp s390x 0.12.12-1build1 [2161 kB] Get:152 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-rsqlite s390x 1.1-2-1build1 [731 kB] Get:153 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-annotationdbi all 1.36.1-2build1 [4240 kB] Get:154 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-lambda.r all 1.1.9-1build1 [84.2 kB] Get:155 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-futile.options all 1.0.0-2build1 [15.7 kB] Get:156 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-futile.logger all 1.4.3-1build1 [93.9 kB] Get:157 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-snow all 1:0.4.2-1build1 [64.5 kB] Get:158 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-biocparallel all 1.10.1-1build1 [656 kB] Get:159 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-xml s390x 3.98-1.9-1build1 [1652 kB] Get:160 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-bitops s390x 1.0-6-1build1 [21.8 kB] Get:161 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-rcurl s390x 1.95-4.8-2build1 [618 kB] Get:162 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-biomart all 2.30.0-1build1 [194 kB] Get:163 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-xvector s390x 0.16.0-1build1 [368 kB] Get:164 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-biostrings s390x 2.44.0-1build1 [13.6 MB] Get:165 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-genomeinfodbdata all 0.99.0-1build1 [16.2 MB] Get:166 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-genomeinfodb all 1.12.2-1build1 [3457 kB] Get:167 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-genomicranges s390x 1.28.2-1build1 [1467 kB] Get:168 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-rsamtools s390x 1.28.0-1build1 [3247 kB] Get:169 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-matrixstats s390x 0.52.2-1build1 [611 kB] Get:170 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-delayedarray all 0.2.7-1build1 [379 kB] Get:171 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-lattice s390x 0.20-35-1build1 [712 kB] Get:172 http://ftpmaster.internal/ubuntu artful/universe s390x r-cran-matrix s390x 1.2-11-1build1 [2320 kB] Get:173 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-summarizedexperiment all 1.6.3-1build1 [1399 kB] Get:174 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-genomicalignments s390x 1.12.1-1build1 [1527 kB] Get:175 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-rtracklayer s390x 1.36.4-1build1 [1865 kB] Get:176 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-bsgenome all 1.42.0-2build1 [6507 kB] Get:177 http://ftpmaster.internal/ubuntu artful/universe s390x r-bioc-genomicfeatures all 1.28.0-1build1 [1088 kB] debconf: delaying package configuration, since 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Setting up libblas3:s390x (3.7.1-3ubuntu2) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode Setting up libjpeg-turbo8-dev:s390x (1.5.2-0ubuntu3) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... Setting up autotools-dev (20161112.1) ... Setting up liburi-perl (1.72-1) ... Processing triggers for systemd (234-2ubuntu12) ... Setting up libhtml-parser-perl (3.72-3build1) ... Setting up libgfortran-7-dev:s390x (7.2.0-8ubuntu2) ... Setting up libreadline-dev:s390x (7.0-0ubuntu2) ... Setting up gfortran-7 (7.2.0-8ubuntu2) ... Setting up libpcrecpp0v5:s390x (2:8.39-4) ... Setting up libpcre32-3:s390x (2:8.39-4) ... Setting up libnet-http-perl (6.16-1) ... Setting up icu-devtools (57.1-6) ... Setting up libpcre16-3:s390x (2:8.39-4) ... Setting up libtcl8.6:s390x (8.6.7+dfsg-1) ... Setting up libthai-data (0.1.26-3) ... Setting up liblzma-dev:s390x (5.2.2-1.3) ... Setting up libxdmcp6:s390x (1:1.1.2-3) ... Setting up bsdmainutils (9.0.12+nmu1ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up x11-common (1:7.7+19ubuntu2) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up xdg-utils (1.1.1-1ubuntu2) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libpython2.7-stdlib:s390x (2.7.14-2ubuntu2) ... Setting up libxau6:s390x (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-4ubuntu1) ... Setting up netbase (5.4) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.038-1) ... Setting up libjpeg8:s390x (8c-2ubuntu8) ... Setting up libpaper1:s390x (1.1.24+nmu5ubuntu1) ... Creating config file /etc/papersize with new version Setting up gfortran (4:7.2.0-1ubuntu1) ... 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 libpaper-utils (1.1.24+nmu5ubuntu1) ... Setting up libpcre3-dev:s390x (2:8.39-4) ... Setting up fontconfig-config (2.11.94-0ubuntu2) ... Setting up libhttp-date-perl (6.02-1) ... Setting up gettext (0.19.8.1-4ubuntu1) ... Setting up libblas-dev:s390x (3.7.1-3ubuntu2) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so to provide /usr/lib/s390x-linux-gnu/libblas.so (libblas.so-s390x-linux-gnu) in auto mode Setting up libnet-ssleay-perl (1.80-1build1) ... Setting up liblapack3:s390x (3.7.1-3ubuntu2) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode Setting up python2.7 (2.7.14-2ubuntu2) ... Setting up libharfbuzz0b:s390x (1.4.2-1) ... Setting up libtiff5:s390x (4.0.8-5) ... Setting up autoconf (2.69-11) ... Setting up libthai0:s390x (0.1.26-3) ... Setting up libicu-dev (57.1-6) ... Setting up file (1:5.32-1) ... Setting up libio-socket-ssl-perl (2.050-1) ... Setting up libhtml-tree-perl (5.03-2) ... Setting up libpython-stdlib:s390x (2.7.14-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libjpeg8-dev:s390x (8c-2ubuntu8) ... Setting up libjpeg-dev:s390x (8c-2ubuntu8) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up libice6:s390x (2:1.0.9-2) ... Setting up libfile-listing-perl (6.04-1) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhttp-message-perl (6.11-1) ... Setting up libpng-dev:s390x (1.6.34-1) ... Setting up libxcb1:s390x (1.11.1-1ubuntu1) ... Setting up python (2.7.14-2ubuntu1) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up liblapack-dev:s390x (3.7.1-3ubuntu2) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so to provide /usr/lib/s390x-linux-gnu/liblapack.so (liblapack.so-s390x-linux-gnu) in auto mode Setting up libtool (2.4.6-2) ... Setting up libfontconfig1:s390x (2.11.94-0ubuntu2) ... Setting up libsm6:s390x (2:1.2.2-1) ... Setting up libxcb-render0:s390x (1.11.1-1ubuntu1) ... Setting up po-debconf (1.0.20) ... Setting up libhttp-cookies-perl (6.01-1) ... Setting up libx11-6:s390x (2:1.6.4-3) ... Setting up python-pkg-resources (36.2.7-2) ... Setting up libxmuu1:s390x (2:1.1.2-2) ... Setting up python-six (1.11.0-1) ... Setting up python-scour (0.32-2) ... Setting up libxcb-shm0:s390x (1.11.1-1ubuntu1) ... Setting up libxt6:s390x (1:1.1.5-1) ... Setting up libxrender1:s390x (1:0.9.10-1) ... Setting up libxft2:s390x (2.3.2-1) ... Setting up fontconfig (2.11.94-0ubuntu2) ... Regenerating fonts cache... done. Setting up libxext6:s390x (2:1.3.3-1) ... Setting up libxss1:s390x (1:1.2.2-1) ... Setting up xauth (1:1.0.9-1ubuntu2) ... Setting up libpango-1.0-0:s390x (1.40.12-1) ... Setting up libcairo2:s390x (1.14.10-1ubuntu1) ... Setting up libtk8.6:s390x (8.6.7-1ubuntu1) ... Setting up libpangoft2-1.0-0:s390x (1.40.12-1) ... Setting up libpangocairo-1.0-0:s390x (1.40.12-1) ... Setting up r-base-core (3.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-littler (0.3.2-1) ... Setting up littler (0.3.2-1) ... Setting up r-bioc-biocgenerics (0.22.0-1build1) ... Setting up r-bioc-biobase (2.36.2-1build1) ... 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Setting up r-bioc-delayedarray (0.2.7-1build1) ... Setting up r-bioc-genomeinfodb (1.12.2-1build1) ... Setting up r-bioc-xvector (0.16.0-1build1) ... Setting up r-bioc-biostrings (2.44.0-1build1) ... Setting up r-bioc-annotationdbi (1.36.1-2build1) ... Setting up r-bioc-genomicranges (1.28.2-1build1) ... Setting up r-bioc-summarizedexperiment (1.6.3-1build1) ... Setting up r-bioc-biomart (2.30.0-1build1) ... Setting up r-bioc-rsamtools (1.28.0-1build1) ... Setting up r-bioc-genomicalignments (1.12.1-1build1) ... Setting up r-bioc-rtracklayer (1.36.4-1build1) ... Setting up r-bioc-genomicfeatures (1.28.0-1build1) ... Setting up r-bioc-bsgenome (1.42.0-2build1) ... Setting up dh-autoreconf (14) ... Setting up liblwp-protocol-https-perl (6.07-2) ... Setting up dh-strip-nondeterminism (0.038-1) ... Setting up libwww-perl (6.15-2) ... Setting up debhelper (10.7.2ubuntu2) ... Setting up libxml-parser-perl (2.44-2build3) ... Setting up intltool (0.51.0-4) ... Setting up dh-translations (131) ... Setting up cdbs (0.4.151ubuntu2) ... Setting up r-base-dev (3.4.2-1) ... Setting up dh-r (20161219) ... Setting up sbuild-build-depends-r-bioc-variantannotation-dummy (0.invalid.0) ... (Reading database ... 22097 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... 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python-six_1.11.0-1 python2.7_2.7.14-2ubuntu2 python2.7-minimal_2.7.14-2ubuntu2 r-base-core_3.4.2-1 r-base-dev_3.4.2-1 r-bioc-annotationdbi_1.36.1-2build1 r-bioc-biobase_2.36.2-1build1 r-bioc-biocgenerics_0.22.0-1build1 r-bioc-biocparallel_1.10.1-1build1 r-bioc-biomart_2.30.0-1build1 r-bioc-biostrings_2.44.0-1build1 r-bioc-bsgenome_1.42.0-2build1 r-bioc-delayedarray_0.2.7-1build1 r-bioc-genomeinfodb_1.12.2-1build1 r-bioc-genomeinfodbdata_0.99.0-1build1 r-bioc-genomicalignments_1.12.1-1build1 r-bioc-genomicfeatures_1.28.0-1build1 r-bioc-genomicranges_1.28.2-1build1 r-bioc-iranges_2.10.2-1ubuntu1 r-bioc-rsamtools_1.28.0-1build1 r-bioc-rtracklayer_1.36.4-1build1 r-bioc-s4vectors_0.14.3-1ubuntu1 r-bioc-summarizedexperiment_1.6.3-1build1 r-bioc-xvector_0.16.0-1build1 r-cran-bitops_1.0-6-1build1 r-cran-dbi_0.7-1build1 r-cran-digest_0.6.12-1build1 r-cran-futile.logger_1.4.3-1build1 r-cran-futile.options_1.0.0-2build1 r-cran-lambda.r_1.1.9-1build1 r-cran-lattice_0.20-35-1build1 r-cran-littler_0.3.2-1 r-cran-matrix_1.2-11-1build1 r-cran-matrixstats_0.52.2-1build1 r-cran-memoise_1.0.0-1build1 r-cran-pkgkitten_0.1.4-1build1 r-cran-rcpp_0.12.12-1build1 r-cran-rcurl_1.95-4.8-2build1 r-cran-rsqlite_1.1-2-1build1 r-cran-snow_1:0.4.2-1build1 r-cran-xml_3.98-1.9-1build1 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-variantannotation-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-2ubuntu12 systemd-sysv_234-2ubuntu12 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-2 tzdata_2017b-2 ubuntu-keyring_2016.10.27 ucf_3.0036 unzip_6.0-21ubuntu1 util-linux_2.30.1-0ubuntu4 x11-common_1:7.7+19ubuntu2 xauth_1:1.0.9-1ubuntu2 xdg-utils_1.1.1-1ubuntu2 xz-utils_5.2.2-1.3 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Oct 3 07:52:17 2017 UTC gpgv: using RSA key gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./r-bioc-variantannotation_1.22.3-1.dsc dpkg-source: info: extracting r-bioc-variantannotation in r-bioc-variantannotation-1.22.3 dpkg-source: info: unpacking r-bioc-variantannotation_1.22.3.orig.tar.gz dpkg-source: info: unpacking r-bioc-variantannotation_1.22.3-1.debian.tar.xz dpkg-source: info: applying use_debian_packaged_zlib.patch dpkg-source: info: applying drop_tests_requiring_large_data_sets.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-13546905 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13546905 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13546905 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package r-bioc-variantannotation dpkg-buildpackage: info: source version 1.22.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build r-bioc-variantannotation-1.22.3 dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean --buildsystem R dh_testdir -O--buildsystem=R dh_auto_clean -O--buildsystem=R dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules build-arch dh build-arch --buildsystem R dh_testdir -a -O--buildsystem=R dh_update_autotools_config -a -O--buildsystem=R dh_autoreconf -a -O--buildsystem=R dh_auto_configure -a -O--buildsystem=R dh_auto_build -a -O--buildsystem=R dh_auto_test -a -O--buildsystem=R create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --buildsystem R dh_testroot -a -O--buildsystem=R dh_prep -a -O--buildsystem=R dh_installdirs -a -O--buildsystem=R dh_auto_install -a -O--buildsystem=R I: R Package: VariantAnnotation Version: 1.22.3 I: Building using R version 3.4.2-1 I: R API version: r-api-3.4 I: Using built-time from d/changelog: Tue, 03 Oct 2017 09:41:55 +0200 mkdir -p /<>/debian/r-bioc-variantannotation/usr/lib/R/site-library R CMD INSTALL -l /<>/debian/r-bioc-variantannotation/usr/lib/R/site-library --clean . "--built-timestamp='Tue, 03 Oct 2017 09:41:55 +0200'" * installing *source* package ‘VariantAnnotation’ ... ** libs make[1]: Entering directory '/<>/src' gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dna_hash.c -o dna_hash.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rle.c -o rle.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c strhash.c -o strhash.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utilities.c -o utilities.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vcffile.c -o vcffile.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vcftype.c -o vcftype.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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/Rsamtools/include" -fPIC -g -O2 -fdebug-prefix-map=/build/r-base-9G6lPO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c writevcf.c -o writevcf.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /usr/lib/R/site-library/Rsamtools/usrlib//libbam.a /usr/lib/R/site-library/Rsamtools/usrlib//libbcf.a /usr/lib/R/site-library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/usr/lib/R/lib -lR make[1]: Leaving directory '/<>/src' make[1]: Entering directory '/<>/src' make[1]: Leaving directory '/<>/src' installing to /<>/debian/r-bioc-variantannotation/usr/lib/R/site-library/VariantAnnotation/libs ** R ** inst ** preparing package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (VariantAnnotation) W: Ignoring specified R dependency: R (>= 2.8.0) I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.15.3) I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.11.4) I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.27.6) I: Using r-bioc-summarizedexperiment for Depends:SummarizedExperiment (>= 1.5.3) I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.23.10) I: Using r-cran-runit for Suggests:RUnit I: Using r-bioc-annotationhub for Suggests:AnnotationHub W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19 W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg19.knownGene W: Cannot find a debian package for Suggests:SNPlocs.Hsapiens.dbSNP.20101109 W: Cannot find a debian package for Suggests:SIFT.Hsapiens.dbSNP132 W: Cannot find a debian package for Suggests:SIFT.Hsapiens.dbSNP137 W: Cannot find a debian package for Suggests:PolyPhen.Hsapiens.dbSNP131 I: Using r-bioc-snpstats for Suggests:snpStats I: Using r-cran-ggplot2 for Suggests:ggplot2 W: Cannot find a debian package for Suggests:BiocStyle I: Using r-cran-dbi for Imports:DBI I: Using r-bioc-biobase for Imports:Biobase I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.13.13) I: Using r-bioc-iranges for Imports:IRanges (>= 2.3.25) I: Using r-bioc-xvector for Imports:XVector (>= 0.5.6) I: Using r-bioc-biostrings for Imports:Biostrings (>= 2.33.5) I: Using r-bioc-annotationdbi for Imports:AnnotationDbi (>= 1.27.9) I: Using r-bioc-bsgenome for Imports:BSgenome (>= 1.37.6) I: Using r-bioc-rtracklayer for Imports:rtracklayer (>= 1.25.16) I: Using r-bioc-genomicfeatures for Imports:GenomicFeatures (>= 1.27.4) dh_install -a -O--buildsystem=R dh_installdocs -a -O--buildsystem=R dh_installchangelogs -a -O--buildsystem=R dh_installexamples -a -O--buildsystem=R dh_installman -a -O--buildsystem=R dh_installcatalogs -a -O--buildsystem=R dh_installcron -a -O--buildsystem=R dh_installdebconf -a -O--buildsystem=R dh_installemacsen -a -O--buildsystem=R dh_installifupdown -a -O--buildsystem=R dh_installinfo -a -O--buildsystem=R dh_systemd_enable -a -O--buildsystem=R dh_installinit -a -O--buildsystem=R dh_systemd_start -a -O--buildsystem=R dh_installmenu -a -O--buildsystem=R dh_installmime -a -O--buildsystem=R dh_installmodules -a -O--buildsystem=R dh_installlogcheck -a -O--buildsystem=R dh_installlogrotate -a -O--buildsystem=R dh_installpam -a -O--buildsystem=R dh_installppp -a -O--buildsystem=R dh_installudev -a -O--buildsystem=R dh_installgsettings -a -O--buildsystem=R dh_bugfiles -a -O--buildsystem=R dh_ucf -a -O--buildsystem=R dh_lintian -a -O--buildsystem=R dh_gconf -a -O--buildsystem=R dh_icons -a -O--buildsystem=R dh_perl -a -O--buildsystem=R dh_usrlocal -a -O--buildsystem=R dh_link -a -O--buildsystem=R dh_installwm -a -O--buildsystem=R dh_installxfonts -a -O--buildsystem=R dh_strip_nondeterminism -a -O--buildsystem=R dh_compress -a -O--buildsystem=R dh_fixperms -a -O--buildsystem=R dh_missing -a -O--buildsystem=R dh_strip -a -O--buildsystem=R dh_makeshlibs -a -O--buildsystem=R dh_shlibdeps -a -O--buildsystem=R dh_installdeb -a -O--buildsystem=R dh_gencontrol -a -O--buildsystem=R dh_md5sums -a -O--buildsystem=R dh_builddeb -a -O--buildsystem=R INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing r-bioc-variantannotation (in debian/r-bioc-variantannotation); do_strip: , oemstrip: pkgstriptranslations: processing r-bioc-variantannotation-dbgsym (in debian/.debhelper/r-bioc-variantannotation/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-bioc-variantannotation/DEBIAN/control, package r-bioc-variantannotation, directory debian/r-bioc-variantannotation pkgstripfiles: Truncating usr/share/doc/r-bioc-variantannotation/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-bioc-variantannotation ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-bioc-variantannotation' in '../r-bioc-variantannotation_1.22.3-1_s390x.deb'. pkgstripfiles: processing control file: debian/.debhelper/r-bioc-variantannotation/dbgsym-root/DEBIAN/control, package r-bioc-variantannotation-dbgsym, directory debian/.debhelper/r-bioc-variantannotation/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-bioc-variantannotation-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-bioc-variantannotation-dbgsym' in 'debian/.debhelper/scratch-space/build-r-bioc-variantannotation/r-bioc-variantannotation-dbgsym_1.22.3-1_s390x.deb'. Renaming r-bioc-variantannotation-dbgsym_1.22.3-1_s390x.deb to r-bioc-variantannotation-dbgsym_1.22.3-1_s390x.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../r-bioc-variantannotation_1.22.3-1_s390x.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build r-bioc-variantannotation-1.22.3 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20171005-2014 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ r-bioc-variantannotation_1.22.3-1_s390x.changes: ------------------------------------------------ Format: 1.8 Date: Tue, 03 Oct 2017 09:41:55 +0200 Source: r-bioc-variantannotation Binary: r-bioc-variantannotation Architecture: s390x Version: 1.22.3-1 Distribution: artful-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: r-bioc-variantannotation - BioConductor annotation of genetic variants Changes: r-bioc-variantannotation (1.22.3-1) unstable; urgency=medium . * New upstream version * Moved packaging from SVN to Git * Standards-Version: 4.1.1 Checksums-Sha1: 982dae54761ce06d3cbe352ff46e07383e310c74 71728 r-bioc-variantannotation-dbgsym_1.22.3-1_s390x.ddeb 7e6cea8462270bc59e94f6aaf46702bbed4d00f5 10940 r-bioc-variantannotation_1.22.3-1_s390x.buildinfo 0857046b3ba8722f879e898f3d02b99173c9a4c4 2369380 r-bioc-variantannotation_1.22.3-1_s390x.deb Checksums-Sha256: 73b01c2b3b14363508f221f95ad9675a9da09dd9178c0a97b7142a0552675bf6 71728 r-bioc-variantannotation-dbgsym_1.22.3-1_s390x.ddeb 075aa5d8bc397eddffa24399cf57ef95dad5794311b6662006c702047c12fbc6 10940 r-bioc-variantannotation_1.22.3-1_s390x.buildinfo b957af6b648e3cf8bc2fe868b8aca08ab2d154f7e06bae4a3d2afab83875925d 2369380 r-bioc-variantannotation_1.22.3-1_s390x.deb Files: c2345ede04d5d200882b630b5034d5ad 71728 debug extra r-bioc-variantannotation-dbgsym_1.22.3-1_s390x.ddeb 7f46a8fc8940070babef21afc423c962 10940 gnu-r optional r-bioc-variantannotation_1.22.3-1_s390x.buildinfo d206a1727d5b0401be5bea7db7179e83 2369380 gnu-r optional r-bioc-variantannotation_1.22.3-1_s390x.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ r-bioc-variantannotation_1.22.3-1_s390x.deb ------------------------------------------- new debian package, version 2.0. size 2369380 bytes: control archive=3004 bytes. 1160 bytes, 14 lines control 6995 bytes, 70 lines md5sums Package: r-bioc-variantannotation Version: 1.22.3-1 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2963 Depends: r-base-core (>= 3.4.2-1), r-api-3.4, r-bioc-biocgenerics (>= 0.15.3), r-bioc-genomeinfodb (>= 1.11.4), r-bioc-genomicranges (>= 1.27.6), r-bioc-summarizedexperiment (>= 1.5.3), r-bioc-rsamtools (>= 1.23.10), r-cran-dbi, r-bioc-biobase, r-bioc-s4vectors (>= 0.13.13), r-bioc-iranges (>= 2.3.25), r-bioc-xvector (>= 0.5.6), r-bioc-biostrings (>= 2.33.5), r-bioc-annotationdbi (>= 1.27.9), r-bioc-bsgenome (>= 1.37.6), r-bioc-rtracklayer (>= 1.25.16), r-bioc-genomicfeatures (>= 1.27.4), libc6 (>= 2.15), zlib1g (>= 1:1.2.3.3) Suggests: r-cran-runit, r-bioc-annotationhub, r-bioc-snpstats, r-cran-ggplot2 Section: gnu-r Priority: optional Homepage: https://bioconductor.org/packages/VariantAnnotation/ Description: BioConductor annotation of genetic variants This BioConductor package provides R functions to annotate variants, compute amino acid coding changess and to predict coding outcomes. drwxr-xr-x root/root 0 2017-10-03 07:41 ./ drwxr-xr-x root/root 0 2017-10-03 07:41 ./usr/ drwxr-xr-x root/root 0 2017-10-03 07:41 ./usr/lib/ drwxr-xr-x root/root 0 2017-10-03 07:41 ./usr/lib/R/ drwxr-xr-x root/root 0 2017-10-03 07:41 ./usr/lib/R/site-library/ drwxr-xr-x root/root 0 2017-10-03 07:41 ./usr/lib/R/site-library/VariantAnnotation/ -rw-r--r-- root/root 1768 2017-10-03 07:41 ./usr/lib/R/site-library/VariantAnnotation/CITATION -rw-r--r-- root/root 1735 2017-10-03 07:41 ./usr/lib/R/site-library/VariantAnnotation/DESCRIPTION -rw-r--r-- root/root 1668 2017-10-03 07:41 ./usr/lib/R/site-library/VariantAnnotation/INDEX drwxr-xr-x root/root 0 2017-10-03 07:41 ./usr/lib/R/site-library/VariantAnnotation/Meta/ -rw-r--r-- root/root 3384 2017-10-03 07:41 ./usr/lib/R/site-library/VariantAnnotation/Meta/Rd.rds -rw-r--r-- root/root 112 2017-10-03 07:41 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+------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 8380 Build-Time: 33 Distribution: artful-proposed Host Architecture: s390x Install-Time: 102 Job: r-bioc-variantannotation_1.22.3-1.dsc Machine Architecture: s390x Package: r-bioc-variantannotation Package-Time: 135 Source-Version: 1.22.3-1 Space: 8380 Status: successful Version: 1.22.3-1 -------------------------------------------------------------------------------- Finished at 20171005-2014 Build needed 00:02:15, 8380k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=artful --arch=s390x PACKAGEBUILD-13546905 Scanning for processes to kill in build PACKAGEBUILD-13546905 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=artful --arch=s390x PACKAGEBUILD-13546905 Stopping target for build PACKAGEBUILD-13546905 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=artful --arch=s390x PACKAGEBUILD-13546905 Removing build PACKAGEBUILD-13546905