DC-Build-Header: r-bioc-shortread 1.34.0-1 / 2017-07-06 19:25:45 +0000 DC-Task: type:rebuild-binarch-only source:r-bioc-shortread version:1.34.0-1 chroot:unstable esttime:503 logfile:/tmp/r-bioc-shortread_1.34.0-1_unstable_clang3.9.log modes:clang:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang r-bioc-shortread_1.34.0-1' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-43-122.eu-central-1.compute.internal +==============================================================================+ | r-bioc-shortread 1.34.0-1 (amd64) Thu, 06 Jul 2017 19:25:45 +0000 | +==============================================================================+ Package: r-bioc-shortread Version: 1.34.0-1 Source Version: 1.34.0-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-6fc18d98-dc06-4df2-bd2a-7fee3d792dec' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang ---------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.9 + echo 'Install of clang-3.9' Install of clang-3.9 + apt-get update Hit:1 http://127.0.0.1:9999/debian unstable InRelease Get:2 http://127.0.0.1:9999/debian unstable/main Translation-en [5730 kB] Fetched 5730 kB in 1s (3955 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.9 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbsd0 libclang-common-3.9-dev libclang1-3.9 libedit2 libjsoncpp1 libllvm3.9 libncurses5 libobjc-6-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.9-doc Recommended packages: llvm-3.9-dev python libgpm2 The following NEW packages will be installed: clang-3.9 libbsd0 libclang-common-3.9-dev libclang1-3.9 libedit2 libjsoncpp1 libllvm3.9 libncurses5 libobjc-6-dev libobjc4 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 57.7 MB of archives. After this operation, 251 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.5-1 [89.6 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5 amd64 6.0+20161126-1 [93.4 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20170329-1 [85.2 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm3.9 amd64 1:3.9.1-10 [11.3 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-3.9 amd64 1:3.9.1-10 [5875 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 7.1.0-9 [51.0 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.4.0-1 [197 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-3.9-dev amd64 1:3.9.1-10 [2573 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 clang-3.9 amd64 1:3.9.1-10 [37.4 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 57.7 MB in 0s (95.2 MB/s) Selecting previously unselected package libbsd0:amd64. (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 ... 9711 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.8.5-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.5-1) ... Selecting previously unselected package libncurses5:amd64. Preparing to unpack .../1-libncurses5_6.0+20161126-1_amd64.deb ... Unpacking libncurses5:amd64 (6.0+20161126-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../2-libedit2_3.1-20170329-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20170329-1) ... Selecting previously unselected package libllvm3.9:amd64. Preparing to unpack .../3-libllvm3.9_1%3a3.9.1-10_amd64.deb ... Unpacking libllvm3.9:amd64 (1:3.9.1-10) ... Selecting previously unselected package libclang1-3.9:amd64. Preparing to unpack .../4-libclang1-3.9_1%3a3.9.1-10_amd64.deb ... Unpacking libclang1-3.9:amd64 (1:3.9.1-10) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../5-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../6-libobjc4_7.1.0-9_amd64.deb ... Unpacking libobjc4:amd64 (7.1.0-9) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../7-libobjc-6-dev_6.4.0-1_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.4.0-1) ... Selecting previously unselected package libclang-common-3.9-dev. Preparing to unpack .../8-libclang-common-3.9-dev_1%3a3.9.1-10_amd64.deb ... Unpacking libclang-common-3.9-dev (1:3.9.1-10) ... Selecting previously unselected package clang-3.9. Preparing to unpack .../9-clang-3.9_1%3a3.9.1-10_amd64.deb ... Unpacking clang-3.9 (1:3.9.1-10) ... Setting up libncurses5:amd64 (6.0+20161126-1) ... Setting up libobjc4:amd64 (7.1.0-9) ... Setting up libbsd0:amd64 (0.8.5-1) ... Processing triggers for libc-bin (2.24-12) ... Setting up libobjc-6-dev:amd64 (6.4.0-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libllvm3.9:amd64 (1:3.9.1-10) ... Setting up libclang-common-3.9-dev (1:3.9.1-10) ... Setting up libclang1-3.9:amd64 (1:3.9.1-10) ... Setting up clang-3.9 (1:3.9.1-10) ... Processing triggers for libc-bin (2.24-12) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.9 g++-4.6 + ln -s clang-3.9 gcc-4.6 + ln -s clang-3.9 cpp-4.6 + ln -s clang-3.9 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.9 g++-4.7 + ln -s clang-3.9 gcc-4.7 + ln -s clang-3.9 cpp-4.7 + ln -s clang-3.9 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.9 g++-4.8 + ln -s clang-3.9 gcc-4.8 + ln -s clang-3.9 cpp-4.8 + ln -s clang-3.9 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.9 g++-4.9 + ln -s clang-3.9 gcc-4.9 + ln -s clang-3.9 cpp-4.9 + ln -s clang-3.9 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.9 g++-5 + ln -s clang-3.9 gcc-5 + ln -s clang-3.9 cpp-5 + ln -s clang-3.9 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-3.9 g++-6 + ln -s clang-3.9 gcc-6 + ln -s clang-3.9 cpp-6 + ln -s clang-3.9 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-3.9 g++-7 + ln -s clang-3.9 gcc-7 + ln -s clang-3.9 cpp-7 + ln -s clang-3.9 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/r-bioc-shortread-w1QaU6 + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'r-bioc-shortread' packaging is maintained in the 'Svn' version control system at: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-shortread/trunk/ Need to get 5153 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main r-bioc-shortread 1.34.0-1 (dsc) [2226 B] Get:2 http://127.0.0.1:9999/debian unstable/main r-bioc-shortread 1.34.0-1 (tar) [5145 kB] Get:3 http://127.0.0.1:9999/debian unstable/main r-bioc-shortread 1.34.0-1 (diff) [5224 B] Fetched 5153 kB in 0s (25.7 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-w1QaU6/r-bioc-shortread-1.34.0' with '<>' I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-w1QaU6' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-6JDKG1/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-6JDKG1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-6JDKG1/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-6JDKG1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-6JDKG1/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-6JDKG1/apt_archive ./ Packages [431 B] Fetched 1737 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 784 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-6JDKG1/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [784 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 784 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10178 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9), dh-r, r-base-dev, r-bioc-biobase (>= 2.26.0), r-bioc-genomicalignments (>= 1.8.0), r-bioc-rsamtools (>= 1.28.0), r-cran-hwriter, r-cran-latticeextra Filtered Build-Depends: debhelper (>= 9), dh-r, r-base-dev, r-bioc-biobase (>= 2.26.0), r-bioc-genomicalignments (>= 1.8.0), r-bioc-rsamtools (>= 1.28.0), r-cran-hwriter, r-cran-latticeextra dpkg-deb: building package 'sbuild-build-depends-r-bioc-shortread-dummy' in '/<>/resolver-6JDKG1/apt_archive/sbuild-build-depends-r-bioc-shortread-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-r-bioc-shortread-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-6JDKG1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-6JDKG1/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-6JDKG1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-6JDKG1/apt_archive ./ Sources [567 B] Get:5 copy:/<>/resolver-6JDKG1/apt_archive ./ Packages [647 B] Fetched 2177 B in 0s (0 B/s) Reading package lists... Reading package lists... Install r-bioc-shortread 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 ca-certificates cdbs dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-common libblas-dev libblas3 libbz2-dev libcairo2 libcroco3 libcurl3 libdatrie1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran-6-dev libgfortran3 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu57 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libncurses5-dev libnghttp2-14 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 libpng16-16 libpsl5 libreadline-dev libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh2-1 libssl1.0.2 libssl1.1 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6 libtool libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1 libxss1 libxt6 lsb-base m4 man-db openssl pkg-config po-debconf r-base-core r-base-dev r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector r-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-hwriter r-cran-lambda.r r-cran-lattice r-cran-latticeextra r-cran-matrix r-cran-matrixstats r-cran-rcolorbrewer r-cran-rcurl r-cran-snow readline-common tzdata 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-6-multilib gfortran-6-doc libgfortran3-dbg libcoarrays-dev groff liblapack-doc krb5-doc krb5-user icu-doc liblzma-doc ncurses-doc readline-doc tcl8.6 tk8.6 libtool-doc gcj-jdk m4-doc less www-browser libmail-box-perl 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-cran-foreach r-cran-batchjobs r-cran-bbmisc r-cran-doparallel r-cran-rmpi r-bioc-shortread r-cran-codetools r-cran-runit r-cran-knitr r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-affy r-bioc-genefilter r-bioc-rtracklayer r-bioc-deseq2 r-bioc-edger r-bioc-annotationdbi r-bioc-annotate r-bioc-gviz r-bioc-variantannotation r-bioc-annotationhub r-cran-digest r-bioc-graph r-cran-data.table r-cran-jsonlite r-cran-testthat r-cran-base64enc r-cran-ggplot2 r-cran-xml 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 krb5-locales libpng-tools publicsuffix libsasl2-modules libltdl-dev 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 NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils ca-certificates cdbs dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-common libblas-dev libblas3 libbz2-dev libcairo2 libcroco3 libcurl3 libdatrie1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran-6-dev libgfortran3 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu57 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libncurses5-dev libnghttp2-14 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 libpng16-16 libpsl5 libreadline-dev libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh2-1 libssl1.0.2 libssl1.1 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6 libtool libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1 libxss1 libxt6 lsb-base m4 man-db openssl pkg-config po-debconf r-base-core r-base-dev r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector r-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-hwriter r-cran-lambda.r r-cran-lattice r-cran-latticeextra r-cran-matrix r-cran-matrixstats r-cran-rcolorbrewer r-cran-rcurl r-cran-snow readline-common sbuild-build-depends-r-bioc-shortread-dummy tzdata ucf unzip x11-common xauth xdg-utils zip zlib1g-dev 0 upgraded, 152 newly installed, 0 to remove and 0 not upgraded. Need to get 145 MB of archives. After this operation, 367 MB of additional disk space will be used. Get:1 copy:/<>/resolver-6JDKG1/apt_archive ./ sbuild-build-depends-r-bioc-shortread-dummy 0.invalid.0 [864 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-9 [1160 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.12+nmu1 [186 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.6.1-2 [1044 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.1-3 [85.6 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libpng16-16 amd64 1.6.29-3 [281 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libfreetype6 amd64 2.8-0.2 [449 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 ucf all 3.0036 [70.2 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 fontconfig-config all 2.12.3-0.1 [303 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libfontconfig1 amd64 2.12.3-0.1 [366 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 fontconfig amd64 2.12.3-0.1 [436 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libpcrecpp0v5 amd64 2:8.39-3 [151 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libxcb1 amd64 1.12-1 [133 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libx11-data all 2:1.6.4-3 [290 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libx11-6 amd64 2:1.6.4-3 [747 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 lsb-base all 9.20161125 [27.9 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 x11-common all 1:7.7+19 [251 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libxss1 amd64 1:1.2.2-1 [17.5 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 tzdata all 2017b-2 [260 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 readline-common all 7.0-3 [70.4 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2l-2 [1294 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.1 amd64 1.1.0f-3 [1342 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.30-1 [222 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.30-1 [111 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.30-1 [63.9 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2+b1 [122 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.15-1 [61.7 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.15-1 [119 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.15-1 [311 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.15-1 [154 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3 [68.2 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3 [105 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 libldap-common all 2.4.44+dfsg-7 [85.2 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-7 [219 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-6 [7701 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-3 [715 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.11-1 [29.9 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-2 [736 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-2 [433 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 openssl amd64 1.1.0f-3 [725 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 ca-certificates all 20161130+nmu1 [196 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 cdbs all 0.4.152 [82.7 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 dctrl-tools amd64 2.24-2+b1 [104 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 14 [15.9 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.035-2 [17.0 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.035-2 [10.7 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.52.3-1 [2742 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-1 [144 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-2+b1 [1301 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 10.6.2 [968 kB] Get:66 http://127.0.0.1:9999/debian unstable/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:67 http://127.0.0.1:9999/debian unstable/main amd64 unzip amd64 6.0-21 [170 kB] Get:68 http://127.0.0.1:9999/debian unstable/main amd64 libpaper1 amd64 1.1.24+nmu5 [21.6 kB] Get:69 http://127.0.0.1:9999/debian unstable/main amd64 libpaper-utils amd64 1.1.24+nmu5 [17.6 kB] Get:70 http://127.0.0.1:9999/debian unstable/main amd64 xdg-utils all 1.1.1-1 [71.1 kB] Get:71 http://127.0.0.1:9999/debian unstable/main amd64 libgfortran3 amd64 6.4.0-1 [265 kB] Get:72 http://127.0.0.1:9999/debian unstable/main amd64 libblas-common amd64 3.7.1-1 [14.6 kB] Get:73 http://127.0.0.1:9999/debian unstable/main amd64 libblas3 amd64 3.7.1-1 [156 kB] Get:74 http://127.0.0.1:9999/debian unstable/main amd64 libpixman-1-0 amd64 0.34.0-1 [530 kB] Get:75 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-render0 amd64 1.12-1 [105 kB] Get:76 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-shm0 amd64 1.12-1 [95.9 kB] Get:77 http://127.0.0.1:9999/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:78 http://127.0.0.1:9999/debian unstable/main amd64 libcairo2 amd64 1.14.10-1 [774 kB] Get:79 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.24.0-1 [81.6 kB] Get:80 http://127.0.0.1:9999/debian unstable/main amd64 libpsl5 amd64 0.17.0-4+b1 [43.0 kB] Get:81 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:82 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.8.0-1 [138 kB] Get:83 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3 amd64 7.52.1-5 [291 kB] Get:84 http://127.0.0.1:9999/debian unstable/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:85 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:86 http://127.0.0.1:9999/debian unstable/main amd64 liblapack3 amd64 3.7.1-1 [2141 kB] Get:87 http://127.0.0.1:9999/debian unstable/main amd64 libthai-data all 0.1.26-1 [166 kB] Get:88 http://127.0.0.1:9999/debian unstable/main amd64 libdatrie1 amd64 0.2.10-4+b1 [36.4 kB] Get:89 http://127.0.0.1:9999/debian unstable/main amd64 libthai0 amd64 0.1.26-1 [52.1 kB] Get:90 http://127.0.0.1:9999/debian unstable/main amd64 libpango-1.0-0 amd64 1.40.6-1 [182 kB] Get:91 http://127.0.0.1:9999/debian unstable/main amd64 libgraphite2-3 amd64 1.3.10-2 [84.3 kB] Get:92 http://127.0.0.1:9999/debian unstable/main amd64 libharfbuzz0b amd64 1.4.2-1 [671 kB] Get:93 http://127.0.0.1:9999/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.40.6-1 [67.0 kB] Get:94 http://127.0.0.1:9999/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.40.6-1 [54.8 kB] Get:95 http://127.0.0.1:9999/debian unstable/main amd64 libsm6 amd64 2:1.2.2-1+b3 [33.3 kB] Get:96 http://127.0.0.1:9999/debian unstable/main amd64 libtcl8.6 amd64 8.6.6+dfsg-1+b1 [985 kB] Get:97 http://127.0.0.1:9999/debian unstable/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:98 http://127.0.0.1:9999/debian unstable/main amd64 libtiff5 amd64 4.0.8-3 [237 kB] Get:99 http://127.0.0.1:9999/debian unstable/main amd64 libxft2 amd64 2.3.2-1+b2 [56.5 kB] Get:100 http://127.0.0.1:9999/debian unstable/main amd64 libtk8.6 amd64 8.6.6-1+b1 [754 kB] Get:101 http://127.0.0.1:9999/debian unstable/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:102 http://127.0.0.1:9999/debian unstable/main amd64 r-base-core amd64 3.4.1-1 [23.2 MB] Get:103 http://127.0.0.1:9999/debian unstable/main amd64 libgfortran-6-dev amd64 6.4.0-1 [299 kB] Get:104 http://127.0.0.1:9999/debian unstable/main amd64 gfortran-6 amd64 6.4.0-1 [6911 kB] Get:105 http://127.0.0.1:9999/debian unstable/main amd64 gfortran amd64 4:6.3.0-4d1 [1362 B] Get:106 http://127.0.0.1:9999/debian unstable/main amd64 libblas-dev amd64 3.7.1-1 [162 kB] Get:107 http://127.0.0.1:9999/debian unstable/main amd64 liblapack-dev amd64 3.7.1-1 [2173 kB] Get:108 http://127.0.0.1:9999/debian unstable/main amd64 libtinfo-dev amd64 6.0+20161126-1 [78.8 kB] Get:109 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5-dev amd64 6.0+20161126-1 [175 kB] Get:110 http://127.0.0.1:9999/debian unstable/main amd64 libreadline-dev amd64 7.0-3 [132 kB] Get:111 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:1.5.1-2 [210 kB] Get:112 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg-dev all 1:1.5.1-2 [56.1 kB] Get:113 http://127.0.0.1:9999/debian unstable/main amd64 libpcre16-3 amd64 2:8.39-3 [258 kB] Get:114 http://127.0.0.1:9999/debian unstable/main amd64 libpcre32-3 amd64 2:8.39-3 [248 kB] Get:115 http://127.0.0.1:9999/debian unstable/main amd64 libpcre3-dev amd64 2:8.39-3 [647 kB] Get:116 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-5 [205 kB] Get:117 http://127.0.0.1:9999/debian unstable/main amd64 libpng-dev amd64 1.6.29-3 [251 kB] Get:118 http://127.0.0.1:9999/debian unstable/main amd64 libbz2-dev amd64 1.0.6-8.1 [29.4 kB] Get:119 http://127.0.0.1:9999/debian unstable/main amd64 liblzma-dev amd64 5.2.2-1.2+b1 [292 kB] Get:120 http://127.0.0.1:9999/debian unstable/main amd64 icu-devtools amd64 57.1-6 [178 kB] Get:121 http://127.0.0.1:9999/debian unstable/main amd64 libicu-dev amd64 57.1-6 [16.5 MB] Get:122 http://127.0.0.1:9999/debian unstable/main amd64 libxmuu1 amd64 2:1.1.2-2 [23.5 kB] Get:123 http://127.0.0.1:9999/debian unstable/main amd64 xauth amd64 1:1.0.9-1+b2 [39.6 kB] Get:124 http://127.0.0.1:9999/debian unstable/main amd64 pkg-config amd64 0.29-4+b1 [63.3 kB] Get:125 http://127.0.0.1:9999/debian unstable/main amd64 r-base-dev all 3.4.1-1 [4412 B] Get:126 http://127.0.0.1:9999/debian unstable/main amd64 dh-r all 20161219 [8794 B] Get:127 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-biocgenerics all 0.22.0-1 [564 kB] Get:128 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-biobase amd64 2.34.0-1 [1989 kB] Get:129 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-lambda.r all 1.1.9-1 [66.7 kB] Get:130 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-futile.options all 1.0.0-2 [15.4 kB] Get:131 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-futile.logger all 1.4.3-1 [90.8 kB] Get:132 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-snow all 1:0.4.2-1 [65.0 kB] Get:133 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-biocparallel all 1.10.1-1 [656 kB] Get:134 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-s4vectors amd64 0.14.3-1 [1163 kB] Get:135 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-iranges amd64 2.10.1-1 [1448 kB] Get:136 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-xvector amd64 0.16.0-1 [375 kB] Get:137 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-biostrings amd64 2.44.0-1 [13.6 MB] Get:138 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-matrixstats amd64 0.52.2-1 [619 kB] Get:139 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-delayedarray all 0.2.7-1 [374 kB] Get:140 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-bitops amd64 1.0-6-1 [22.3 kB] Get:141 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-rcurl amd64 1.95-4.8-2 [607 kB] Get:142 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-genomeinfodbdata all 0.99.0-1 [16.2 MB] Get:143 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-genomeinfodb all 1.12.0-1 [3461 kB] Get:144 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-genomicranges amd64 1.28.2-1 [1468 kB] Get:145 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-lattice amd64 0.20-35-1 [722 kB] Get:146 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-matrix amd64 1.2-10-1 [2380 kB] Get:147 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-summarizedexperiment all 1.6.3-1 [1400 kB] Get:148 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-rsamtools amd64 1.28.0-1 [3266 kB] Get:149 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-genomicalignments amd64 1.12.1-1 [1529 kB] Get:150 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-hwriter all 1.3.2-1 [137 kB] Get:151 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-2-1 [26.0 kB] Get:152 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-latticeextra amd64 0.6-28-2 [2059 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 145 MB in 2s (66.5 MB/s) Selecting previously unselected package groff-base. (Reading database ... 10178 files and directories currently installed.) Preparing to unpack .../000-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_9.0.12+nmu1_amd64.deb ... Unpacking bsdmainutils (9.0.12+nmu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../002-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../003-man-db_2.7.6.1-2_amd64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../004-libexpat1_2.2.1-3_amd64.deb ... Unpacking libexpat1:amd64 (2.2.1-3) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../005-libpng16-16_1.6.29-3_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.29-3) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../006-libfreetype6_2.8-0.2_amd64.deb ... Unpacking libfreetype6:amd64 (2.8-0.2) ... Selecting previously unselected package ucf. Preparing to unpack .../007-ucf_3.0036_all.deb ... Moving old data out of the way Unpacking ucf (3.0036) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../008-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../009-fontconfig-config_2.12.3-0.1_all.deb ... Unpacking fontconfig-config (2.12.3-0.1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../010-libfontconfig1_2.12.3-0.1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.12.3-0.1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../011-fontconfig_2.12.3-0.1_amd64.deb ... Unpacking fontconfig (2.12.3-0.1) ... 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Setting up libsigsegv2:amd64 (2.11-1) ... Setting up libldap-common (2.4.44+dfsg-7) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libblas-common (3.7.1-1) ... Setting up libpsl5:amd64 (0.17.0-4+b1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jul 6 19:26:18 UTC 2017. Universal Time is now: Thu Jul 6 19:26:18 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgfortran3:amd64 (6.4.0-1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:amd64 (2.52.3-1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3) ... Setting up libgfortran-6-dev:amd64 (6.4.0-1) ... Setting up unzip (6.0-21) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3) ... Setting up libtinfo-dev:amd64 (6.0+20161126-1) ... Setting up dctrl-tools (2.24-2+b1) ... Setting up libdatrie1:amd64 (0.2.10-4+b1) ... 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Processing triggers for libc-bin (2.24-12) ... Setting up autotools-dev (20161112.1) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-7) ... Setting up libssl1.1:amd64 (1.1.0f-3) ... Setting up openssl (1.1.0f-3) ... Setting up libreadline-dev:amd64 (7.0-3) ... Setting up libpcrecpp0v5:amd64 (2:8.39-3) ... Setting up libpcre32-3:amd64 (2:8.39-3) ... Setting up icu-devtools (57.1-6) ... Setting up libpcre16-3:amd64 (2:8.39-3) ... Setting up libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Setting up libthai-data (0.1.26-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:1.5.1-2) ... Setting up liblzma-dev:amd64 (5.2.2-1.2+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.12+nmu1) ... 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+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up xdg-utils (1.1.1-1) ... Setting up ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 166 added, 0 removed; done. Setting up libx11-data (2:1.6.4-3) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-2) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up libpaper1:amd64 (1.1.24+nmu5) ... Creating config file /etc/papersize with new version Setting up gfortran-6 (6.4.0-1) ... Setting up libpaper-utils (1.1.24+nmu5) ... Setting up libpcre3-dev:amd64 (2:8.39-3) ... Setting up fontconfig-config (2.12.3-0.1) ... Setting up gettext (0.19.8.1-2+b1) ... Setting up liblapack3 (3.7.1-1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libharfbuzz0b:amd64 (1.4.2-1) ... Setting up autoconf (2.69-10) ... Setting up libthai0:amd64 (0.1.26-1) ... Setting up libicu-dev (57.1-6) ... Setting up file (1:5.30-1) ... Setting up libkrb5support0:amd64 (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libjpeg-dev (1:1.5.1-2) ... Setting up automake (1:1.15.1-2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up libice6:amd64 (2:1.0.9-2) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpng-dev:amd64 (1.6.29-3) ... Setting up libxcb1:amd64 (1.12-1) ... Setting up libtool (2.4.6-2) ... Setting up gfortran (4:6.3.0-4d1) ... 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 libfontconfig1:amd64 (2.12.3-0.1) ... Setting up libsm6:amd64 (2:1.2.2-1+b3) ... Setting up libk5crypto3:amd64 (1.15-1) ... Setting up libxcb-render0:amd64 (1.12-1) ... Setting up po-debconf (1.0.20) ... Setting up libblas-dev (3.7.1-1) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libx11-6:amd64 (2:1.6.4-3) ... Setting up libxmuu1:amd64 (2:1.1.2-2) ... Setting up libxcb-shm0:amd64 (1.12-1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libkrb5-3:amd64 (1.15-1) ... Setting up libxft2:amd64 (2.3.2-1+b2) ... Setting up fontconfig (2.12.3-0.1) ... Regenerating fonts cache... done. Setting up liblapack-dev (3.7.1-1) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxss1:amd64 (1:1.2.2-1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1) ... Setting up xauth (1:1.0.9-1+b2) ... Setting up libpango-1.0-0:amd64 (1.40.6-1) ... Setting up libcairo2:amd64 (1.14.10-1) ... Setting up libcurl3:amd64 (7.52.1-5) ... Setting up libtk8.6:amd64 (8.6.6-1+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.40.6-1) ... Setting up libpangocairo-1.0-0:amd64 (1.40.6-1) ... Setting up r-base-core (3.4.1-1) ... Creating config file /etc/R/Renviron with new version Setting up r-base-dev (3.4.1-1) ... Setting up r-bioc-biocgenerics (0.22.0-1) ... Setting up r-bioc-biobase (2.34.0-1) ... Setting up r-cran-rcolorbrewer (1.1-2-1) ... Setting up r-cran-bitops (1.0-6-1) ... Setting up r-cran-futile.options (1.0.0-2) ... Setting up r-cran-rcurl (1.95-4.8-2) ... Setting up r-cran-hwriter (1.3.2-1) ... Setting up r-cran-lambda.r (1.1.9-1) ... Setting up r-cran-matrixstats (0.52.2-1) ... Setting up r-cran-snow (1:0.4.2-1) ... Setting up r-bioc-s4vectors (0.14.3-1) ... Setting up r-cran-lattice (0.20-35-1) ... Setting up r-cran-latticeextra (0.6-28-2) ... Setting up r-bioc-genomeinfodbdata (0.99.0-1) ... Setting up r-cran-futile.logger (1.4.3-1) ... Setting up r-bioc-iranges (2.10.1-1) ... Setting up r-bioc-biocparallel (1.10.1-1) ... Setting up r-cran-matrix (1.2-10-1) ... Setting up r-bioc-delayedarray (0.2.7-1) ... Setting up r-bioc-genomeinfodb (1.12.0-1) ... Setting up r-bioc-xvector (0.16.0-1) ... Setting up r-bioc-biostrings (2.44.0-1) ... Setting up r-bioc-genomicranges (1.28.2-1) ... Setting up r-bioc-summarizedexperiment (1.6.3-1) ... Setting up r-bioc-rsamtools (1.28.0-1) ... Setting up r-bioc-genomicalignments (1.12.1-1) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up debhelper (10.6.2) ... Setting up dh-r (20161219) ... Setting up sbuild-build-depends-r-bioc-shortread-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-12) ... Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-2-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1 gcc-6_6.4.0-1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 linux-libc-dev_4.11.6-1 Package versions: adduser_3.115 apt_1.5~beta1 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 cdbs_0.4.152 clang-3.9_1:3.9.1-10 coreutils_8.26-3 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1 dash_0.5.8-2.4 dctrl-tools_2.24-2+b1 debconf_1.5.62 debfoster_2.7-2.1+b1 debhelper_10.6.2 debian-archive-keyring_2017.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-r_20161219 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 eatmydata_105-5 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-2 fontconfig_2.12.3-0.1 fontconfig-config_2.12.3-0.1 fonts-dejavu-core_2.37-1 g++_4:6.3.0-4d1 g++-6_6.4.0-1 gcc_4:6.3.0-4d1 gcc-6_6.4.0-1 gcc-6-base_6.4.0-1 gcc-7-base_7.1.0-9 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gfortran_4:6.3.0-4d1 gfortran-6_6.4.0-1 gpgv_2.1.18-8 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5+b1 hostname_3.18+b1 icu-devtools_57.1-6 init-system-helpers_1.48 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1 libatomic1_7.1.0-9 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libblas-common_3.7.1-1 libblas-dev_3.7.1-1 libblas3_3.7.1-1 libblkid1_2.29.2-1 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcairo2_1.14.10-1 libcap-ng0_0.7.7-3+b1 libcc1-0_7.1.0-9 libcilkrts5_7.1.0-9 libclang-common-3.9-dev_1:3.9.1-10 libclang1-3.9_1:3.9.1-10 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcurl3_7.52.1-5 libdatrie1_0.2.10-4+b1 libdb5.3_5.3.28-12+b1 libdebconfclient0_0.229 libdpkg-perl_1.18.24 libeatmydata1_105-5 libedit2_3.1-20170329-1 libexpat1_2.2.1-3 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.035-2 libfontconfig1_2.12.3-0.1 libfreetype6_2.8-0.2 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.4.0-1 libgcc1_1:7.1.0-9 libgcrypt20_1.7.8-1 libgdbm3_1.8.3-14 libgfortran-6-dev_6.4.0-1 libgfortran3_6.4.0-1 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.13-2 libgomp1_7.1.0-9 libgpg-error0_1.27-3 libgraphite2-3_1.3.10-2 libgssapi-krb5-2_1.15-1 libharfbuzz0b_1.4.2-1 libhogweed4_3.3-1+b1 libice6_2:1.0.9-2 libicu-dev_57.1-6 libicu57_57.1-6 libidn2-0_0.16-1+b1 libisl15_0.18-1 libitm1_7.1.0-9 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.1-2 libjpeg62-turbo_1:1.5.1-2 libjpeg62-turbo-dev_1:1.5.1-2 libjsoncpp1_1.7.4-3 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libkrb5-3_1.15-1 libkrb5support0_1.15-1 liblapack-dev_3.7.1-1 liblapack3_3.7.1-1 libldap-2.4-2_2.4.44+dfsg-7 libldap-common_2.4.44+dfsg-7 libllvm3.9_1:3.9.1-10 liblsan0_7.1.0-9 liblz4-1_0.0~r131-2+b1 liblzma-dev_5.2.2-1.2+b1 liblzma5_5.2.2-1.2+b1 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-1 libmpc3_1.0.3-1+b2 libmpfr4_3.1.5-1 libmpx2_7.1.0-9 libncurses5_6.0+20161126-1 libncurses5-dev_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnettle6_3.3-1+b1 libnghttp2-14_1.24.0-1 libobjc-6-dev_6.4.0-1 libobjc4_7.1.0-9 libp11-kit0_0.23.7-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpango-1.0-0_1.40.6-1 libpangocairo-1.0-0_1.40.6-1 libpangoft2-1.0-0_1.40.6-1 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre16-3_2:8.39-3 libpcre3_2:8.39-3 libpcre3-dev_2:8.39-3 libpcre32-3_2:8.39-3 libpcrecpp0v5_2:8.39-3 libperl5.24_5.24.1-6 libpipeline1_1.4.1-2 libpixman-1-0_0.34.0-1 libpng-dev_1.6.29-3 libpng16-16_1.6.29-3 libpsl5_0.17.0-4+b1 libquadmath0_7.1.0-9 libreadline-dev_7.0-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1+b1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libselinux1_2.6-3+b2 libsemanage-common_2.6-2 libsemanage1_2.6-2+b1 libsepol1_2.6-2 libsigsegv2_2.11-1 libsm6_2:1.2.2-1+b3 libsmartcols1_2.29.2-1 libss2_1.43.4-2 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2l-2 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 libsystemd0_233-10 libtasn1-6_4.12-2 libtcl8.6_8.6.6+dfsg-1+b1 libthai-data_0.1.26-1 libthai0_0.1.26-1 libtiff5_4.0.8-3 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20161126-1 libtinfo5_6.0+20161126-1 libtk8.6_8.6.6-1+b1 libtool_2.4.6-2 libtsan0_7.1.0-9 libubsan0_7.1.0-9 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1 libxcb-render0_1.12-1 libxcb-shm0_1.12-1 libxcb1_1.12-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-1+b2 libxml2_2.9.4+dfsg1-3 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 linux-libc-dev_4.11.6-1 login_1:4.4-4.1 lsb-base_9.20161125 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17+b3 mount_2.29.2-1 multiarch-support_2.24-12 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 openssl_1.1.0f-3 passwd_1:4.4-4.1 patch_2.7.5-1+b2 perl_5.24.1-6 perl-base_5.24.1-6 perl-modules-5.24_5.24.1-6 pkg-config_0.29-4+b1 po-debconf_1.0.20 r-base-core_3.4.1-1 r-base-dev_3.4.1-1 r-bioc-biobase_2.34.0-1 r-bioc-biocgenerics_0.22.0-1 r-bioc-biocparallel_1.10.1-1 r-bioc-biostrings_2.44.0-1 r-bioc-delayedarray_0.2.7-1 r-bioc-genomeinfodb_1.12.0-1 r-bioc-genomeinfodbdata_0.99.0-1 r-bioc-genomicalignments_1.12.1-1 r-bioc-genomicranges_1.28.2-1 r-bioc-iranges_2.10.1-1 r-bioc-rsamtools_1.28.0-1 r-bioc-s4vectors_0.14.3-1 r-bioc-summarizedexperiment_1.6.3-1 r-bioc-xvector_0.16.0-1 r-cran-bitops_1.0-6-1 r-cran-futile.logger_1.4.3-1 r-cran-futile.options_1.0.0-2 r-cran-hwriter_1.3.2-1 r-cran-lambda.r_1.1.9-1 r-cran-lattice_0.20-35-1 r-cran-latticeextra_0.6-28-2 r-cran-matrix_1.2-10-1 r-cran-matrixstats_0.52.2-1 r-cran-rcolorbrewer_1.1-2-1 r-cran-rcurl_1.95-4.8-2 r-cran-snow_1:0.4.2-1 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-shortread-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 tzdata_2017b-2 ucf_3.0036 unzip_6.0-21 util-linux_2.29.2-1 x11-common_1:7.7+19 xauth_1:1.0.9-1+b2 xdg-utils_1.1.1-1 xz-utils_5.2.2-1.2+b1 zip_3.0-11+b1 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon May 29 13:20:55 2017 UTC gpgv: using RSA key AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./r-bioc-shortread_1.34.0-1.dsc dpkg-source: info: extracting r-bioc-shortread in /<> dpkg-source: info: unpacking r-bioc-shortread_1.34.0.orig.tar.gz dpkg-source: info: unpacking r-bioc-shortread_1.34.0-1.debian.tar.xz dpkg-source: info: applying use_debian_packaged_zlib.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=unstable-amd64-sbuild-6fc18d98-dc06-4df2-bd2a-7fee3d792dec SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package r-bioc-shortread dpkg-buildpackage: info: source version 1.34.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Graham Inggs dpkg-source --before-build r-bioc-shortread-1.34.0 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --buildsystem R dh_testdir -O--buildsystem=R dh_auto_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_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 create-stamp debian/debhelper-build-stamp 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: ShortRead Version: 1.34.0 I: Building using R version 3.4.1-1 I: R API version: r-api-3 I: Using built-time from d/changelog: Mon, 29 May 2017 15:13:59 +0200 mkdir -p /<>/debian/r-bioc-shortread/usr/lib/R/site-library R CMD INSTALL -l /<>/debian/r-bioc-shortread/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 29 May 2017 15:13:59 +0200'" * installing *source* package 'ShortRead' ... checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc -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... 8 configure: creating ./config.status config.status: creating src/Makevars ** libs make[1]: Entering directory '/<>/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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_soap.c -o io_soap.o g++ -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" -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=8 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readBfaToc.cc -o readBfaToc.o g++ -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" -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=8 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xsnap.c -o xsnap.o g++ -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 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 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) /usr/share/R/share/make/shlib.mk:6: recipe for target 'ShortRead.so' failed make[1]: *** [ShortRead.so] Error 1 make[1]: Leaving directory '/<>/src' make[1]: Entering directory '/<>/src' make[1]: Leaving directory '/<>/src' ERROR: compilation failed for package 'ShortRead' * removing '/<>/debian/r-bioc-shortread/usr/lib/R/site-library/ShortRead' dh_auto_install: R CMD INSTALL -l /<>/debian/r-bioc-shortread/usr/lib/R/site-library --clean . --built-timestamp='Mon, 29 May 2017 15:13:59 +0200' returned exit code 1 debian/rules:4: recipe for target 'binary-arch' failed make: *** [binary-arch] Error 25 dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2017-07-06T19:26:30Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 8540 Build-Time: 7 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 23 Job: r-bioc-shortread_1.34.0-1 Machine Architecture: amd64 Package: r-bioc-shortread Package-Time: 45 Source-Version: 1.34.0-1 Space: 8540 Status: attempted Version: 1.34.0-1 -------------------------------------------------------------------------------- Finished at 2017-07-06T19:26:30Z Build needed 00:00:45, 8540k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 45.786742162s DC-Time-Estimation: 45.786742162 versus expected 503 (r/m: 9.985712812244088 ; m: 45.786742162)