DC-Build-Header: r-bioc-rsamtools 1.28.0-1 / 2017-07-06 19:20:20 +0000 DC-Task: type:rebuild-binarch-only source:r-bioc-rsamtools version:1.28.0-1 chroot:unstable esttime:520 logfile:/tmp/r-bioc-rsamtools_1.28.0-1_unstable_clang4.0.log modes:clang40:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang40 r-bioc-rsamtools_1.28.0-1' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-38-146.eu-central-1.compute.internal +==============================================================================+ | r-bioc-rsamtools 1.28.0-1 (amd64) Thu, 06 Jul 2017 19:20:21 +0000 | +==============================================================================+ Package: r-bioc-rsamtools Version: 1.28.0-1 Source Version: 1.28.0-1 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-fbd67dcd-e45b-4243-bb6b-acd8f8fa3b35' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang40 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=4.0 + echo 'Install of clang-4.0' Install of clang-4.0 + 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 (3845 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-4.0 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbsd0 libclang-common-4.0-dev libclang1-4.0 libedit2 libjsoncpp1 libllvm4.0 libncurses5 libobjc-6-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-4.0-doc libomp-dev Recommended packages: llvm-4.0-dev python libgpm2 The following NEW packages will be installed: clang-4.0 libbsd0 libclang-common-4.0-dev libclang1-4.0 libedit2 libjsoncpp1 libllvm4.0 libncurses5 libobjc-6-dev libobjc4 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 74.4 MB of archives. After this operation, 320 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 libllvm4.0 amd64 1:4.0.1-1 [12.3 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-4.0 amd64 1:4.0.1-1 [6355 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-4.0-dev amd64 1:4.0.1-1 [2495 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 clang-4.0 amd64 1:4.0.1-1 [52.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.4 MB in 0s (94.6 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 libllvm4.0:amd64. Preparing to unpack .../3-libllvm4.0_1%3a4.0.1-1_amd64.deb ... Unpacking libllvm4.0:amd64 (1:4.0.1-1) ... Selecting previously unselected package libclang1-4.0:amd64. Preparing to unpack .../4-libclang1-4.0_1%3a4.0.1-1_amd64.deb ... Unpacking libclang1-4.0:amd64 (1:4.0.1-1) ... 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-4.0-dev. Preparing to unpack .../8-libclang-common-4.0-dev_1%3a4.0.1-1_amd64.deb ... Unpacking libclang-common-4.0-dev (1:4.0.1-1) ... Selecting previously unselected package clang-4.0. Preparing to unpack .../9-clang-4.0_1%3a4.0.1-1_amd64.deb ... Unpacking clang-4.0 (1:4.0.1-1) ... 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 libllvm4.0:amd64 (1:4.0.1-1) ... Setting up libclang1-4.0:amd64 (1:4.0.1-1) ... Setting up libclang-common-4.0-dev (1:4.0.1-1) ... Setting up clang-4.0 (1:4.0.1-1) ... 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++-4.0 g++-4.6 + ln -s clang-4.0 gcc-4.6 + ln -s clang-4.0 cpp-4.6 + ln -s clang-4.0 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++-4.0 g++-4.7 + ln -s clang-4.0 gcc-4.7 + ln -s clang-4.0 cpp-4.7 + ln -s clang-4.0 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++-4.0 g++-4.8 + ln -s clang-4.0 gcc-4.8 + ln -s clang-4.0 cpp-4.8 + ln -s clang-4.0 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++-4.0 g++-4.9 + ln -s clang-4.0 gcc-4.9 + ln -s clang-4.0 cpp-4.9 + ln -s clang-4.0 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++-4.0 g++-5 + ln -s clang-4.0 gcc-5 + ln -s clang-4.0 cpp-5 + ln -s clang-4.0 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++-4.0 g++-6 + ln -s clang-4.0 gcc-6 + ln -s clang-4.0 cpp-6 + ln -s clang-4.0 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++-4.0 g++-7 + ln -s clang-4.0 gcc-7 + ln -s clang-4.0 cpp-7 + ln -s clang-4.0 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-rsamtools-vnWCls + 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/clang40'. 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-rsamtools' packaging is maintained in the 'Svn' version control system at: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/ Need to get 2993 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main r-bioc-rsamtools 1.28.0-1 (dsc) [2208 B] Get:2 http://127.0.0.1:9999/debian unstable/main r-bioc-rsamtools 1.28.0-1 (tar) [2985 kB] Get:3 http://127.0.0.1:9999/debian unstable/main r-bioc-rsamtools 1.28.0-1 (diff) [6036 B] Fetched 2993 kB in 0s (44.4 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-vnWCls/r-bioc-rsamtools-1.28.0' with '<>' I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-vnWCls' 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-L3mmGl/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-L3mmGl/apt_archive ./ InRelease Get:2 copy:/<>/resolver-L3mmGl/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-L3mmGl/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-L3mmGl/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-L3mmGl/apt_archive ./ Packages [432 B] Fetched 1738 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 782 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-L3mmGl/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [782 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 782 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10206 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 (>= 10), dh-r, r-base-dev, r-cran-bitops, r-bioc-biostrings (>= 2.40.0), r-bioc-genomicranges (>= 1.24.0), r-bioc-biocparallel, libbam-dev Filtered Build-Depends: debhelper (>= 10), dh-r, r-base-dev, r-cran-bitops, r-bioc-biostrings (>= 2.40.0), r-bioc-genomicranges (>= 1.24.0), r-bioc-biocparallel, libbam-dev dpkg-deb: building package 'sbuild-build-depends-r-bioc-rsamtools-dummy' in '/<>/resolver-L3mmGl/apt_archive/sbuild-build-depends-r-bioc-rsamtools-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-rsamtools-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-L3mmGl/apt_archive ./ InRelease Get:2 copy:/<>/resolver-L3mmGl/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-L3mmGl/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-L3mmGl/apt_archive ./ Sources [560 B] Get:5 copy:/<>/resolver-L3mmGl/apt_archive ./ Packages [643 B] Fetched 2166 B in 0s (0 B/s) Reading package lists... Reading package lists... Install r-bioc-rsamtools 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 libbam-dev 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-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors r-bioc-xvector r-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-lambda.r 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-rsamtools r-bioc-genomicalignments r-bioc-shortread r-cran-codetools r-cran-runit r-cran-knitr r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-affy r-bioc-biobase r-bioc-annotationdbi r-bioc-annotate r-bioc-summarizedexperiment r-cran-matrix r-bioc-rtracklayer r-bioc-gviz r-bioc-variantannotation r-bioc-annotationhub r-bioc-deseq2 r-bioc-edger r-cran-digest r-bioc-graph r-cran-data.table r-cran-testthat r-cran-jsonlite 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 libbam-dev 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-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors r-bioc-xvector r-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-rcurl r-cran-snow readline-common sbuild-build-depends-r-bioc-rsamtools-dummy tzdata ucf unzip x11-common xauth xdg-utils zip zlib1g-dev 0 upgraded, 142 newly installed, 0 to remove and 0 not upgraded. Need to get 131 MB of archives. After this operation, 344 MB of additional disk space will be used. Get:1 copy:/<>/resolver-L3mmGl/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [858 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 libbam-dev amd64 0.1.19-2 [123 kB] Get:128 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-biocgenerics all 0.22.0-1 [564 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-bitops amd64 1.0-6-1 [22.3 kB] Get:139 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-rcurl amd64 1.95-4.8-2 [607 kB] Get:140 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-genomeinfodbdata all 0.99.0-1 [16.2 MB] Get:141 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-genomeinfodb all 1.12.0-1 [3461 kB] Get:142 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-genomicranges amd64 1.28.2-1 [1468 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 131 MB in 1s (91.4 MB/s) Selecting previously unselected package groff-base. (Reading database ... 10206 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) ... Selecting previously unselected package libpcrecpp0v5:amd64. Preparing to unpack .../012-libpcrecpp0v5_2%3a8.39-3_amd64.deb ... Unpacking libpcrecpp0v5:amd64 (2:8.39-3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../013-libxau6_1%3a1.0.8-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../014-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../015-libxcb1_1.12-1_amd64.deb ... Unpacking libxcb1:amd64 (1.12-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../016-libx11-data_2%3a1.6.4-3_all.deb ... Unpacking libx11-data (2:1.6.4-3) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../017-libx11-6_2%3a1.6.4-3_amd64.deb ... Unpacking libx11-6:amd64 (2:1.6.4-3) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../018-libxext6_2%3a1.3.3-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.3-1+b2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../019-lsb-base_9.20161125_all.deb ... Unpacking lsb-base (9.20161125) ... Selecting previously unselected package x11-common. Preparing to unpack .../020-x11-common_1%3a7.7+19_all.deb ... Unpacking x11-common (1:7.7+19) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../021-libxss1_1%3a1.2.2-1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.2-1) ... Selecting previously unselected package tzdata. Preparing to unpack .../022-tzdata_2017b-2_all.deb ... Unpacking tzdata (2017b-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../023-readline-common_7.0-3_all.deb ... Unpacking readline-common (7.0-3) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../024-libreadline7_7.0-3_amd64.deb ... Unpacking libreadline7:amd64 (7.0-3) ... Selecting previously unselected package libssl1.0.2:amd64. Preparing to unpack .../025-libssl1.0.2_1.0.2l-2_amd64.deb ... Unpacking libssl1.0.2:amd64 (1.0.2l-2) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../026-libssl1.1_1.1.0f-3_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0f-3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../027-libmagic-mgc_1%3a5.30-1_amd64.deb ... Unpacking libmagic-mgc (1:5.30-1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../028-libmagic1_1%3a5.30-1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.30-1) ... Selecting previously unselected package file. Preparing to unpack .../029-file_1%3a5.30-1_amd64.deb ... Unpacking file (1:5.30-1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../030-gettext-base_0.19.8.1-2+b1_amd64.deb ... Unpacking gettext-base (0.19.8.1-2+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../031-libkeyutils1_1.5.9-9_amd64.deb ... Unpacking libkeyutils1:amd64 (1.5.9-9) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../032-libkrb5support0_1.15-1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.15-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../033-libk5crypto3_1.15-1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.15-1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../034-libkrb5-3_1.15-1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.15-1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../035-libgssapi-krb5-2_1.15-1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.15-1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../036-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../037-libsasl2-2_2.1.27~101-g0780600+dfsg-3_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3) ... Selecting previously unselected package libldap-common. Preparing to unpack .../038-libldap-common_2.4.44+dfsg-7_all.deb ... Unpacking libldap-common (2.4.44+dfsg-7) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../039-libldap-2.4-2_2.4.44+dfsg-7_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.44+dfsg-7) ... Selecting previously unselected package libicu57:amd64. Preparing to unpack .../040-libicu57_57.1-6_amd64.deb ... Unpacking libicu57:amd64 (57.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../041-libxml2_2.9.4+dfsg1-3_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-3) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../042-libsigsegv2_2.11-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.11-1) ... Selecting previously unselected package m4. Preparing to unpack .../043-m4_1.4.18-1_amd64.deb ... Unpacking m4 (1.4.18-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../044-autoconf_2.69-10_all.deb ... Unpacking autoconf (2.69-10) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../045-autotools-dev_20161112.1_all.deb ... Unpacking autotools-dev (20161112.1) ... Selecting previously unselected package automake. Preparing to unpack .../046-automake_1%3a1.15.1-2_all.deb ... Unpacking automake (1:1.15.1-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../047-autopoint_0.19.8.1-2_all.deb ... Unpacking autopoint (0.19.8.1-2) ... Selecting previously unselected package openssl. Preparing to unpack .../048-openssl_1.1.0f-3_amd64.deb ... Unpacking openssl (1.1.0f-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../049-ca-certificates_20161130+nmu1_all.deb ... Unpacking ca-certificates (20161130+nmu1) ... Selecting previously unselected package cdbs. Preparing to unpack .../050-cdbs_0.4.152_all.deb ... Unpacking cdbs (0.4.152) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../051-dctrl-tools_2.24-2+b1_amd64.deb ... Unpacking dctrl-tools (2.24-2+b1) ... Selecting previously unselected package libtool. Preparing to unpack .../052-libtool_2.4.6-2_all.deb ... Unpacking libtool (2.4.6-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../053-dh-autoreconf_14_all.deb ... Unpacking dh-autoreconf (14) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../054-libarchive-zip-perl_1.59-1_all.deb ... Unpacking libarchive-zip-perl (1.59-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../055-libfile-stripnondeterminism-perl_0.035-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.035-2) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../056-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../057-dh-strip-nondeterminism_0.035-2_all.deb ... Unpacking dh-strip-nondeterminism (0.035-2) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../058-libglib2.0-0_2.52.3-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.52.3-1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../059-libcroco3_0.6.12-1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-1) ... Selecting previously unselected package gettext. Preparing to unpack .../060-gettext_0.19.8.1-2+b1_amd64.deb ... Unpacking gettext (0.19.8.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../061-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../062-po-debconf_1.0.20_all.deb ... Unpacking po-debconf (1.0.20) ... Selecting previously unselected package debhelper. Preparing to unpack .../063-debhelper_10.6.2_all.deb ... Unpacking debhelper (10.6.2) ... Selecting previously unselected package zip. Preparing to unpack .../064-zip_3.0-11+b1_amd64.deb ... Unpacking zip (3.0-11+b1) ... Selecting previously unselected package unzip. Preparing to unpack .../065-unzip_6.0-21_amd64.deb ... Unpacking unzip (6.0-21) ... Selecting previously unselected package libpaper1:amd64. Preparing to unpack .../066-libpaper1_1.1.24+nmu5_amd64.deb ... Unpacking libpaper1:amd64 (1.1.24+nmu5) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../067-libpaper-utils_1.1.24+nmu5_amd64.deb ... Unpacking libpaper-utils (1.1.24+nmu5) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../068-xdg-utils_1.1.1-1_all.deb ... Unpacking xdg-utils (1.1.1-1) ... Selecting previously unselected package libgfortran3:amd64. Preparing to unpack .../069-libgfortran3_6.4.0-1_amd64.deb ... Unpacking libgfortran3:amd64 (6.4.0-1) ... Selecting previously unselected package libblas-common. Preparing to unpack .../070-libblas-common_3.7.1-1_amd64.deb ... Unpacking libblas-common (3.7.1-1) ... Selecting previously unselected package libblas3. Preparing to unpack .../071-libblas3_3.7.1-1_amd64.deb ... Unpacking libblas3 (3.7.1-1) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../072-libpixman-1-0_0.34.0-1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.34.0-1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../073-libxcb-render0_1.12-1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.12-1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../074-libxcb-shm0_1.12-1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.12-1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../075-libxrender1_1%3a0.9.10-1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../076-libcairo2_1.14.10-1_amd64.deb ... Unpacking libcairo2:amd64 (1.14.10-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../077-libnghttp2-14_1.24.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.24.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../078-libpsl5_0.17.0-4+b1_amd64.deb ... Unpacking libpsl5:amd64 (0.17.0-4+b1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../079-librtmp1_2.4+20151223.gitfa8646d.1-1+b1_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../080-libssh2-1_1.8.0-1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-1) ... Selecting previously unselected package libcurl3:amd64. Preparing to unpack .../081-libcurl3_7.52.1-5_amd64.deb ... Unpacking libcurl3:amd64 (7.52.1-5) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../082-libice6_2%3a1.0.9-2_amd64.deb ... Unpacking libice6:amd64 (2:1.0.9-2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../083-libjpeg62-turbo_1%3a1.5.1-2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.1-2) ... Selecting previously unselected package liblapack3. Preparing to unpack .../084-liblapack3_3.7.1-1_amd64.deb ... Unpacking liblapack3 (3.7.1-1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../085-libthai-data_0.1.26-1_all.deb ... Unpacking libthai-data (0.1.26-1) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../086-libdatrie1_0.2.10-4+b1_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.10-4+b1) ... Selecting previously unselected package libthai0:amd64. Preparing to unpack .../087-libthai0_0.1.26-1_amd64.deb ... Unpacking libthai0:amd64 (0.1.26-1) ... Selecting previously unselected package libpango-1.0-0:amd64. Preparing to unpack .../088-libpango-1.0-0_1.40.6-1_amd64.deb ... Unpacking libpango-1.0-0:amd64 (1.40.6-1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../089-libgraphite2-3_1.3.10-2_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.10-2) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../090-libharfbuzz0b_1.4.2-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (1.4.2-1) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Preparing to unpack .../091-libpangoft2-1.0-0_1.40.6-1_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.40.6-1) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Preparing to unpack .../092-libpangocairo-1.0-0_1.40.6-1_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.40.6-1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../093-libsm6_2%3a1.2.2-1+b3_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.2-1+b3) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../094-libtcl8.6_8.6.6+dfsg-1+b1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../095-libjbig0_2.1-3.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-3.1+b2) ... Selecting previously unselected package libtiff5:amd64. Preparing to unpack .../096-libtiff5_4.0.8-3_amd64.deb ... Unpacking libtiff5:amd64 (4.0.8-3) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../097-libxft2_2.3.2-1+b2_amd64.deb ... Unpacking libxft2:amd64 (2.3.2-1+b2) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../098-libtk8.6_8.6.6-1+b1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.6-1+b1) ... Selecting previously unselected package libxt6:amd64. Preparing to unpack .../099-libxt6_1%3a1.1.5-1_amd64.deb ... Unpacking libxt6:amd64 (1:1.1.5-1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../100-r-base-core_3.4.1-1_amd64.deb ... Unpacking r-base-core (3.4.1-1) ... Selecting previously unselected package libgfortran-6-dev:amd64. Preparing to unpack .../101-libgfortran-6-dev_6.4.0-1_amd64.deb ... Unpacking libgfortran-6-dev:amd64 (6.4.0-1) ... Selecting previously unselected package gfortran-6. Preparing to unpack .../102-gfortran-6_6.4.0-1_amd64.deb ... Unpacking gfortran-6 (6.4.0-1) ... Selecting previously unselected package gfortran. Preparing to unpack .../103-gfortran_4%3a6.3.0-4d1_amd64.deb ... Unpacking gfortran (4:6.3.0-4d1) ... Selecting previously unselected package libblas-dev. Preparing to unpack .../104-libblas-dev_3.7.1-1_amd64.deb ... Unpacking libblas-dev (3.7.1-1) ... Selecting previously unselected package liblapack-dev. Preparing to unpack .../105-liblapack-dev_3.7.1-1_amd64.deb ... Unpacking liblapack-dev (3.7.1-1) ... Selecting previously unselected package libtinfo-dev:amd64. Preparing to unpack .../106-libtinfo-dev_6.0+20161126-1_amd64.deb ... Unpacking libtinfo-dev:amd64 (6.0+20161126-1) ... Selecting previously unselected package libncurses5-dev:amd64. Preparing to unpack .../107-libncurses5-dev_6.0+20161126-1_amd64.deb ... Unpacking libncurses5-dev:amd64 (6.0+20161126-1) ... Selecting previously unselected package libreadline-dev:amd64. Preparing to unpack .../108-libreadline-dev_7.0-3_amd64.deb ... Unpacking libreadline-dev:amd64 (7.0-3) ... Selecting previously unselected package libjpeg62-turbo-dev:amd64. Preparing to unpack .../109-libjpeg62-turbo-dev_1%3a1.5.1-2_amd64.deb ... Unpacking libjpeg62-turbo-dev:amd64 (1:1.5.1-2) ... Selecting previously unselected package libjpeg-dev. Preparing to unpack .../110-libjpeg-dev_1%3a1.5.1-2_all.deb ... Unpacking libjpeg-dev (1:1.5.1-2) ... Selecting previously unselected package libpcre16-3:amd64. Preparing to unpack .../111-libpcre16-3_2%3a8.39-3_amd64.deb ... Unpacking libpcre16-3:amd64 (2:8.39-3) ... Selecting previously unselected package libpcre32-3:amd64. Preparing to unpack .../112-libpcre32-3_2%3a8.39-3_amd64.deb ... Unpacking libpcre32-3:amd64 (2:8.39-3) ... Selecting previously unselected package libpcre3-dev:amd64. Preparing to unpack .../113-libpcre3-dev_2%3a8.39-3_amd64.deb ... Unpacking libpcre3-dev:amd64 (2:8.39-3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../114-zlib1g-dev_1%3a1.2.8.dfsg-5_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Selecting previously unselected package libpng-dev:amd64. Preparing to unpack .../115-libpng-dev_1.6.29-3_amd64.deb ... Unpacking libpng-dev:amd64 (1.6.29-3) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../116-libbz2-dev_1.0.6-8.1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.6-8.1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../117-liblzma-dev_5.2.2-1.2+b1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.2.2-1.2+b1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../118-icu-devtools_57.1-6_amd64.deb ... Unpacking icu-devtools (57.1-6) ... Selecting previously unselected package libicu-dev. Preparing to unpack .../119-libicu-dev_57.1-6_amd64.deb ... Unpacking libicu-dev (57.1-6) ... Selecting previously unselected package libxmuu1:amd64. Preparing to unpack .../120-libxmuu1_2%3a1.1.2-2_amd64.deb ... Unpacking libxmuu1:amd64 (2:1.1.2-2) ... Selecting previously unselected package xauth. Preparing to unpack .../121-xauth_1%3a1.0.9-1+b2_amd64.deb ... Unpacking xauth (1:1.0.9-1+b2) ... Selecting previously unselected package pkg-config. Preparing to unpack .../122-pkg-config_0.29-4+b1_amd64.deb ... Unpacking pkg-config (0.29-4+b1) ... Selecting previously unselected package r-base-dev. Preparing to unpack .../123-r-base-dev_3.4.1-1_all.deb ... Unpacking r-base-dev (3.4.1-1) ... Selecting previously unselected package dh-r. Preparing to unpack .../124-dh-r_20161219_all.deb ... Unpacking dh-r (20161219) ... Selecting previously unselected package libbam-dev. Preparing to unpack .../125-libbam-dev_0.1.19-2_amd64.deb ... Unpacking libbam-dev (0.1.19-2) ... Selecting previously unselected package r-bioc-biocgenerics. Preparing to unpack .../126-r-bioc-biocgenerics_0.22.0-1_all.deb ... Unpacking r-bioc-biocgenerics (0.22.0-1) ... Selecting previously unselected package r-cran-lambda.r. Preparing to unpack .../127-r-cran-lambda.r_1.1.9-1_all.deb ... Unpacking r-cran-lambda.r (1.1.9-1) ... Selecting previously unselected package r-cran-futile.options. Preparing to unpack .../128-r-cran-futile.options_1.0.0-2_all.deb ... Unpacking r-cran-futile.options (1.0.0-2) ... Selecting previously unselected package r-cran-futile.logger. Preparing to unpack .../129-r-cran-futile.logger_1.4.3-1_all.deb ... Unpacking r-cran-futile.logger (1.4.3-1) ... Selecting previously unselected package r-cran-snow. Preparing to unpack .../130-r-cran-snow_1%3a0.4.2-1_all.deb ... Unpacking r-cran-snow (1:0.4.2-1) ... Selecting previously unselected package r-bioc-biocparallel. Preparing to unpack .../131-r-bioc-biocparallel_1.10.1-1_all.deb ... Unpacking r-bioc-biocparallel (1.10.1-1) ... Selecting previously unselected package r-bioc-s4vectors. Preparing to unpack .../132-r-bioc-s4vectors_0.14.3-1_amd64.deb ... Unpacking r-bioc-s4vectors (0.14.3-1) ... Selecting previously unselected package r-bioc-iranges. Preparing to unpack .../133-r-bioc-iranges_2.10.1-1_amd64.deb ... Unpacking r-bioc-iranges (2.10.1-1) ... Selecting previously unselected package r-bioc-xvector. Preparing to unpack .../134-r-bioc-xvector_0.16.0-1_amd64.deb ... Unpacking r-bioc-xvector (0.16.0-1) ... Selecting previously unselected package r-bioc-biostrings. Preparing to unpack .../135-r-bioc-biostrings_2.44.0-1_amd64.deb ... Unpacking r-bioc-biostrings (2.44.0-1) ... Selecting previously unselected package r-cran-bitops. Preparing to unpack .../136-r-cran-bitops_1.0-6-1_amd64.deb ... Unpacking r-cran-bitops (1.0-6-1) ... Selecting previously unselected package r-cran-rcurl. Preparing to unpack .../137-r-cran-rcurl_1.95-4.8-2_amd64.deb ... Unpacking r-cran-rcurl (1.95-4.8-2) ... Selecting previously unselected package r-bioc-genomeinfodbdata. Preparing to unpack .../138-r-bioc-genomeinfodbdata_0.99.0-1_all.deb ... Unpacking r-bioc-genomeinfodbdata (0.99.0-1) ... Selecting previously unselected package r-bioc-genomeinfodb. Preparing to unpack .../139-r-bioc-genomeinfodb_1.12.0-1_all.deb ... Unpacking r-bioc-genomeinfodb (1.12.0-1) ... Selecting previously unselected package r-bioc-genomicranges. Preparing to unpack .../140-r-bioc-genomicranges_1.28.2-1_amd64.deb ... Unpacking r-bioc-genomicranges (1.28.2-1) ... Selecting previously unselected package sbuild-build-depends-r-bioc-rsamtools-dummy. Preparing to unpack .../141-sbuild-build-depends-r-bioc-rsamtools-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ... Setting up cdbs (0.4.152) ... Setting up readline-common (7.0-3) ... Setting up libexpat1:amd64 (2.2.1-3) ... Setting up libbz2-dev:amd64 (1.0.6-8.1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.1-2) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libnghttp2-14:amd64 (1.24.0-1) ... Setting up libpng16-16:amd64 (1.6.29-3) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... 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 19:20:53 UTC 2017. Universal Time is now: Thu Jul 6 19:20:53 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) ... Setting up libtiff5:amd64 (4.0.8-3) ... Setting up gettext-base (0.19.8.1-2+b1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:amd64 (57.1-6) ... Setting up ucf (3.0036) ... Setting up libxml2:amd64 (2.9.4+dfsg1-3) ... Setting up zip (3.0-11+b1) ... Setting up libfreetype6:amd64 (2.8-0.2) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:amd64 (1:5.30-1) ... Setting up lsb-base (9.20161125) ... Setting up libgraphite2-3:amd64 (1.3.10-2) ... Setting up libcroco3:amd64 (0.6.12-1) ... Setting up libncurses5-dev:amd64 (6.0+20161126-1) ... Setting up libssl1.0.2:amd64 (1.0.2l-2) ... Setting up pkg-config (0.29-4+b1) ... Setting up libpixman-1-0:amd64 (0.34.0-1) ... Setting up libblas3 (3.7.1-1) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libssh2-1:amd64 (1.8.0-1) ... 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 libbam-dev (0.1.19-2) ... 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-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-lambda.r (1.1.9-1) ... Setting up r-cran-snow (1:0.4.2-1) ... Setting up r-bioc-s4vectors (0.14.3-1) ... 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-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 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-rsamtools-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-4.0_1:4.0.1-1 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 libbam-dev_0.1.19-2 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-4.0-dev_1:4.0.1-1 libclang1-4.0_1:4.0.1-1 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 libllvm4.0_1:4.0.1-1 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-biocgenerics_0.22.0-1 r-bioc-biocparallel_1.10.1-1 r-bioc-biostrings_2.44.0-1 r-bioc-genomeinfodb_1.12.0-1 r-bioc-genomeinfodbdata_0.99.0-1 r-bioc-genomicranges_1.28.2-1 r-bioc-iranges_2.10.1-1 r-bioc-s4vectors_0.14.3-1 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-lambda.r_1.1.9-1 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-rsamtools-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 12:08:52 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-rsamtools_1.28.0-1.dsc dpkg-source: info: extracting r-bioc-rsamtools in /<> dpkg-source: info: unpacking r-bioc-rsamtools_1.28.0.orig.tar.gz dpkg-source: info: unpacking r-bioc-rsamtools_1.28.0-1.debian.tar.xz dpkg-source: info: applying use_debian_packaged_zlib.patch dpkg-source: info: applying skip_test_requiring_network.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-fbd67dcd-e45b-4243-bb6b-acd8f8fa3b35 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package r-bioc-rsamtools dpkg-buildpackage: info: source version 1.28.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Graham Inggs dpkg-source --before-build r-bioc-rsamtools-1.28.0 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_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: Rsamtools Version: 1.28.0 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 13:43:34 +0200 mkdir -p /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library R CMD INSTALL -l /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 29 May 2017 13:43:34 +0200'" * installing *source* package 'Rsamtools' ... ** 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 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" -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 PileupBuffer.cpp -o PileupBuffer.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" -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 PosCacheColl.cpp -o PosCacheColl.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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_Rsamtools.c -o R_init_Rsamtools.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" -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 ResultManager.cpp -o ResultManager.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 as_bam.c -o as_bam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 bam_data.c -o bam_data.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" -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 bam_mate_iter.cpp -o bam_mate_iter.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 bambuffer.c -o bambuffer.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 bamfile.c -o bamfile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 bcffile.c -o bcffile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 encode.c -o encode.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 fafile.c -o fafile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 idxstats.c -o idxstats.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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_sam.c -o io_sam.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" -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 pbuffer_wrapper.cpp -o pbuffer_wrapper.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" -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 pileup.cpp -o pileup.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 pileupbam.c -o pileupbam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools_patch.c -o samtools_patch.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 scan_bam_data.c -o scan_bam_data.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 tabixfile.c -o tabixfile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 tagfilter.c -o tagfilter.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 utilities.c -o utilities.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 zip_compression.c -o zip_compression.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bgzf.c -o samtools/bgzf.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/kstring.c -o samtools/kstring.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_aux.c -o samtools/bam_aux.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam.c -o samtools/bam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_import.c -o samtools/bam_import.o In file included from samtools/bam_import.c:3: In file included from /usr/include/zlib.h:34: In file included from /usr/include/zconf.h:395: In file included from /usr/lib/llvm-4.0/bin/../lib/clang/4.0.1/include/limits.h:37: In file included from /usr/include/limits.h:25: /usr/include/features.h:148:3: warning: "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-W#warnings] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ 1 warning generated. 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/sam.c -o samtools/sam.o In file included from samtools/sam.c:3: In file included from /usr/include/string.h:25: /usr/include/features.h:148:3: warning: "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-W#warnings] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ 1 warning generated. 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_index.c -o samtools/bam_index.o samtools/bam_index.c:358:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&key, 4, 1, fp); ^~~~~ ~~~~~~~~~~~~~~ samtools/bam_index.c:362:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&p->n, 4, 1, fp); ^~~~~ ~~~~~~~~~~~~~~~ samtools/bam_index.c:366:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(p->list, 16, p->n, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:355:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&size, 4, 1, fp); ^~~~~ ~~~~~~~~~~~~~~~ samtools/bam_index.c:376:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&index2->n, 4, 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:380:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(index2->offset, index2->n, 8, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:335:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(magic, 1, 4, fp); ^~~~~ ~~~~~~~~~~~~~~~ samtools/bam_index.c:342:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&idx->n, 4, 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~ 8 warnings generated. 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_pileup.c -o samtools/bam_pileup.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_lpileup.c -o samtools/bam_lpileup.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_md.c -o samtools/bam_md.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/razf.c -o samtools/razf.o samtools/razf.c:99:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(fd, &v32, sizeof(uint32_t)); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:96:12: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] if(is_be) write(fd, &rz->index->size, sizeof(int)); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:106:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:107:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:201:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:221:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:234:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:258:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:810:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(rz->x.fpw, &rz->in, sizeof(int64_t)); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:811:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(rz->x.fpw, &rz->out, sizeof(int64_t)); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:814:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:816:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 12 warnings generated. 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/faidx.c -o samtools/faidx.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/knetfile.c -o samtools/knetfile.o In file included from samtools/knetfile.c:33: In file included from /usr/include/time.h:27: /usr/include/features.h:148:3: warning: "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-W#warnings] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ samtools/knetfile.c:239:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./samtools/knetfile.h:9:32: note: expanded from macro 'netwrite' #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~ ~~~~~~~~~~~~ samtools/knetfile.c:418:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] netwrite(fp->fd, buf, l); ^~~~~~~~~~~~~~~~~~~~~~~~ ./samtools/knetfile.h:9:32: note: expanded from macro 'netwrite' #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~ ~~~~~~~~~~~~ 3 warnings generated. 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_sort.c -o samtools/bam_sort.o In file included from samtools/bam_sort.c:3: In file included from /usr/include/stdlib.h:24: /usr/include/features.h:148:3: warning: "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-W#warnings] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ 1 warning generated. 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/sam_header.c -o samtools/sam_header.o In file included from samtools/sam_header.c:3: In file included from /usr/include/stdio.h:27: /usr/include/features.h:148:3: warning: "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-W#warnings] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ 1 warning generated. 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_reheader.c -o samtools/bam_reheader.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/kprobaln.c -o samtools/kprobaln.o ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/bcf.c -o samtools/bcftools/bcf.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o In file included from samtools/bcftools/vcf.c:3: In file included from /usr/include/zlib.h:34: In file included from /usr/include/zconf.h:395: In file included from /usr/lib/llvm-4.0/bin/../lib/clang/4.0.1/include/limits.h:37: In file included from /usr/include/limits.h:25: /usr/include/features.h:148:3: warning: "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-W#warnings] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ 1 warning generated. 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o In file included from samtools/bcftools/bcfutils.c:3: In file included from /usr/include/alloca.h:21: /usr/include/features.h:148:3: warning: "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-W#warnings] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ 1 warning generated. 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/prob1.c -o samtools/bcftools/prob1.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/index.c -o samtools/bcftools/index.o In file included from samtools/bcftools/index.c:2: In file included from /usr/include/assert.h:35: /usr/include/features.h:148:3: warning: "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-W#warnings] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ 1 warning generated. 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/fet.c -o samtools/bcftools/fet.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 tabix/index.c -o tabix/index.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 tabix/bedidx.c -o tabix/bedidx.o ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools" mkdir -p "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix" cp samtools/*.h "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/" cp samtools/bcftools/*h "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/" cp tabix/*h "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/" cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \ "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/" mkdir -p "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib" cp libbam.a libbcf.a libtabix.a "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib" g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbam.a /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbcf.a /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libtabix.a -lz -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 'Rsamtools.so' failed make[1]: *** [Rsamtools.so] Error 1 make[1]: Leaving directory '/<>/src' make[1]: Entering directory '/<>/src' make[1]: Leaving directory '/<>/src' ERROR: compilation failed for package 'Rsamtools' * removing '/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools' dh_auto_install: R CMD INSTALL -l /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean . --built-timestamp='Mon, 29 May 2017 13:43:34 +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 2017-07-06T19:21:17Z 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: 7964 Build-Time: 18 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 21 Job: r-bioc-rsamtools_1.28.0-1 Machine Architecture: amd64 Package: r-bioc-rsamtools Package-Time: 56 Source-Version: 1.28.0-1 Space: 7964 Status: attempted Version: 1.28.0-1 -------------------------------------------------------------------------------- Finished at 2017-07-06T19:21:17Z Build needed 00:00:56, 7964k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 57.911185231s DC-Time-Estimation: 57.911185231 versus expected 520 (r/m: 7.979267095394254 ; m: 57.911185231)