DC-Build-Header: r-bioc-rsamtools 1.24.0-1 / 2016-08-29 16:23:09 +0000 DC-Task: type:rebuild-binarch-only source:r-bioc-rsamtools version:1.24.0-1 chroot:unstable esttime:520 logfile:/tmp/r-bioc-rsamtools_1.24.0-1_unstable_clang3.8.log modes:clang:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang r-bioc-rsamtools_1.24.0-1' sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on ip-172-31-8-35.eu-central-1.compute.internal +==============================================================================+ | r-bioc-rsamtools 1.24.0-1 (amd64) Mon, 29 Aug 2016 16:23:09 +0000 | +==============================================================================+ Package: r-bioc-rsamtools Version: 1.24.0-1 Source Version: 1.24.0-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-44723ddf-dd77-441e-86d6-f08c395d9c77' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang ---------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.8 + echo 'Install of clang-3.8' Install of clang-3.8 + apt-get update Get:1 http://127.0.0.1:9999/debian unstable InRelease [209 kB] Get:2 http://127.0.0.1:9999/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian unstable/main Translation-en [5451 kB] Get:5 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0319.00.pdiff [16.7 kB] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0916.07.pdiff [5442 B] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0916.07.pdiff [5442 B] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0319.00.pdiff [13.2 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0916.07.pdiff [3300 B] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0916.07.pdiff [3300 B] Fetched 5755 kB in 2s (2029 kB/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges + apt-get install --yes --no-install-recommends --force-yes clang-3.8 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbsd0 libclang-common-3.8-dev libclang1-3.8 libedit2 libffi6 libllvm3.8 libobjc-6-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.8-doc Recommended packages: llvm-3.8-dev python The following NEW packages will be installed: clang-3.8 libbsd0 libclang-common-3.8-dev libclang1-3.8 libedit2 libffi6 libllvm3.8 libobjc-6-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 1 not upgraded. Need to get 38.3 MB of archives. After this operation, 162 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20150325-1+b1 [85.2 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libffi6 amd64 3.2.1-4 [20.4 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm3.8 amd64 1:3.8.1-9 [10.3 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 6.2.0-1 [110 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.2.0-1 [394 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-3.8 amd64 1:3.8.1-9 [4188 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-3.8-dev amd64 1:3.8.1-9 [1477 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 clang-3.8 amd64 1:3.8.1-9 [21.6 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.3 MB in 1s (19.7 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 ... 9446 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.8.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.3-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../1-libedit2_3.1-20150325-1+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20150325-1+b1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../2-libffi6_3.2.1-4_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-4) ... Selecting previously unselected package libllvm3.8:amd64. Preparing to unpack .../3-libllvm3.8_1%3a3.8.1-9_amd64.deb ... Unpacking libllvm3.8:amd64 (1:3.8.1-9) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../4-libobjc4_6.2.0-1_amd64.deb ... Unpacking libobjc4:amd64 (6.2.0-1) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../5-libobjc-6-dev_6.2.0-1_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.2.0-1) ... Selecting previously unselected package libclang1-3.8:amd64. Preparing to unpack .../6-libclang1-3.8_1%3a3.8.1-9_amd64.deb ... Unpacking libclang1-3.8:amd64 (1:3.8.1-9) ... Selecting previously unselected package libclang-common-3.8-dev. Preparing to unpack .../7-libclang-common-3.8-dev_1%3a3.8.1-9_amd64.deb ... Unpacking libclang-common-3.8-dev (1:3.8.1-9) ... Selecting previously unselected package clang-3.8. Preparing to unpack .../8-clang-3.8_1%3a3.8.1-9_amd64.deb ... Unpacking clang-3.8 (1:3.8.1-9) ... Setting up libobjc4:amd64 (6.2.0-1) ... Setting up libbsd0:amd64 (0.8.3-1) ... Processing triggers for libc-bin (2.23-5) ... Setting up libobjc-6-dev:amd64 (6.2.0-1) ... Setting up libffi6:amd64 (3.2.1-4) ... Setting up libedit2:amd64 (3.1-20150325-1+b1) ... Setting up libllvm3.8:amd64 (1:3.8.1-9) ... Setting up libclang-common-3.8-dev (1:3.8.1-9) ... Setting up libclang1-3.8:amd64 (1:3.8.1-9) ... Setting up clang-3.8 (1:3.8.1-9) ... Processing triggers for libc-bin (2.23-5) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. W: No sandbox user '_apt' on the system, can not drop privileges + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.8 g++-4.6 + ln -s clang-3.8 gcc-4.6 + ln -s clang-3.8 cpp-4.6 + ln -s clang-3.8 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.8 g++-4.7 + ln -s clang-3.8 gcc-4.7 + ln -s clang-3.8 cpp-4.7 + ln -s clang-3.8 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in 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 + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in 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 + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.8 g++-4.8 + ln -s clang-3.8 gcc-4.8 + ln -s clang-3.8 cpp-4.8 + ln -s clang-3.8 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.8 g++-4.9 + ln -s clang-3.8 gcc-4.9 + ln -s clang-3.8 cpp-4.9 + ln -s clang-3.8 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in 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 + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in 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 + for VERSION in '$VERSIONS' + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.8 g++-5 + ln -s clang-3.8 gcc-5 + ln -s clang-3.8 cpp-5 + ln -s clang-3.8 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-3.8 g++-6 + ln -s clang-3.8 gcc-6 + ln -s clang-3.8 cpp-6 + ln -s clang-3.8 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + cd - /build/r-bioc-rsamtools-kflEPd + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: linux-libc-dev 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1158 kB of archives. After this operation, 60.4 kB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 linux-libc-dev amd64 4.7.2-1 [1158 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1158 kB in 0s (69.9 MB/s) (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 ... 9769 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_4.7.2-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (4.7.2-1) over (4.6.4-1) ... Setting up linux-libc-dev:amd64 (4.7.2-1) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | 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 2994 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main r-bioc-rsamtools 1.24.0-1 (dsc) [2232 B] Get:2 http://127.0.0.1:9999/debian unstable/main r-bioc-rsamtools 1.24.0-1 (tar) [2985 kB] Get:3 http://127.0.0.1:9999/debian unstable/main r-bioc-rsamtools 1.24.0-1 (diff) [6892 B] Fetched 2994 kB in 0s (15.3 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-kflEPd/r-bioc-rsamtools-1.24.0' with '<>' I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-kflEPd' 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-d7Qp7a/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-d7Qp7a/apt_archive ./ InRelease Get:2 copy:/<>/resolver-d7Qp7a/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-d7Qp7a/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-d7Qp7a/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-d7Qp7a/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (0 B/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges 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 770 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-d7Qp7a/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 9775 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) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9), cdbs, 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 (>= 9), cdbs, 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-T7luyO/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-r-bioc-rsamtools-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-T7luyO/apt_archive ./ InRelease Get:2 copy:/<>/resolver-T7luyO/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-T7luyO/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-T7luyO/apt_archive ./ Sources [415 B] Get:5 copy:/<>/resolver-T7luyO/apt_archive ./ Packages [504 B] Fetched 1876 B in 0s (0 B/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges 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 debhelper dh-autoreconf 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 libgnutls30 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed4 libice6 libicu-dev libicu57 libidn11 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libncurses5-dev libnettle6 libnghttp2-14 libp11-kit0 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 libreadline-dev libreadline6 libreadline6-dev librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsqlite3-0 libssh2-1 libssl1.0.2 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6 libtool libunistring0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler lsb-base m4 man-db openssl po-debconf r-base-core r-base-dev r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors r-bioc-xvector r-cran-base64enc r-cran-batchjobs r-cran-bbmisc r-cran-bitops r-cran-brew r-cran-checkmate r-cran-codetools r-cran-dbi r-cran-digest r-cran-fail r-cran-foreach r-cran-futile.logger r-cran-futile.options r-cran-iterators r-cran-lambda.r r-cran-littler r-cran-magrittr r-cran-pkgkitten r-cran-plyr r-cran-rcpp r-cran-rsqlite r-cran-sendmailr r-cran-snow r-cran-stringi r-cran-stringr readline-common tzdata ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation devscripts 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-man liblapack-doc gnutls-bin krb5-doc krb5-user icu-doc liblzma-doc ncurses-doc readline-doc tcl8.6 tk8.6 libtool-doc gcj-jdk 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-mpi r-cran-rmysql r-cran-getopt r-cran-inline r-cran-runit r-cran-rmpi r-cran-rsprng r-cran-rlecuyer gvfs-bin Recommended packages: curl | wget | lynx-cur bzip2-doc libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libpng-tools libsasl2-modules libltdl-dev xml-core libmail-sendmail-perl r-recommended r-doc-html r-cran-doparallel r-bioc-rsamtools r-cran-mass r-cran-crayon r-cran-domc r-cran-abind 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 debhelper dh-autoreconf 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 libgnutls30 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed4 libice6 libicu-dev libicu57 libidn11 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libncurses5-dev libnettle6 libnghttp2-14 libp11-kit0 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 libreadline-dev libreadline6 libreadline6-dev librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsqlite3-0 libssh2-1 libssl1.0.2 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6 libtool libunistring0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler lsb-base m4 man-db openssl po-debconf r-base-core r-base-dev r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors r-bioc-xvector r-cran-base64enc r-cran-batchjobs r-cran-bbmisc r-cran-bitops r-cran-brew r-cran-checkmate r-cran-codetools r-cran-dbi r-cran-digest r-cran-fail r-cran-foreach r-cran-futile.logger r-cran-futile.options r-cran-iterators r-cran-lambda.r r-cran-littler r-cran-magrittr r-cran-pkgkitten r-cran-plyr r-cran-rcpp r-cran-rsqlite r-cran-sendmailr r-cran-snow r-cran-stringi r-cran-stringr readline-common sbuild-build-depends-r-bioc-rsamtools-dummy tzdata ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 162 newly installed, 0 to remove and 0 not upgraded. Need to get 157 MB of archives. After this operation, 486 MB of additional disk space will be used. Get:1 copy:/<>/resolver-T7luyO/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [848 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-8 [1162 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.10 [184 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 2.7.5-1 [1003 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.0-1 [82.0 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libpng16-16 amd64 1.6.24-2 [279 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libfreetype6 amd64 2.6.3-3+b1 [437 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 2.11.0-6.7 [271 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libfontconfig1 amd64 2.11.0-6.7 [331 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 fontconfig amd64 2.11.0-6.7 [403 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 lsb-base all 9.20160629 [27.6 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 x11-common all 1:7.7+16 [251 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libice6 amd64 2:1.0.9-1+b1 [58.8 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libpaper1 amd64 1.1.24+nmu4 [22.0 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libpcrecpp0v5 amd64 2:8.39-2 [151 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libsm6 amd64 2:1.2.2-1+b1 [33.6 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-1.1 [26.2 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libxcb1 amd64 1.11.1-1.1 [45.3 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libx11-data all 2:1.6.3-1 [128 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libx11-6 amd64 2:1.6.3-1 [742 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1 [52.7 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libxrender1 amd64 1:0.9.9-2 [31.8 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libxft2 amd64 2.3.2-1 [55.4 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libxss1 amd64 1:1.2.2-1 [17.5 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libjbig0 amd64 2.1-3.1 [30.7 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 tzdata all 2016f-1 [219 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 readline-common all 6.3-8 [57.7 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libreadline6 amd64 6.3-8+b4 [142 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2h-1 [1287 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.28-4 [210 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.28-4 [109 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.28-4 [62.9 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-1 [121 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 libnettle6 amd64 3.2-1 [191 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 libhogweed4 amd64 3.2-1 [136 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 libidn11 amd64 1.33-1 [115 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libp11-kit0 amd64 0.23.2-5 [111 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libtasn1-6 amd64 4.9-4 [50.0 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 libgnutls30 amd64 3.5.3-3 [801 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.14.3+dfsg-1 [61.0 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.14.3+dfsg-1 [115 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.14.3+dfsg-1 [311 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.14.3+dfsg-1 [154 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-15 [66.9 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-15 [103 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2+b2 [222 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libsqlite3-0 amd64 3.14.1-1 [559 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-3 [7676 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-1+b1 [919 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.17-5 [255 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20160430.1 [72.6 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15-4 [735 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-1 [433 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 openssl amd64 1.0.2h-1 [681 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 ca-certificates all 20160104 [200 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 cdbs all 0.4.143 [80.9 kB] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.48.1-3 [2707 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.11-1 [143 kB] Get:66 http://127.0.0.1:9999/debian unstable/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:67 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-1 [1493 kB] Get:68 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:69 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.19 [249 kB] Get:70 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:71 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.023-2 [13.4 kB] Get:72 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:73 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.023-2 [8202 B] Get:74 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:75 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 12 [15.8 kB] Get:76 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 9.20160814 [800 kB] Get:77 http://127.0.0.1:9999/debian unstable/main amd64 libgfortran3 amd64 6.2.0-1 [264 kB] Get:78 http://127.0.0.1:9999/debian unstable/main amd64 libgfortran-6-dev amd64 6.2.0-1 [295 kB] Get:79 http://127.0.0.1:9999/debian unstable/main amd64 gfortran-6 amd64 6.2.0-1 [31.7 MB] Get:80 http://127.0.0.1:9999/debian unstable/main amd64 gfortran amd64 4:6.1.1-1 [1352 B] Get:81 http://127.0.0.1:9999/debian unstable/main amd64 icu-devtools amd64 57.1-3 [172 kB] Get:82 http://127.0.0.1:9999/debian unstable/main amd64 libbam-dev amd64 0.1.19-2 [123 kB] Get:83 http://127.0.0.1:9999/debian unstable/main amd64 libblas-common amd64 3.6.1-2 [13.9 kB] Get:84 http://127.0.0.1:9999/debian unstable/main amd64 libblas3 amd64 3.6.1-2 [157 kB] Get:85 http://127.0.0.1:9999/debian unstable/main amd64 libblas-dev amd64 3.6.1-2 [18.9 kB] Get:86 http://127.0.0.1:9999/debian unstable/main amd64 libbz2-dev amd64 1.0.6-8 [29.0 kB] Get:87 http://127.0.0.1:9999/debian unstable/main amd64 libpixman-1-0 amd64 0.33.6-1 [532 kB] Get:88 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-render0 amd64 1.11.1-1.1 [17.5 kB] Get:89 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-shm0 amd64 1.11.1-1.1 [11.6 kB] Get:90 http://127.0.0.1:9999/debian unstable/main amd64 libcairo2 amd64 1.14.6-1+b1 [767 kB] Get:91 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.13.0-1 [79.4 kB] Get:92 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1 [60.0 kB] Get:93 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.7.0-1 [138 kB] Get:94 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3 amd64 7.50.1-1 [280 kB] Get:95 http://127.0.0.1:9999/debian unstable/main amd64 libdatrie1 amd64 0.2.10-2 [35.8 kB] Get:96 http://127.0.0.1:9999/debian unstable/main amd64 libgraphite2-3 amd64 1.3.8-1 [76.4 kB] Get:97 http://127.0.0.1:9999/debian unstable/main amd64 libharfbuzz0b amd64 1.2.7-1+b1 [612 kB] Get:98 http://127.0.0.1:9999/debian unstable/main amd64 libicu-dev amd64 57.1-3 [16.3 MB] Get:99 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.0-1 [132 kB] Get:100 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:1.5.0-1 [210 kB] Get:101 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg-dev all 1:1.5.0-1 [54.8 kB] Get:102 http://127.0.0.1:9999/debian unstable/main amd64 liblapack3 amd64 3.6.1-2 [1963 kB] Get:103 http://127.0.0.1:9999/debian unstable/main amd64 liblapack-dev amd64 3.6.1-2 [1977 kB] Get:104 http://127.0.0.1:9999/debian unstable/main amd64 liblzma-dev amd64 5.1.1alpha+20120614-2.1 [255 kB] Get:105 http://127.0.0.1:9999/debian unstable/main amd64 libtinfo-dev amd64 6.0+20160625-1 [77.1 kB] Get:106 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5-dev amd64 6.0+20160625-1 [174 kB] Get:107 http://127.0.0.1:9999/debian unstable/main amd64 libthai-data all 0.1.25-1 [165 kB] Get:108 http://127.0.0.1:9999/debian unstable/main amd64 libthai0 amd64 0.1.25-1 [51.6 kB] Get:109 http://127.0.0.1:9999/debian unstable/main amd64 libpango-1.0-0 amd64 1.40.1-1 [311 kB] Get:110 http://127.0.0.1:9999/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.40.1-1 [236 kB] Get:111 http://127.0.0.1:9999/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.40.1-1 [223 kB] Get:112 http://127.0.0.1:9999/debian unstable/main amd64 libpaper-utils amd64 1.1.24+nmu4 [17.5 kB] Get:113 http://127.0.0.1:9999/debian unstable/main amd64 libpcre16-3 amd64 2:8.39-2 [258 kB] Get:114 http://127.0.0.1:9999/debian unstable/main amd64 libpcre32-3 amd64 2:8.39-2 [248 kB] Get:115 http://127.0.0.1:9999/debian unstable/main amd64 libpcre3-dev amd64 2:8.39-2 [645 kB] Get:116 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB] Get:117 http://127.0.0.1:9999/debian unstable/main amd64 libpng-dev amd64 1.6.24-2 [247 kB] Get:118 http://127.0.0.1:9999/debian unstable/main amd64 libreadline6-dev amd64 6.3-8+b4 [123 kB] Get:119 http://127.0.0.1:9999/debian unstable/main amd64 libreadline-dev amd64 6.3-8+b4 [956 B] Get:120 http://127.0.0.1:9999/debian unstable/main amd64 libtcl8.6 amd64 8.6.6+dfsg-1 [984 kB] Get:121 http://127.0.0.1:9999/debian unstable/main amd64 libtiff5 amd64 4.0.6-2 [222 kB] Get:122 http://127.0.0.1:9999/debian unstable/main amd64 libtk8.6 amd64 8.6.6-1 [752 kB] Get:123 http://127.0.0.1:9999/debian unstable/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:124 http://127.0.0.1:9999/debian unstable/main amd64 zip amd64 3.0-11 [229 kB] Get:125 http://127.0.0.1:9999/debian unstable/main amd64 unzip amd64 6.0-20 [161 kB] Get:126 http://127.0.0.1:9999/debian unstable/main amd64 xdg-utils all 1.1.1-1 [71.1 kB] Get:127 http://127.0.0.1:9999/debian unstable/main amd64 r-base-core amd64 3.3.1-1+b1 [21.0 MB] Get:128 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-littler amd64 0.3.1-1 [59.1 kB] Get:129 http://127.0.0.1:9999/debian unstable/main amd64 littler all 0.3.1-1 [11.7 kB] Get:130 http://127.0.0.1:9999/debian unstable/main amd64 r-base-dev all 3.3.1-1 [4306 B] Get:131 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-biocgenerics all 0.18.0-1 [475 kB] Get:132 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-checkmate amd64 1.6.0-1 [270 kB] Get:133 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-bbmisc amd64 1.9-2 [279 kB] Get:134 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-brew amd64 1.0-6-1 [61.4 kB] Get:135 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-digest amd64 0.6.10-1 [110 kB] Get:136 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-dbi amd64 0.5-1 [331 kB] Get:137 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-rsqlite amd64 1.0.0-2 [305 kB] Get:138 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-pkgkitten all 0.1.3-1 [18.3 kB] Get:139 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-rcpp amd64 0.12.6-1 [2166 kB] Get:140 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-plyr amd64 1.8.3-2 [730 kB] Get:141 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-magrittr amd64 1.5-3 [147 kB] Get:142 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-stringi amd64 1.0-1-1+b1 [657 kB] Get:143 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-stringr all 1.0.0-1 [76.6 kB] Get:144 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-base64enc amd64 0.1-2-1 [19.9 kB] Get:145 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-sendmailr amd64 1.2-1-1 [29.0 kB] Get:146 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-fail amd64 1.3-1 [43.1 kB] Get:147 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-batchjobs amd64 1.6-1 [422 kB] Get:148 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-codetools all 0.2-14-2 [46.4 kB] Get:149 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-iterators all 1.0.8-1 [306 kB] Get:150 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-foreach all 1.4.3-1 [371 kB] Get:151 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-lambda.r all 1.1.7-3 [66.4 kB] Get:152 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-futile.options all 1.0.0-2 [15.4 kB] Get:153 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-futile.logger all 1.4.1-3 [84.3 kB] Get:154 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-snow all 1:0.4.1-2 [64.9 kB] Get:155 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-biocparallel all 1.6.0-1 [626 kB] Get:156 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-s4vectors amd64 0.10.2-1 [925 kB] Get:157 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-iranges amd64 2.6.1-1 [1424 kB] Get:158 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-xvector amd64 0.12.0-2 [334 kB] Get:159 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-biostrings amd64 2.40.2-1 [13.5 MB] Get:160 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-genomeinfodb all 1.8.0-1 [19.1 MB] Get:161 http://127.0.0.1:9999/debian unstable/main amd64 r-bioc-genomicranges amd64 1.24.0-1 [1302 kB] Get:162 http://127.0.0.1:9999/debian unstable/main amd64 r-cran-bitops amd64 1.0-6-1 [22.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 157 MB in 19s (8212 kB/s) Selecting previously unselected package groff-base. 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Current default time zone: 'Etc/UTC' Local time is now: Mon Aug 29 16:28:07 UTC 2016. Universal Time is now: Mon Aug 29 16:28:07 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgfortran3:amd64 (6.2.0-1) ... Setting up groff-base (1.22.3-8) ... Setting up libglib2.0-0:amd64 (2.48.1-3) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-15) ... Setting up libgfortran-6-dev:amd64 (6.2.0-1) ... Setting up unzip (6.0-20) ... Setting up libsasl2-2:amd64 (2.1.26.dfsg1-15) ... Setting up libtinfo-dev:amd64 (6.0+20160625-1) ... Setting up libdatrie1:amd64 (0.2.10-2) ... Setting up libtiff5:amd64 (4.0.6-2) ... Setting up gettext-base (0.19.8.1-1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up m4 (1.4.17-5) ... Setting up libicu57:amd64 (57.1-3) ... Setting up ucf (3.0036) ... Setting up libxml2:amd64 (2.9.4+dfsg1-1+b1) ... Setting up zip (3.0-11) ... Setting up libfreetype6:amd64 (2.6.3-3+b1) ... 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Setting up libpcre32-3:amd64 (2:8.39-2) ... Setting up icu-devtools (57.1-3) ... Setting up libpcre16-3:amd64 (2:8.39-2) ... Setting up libtcl8.6:amd64 (8.6.6+dfsg-1) ... Setting up libthai-data (0.1.25-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:1.5.0-1) ... Setting up liblzma-dev:amd64 (5.1.1alpha+20120614-2.1) ... Setting up libxdmcp6:amd64 (1:1.1.2-1.1) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.10) ... 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+16) ... 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 (20160104) ... Setting up libx11-data (2:1.6.3-1) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-1) ... Setting up libidn11:amd64 (1.33-1) ... Setting up libreadline6:amd64 (6.3-8+b4) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Setting up libfile-stripnondeterminism-perl (0.023-2) ... Setting up libpaper1:amd64 (1.1.24+nmu4) ... Creating config file /etc/papersize with new version Setting up gfortran-6 (6.2.0-1) ... Setting up libpaper-utils (1.1.24+nmu4) ... Setting up libpcre3-dev:amd64 (2:8.39-2) ... Setting up fontconfig-config (2.11.0-6.7) ... Setting up gettext (0.19.8.1-1) ... Setting up liblapack3 (3.6.1-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libgnutls30:amd64 (3.5.3-3) ... Setting up libreadline6-dev:amd64 (6.3-8+b4) ... Setting up libharfbuzz0b:amd64 (1.2.7-1+b1) ... Setting up autoconf (2.69-10) ... Setting up libthai0:amd64 (0.1.25-1) ... 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Setting up gfortran (4:6.1.1-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libfontconfig1:amd64 (2.11.0-6.7) ... Setting up libsm6:amd64 (2:1.2.2-1+b1) ... Setting up libk5crypto3:amd64 (1.14.3+dfsg-1) ... Setting up libxcb-render0:amd64 (1.11.1-1.1) ... Setting up po-debconf (1.0.19) ... Setting up libblas-dev (3.6.1-2) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libx11-6:amd64 (2:1.6.3-1) ... Setting up libxcb-shm0:amd64 (1.11.1-1.1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.9-2) ... Setting up libkrb5-3:amd64 (1.14.3+dfsg-1) ... Setting up libxft2:amd64 (2.3.2-1) ... Setting up fontconfig (2.11.0-6.7) ... Regenerating fonts cache... done. Setting up liblapack-dev (3.6.1-2) ... 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) ... Setting up libxss1:amd64 (1:1.2.2-1) ... Setting up libgssapi-krb5-2:amd64 (1.14.3+dfsg-1) ... Setting up libpango-1.0-0:amd64 (1.40.1-1) ... Setting up libcairo2:amd64 (1.14.6-1+b1) ... Setting up libcurl3:amd64 (7.50.1-1) ... Setting up libtk8.6:amd64 (8.6.6-1) ... Setting up libpangoft2-1.0-0:amd64 (1.40.1-1) ... Setting up libpangocairo-1.0-0:amd64 (1.40.1-1) ... Setting up r-base-core (3.3.1-1+b1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-littler (0.3.1-1) ... Setting up littler (0.3.1-1) ... Setting up r-base-dev (3.3.1-1) ... Setting up r-bioc-biocgenerics (0.18.0-1) ... Setting up r-cran-brew (1.0-6-1) ... Setting up r-cran-bitops (1.0-6-1) ... Setting up r-cran-dbi (0.5-1) ... Setting up r-cran-stringi (1.0-1-1+b1) ... Setting up r-cran-pkgkitten (0.1.3-1) ... Setting up r-cran-futile.options (1.0.0-2) ... Setting up r-cran-rcpp (0.12.6-1) ... Setting up r-cran-plyr (1.8.3-2) ... Setting up r-cran-digest (0.6.10-1) ... Setting up r-cran-rsqlite (1.0.0-2) ... Setting up r-cran-magrittr (1.5-3) ... Setting up r-cran-lambda.r (1.1.7-3) ... Setting up r-cran-snow (1:0.4.1-2) ... Setting up r-bioc-s4vectors (0.10.2-1) ... Setting up r-cran-codetools (0.2-14-2) ... Setting up r-cran-iterators (1.0.8-1) ... Setting up r-cran-base64enc (0.1-2-1) ... Setting up r-cran-checkmate (1.6.0-1) ... Setting up r-cran-stringr (1.0.0-1) ... Setting up r-cran-foreach (1.4.3-1) ... Setting up r-cran-sendmailr (1.2-1-1) ... Setting up r-cran-futile.logger (1.4.1-3) ... Setting up r-bioc-iranges (2.6.1-1) ... Setting up r-cran-bbmisc (1.9-2) ... Setting up r-bioc-genomeinfodb (1.8.0-1) ... Setting up r-bioc-xvector (0.12.0-2) ... Setting up r-cran-fail (1.3-1) ... Setting up r-bioc-biostrings (2.40.2-1) ... Setting up r-bioc-genomicranges (1.24.0-1) ... Setting up r-cran-batchjobs (1.6-1) ... Setting up r-bioc-biocparallel (1.6.0-1) ... Setting up dh-autoreconf (12) ... Setting up debhelper (9.20160814) ... Setting up sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.023-2) ... Processing triggers for libc-bin (2.23-5) ... Processing triggers for ca-certificates (20160104) ... Updating certificates in /etc/ssl/certs... 173 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.27-6 dpkg-dev_1.18.10 g++-6_6.2.0-1 gcc-6_6.2.0-1 libc6-dev_2.23-5 libstdc++-6-dev_6.2.0-1 libstdc++6_6.2.0-1 linux-libc-dev_4.7.2-1 Package versions: adduser_3.115 apt_1.3~rc2 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6 base-passwd_3.5.40 bash_4.3-15 binutils_2.27-6 bsdmainutils_9.0.10 bsdutils_1:2.28.1-1 build-essential_12.2 bzip2_1.0.6-8 ca-certificates_20160104 cdbs_0.4.143 clang-3.8_1:3.8.1-9 coreutils_8.25-2 cpp_4:6.1.1-1 cpp-6_6.2.0-1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_9.20160814 debian-archive-keyring_2014.3 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.023-2 diffutils_1:3.3-3 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 eatmydata_105-3 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fontconfig_2.11.0-6.7 fontconfig-config_2.11.0-6.7 fonts-dejavu-core_2.37-1 g++_4:6.1.1-1 g++-6_6.2.0-1 gcc_4:6.1.1-1 gcc-6_6.2.0-1 gcc-6-base_6.2.0-1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gfortran_4:6.1.1-1 gfortran-6_6.2.0-1 gpgv_2.1.14-5 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-3 init-system-helpers_1.42 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapt-pkg5.0_1.3~rc2 libarchive-zip-perl_1.59-1 libasan3_6.2.0-1 libatomic1_6.2.0-1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1 libaudit1_1:2.6.6-1 libbam-dev_0.1.19-2 libblas-common_3.6.1-2 libblas-dev_3.6.1-2 libblas3_3.6.1-2 libblkid1_2.28.1-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.23-5 libc-dev-bin_2.23-5 libc6_2.23-5 libc6-dev_2.23-5 libcairo2_1.14.6-1+b1 libcap-ng0_0.7.7-3 libcc1-0_6.2.0-1 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libxft2_2.3.2-1 libxml2_2.9.4+dfsg1-1+b1 libxrender1_1:0.9.9-2 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 linux-libc-dev_4.7.2-1 littler_0.3.1-1 login_1:4.2-3.1 lsb-base_9.20160629 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17 mount_2.28.1-1 multiarch-support_2.23-5 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 openssl_1.0.2h-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 po-debconf_1.0.19 r-base-core_3.3.1-1+b1 r-base-dev_3.3.1-1 r-bioc-biocgenerics_0.18.0-1 r-bioc-biocparallel_1.6.0-1 r-bioc-biostrings_2.40.2-1 r-bioc-genomeinfodb_1.8.0-1 r-bioc-genomicranges_1.24.0-1 r-bioc-iranges_2.6.1-1 r-bioc-s4vectors_0.10.2-1 r-bioc-xvector_0.12.0-2 r-cran-base64enc_0.1-2-1 r-cran-batchjobs_1.6-1 r-cran-bbmisc_1.9-2 r-cran-bitops_1.0-6-1 r-cran-brew_1.0-6-1 r-cran-checkmate_1.6.0-1 r-cran-codetools_0.2-14-2 r-cran-dbi_0.5-1 r-cran-digest_0.6.10-1 r-cran-fail_1.3-1 r-cran-foreach_1.4.3-1 r-cran-futile.logger_1.4.1-3 r-cran-futile.options_1.0.0-2 r-cran-iterators_1.0.8-1 r-cran-lambda.r_1.1.7-3 r-cran-littler_0.3.1-1 r-cran-magrittr_1.5-3 r-cran-pkgkitten_0.1.3-1 r-cran-plyr_1.8.3-2 r-cran-rcpp_0.12.6-1 r-cran-rsqlite_1.0.0-2 r-cran-sendmailr_1.2-1-1 r-cran-snow_1:0.4.1-2 r-cran-stringi_1.0-1-1+b1 r-cran-stringr_1.0.0-1 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rsamtools-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016f-1 ucf_3.0036 unzip_6.0-20 util-linux_2.28.1-1 x11-common_1:7.7+16 xdg-utils_1.1.1-1 xz-utils_5.1.1alpha+20120614-2.1 zip_3.0-11 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1 +------------------------------------------------------------------------------+ | 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 9 06:25:57 2016 UTC using RSA key ID gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./r-bioc-rsamtools_1.24.0-1.dsc dpkg-source: info: extracting r-bioc-rsamtools in /<> dpkg-source: info: unpacking r-bioc-rsamtools_1.24.0.orig.tar.gz dpkg-source: info: unpacking r-bioc-rsamtools_1.24.0-1.debian.tar.xz dpkg-source: info: applying use_debian_packaged_zlib.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-44723ddf-dd77-441e-86d6-f08c395d9c77 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 1.24.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build r-bioc-rsamtools-1.24.0 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean test -x debian/rules dh_clean if test -d src; then \ find src -regex ".*\.o" | \ xargs --no-run-if-empty -r rm; \ fi rm -f config.log config.status dh_clean rm -f src/*.a debian/rules build-arch test -x debian/rules mkdir -p "." fakeroot debian/rules binary-arch test -x debian/rules dh_testroot dh_prep dh_installdirs -A mkdir -p "." dh_installdirs usr/lib/R/site-library echo "R:Depends=r-base-core (>= 3.3.1-1), r-api-3" >> debian/r-bioc-rsamtools.substvars if test -f /usr/bin/xvfb-run; then \ xvfb-run -a \ R CMD INSTALL -l /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean \ . \ "--built-timestamp=\"Sun, 08 May 2016 21:06:24 +0200\"" \ ; \ else \ R CMD INSTALL -l /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library \ --clean . \ "--built-timestamp=\"Sun, 08 May 2016 21:06:24 +0200\"" \ ; \ fi * 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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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/x86_64-linux-gnu/zconf.h:395: In file included from /usr/lib/llvm-3.8/bin/../lib/clang/3.8.1/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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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/x86_64-linux-gnu/zconf.h:395: In file included from /usr/lib/llvm-3.8/bin/../lib/clang/3.8.1/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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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-NmmxMb/r-base-3.3.1=. -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 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' /usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed make: *** [R_any_arch] Error 1 dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2016-08-29T16:28:30Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 0 Build-Time: 18 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 172 Job: r-bioc-rsamtools_1.24.0-1 Machine Architecture: amd64 Package: r-bioc-rsamtools Package-Time: 321 Source-Version: 1.24.0-1 Space: 0 Status: failed Version: 1.24.0-1 -------------------------------------------------------------------------------- Finished at 2016-08-29T16:28:30Z Build needed 00:00:00, 0k disc space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 321.793716059s DC-Time-Estimation: 321.793716059 versus expected 520 (r/m: 0.6159420586841398 ; m: 321.793716059)