r-bioc-shortread →
1.22.0-1 →
armhf → 2014-07-30 06:15:13
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-03
╔══════════════════════════════════════════════════════════════════════════════╗
║ r-bioc-shortread 1.22.0-1 (armhf) 30 Jul 2014 05:58 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: r-bioc-shortread
Version: 1.22.0-1
Source Version: 1.22.0-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-wUh2JU/r-bioc-shortread-1.22.0' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-wUh2JU' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-ca8068ab-2fc4-4033-af2e-db83a3f9f696' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7433 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8431 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'r-bioc-shortread' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-shortread/trunk/
Need to get 5159 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main r-bioc-shortread 1.22.0-1 (dsc) [2330 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main r-bioc-shortread 1.22.0-1 (tar) [5152 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main r-bioc-shortread 1.22.0-1 (diff) [4860 B]
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-OK6QAo/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 42 not upgraded.
Need to get 0 B/816 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11827 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), cdbs, r-base-dev, r-cran-latticeextra, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-biocparallel, r-bioc-genomicalignments, r-bioc-genomicranges, r-bioc-iranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-xvector, r-cran-hwriter
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), cdbs, r-base-dev, r-cran-latticeextra, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-biocparallel, r-bioc-genomicalignments, r-bioc-genomicranges, r-bioc-iranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-xvector, r-cran-hwriter
dpkg-deb: building package `sbuild-build-depends-r-bioc-shortread-dummy' in `/«BUILDDIR»/resolver-6IxXxO/apt_archive/sbuild-build-depends-r-bioc-shortread-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install r-bioc-shortread build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils cdbs cpp cpp-4.9 debhelper file fontconfig fontconfig-config
fonts-dejavu-core g++-4.9 gcc gcc-4.9 gcc-4.9-base gettext gettext-base
gfortran gfortran-4.9 groff-base intltool-debian libasan1 libasprintf0c2
libatomic1 libblas-dev libblas3 libbz2-dev libcairo2 libcroco3 libdatrie1
libdrm2 libexpat1 libffi6 libfontconfig1 libfreetype6 libgcc-4.9-dev libgcc1
libgfortran-4.9-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0
libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg8 libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libmagic1 libncurses5-dev
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0
libpng12-0 libpng12-dev libreadline-dev libreadline6-dev libsm6 libsqlite3-0
libstdc++-4.9-dev libstdc++6 libtcl8.5 libthai-data libthai0 libtiff5
libtinfo-dev libtk8.5 libubsan0 libunistring0 libx11-6 libx11-data
libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1 libxdmcp6
libxext6 libxfixes3 libxft2 libxml2 libxrender1 libxshmfence1 libxss1 libxt6
libxxf86vm1 littler man-db po-debconf r-base-core r-base-dev r-bioc-biobase
r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-bsgenome
r-bioc-genomeinfodb r-bioc-genomicalignments r-bioc-genomicranges
r-bioc-iranges r-bioc-rsamtools r-bioc-xvector r-cran-base64enc
r-cran-batchjobs r-cran-bbmisc r-cran-bitops r-cran-brew r-cran-codetools
r-cran-dbi r-cran-digest r-cran-fail r-cran-foreach r-cran-hwriter
r-cran-iterators r-cran-lattice r-cran-latticeextra r-cran-plyr
r-cran-rcolorbrewer r-cran-rcpp r-cran-rsqlite r-cran-sendmailr
r-cran-stringr ucf unzip x11-common xdg-utils zip zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation devscripts cpp-doc gcc-4.9-locales dh-make
gcc-4.9-doc libstdc++6-4.9-dbg gcc-multilib manpages-dev autoconf automake
libtool flex bison gdb gcc-doc libgcc1-dbg libgomp1-dbg libitm1-dbg
libatomic1-dbg libasan1-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg
libvtv0-dbg libcilkrts5-dbg libquadmath-dbg gettext-doc gfortran-doc
gfortran-4.9-doc libgfortran3-dbg groff liblzma-doc ncurses-doc ttf-baekmuk
ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp
ttf-arphic-bkai00mp libstdc++-4.9-doc tcl8.5 tk8.5 r-cran-getopt less
www-browser libmail-box-perl 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-rmysql
r-cran-inline r-cran-runit gvfs-bin
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libgl1-mesa-dri libglib2.0-data shared-mime-info xml-core
libmail-sendmail-perl r-recommended r-doc-html r-cran-doparallel
r-bioc-shortread r-cran-domc libfile-mimeinfo-perl libnet-dbus-perl
libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base gfortran gfortran-4.9 groff-base
intltool-debian libasprintf0c2 libblas-dev libblas3 libbz2-dev libcairo2
libcroco3 libdatrie1 libdrm2 libexpat1 libffi6 libfontconfig1 libfreetype6
libgfortran-4.9-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0
libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg8 libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libmagic1 libncurses5-dev
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-0
libpng12-dev libreadline-dev libreadline6-dev libsm6 libsqlite3-0 libtcl8.5
libthai-data libthai0 libtiff5 libtinfo-dev libtk8.5 libunistring0 libx11-6
libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0
libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1
libxdmcp6 libxext6 libxfixes3 libxft2 libxml2 libxrender1 libxshmfence1
libxss1 libxt6 libxxf86vm1 littler man-db po-debconf r-base-core r-base-dev
r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings
r-bioc-bsgenome r-bioc-genomeinfodb r-bioc-genomicalignments
r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-xvector
r-cran-base64enc r-cran-batchjobs r-cran-bbmisc r-cran-bitops r-cran-brew
r-cran-codetools r-cran-dbi r-cran-digest r-cran-fail r-cran-foreach
r-cran-hwriter r-cran-iterators r-cran-lattice r-cran-latticeextra
r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-rsqlite r-cran-sendmailr
r-cran-stringr sbuild-build-depends-r-bioc-shortread-dummy ucf unzip
x11-common xdg-utils zip zlib1g-dev
The following packages will be upgraded:
cpp cpp-4.9 g++-4.9 gcc gcc-4.9 gcc-4.9-base libasan1 libatomic1
libgcc-4.9-dev libgcc1 libgomp1 libpcre3 libstdc++-4.9-dev libstdc++6
libubsan0
15 upgraded, 129 newly installed, 0 to remove and 27 not upgraded.
Need to get 87.5 MB/87.5 MB of archives.
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Get:87 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140613 [692 kB]
Get:88 http://172.17.0.1/private/ jessie-staging/main gcc armhf 4:4.9.1-1 [5134 B]
Get:89 http://172.17.0.1/private/ jessie-staging/main libgfortran-4.9-dev armhf 4.9.1-1 [181 kB]
Get:90 http://172.17.0.1/private/ jessie-staging/main gfortran-4.9 armhf 4.9.1-1 [4509 kB]
Get:91 http://172.17.0.1/private/ jessie-staging/main gfortran armhf 4:4.9.1-1 [1288 B]
Get:92 http://172.17.0.1/private/ jessie-staging/main libblas3 armhf 1.2.20110419-7 [186 kB]
Get:93 http://172.17.0.1/private/ jessie-staging/main libblas-dev armhf 1.2.20110419-7 [201 kB]
Get:94 http://172.17.0.1/private/ jessie-staging/main libbz2-dev armhf 1.0.6-5 [33.8 kB]
Get:95 http://172.17.0.1/private/ jessie-staging/main libjpeg8-dev armhf 8d1-1 [205 kB]
Get:96 http://172.17.0.1/private/ jessie-staging/main liblapack3 armhf 3.5.0-2 [2416 kB]
Get:97 http://172.17.0.1/private/ jessie-staging/main liblapack-dev armhf 3.5.0-2 [2716 kB]
Get:98 http://172.17.0.1/private/ jessie-staging/main liblzma-dev armhf 5.1.1alpha+20120614-2 [272 kB]
Get:99 http://172.17.0.1/private/ jessie-staging/main libtinfo-dev armhf 5.9+20140118-1 [64.8 kB]
Get:100 http://172.17.0.1/private/ jessie-staging/main libncurses5-dev armhf 5.9+20140118-1 [152 kB]
Get:101 http://172.17.0.1/private/ jessie-staging/main libpaper-utils armhf 1.1.24+nmu3 [17.0 kB]
Get:102 http://172.17.0.1/private/ jessie-staging/main libpcre3-dev armhf 1:8.35-3 [407 kB]
Get:103 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1+rpi1 [192 kB]
Get:104 http://172.17.0.1/private/ jessie-staging/main libpng12-dev armhf 1.2.50-1 [260 kB]
Get:105 http://172.17.0.1/private/ jessie-staging/main libreadline6-dev armhf 6.3-6 [194 kB]
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Get:107 http://172.17.0.1/private/ jessie-staging/main zip armhf 3.0-8 [326 kB]
Get:108 http://172.17.0.1/private/ jessie-staging/main unzip armhf 6.0-12 [152 kB]
Get:109 http://172.17.0.1/private/ jessie-staging/main xdg-utils all 1.1.0~rc1+git20111210-7.1 [64.6 kB]
Get:110 http://172.17.0.1/private/ jessie-staging/main r-base-core armhf 3.1.1-1 [19.5 MB]
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Get:112 http://172.17.0.1/private/ jessie-staging/main r-base-dev all 3.1.1-1 [4018 B]
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Get:115 http://172.17.0.1/private/ jessie-staging/main r-cran-codetools all 0.2-8-2 [45.4 kB]
Get:116 http://172.17.0.1/private/ jessie-staging/main r-cran-iterators all 1.0.7-1 [306 kB]
Get:117 http://172.17.0.1/private/ jessie-staging/main r-cran-foreach all 1.4.2-1 [371 kB]
Get:118 http://172.17.0.1/private/ jessie-staging/main r-cran-bbmisc armhf 1.6-1 [228 kB]
Get:119 http://172.17.0.1/private/ jessie-staging/main r-cran-brew armhf 1.0-6-1 [61.3 kB]
Get:120 http://172.17.0.1/private/ jessie-staging/main r-cran-digest armhf 0.6.4-1 [89.6 kB]
Get:121 http://172.17.0.1/private/ jessie-staging/main r-cran-dbi armhf 0.2-7-1 [274 kB]
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Get:123 http://172.17.0.1/private/ jessie-staging/main r-cran-rcpp armhf 0.11.2-1 [2014 kB]
Get:124 http://172.17.0.1/private/ jessie-staging/main r-cran-plyr armhf 1.8.1-1 [735 kB]
Get:125 http://172.17.0.1/private/ jessie-staging/main r-cran-stringr all 0.6.2-2 [71.8 kB]
Get:126 http://172.17.0.1/private/ jessie-staging/main r-cran-base64enc armhf 0.1-1-4 [19.1 kB]
Get:127 http://172.17.0.1/private/ jessie-staging/main r-cran-sendmailr armhf 1.1-2-1 [29.4 kB]
Get:128 http://172.17.0.1/private/ jessie-staging/main r-cran-fail armhf 1.2-1 [42.6 kB]
Get:129 http://172.17.0.1/private/ jessie-staging/main r-cran-batchjobs armhf 1.2-1 [367 kB]
Get:130 http://172.17.0.1/private/ jessie-staging/main r-bioc-biocparallel all 0.6.1-1 [321 kB]
Get:131 http://172.17.0.1/private/ jessie-staging/main r-bioc-iranges armhf 1.22.8-1 [1807 kB]
Get:132 http://172.17.0.1/private/ jessie-staging/main r-bioc-xvector armhf 0.4.0-1 [328 kB]
Get:133 http://172.17.0.1/private/ jessie-staging/main r-bioc-biostrings armhf 2.32.0-1 [2235 kB]
Get:134 http://172.17.0.1/private/ jessie-staging/main r-bioc-genomeinfodb all 1.0.2-1 [221 kB]
Get:135 http://172.17.0.1/private/ jessie-staging/main r-bioc-genomicranges armhf 1.16.3-1 [1097 kB]
Get:136 http://172.17.0.1/private/ jessie-staging/main r-cran-bitops armhf 1.0-6-1 [23.6 kB]
Get:137 http://172.17.0.1/private/ jessie-staging/main r-bioc-rsamtools armhf 1.16.1-2 [3091 kB]
Get:138 http://172.17.0.1/private/ jessie-staging/main r-bioc-bsgenome all 1.32.0-1 [763 kB]
Get:139 http://172.17.0.1/private/ jessie-staging/main r-bioc-genomicalignments armhf 1.0.2-1 [1240 kB]
Get:140 http://172.17.0.1/private/ jessie-staging/main r-cran-hwriter all 1.3-1 [137 kB]
Get:141 http://172.17.0.1/private/ jessie-staging/main r-cran-lattice armhf 0.20-29-1 [712 kB]
Get:142 http://172.17.0.1/private/ jessie-staging/main r-cran-rcolorbrewer all 1.0-5-2 [25.5 kB]
Get:143 http://172.17.0.1/private/ jessie-staging/main r-cran-latticeextra armhf 0.6-26-1 [1469 kB]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.15-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140617-1 dpkg-dev_1.17.10 g++-4.9_4.9.1-1 gcc-4.8_4.8.3-4 gcc-4.9_4.9.1-1 libc6-dev_2.19-7 libstdc++-4.9-dev_4.9.1-1 libstdc++6_4.9.1-1 linux-libc-dev_3.14.4-1+rpi1
Package versions: apt_1.0.6 base-files_7.3+rpi1 base-passwd_3.5.28 bash_4.3-7 binutils_2.24.51.20140617-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.6 bzip2_1.0.6-5 cdbs_0.4.125 coreutils_8.21-1.2 cpio_2.11+dfsg-2 cpp_4:4.9.1-1 cpp-4.8_4.8.3-4 cpp-4.9_4.9.1-1 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140613 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.10 dpkg-dev_1.17.10 e2fslibs_1.42.10-1.1 e2fsprogs_1.42.10-1.1 fakeroot_1.18.4-2 file_1:5.19-1 findutils_4.4.2-9 fontconfig_2.11.0-5 fontconfig-config_2.11.0-5 fonts-dejavu-core_2.34-1 g++_4:4.9.0-4 g++-4.9_4.9.1-1 gcc_4:4.9.1-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.3-4 gcc-4.8-base_4.8.3-4 gcc-4.9_4.9.1-1 gcc-4.9-base_4.9.1-1 gettext_0.18.3.2-4 gettext-base_0.18.3.2-4 gfortran_4:4.9.1-1 gfortran-4.9_4.9.1-1 gnupg_1.4.18-2 gpgv_1.4.18-2 grep_2.18-2 groff-base_1.22.2-6 gzip_1.6-3 hostname_3.15 init-system-helpers_1.19 initramfs-tools_0.115 initscripts_2.88dsf-53.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.3-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_1.0.6 libasan0_4.8.3-4 libasan1_4.9.1-1 libasprintf0c2_0.18.3.2-4 libatomic1_4.9.1-1 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libblas-dev_1.2.20110419-7 libblas3_1.2.20110419-7 libblkid1_2.20.1-5.8 libbz2-1.0_1.0.6-5 libbz2-dev_1.0.6-5 libc-bin_2.19-7 libc-dev-bin_2.19-7 libc6_2.19-7 libc6-dev_2.19-7 libcairo2_1.12.16-2+rpi1 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.10-1.1 libcroco3_0.6.8-2 libdatrie1_0.2.8-1 libdb5.1_5.1.29-6 libdb5.3_5.3.28-5 libdbus-1-3_1.8.6-1 libdpkg-perl_1.17.10 libdrm2_2.4.54-1 libexpat1_2.1.0-6 libffi6_3.1-2 libfontconfig1_2.11.0-5 libfreetype6_2.5.2-1 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.3-4 libgcc-4.9-dev_4.9.1-1 libgcc1_1:4.9.1-1 libgdbm3_1.8.3-12 libgfortran-4.9-dev_4.9.1-1 libgfortran3_4.9.1-1 libgl1-mesa-glx_10.2.4-1 libglapi-mesa_10.2.4-1 libglib2.0-0_2.40.0-3 libgmp10_2:6.0.0+dfsg-4+rpi1 libgomp1_4.9.1-1 libgraphite2-3_1.2.4-3 libharfbuzz0b_0.9.29-1 libice6_2:1.0.9-1 libisl10_0.12.2-2 libjbig0_2.1-3 libjpeg8_8d1-1 libjpeg8-dev_8d1-1 libklibc_2.0.3-1+rpi1 libkmod2_16-2 liblapack-dev_3.5.0-2 liblapack3_3.5.0-2 liblocale-gettext-perl_1.05-8 liblzma-dev_5.1.1alpha+20120614-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.19-1 libmount1_2.20.1-5.8 libmpc3_1.0.2-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncurses5-dev_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpango-1.0-0_1.36.3-1 libpangocairo-1.0-0_1.36.3-1 libpangoft2-1.0-0_1.36.3-1 libpaper-utils_1.1.24+nmu3 libpaper1_1.1.24+nmu3 libpcre3_1:8.35-3 libpcre3-dev_1:8.35-3 libpcrecpp0_1:8.35-3 libpipeline1_1.3.0-1 libpixman-1-0_0.32.6-1 libpng12-0_1.2.50-1 libpng12-dev_1.2.50-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-5 libreadline-dev_6.3-6 libreadline6_6.3-6 libreadline6-dev_6.3-6 libselinux1_2.3-1 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-1 libslang2_2.2.4-17 libsm6_2:1.2.2-1 libsqlite3-0_3.8.5-2 libss2_1.42.10-1.1 libstdc++-4.9-dev_4.9.1-1 libstdc++6_4.9.1-1 libtcl8.5_8.5.15-4 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.20-3 libthai0_0.1.20-3 libtiff5_4.0.3-9 libtimedate-perl_2.3000-2 libtinfo-dev_5.9+20140118-1 libtinfo5_5.9+20140118-1 libtk8.5_8.5.15-4 libubsan0_4.9.1-1 libudev1_204-14 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-24 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libx11-6_2:1.6.2-2 libx11-data_2:1.6.2-2 libx11-xcb1_2:1.6.2-2 libxau6_1:1.0.8-1 libxcb-dri2-0_1.10-3 libxcb-dri3-0_1.10-3 libxcb-glx0_1.10-3 libxcb-present0_1.10-3 libxcb-render0_1.10-3 libxcb-shm0_1.10-3 libxcb-sync1_1.10-3 libxcb1_1.10-3 libxdamage1_1:1.1.4-2 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.2-1 libxfixes3_1:5.0.1-2 libxft2_2.3.2-1 libxml2_2.9.1+dfsg1-4 libxrender1_1:0.9.8-1 libxshmfence1_1.1-2 libxss1_1:1.2.2-1 libxt6_1:1.1.4-1 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.14.4-1+rpi1 littler_0.1.5-1 login_1:4.2-2 lsb-base_4.1+Debian13+rpi1 make_4.0-8 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.8 multiarch-support_2.19-7 nano_2.2.6-1.1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.2-2 patch_2.7.1-5 perl_5.18.2-6 perl-base_5.18.2-6 perl-modules_5.18.2-6 plymouth_0.9.0-4 po-debconf_1.0.16+nmu3 procps_1:3.3.9-5 r-base-core_3.1.1-1 r-base-dev_3.1.1-1 r-bioc-biobase_2.24.0-1 r-bioc-biocgenerics_0.10.0-1 r-bioc-biocparallel_0.6.1-1 r-bioc-biostrings_2.32.0-1 r-bioc-bsgenome_1.32.0-1 r-bioc-genomeinfodb_1.0.2-1 r-bioc-genomicalignments_1.0.2-1 r-bioc-genomicranges_1.16.3-1 r-bioc-iranges_1.22.8-1 r-bioc-rsamtools_1.16.1-2 r-bioc-xvector_0.4.0-1 r-cran-base64enc_0.1-1-4 r-cran-batchjobs_1.2-1 r-cran-bbmisc_1.6-1 r-cran-bitops_1.0-6-1 r-cran-brew_1.0-6-1 r-cran-codetools_0.2-8-2 r-cran-dbi_0.2-7-1 r-cran-digest_0.6.4-1 r-cran-fail_1.2-1 r-cran-foreach_1.4.2-1 r-cran-hwriter_1.3-1 r-cran-iterators_1.0.7-1 r-cran-lattice_0.20-29-1 r-cran-latticeextra_0.6-26-1 r-cran-plyr_1.8.1-1 r-cran-rcolorbrewer_1.0-5-2 r-cran-rcpp_0.11.2-1 r-cran-rsqlite_0.11.4-1 r-cran-sendmailr_1.1-2-1 r-cran-stringr_0.6.2-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-6 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-shortread-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sysv-rc_2.88dsf-53.2 sysvinit_2.88dsf-53.2 sysvinit-core_2.88dsf-53.2 sysvinit-utils_2.88dsf-53.2 tar_1.27.1-2 tzdata_2014e-1 ucf_3.0030 udev_204-14 unzip_6.0-12 util-linux_2.20.1-5.8 x11-common_1:7.7+7 xdg-utils_1.1.0~rc1+git20111210-7.1 xz-utils_5.1.1alpha+20120614-2 zip_3.0-8 zlib1g_1:1.2.8.dfsg-1+rpi1 zlib1g-dev_1:1.2.8.dfsg-1+rpi1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Jul 24 09:43:57 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./r-bioc-shortread_1.22.0-1.dsc
dpkg-source: info: extracting r-bioc-shortread in r-bioc-shortread-1.22.0
dpkg-source: info: unpacking r-bioc-shortread_1.22.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-shortread_1.22.0-1.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
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-ca8068ab-2fc4-4033-af2e-db83a3f9f696
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package r-bioc-shortread
dpkg-buildpackage: source version 1.22.0-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build r-bioc-shortread-1.22.0
dpkg-buildpackage: host architecture armhf
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
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 (>= 3.1.1-1)" >> debian/r-bioc-shortread.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library --clean \
. ; \
else \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library \
--clean . ;\
fi
* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 4
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make[1]: Entering directory '/«PKGBUILDDIR»/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c io.c -o io.o
io.c: In function '_count_ipar_int_recs':
io.c:148:44: warning: passing argument 1 of 'gzread' from incompatible pointer type
while (*n_cycles == 0 && (bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
^
In file included from io.c:3:0:
/usr/include/zlib.h:1313:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
io.c:165:26: warning: passing argument 1 of 'gzread' from incompatible pointer type
while ((bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
^
In file included from io.c:3:0:
/usr/include/zlib.h:1313:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
io.c: In function 'count_ipar_int_recs':
io.c:200:9: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c: In function 'read_prb_as_character':
io.c:226:9: warning: passing argument 1 of 'gzgets' from incompatible pointer type
if (gzgets(file, buf, LINEBUF_SIZE) == Z_NULL) {
^
In file included from io.c:3:0:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:227:9: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:236:5: warning: passing argument 1 of 'gzrewind' from incompatible pointer type
gzrewind(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1447:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzrewind OF((gzFile file));
^
io.c:241:12: warning: passing argument 1 of 'gzgets' from incompatible pointer type
while (gzgets(file, buf, LINEBUF_SIZE) != Z_NULL) {
^
In file included from io.c:3:0:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:243:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:253:17: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:262:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:268:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c: In function '_read_solexa_fastq_file':
io.c:285:12: warning: passing argument 1 of 'gzgets' from incompatible pointer type
while (gzgets(file, linebuf, LINEBUF_SIZE) != NULL) {
^
In file included from io.c:3:0:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:293:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:296:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:319:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c: In function '_io_XStringSet_columns':
io.c:380:9: warning: passing argument 1 of 'gzgets' from incompatible pointer type
gzgets(file, linebuf, LINEBUF_SIZE);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:382:9: warning: passing argument 1 of 'gzgets' from incompatible pointer type
gzgets(file, linebuf, LINEBUF_SIZE);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:384:28: warning: passing argument 1 of 'gzgets' from incompatible pointer type
while (recno < nrow && gzgets(file, linebuf, LINEBUF_SIZE) != NULL) {
^
In file included from io.c:3:0:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:405:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c: In function '_read_solexa_export_file':
io.c:610:12: warning: passing argument 1 of 'gzgets' from incompatible pointer type
while (gzgets(file, linebuf, LINEBUF_SIZE) != NULL) {
^
In file included from io.c:3:0:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:619:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:656:17: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:674:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from io.c:3:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c io_bowtie.c -o io_bowtie.o
io_bowtie.c: In function '_read_bowtie':
io_bowtie.c:35:12: warning: passing argument 1 of 'gzgets' from incompatible pointer type
while (gzgets(file, linebuf, LINEBUF_SIZE) != NULL) {
^
In file included from ShortRead.h:8:0,
from io_bowtie.c:2:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io_bowtie.c:45:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io_bowtie.c:2:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c io_soap.c -o io_soap.o
io_soap.c: In function '_read_soap':
io_soap.c:38:12: warning: passing argument 1 of 'gzgets' from incompatible pointer type
while (gzgets(file, linebuf, LINEBUF_SIZE) != NULL) {
^
In file included from ShortRead.h:8:0,
from io_soap.c:2:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pileup.c -o pileup.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c readBfaToc.cc -o readBfaToc.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sampler.c -o sampler.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c trim.c -o trim.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o
util.c: In function '_fopen':
util.c:229:20: warning: initialization from incompatible pointer type
gzFile *file = gzopen(fname, mode);
^
util.c: In function '_linebuf_skip_p':
util.c:244:9: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from ShortRead.h:8:0,
from util.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
util.c:247:9: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from ShortRead.h:8:0,
from util.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
util.c: In function '_count_lines':
util.c:349:26: warning: passing argument 1 of 'gzread' from incompatible pointer type
while ((bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
^
In file included from ShortRead.h:8:0,
from util.c:3:
/usr/include/zlib.h:1313:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
util.c: In function 'count_lines':
util.c:385:9: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(file);
^
In file included from ShortRead.h:8:0,
from util.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xsnap.c -o xsnap.o
g++ -shared -Wl,-z,relro -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/«PKGBUILDDIR»/src'
make[1]: Entering directory '/«PKGBUILDDIR»/src'
make[1]: Leaving directory '/«PKGBUILDDIR»/src'
installing to /«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library/ShortRead/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ShortRead)
rm -vf /«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library/R.css \
/«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library/ShortRead/COPYING \
/«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library/ShortRead/LICENSE.txt
if test -f debian/overrides; then \
install -d /«PKGBUILDDIR»/debian/r-bioc-shortread/usr/share/lintian/overrides ; \
install -m 0644 debian/overrides \
/«PKGBUILDDIR»/debian/r-bioc-shortread/usr/share/lintian/overrides/r-bioc-shortread; \
fi
Adding cdbs dependencies to debian/r-bioc-shortread.substvars
dh_installdirs -pr-bioc-shortread
dh_installdocs -pr-bioc-shortread ./NEWS
dh_installexamples -pr-bioc-shortread
dh_installman -pr-bioc-shortread
dh_installinfo -pr-bioc-shortread
dh_installmenu -pr-bioc-shortread
dh_installcron -pr-bioc-shortread
dh_installinit -pr-bioc-shortread
dh_installdebconf -pr-bioc-shortread
dh_installemacsen -pr-bioc-shortread
dh_installcatalogs -pr-bioc-shortread
dh_installpam -pr-bioc-shortread
dh_installlogrotate -pr-bioc-shortread
dh_installlogcheck -pr-bioc-shortread
dh_installchangelogs -pr-bioc-shortread
dh_installudev -pr-bioc-shortread
dh_lintian -pr-bioc-shortread
dh_bugfiles -pr-bioc-shortread
dh_install -pr-bioc-shortread
dh_link -pr-bioc-shortread
dh_installmime -pr-bioc-shortread
dh_installgsettings -pr-bioc-shortread
dh_strip -pr-bioc-shortread
dh_compress -pr-bioc-shortread
dh_fixperms -pr-bioc-shortread
dh_makeshlibs -pr-bioc-shortread
dh_installdeb -pr-bioc-shortread
dh_perl -pr-bioc-shortread
dh_shlibdeps -pr-bioc-shortread
dh_gencontrol -pr-bioc-shortread
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -pr-bioc-shortread
dh_builddeb -pr-bioc-shortread
dpkg-deb: building package `r-bioc-shortread' in `../r-bioc-shortread_1.22.0-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-shortread_1.22.0-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build r-bioc-shortread-1.22.0
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140730-0614
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-shortread_1.22.0-1_armhf.changes:
────────────────────────────────────────
Format: 1.8
Date: Thu, 24 Jul 2014 11:38:30 +0200
Source: r-bioc-shortread
Binary: r-bioc-shortread
Architecture: armhf
Version: 1.22.0-1
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-shortread - GNU R classes and methods for high-throughput short-read sequenci
Closes: 753224
Changes:
r-bioc-shortread (1.22.0-1) unstable; urgency=medium
.
* New upstream version
* Moved debian/upstream to debian/upstream/metadata
* Add autopkgtest
* (Build-)Depends: r-bioc-genomicalignments
Closes: #753224
Checksums-Sha1:
ef3cacee31cc191806da6156bd4e0c9cc45e8102 4156904 r-bioc-shortread_1.22.0-1_armhf.deb
Checksums-Sha256:
e1dbeb7b520d5a9bd0303d4ec79db664ac03c60ee747f467cc1ceca3faaf835b 4156904 r-bioc-shortread_1.22.0-1_armhf.deb
Files:
6fe7c6e7f9e613bbb25240ac539ac6f3 4156904 gnu-r optional r-bioc-shortread_1.22.0-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-shortread_1.22.0-1_armhf.deb
───────────────────────────────────
new debian package, version 2.0.
size 4156904 bytes: control archive=4643 bytes.
1079 bytes, 16 lines control
10895 bytes, 114 lines md5sums
Package: r-bioc-shortread
Version: 1.22.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5788
Depends: r-base-core (>= 3.1.1-1), libc6 (>= 2.7), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.9), libstdc++6 (>= 4.3.0), zlib1g (>= 1:1.1.4), r-cran-latticeextra, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-biocparallel, r-bioc-genomicalignments, r-bioc-genomicranges, r-bioc-iranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-xvector, r-cran-hwriter
Section: gnu-r
Priority: optional
Homepage: http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html
Description: GNU R classes and methods for high-throughput short-read sequencing data
This BioConductor module is a package for input, quality assessment,
manipulation and output of high-throughput sequencing data. ShortRead is
provided in the R and Bioconductor environments, allowing ready access
to additional facilities for advanced statistical analysis, data
transformation, visualization and integration with diverse genomic
resources.
drwxr-xr-x root/root 0 2014-07-30 06:13 ./
drwxr-xr-x root/root 0 2014-07-30 06:13 ./usr/
drwxr-xr-x root/root 0 2014-07-30 06:10 ./usr/lib/
drwxr-xr-x root/root 0 2014-07-30 06:10 ./usr/lib/R/
drwxr-xr-x root/root 0 2014-07-30 06:13 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/
-rw-r--r-- root/root 4084 2014-07-30 06:10 ./usr/lib/R/site-library/ShortRead/NAMESPACE
-rw-r--r-- root/root 10504 2014-07-30 06:10 ./usr/lib/R/site-library/ShortRead/NEWS
-rw-r--r-- root/root 1225 2014-07-30 06:10 ./usr/lib/R/site-library/ShortRead/DESCRIPTION
drwxr-xr-x root/root 0 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/Meta/
-rw-r--r-- root/root 1288 2014-07-30 06:10 ./usr/lib/R/site-library/ShortRead/Meta/package.rds
-rw-r--r-- root/root 5634 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/Meta/Rd.rds
-rw-r--r-- root/root 5785 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/Meta/hsearch.rds
-rw-r--r-- root/root 4131 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/Meta/links.rds
-rw-r--r-- root/root 261 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/Meta/vignette.rds
-rw-r--r-- root/root 1885 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/Meta/nsInfo.rds
drwxr-xr-x root/root 0 2014-07-30 06:13 ./usr/lib/R/site-library/ShortRead/libs/
-rw-r--r-- root/root 100728 2014-07-30 06:13 ./usr/lib/R/site-library/ShortRead/libs/ShortRead.so
drwxr-xr-x root/root 0 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/R/
-rw-r--r-- root/root 1056 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/R/ShortRead
-rw-r--r-- root/root 758707 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/R/ShortRead.rdb
-rw-r--r-- root/root 11675 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/R/ShortRead.rdx
drwxr-xr-x root/root 0 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/doc/
-rw-r--r-- root/root 5960 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/doc/Overview.R
-rw-r--r-- root/root 15598 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/doc/Overview.Rnw
-rw-r--r-- root/root 149829 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/doc/Overview.pdf
-rw-r--r-- root/root 1162 2014-07-30 06:12 ./usr/lib/R/site-library/ShortRead/doc/index.html
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/
-rw-r--r-- root/root 31740 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt
-rw-r--r-- root/root 121368 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt
-rw-r--r-- root/root 90912 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_5_0001_realign.txt
-rw-r--r-- root/root 184320 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_prb.txt
-rw-r--r-- root/root 12452 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_seq.txt
-rw-r--r-- root/root 21534 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/s_1_1_0001_qseq.txt
-rw-r--r-- root/root 261216 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/s_1_0001_int.txt
-rw-r--r-- root/root 261028 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/s_1_0001_nse.txt
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/E-MTAB-1147/
-rw-r--r-- root/root 1408765 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz
-rw-r--r-- root/root 1402866 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/bowtie/
-rw-r--r-- root/root 117004 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/bowtie/s_1_aligned_bowtie.txt
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/maq/
-rw-r--r-- root/root 131501 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/maq/out.aln.1.txt
-rw-r--r-- root/root 133413 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/extdata/maq/out.aln.2.txt
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/script/
-rw-r--r-- root/root 450 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/script/qa-test.R
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/template/
drwxr-xr-x root/root 0 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/template/image/
-rw-r--r-- root/root 7692 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/template/image/bioclogo-small.gif
-rw-r--r-- root/root 671 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/template/0000-Header.html
-rw-r--r-- root/root 578 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/template/1000-Overview.html
-rw-r--r-- root/root 140 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/template/1100-Overview-SolexaRealign.html
-rw-r--r-- root/root 1177 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/template/2000-RunSummary.html
-rw-r--r-- root/root 1998 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/template/3000-ReadDistribution.html
-rw-r--r-- root/root 1209 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/template/4000-CycleSpecific.html
-rw-r--r-- root/root 2439 2014-07-30 06:11 ./usr/lib/R/site-library/ShortRead/template/5000-PerTile.html
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
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Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 18612
Build-Time: 251
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 645
Job: r-bioc-shortread_1.22.0-1
Machine Architecture: armhf
Package: r-bioc-shortread
Package-Time: 953
Source-Version: 1.22.0-1
Space: 18612
Status: successful
Version: 1.22.0-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140730-0614
Build needed 00:15:53, 18612k disc space