r-bioc-rsamtools →
1.14.2-1 →
armhf → 2013-12-12 08:19:37
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on testwandboard
╔══════════════════════════════════════════════════════════════════════════════╗
║ r-bioc-rsamtools 1.14.2-1 (armhf) 12 Dec 2013 08:06 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: r-bioc-rsamtools
Version: 1.14.2-1
Source Version: 1.14.2-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-PUtmqb/r-bioc-rsamtools-1.14.2' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-PUtmqb' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-9468cabd-1c1b-4256-b974-6ad57b1527e6' 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 [7093 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8215 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.3 MB in 37s (408 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
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 2963 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main r-bioc-rsamtools 1.14.2-1 (dsc) [1588 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main r-bioc-rsamtools 1.14.2-1 (tar) [2955 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main r-bioc-rsamtools 1.14.2-1 (diff) [6548 B]
Fetched 2963 kB in 3s (876 kB/s)
Download complete and in download only mode
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-S2oMQV/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 32 not upgraded.
Need to get 0 B/706 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 ... 12190 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
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-bitops, r-bioc-biocgenerics, r-bioc-iranges, r-bioc-biostrings, r-bioc-genomicranges, r-bioc-xvector, libbam-dev
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-bitops, r-bioc-biocgenerics, r-bioc-iranges, r-bioc-biostrings, r-bioc-genomicranges, r-bioc-xvector, libbam-dev
dpkg-deb: building package `sbuild-build-depends-r-bioc-rsamtools-dummy' in `/«BUILDDIR»/resolver-KYkMsZ/apt_archive/sbuild-build-depends-r-bioc-rsamtools-dummy.deb'.
OK
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 extra packages will be installed:
bsdmainutils cdbs debhelper file fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base gfortran gfortran-4.8 groff-base
intltool-debian libasprintf0c2 libbam-dev libblas-dev libblas3 libbz2-dev
libcairo2 libcroco3 libdatrie1 libdrm2 libegl1-mesa libexpat1 libffi6
libfontconfig1 libfreetype6 libgbm1 libgfortran-4.8-dev libgfortran3
libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3 libharfbuzz0a
libice6 libjbig0 libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libllvm3.3
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 libthai-data libthai0 libtiff5 libtinfo-dev
libunistring0 libwayland-client0 libwayland-server0 libx11-6 libx11-data
libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-glx0 libxcb-render0 libxcb-shape0
libxcb-shm0 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3
libxft2 libxml2 libxrender1 libxss1 libxt6 libxxf86vm1 man-db po-debconf
r-base-core r-base-dev r-bioc-biocgenerics r-bioc-biostrings
r-bioc-genomicranges r-bioc-iranges r-bioc-xvector r-cran-bitops tcl8.5
tk8.5 ucf unzip x11-common xdg-utils zip zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc
gfortran-doc gfortran-4.8-doc libgfortran3-dbg groff ncurses-doc ttf-baekmuk
ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp
ttf-arphic-bkai00mp 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
texi2html tcl-tclreadline gvfs-bin
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libegl1-mesa-drivers libgl1-mesa-dri libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl r-recommended r-doc-html xterm
x-terminal-emulator 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-4.8 groff-base
intltool-debian libasprintf0c2 libbam-dev libblas-dev libblas3 libbz2-dev
libcairo2 libcroco3 libdatrie1 libdrm2 libegl1-mesa libexpat1 libffi6
libfontconfig1 libfreetype6 libgbm1 libgfortran-4.8-dev libgfortran3
libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3 libharfbuzz0a
libice6 libjbig0 libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libllvm3.3
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 libthai-data libthai0 libtiff5 libtinfo-dev
libunistring0 libwayland-client0 libwayland-server0 libx11-6 libx11-data
libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-glx0 libxcb-render0 libxcb-shape0
libxcb-shm0 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3
libxft2 libxml2 libxrender1 libxss1 libxt6 libxxf86vm1 man-db po-debconf
r-base-core r-base-dev r-bioc-biocgenerics r-bioc-biostrings
r-bioc-genomicranges r-bioc-iranges r-bioc-xvector r-cran-bitops
sbuild-build-depends-r-bioc-rsamtools-dummy tcl8.5 tk8.5 ucf unzip
x11-common xdg-utils zip zlib1g-dev
0 upgraded, 105 newly installed, 0 to remove and 32 not upgraded.
Need to get 72.1 MB/72.1 MB of archives.
After this operation, 143 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.4-1 [36.9 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-3 [666 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.5-2 [949 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.1-2 [29.5 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.14-2 [213 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libdrm2 armhf 2.4.49-2 [474 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-4 [19.8 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libglapi-mesa armhf 9.2.2-1 [63.2 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libllvm3.3 armhf 1:3.3-12 [8302 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libwayland-client0 armhf 1.3.0-1+rpi1 [20.7 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libwayland-server0 armhf 1.3.0-1+rpi1 [24.9 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libxdmcp6 armhf 1:1.1.1-1 [24.6 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libxcb1 armhf 1.9.1-3.1 [42.6 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libxcb-dri2-0 armhf 1.9.1-3.1 [12.4 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main libgbm1 armhf 9.2.2-1 [418 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main libx11-data all 2:1.6.2-1 [125 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main libx11-6 armhf 2:1.6.2-1 [867 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main libx11-xcb1 armhf 2:1.6.2-1 [163 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main libxcb-render0 armhf 1.9.1-3.1 [17.4 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main libxcb-shape0 armhf 1.9.1-3.1 [11.3 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main libxcb-xfixes0 armhf 1.9.1-3.1 [14.0 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main libegl1-mesa armhf 9.2.2-1 [74.6 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-4 [117 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main libpng12-0 armhf 1.2.49-5 [179 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main libfreetype6 armhf 2.5.1-1 [460 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main ucf all 3.0027+nmu1 [70.6 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-core all 2.33+svn2514-3 [1042 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main fontconfig-config all 2.11.0-2 [270 kB]
Get:32 http://172.17.0.1/private/ jessie-staging/main libfontconfig1 armhf 2.11.0-2 [329 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main libxcb-glx0 armhf 1.9.1-3.1 [27.0 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main libxfixes3 armhf 1:5.0.1-1 [21.0 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libxdamage1 armhf 1:1.1.4-1 [14.6 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main libxext6 armhf 2:1.3.2-1 [51.1 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main libxxf86vm1 armhf 1:1.1.3-1 [20.0 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-glx armhf 9.2.2-1 [128 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main libpixman-1-0 armhf 0.30.2-2 [460 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0 armhf 1.9.1-3.1 [10.8 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:42 http://172.17.0.1/private/ jessie-staging/main libcairo2 armhf 1.12.16-2 [998 kB]
Get:43 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.4-1 [1907 kB]
Get:44 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:45 http://172.17.0.1/private/ jessie-staging/main libdatrie1 armhf 0.2.7.1-1 [28.1 kB]
Get:46 http://172.17.0.1/private/ jessie-staging/main libgfortran3 armhf 4.8.2-1+rpi1 [226 kB]
Get:47 http://172.17.0.1/private/ jessie-staging/main libgraphite2-3 armhf 1.2.4-1 [57.9 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main libharfbuzz0a armhf 0.9.19-1 [432 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main x11-common all 1:7.7+4 [282 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main libice6 armhf 2:1.0.8-2 [56.2 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main libjpeg8 armhf 8d-2 [133 kB]
Get:52 http://172.17.0.1/private/ jessie-staging/main libthai-data all 0.1.20-1 [157 kB]
Get:53 http://172.17.0.1/private/ jessie-staging/main libthai0 armhf 0.1.20-1 [41.4 kB]
Get:54 http://172.17.0.1/private/ jessie-staging/main fontconfig armhf 2.11.0-2 [407 kB]
Get:55 http://172.17.0.1/private/ jessie-staging/main libpango-1.0-0 armhf 1.36.0-1 [257 kB]
Get:56 http://172.17.0.1/private/ jessie-staging/main libpangoft2-1.0-0 armhf 1.36.0-1 [191 kB]
Get:57 http://172.17.0.1/private/ jessie-staging/main libpangocairo-1.0-0 armhf 1.36.0-1 [181 kB]
Get:58 http://172.17.0.1/private/ jessie-staging/main libpaper1 armhf 1.1.24+nmu2 [20.9 kB]
Get:59 http://172.17.0.1/private/ jessie-staging/main libpcrecpp0 armhf 1:8.31-2 [125 kB]
Get:60 http://172.17.0.1/private/ jessie-staging/main libsm6 armhf 2:1.2.1-2 [32.5 kB]
Get:61 http://172.17.0.1/private/ jessie-staging/main libjbig0 armhf 2.0-2 [31.5 kB]
Get:62 http://172.17.0.1/private/ jessie-staging/main libtiff5 armhf 4.0.3-5 [227 kB]
Get:63 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:64 http://172.17.0.1/private/ jessie-staging/main libxft2 armhf 2.3.1-1 [55.4 kB]
Get:65 http://172.17.0.1/private/ jessie-staging/main libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:66 http://172.17.0.1/private/ jessie-staging/main libxt6 armhf 1:1.1.4-1 [183 kB]
Get:67 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.14-2 [53.8 kB]
Get:68 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.1-2 [135 kB]
Get:69 http://172.17.0.1/private/ jessie-staging/main cdbs all 0.4.122 [81.4 kB]
Get:70 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.1-2 [1829 kB]
Get:71 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:72 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:73 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20131127 [687 kB]
Get:74 http://172.17.0.1/private/ jessie-staging/main libgfortran-4.8-dev armhf 4.8.2-1+rpi1 [300 kB]
Get:75 http://172.17.0.1/private/ jessie-staging/main gfortran-4.8 armhf 4.8.2-1+rpi1 [5704 kB]
Get:76 http://172.17.0.1/private/ jessie-staging/main gfortran armhf 4:4.8.1-3 [1134 B]
Get:77 http://172.17.0.1/private/ jessie-staging/main libbam-dev armhf 0.1.19-1 [110 kB]
Get:78 http://172.17.0.1/private/ jessie-staging/main libblas3 armhf 1.2.20110419-7 [186 kB]
Get:79 http://172.17.0.1/private/ jessie-staging/main libblas-dev armhf 1.2.20110419-7 [201 kB]
Get:80 http://172.17.0.1/private/ jessie-staging/main libbz2-dev armhf 1.0.6-5 [33.8 kB]
Get:81 http://172.17.0.1/private/ jessie-staging/main libjpeg8-dev armhf 8d-2 [238 kB]
Get:82 http://172.17.0.1/private/ jessie-staging/main liblapack3 armhf 3.5.0-2 [2416 kB]
Get:83 http://172.17.0.1/private/ jessie-staging/main liblapack-dev armhf 3.5.0-2 [2716 kB]
Get:84 http://172.17.0.1/private/ jessie-staging/main libtinfo-dev armhf 5.9+20130608-1 [92.5 kB]
Get:85 http://172.17.0.1/private/ jessie-staging/main libncurses5-dev armhf 5.9+20130608-1 [201 kB]
Get:86 http://172.17.0.1/private/ jessie-staging/main libpaper-utils armhf 1.1.24+nmu2 [17.9 kB]
Get:87 http://172.17.0.1/private/ jessie-staging/main libpcre3-dev armhf 1:8.31-2 [350 kB]
Get:88 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1 [212 kB]
Get:89 http://172.17.0.1/private/ jessie-staging/main libpng12-dev armhf 1.2.49-5 [258 kB]
Get:90 http://172.17.0.1/private/ jessie-staging/main libreadline6-dev armhf 6.2+dfsg-0.1 [164 kB]
Get:91 http://172.17.0.1/private/ jessie-staging/main libreadline-dev armhf 6.2+dfsg-0.1 [898 B]
Get:92 http://172.17.0.1/private/ jessie-staging/main zip armhf 3.0-8 [326 kB]
Get:93 http://172.17.0.1/private/ jessie-staging/main unzip armhf 6.0-10 [192 kB]
Get:94 http://172.17.0.1/private/ jessie-staging/main xdg-utils all 1.1.0~rc1+git20111210-7 [83.7 kB]
Get:95 http://172.17.0.1/private/ jessie-staging/main tcl8.5 armhf 8.5.14-2 [1579 kB]
Get:96 http://172.17.0.1/private/ jessie-staging/main tk8.5 armhf 8.5.14-2 [1123 kB]
Get:97 http://172.17.0.1/private/ jessie-staging/main r-base-core armhf 3.0.2-1 [21.2 MB]
Get:98 http://172.17.0.1/private/ jessie-staging/main r-base-dev all 3.0.2-1 [3926 B]
Get:99 http://172.17.0.1/private/ jessie-staging/main r-bioc-biocgenerics all 0.8.0-1 [379 kB]
Get:100 http://172.17.0.1/private/ jessie-staging/main r-bioc-iranges armhf 1.20.4-1 [1890 kB]
Get:101 http://172.17.0.1/private/ jessie-staging/main r-bioc-xvector armhf 0.2.0-1 [333 kB]
Get:102 http://172.17.0.1/private/ jessie-staging/main r-bioc-biostrings armhf 2.30.1-1 [2293 kB]
Get:103 http://172.17.0.1/private/ jessie-staging/main r-bioc-genomicranges armhf 1.14.3-1 [2988 kB]
Get:104 http://172.17.0.1/private/ jessie-staging/main r-cran-bitops armhf 1.0-6-1 [23.6 kB]
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Setting up libreadline-dev:armhf (6.2+dfsg-0.1) ...
Setting up zip (3.0-8) ...
Setting up unzip (6.0-10) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-7) ...
Setting up tcl8.5 (8.5.14-2) ...
update-alternatives: using /usr/bin/tclsh8.5 to provide /usr/bin/tclsh (tclsh) in auto mode
Setting up tk8.5 (8.5.14-2) ...
update-alternatives: using /usr/bin/wish8.5 to provide /usr/bin/wish (wish) in auto mode
Setting up r-base-core (3.0.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.0.2-1) ...
Setting up r-bioc-biocgenerics (0.8.0-1) ...
Setting up r-bioc-iranges (1.20.4-1) ...
Setting up r-bioc-xvector (0.2.0-1) ...
Setting up r-bioc-biostrings (2.30.1-1) ...
Setting up r-bioc-genomicranges (1.14.3-1) ...
Setting up r-cran-bitops (1.0-6-1) ...
Setting up sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.11.0-armv7-x13 armhf (armv7l)
Toolchain package versions: binutils_2.23.90.20131017-1 dpkg-dev_1.16.12 g++-4.6_4.6.4-4+rpi1 g++-4.8_4.8.2-1+rpi1 gcc-4.6_4.6.4-4+rpi1 gcc-4.8_4.8.2-1+rpi1 libc6-dev_2.17-93 libstdc++-4.8-dev_4.8.2-1+rpi1 libstdc++6_4.8.2-1+rpi1 libstdc++6-4.6-dev_4.6.4-4+rpi1 linux-libc-dev_3.10.1-1+rpi1+b2
Package versions: apt_0.9.12.1+rpi1 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.23.90.20131017-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-5 cdbs_0.4.122 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.1-3 cpp-4.6_4.6.4-4+rpi1 cpp-4.8_4.8.2-1+rpi1 dash_0.5.7-3 debconf_1.5.51 debfoster_2.7-1.2 debhelper_9.20131127 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.16.12 dpkg-dev_1.16.12 e2fslibs_1.42.8-1 e2fsprogs_1.42.8-1 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-6 fontconfig_2.11.0-2 fontconfig-config_2.11.0-2 fonts-dejavu-core_2.33+svn2514-3 g++_4:4.8.1-3 g++-4.6_4.6.4-4+rpi1 g++-4.8_4.8.2-1+rpi1 gcc_4:4.8.1-3 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.4-4+rpi1 gcc-4.6-base_4.6.4-4+rpi1 gcc-4.7-base_4.7.3-4+rpi1 gcc-4.8_4.8.2-1+rpi1 gcc-4.8-base_4.8.2-1+rpi1 gettext_0.18.3.1-2 gettext-base_0.18.3.1-2 gfortran_4:4.8.1-3 gfortran-4.8_4.8.2-1+rpi1 gnupg_1.4.15-1.1 gpgv_1.4.15-1.1 grep_2.14-4 groff-base_1.22.2-3 gzip_1.6-2 hostname_3.14 initramfs-tools_0.114 initscripts_2.88dsf-43 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.1-3.1+rpi1 kmod_9-3 libacl1_2.2.52-1 libapt-pkg4.12_0.9.12.1+rpi1 libarchive-extract-perl_0.68-1 libasan0_4.8.2-1+rpi1 libasprintf0c2_0.18.3.1-2 libatomic1_4.8.2-1+rpi1 libattr1_1:2.4.47-1 libbam-dev_0.1.19-1 libblas-dev_1.2.20110419-7 libblas3_1.2.20110419-7 libblkid1_2.20.1-5.5 libbz2-1.0_1.0.6-5 libbz2-dev_1.0.6-5 libc-bin_2.17-93 libc-dev-bin_2.17-93 libc6_2.17-93 libc6-dev_2.17-93 libcairo2_1.12.16-2 libcap2_1:2.22-1.2 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.1-1 libcomerr2_1.42.8-1 libcroco3_0.6.8-2 libdatrie1_0.2.7.1-1 libdb5.1_5.1.29-6 libdbus-1-3_1.6.18-1 libdpkg-perl_1.16.12 libdrm2_2.4.49-2 libegl1-mesa_9.2.2-1 libexpat1_2.1.0-4 libffi6_3.0.13-4 libfontconfig1_2.11.0-2 libfreetype6_2.5.1-1 libgbm1_9.2.2-1 libgc1c2_1:7.2d-5 libgcc-4.8-dev_4.8.2-1+rpi1 libgcc1_1:4.8.2-1+rpi1 libgdbm3_1.8.3-12 libgfortran-4.8-dev_4.8.2-1+rpi1 libgfortran3_4.8.2-1+rpi1 libgl1-mesa-glx_9.2.2-1 libglapi-mesa_9.2.2-1 libglib2.0-0_2.36.4-1 libgmp10_2:5.1.2+dfsg-3 libgomp1_4.8.2-1+rpi1 libgraphite2-3_1.2.4-1 libharfbuzz0a_0.9.19-1 libice6_2:1.0.8-2 libisl10_0.12.1-1 libjbig0_2.0-2 libjpeg8_8d-2 libjpeg8-dev_8d-2 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 liblapack-dev_3.5.0-2 liblapack3_3.5.0-2 libllvm3.3_1:3.3-12 liblog-message-simple-perl_0.10-1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmodule-pluggable-perl_4.8-1 libmount1_2.20.1-5.5 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20130608-1 libncurses5-dev_5.9+20130608-1 libncursesw5_5.9+20130608-1 libnih-dbus1_1.0.3-4.1+b1 libnih1_1.0.3-4.1+b1 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpango-1.0-0_1.36.0-1 libpangocairo-1.0-0_1.36.0-1 libpangoft2-1.0-0_1.36.0-1 libpaper-utils_1.1.24+nmu2 libpaper1_1.1.24+nmu2 libpcre3_1:8.31-2 libpcre3-dev_1:8.31-2 libpcrecpp0_1:8.31-2 libpipeline1_1.2.4-1 libpixman-1-0_0.30.2-2 libpng12-0_1.2.49-5 libpng12-dev_1.2.49-5 libpod-latex-perl_0.61-1 libprocps0_1:3.3.4-2 libreadline-dev_6.2+dfsg-0.1 libreadline6_6.2+dfsg-0.1 libreadline6-dev_6.2+dfsg-0.1 libselinux1_2.1.13-3+rpi1 libsemanage-common_2.1.10-3+rpi1 libsemanage1_2.1.10-3+rpi1 libsepol1_2.1.9-2 libslang2_2.2.4-15 libsm6_2:1.2.1-2 libss2_1.42.8-1 libstdc++-4.8-dev_4.8.2-1+rpi1 libstdc++6_4.8.2-1+rpi1 libstdc++6-4.6-dev_4.6.4-4+rpi1 libswitch-perl_2.16-2 libterm-ui-perl_0.38-1 libthai-data_0.1.20-1 libthai0_0.1.20-1 libtiff5_4.0.3-5 libtimedate-perl_1.2000-1 libtinfo-dev_5.9+20130608-1 libtinfo5_5.9+20130608-1 libudev0_175-7.2 libudev1_204-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libwayland-client0_1.3.0-1+rpi1 libwayland-server0_1.3.0-1+rpi1 libx11-6_2:1.6.2-1 libx11-data_2:1.6.2-1 libx11-xcb1_2:1.6.2-1 libxau6_1:1.0.8-1 libxcb-dri2-0_1.9.1-3.1 libxcb-glx0_1.9.1-3.1 libxcb-render0_1.9.1-3.1 libxcb-shape0_1.9.1-3.1 libxcb-shm0_1.9.1-3.1 libxcb-xfixes0_1.9.1-3.1 libxcb1_1.9.1-3.1 libxdamage1_1:1.1.4-1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.2-1 libxfixes3_1:5.0.1-1 libxft2_2.3.1-1 libxml2_2.9.1+dfsg1-3 libxrender1_1:0.9.8-1 libxss1_1:1.2.2-1 libxt6_1:1.1.4-1 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.10.1-1+rpi1+b2 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.2 makedev_2.3.1-93 man-db_2.6.5-2 mawk_1.3.3-17 mount_2.20.1-5.5 mountall_2.52 multiarch-support_2.17-93 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 passwd_1:4.1.5.1-1 patch_2.7.1-3 perl_5.18.1-4 perl-base_5.18.1-4 perl-modules_5.18.1-4 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 r-base-core_3.0.2-1 r-base-dev_3.0.2-1 r-bioc-biocgenerics_0.8.0-1 r-bioc-biostrings_2.30.1-1 r-bioc-genomicranges_1.14.3-1 r-bioc-iranges_1.20.4-1 r-bioc-xvector_0.2.0-1 r-cran-bitops_1.0-6-1 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rsamtools-dummy_0.invalid.0 sed_4.2.2-2 sensible-utils_0.0.9 sysv-rc_2.88dsf-43 sysvinit_2.88dsf-43 sysvinit-utils_2.88dsf-43 tar_1.26+dfsg-8 tcl8.5_8.5.14-2 tk8.5_8.5.14-2 tzdata_2013d-1 ucf_3.0027+nmu1 udev_204-5 unzip_6.0-10 util-linux_2.20.1-5.5 x11-common_1:7.7+4 xdg-utils_1.1.0~rc1+git20111210-7 xz-utils_5.1.1alpha+20120614-2 zip_3.0-8 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun Dec 1 08:59:48 2013 UTC using DSA key ID C09FD35A
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./r-bioc-rsamtools_1.14.2-1.dsc
dpkg-source: info: extracting r-bioc-rsamtools in r-bioc-rsamtools-1.14.2
dpkg-source: info: unpacking r-bioc-rsamtools_1.14.2.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rsamtools_1.14.2-1.debian.tar.gz
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
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=POSIX
LOGNAME=root
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/root
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-9468cabd-1c1b-4256-b974-6ad57b1527e6
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=192.168.1.2 56144 22
SSH_CONNECTION=192.168.1.2 56144 192.168.1.46 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=root
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package r-bioc-rsamtools
dpkg-buildpackage: source version 1.14.2-1
dpkg-source --before-build r-bioc-rsamtools-1.14.2
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
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 (>= 3.0.2-1)" >> debian/r-bioc-rsamtools.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean \
. ; \
else \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library \
--clean . ;\
fi
* installing *source* package 'Rsamtools' ...
** 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c R_init_Rsamtools.c -o R_init_Rsamtools.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c as_bam.c -o as_bam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c bam_data.c -o bam_data.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" -fpic -O3 -pipe -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/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 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c bambuffer.c -o bambuffer.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c bamfile.c -o bamfile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c bcffile.c -o bcffile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c encode.c -o encode.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c fafile.c -o fafile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c io_sam.c -o io_sam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c pileupbam.c -o pileupbam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools_patch.c -o samtools_patch.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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/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 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c tabixfile.c -o tabixfile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c utilities.c -o utilities.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c zip_compression.c -o zip_compression.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/bgzf.c -o samtools/bgzf.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/kstring.c -o samtools/kstring.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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/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 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/bam.c -o samtools/bam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/bam_import.c -o samtools/bam_import.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/sam.c -o samtools/sam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/bam_index.c -o samtools/bam_index.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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/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 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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/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 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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/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 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/razf.c -o samtools/razf.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/faidx.c -o samtools/faidx.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/knetfile.c -o samtools/knetfile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/bam_sort.c -o samtools/bam_sort.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/sam_header.c -o samtools/sam_header.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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/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 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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/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 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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/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 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c samtools/bcftools/index.c -o samtools/bcftools/index.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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/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 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c tabix/index.c -o tabix/index.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O3 -pipe -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
mkdir -p "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usretc"
cp ../Rsamtools.mk "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usretc"
mkdir -p "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools"
mkdir -p "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix"
cp samtools/*.h "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/"
mkdir -p "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib"
g++ -shared -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.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 pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o utilities.o zip_compression.o -pthread -fopenmp /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbam.a /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbcf.a /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libtabix.a -lz -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-rsamtools/usr/lib/R/site-library/Rsamtools/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 (Rsamtools)
rm -vf /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/R.css \
/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/COPYING \
/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE.txt
if test -f debian/overrides; then \
install -d /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/share/lintian/overrides ; \
install -m 0644 debian/overrides \
/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/share/lintian/overrides/r-bioc-rsamtools; \
fi
Adding cdbs dependencies to debian/r-bioc-rsamtools.substvars
dh_installdirs -pr-bioc-rsamtools
rm -rf debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE
dh_installdocs -pr-bioc-rsamtools ./NEWS
dh_installexamples -pr-bioc-rsamtools
dh_installman -pr-bioc-rsamtools
dh_installinfo -pr-bioc-rsamtools
dh_installmenu -pr-bioc-rsamtools
dh_installcron -pr-bioc-rsamtools
dh_installinit -pr-bioc-rsamtools
dh_installdebconf -pr-bioc-rsamtools
dh_installemacsen -pr-bioc-rsamtools
dh_installcatalogs -pr-bioc-rsamtools
dh_installpam -pr-bioc-rsamtools
dh_installlogrotate -pr-bioc-rsamtools
dh_installlogcheck -pr-bioc-rsamtools
dh_installchangelogs -pr-bioc-rsamtools
dh_installudev -pr-bioc-rsamtools
dh_lintian -pr-bioc-rsamtools
dh_bugfiles -pr-bioc-rsamtools
dh_install -pr-bioc-rsamtools
dh_link -pr-bioc-rsamtools
dh_installmime -pr-bioc-rsamtools
dh_installgsettings -pr-bioc-rsamtools
dh_strip -pr-bioc-rsamtools
dh_compress -pr-bioc-rsamtools
dh_fixperms -pr-bioc-rsamtools
dh_makeshlibs -pr-bioc-rsamtools
dh_installdeb -pr-bioc-rsamtools
dh_perl -pr-bioc-rsamtools
dh_shlibdeps -pr-bioc-rsamtools
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/libs/Rsamtools.so was not linked against libgomp.so.1 (it uses none of the library's symbols)
dh_gencontrol -pr-bioc-rsamtools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -pr-bioc-rsamtools
dh_builddeb -pr-bioc-rsamtools
dpkg-deb: building package `r-bioc-rsamtools' in `../r-bioc-rsamtools_1.14.2-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-rsamtools_1.14.2-1_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-rsamtools-1.14.2
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20131212-0819
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-rsamtools_1.14.2-1_armhf.changes:
────────────────────────────────────────
Format: 1.8
Date: Sun, 01 Dec 2013 09:45:58 +0100
Source: r-bioc-rsamtools
Binary: r-bioc-rsamtools
Architecture: armhf
Version: 1.14.2-1
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix file i
Closes: 730984
Changes:
r-bioc-rsamtools (1.14.2-1) unstable; urgency=low
.
* New upstream version (adapted patch)
Closes: #730984
* Build-Depends: r-bioc-xvector
Checksums-Sha1:
ec338d70759c2615bc4c17fb99cac0a9dda74bc8 3560164 r-bioc-rsamtools_1.14.2-1_armhf.deb
Checksums-Sha256:
307261de208a58b7adc64a66001b957f8d3c81d57c27c0c52ad444f9bd4e5a3f 3560164 r-bioc-rsamtools_1.14.2-1_armhf.deb
Files:
0754e5ce5fc8cdc080cb273e449b1e3d 3560164 gnu-r optional r-bioc-rsamtools_1.14.2-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
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r-bioc-rsamtools_1.14.2-1_armhf.deb
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new debian package, version 2.0.
size 3560164 bytes: control archive=4034 bytes.
885 bytes, 15 lines control
10300 bytes, 113 lines md5sums
Package: r-bioc-rsamtools
Version: 1.14.2-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4835
Depends: r-base-core (>= 3.0.2-1), libc6 (>= 2.7), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.2.3.3), r-cran-bitops, r-bioc-biocgenerics, r-bioc-iranges, r-bioc-biostrings, r-bioc-genomicranges, r-bioc-xvector
Suggests: r-bioc-pasillabamsubset, r-bioc-shortread
Section: gnu-r
Priority: optional
Homepage: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html
Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
This package provides an interface to the 'samtools', 'bcftools', and
'tabix' utilities for manipulating SAM (Sequence Alignment / Map),
binary variant call (BCF) and compressed indexed tab-delimited (tabix)
files.
drwxr-xr-x root/root 0 2013-12-12 08:19 ./
drwxr-xr-x root/root 0 2013-12-12 08:19 ./usr/
drwxr-xr-x root/root 0 2013-12-12 08:15 ./usr/lib/
drwxr-xr-x root/root 0 2013-12-12 08:15 ./usr/lib/R/
drwxr-xr-x root/root 0 2013-12-12 08:19 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2013-12-12 08:19 ./usr/lib/R/site-library/Rsamtools/
-rw-r--r-- root/root 1468 2013-12-12 08:15 ./usr/lib/R/site-library/Rsamtools/NAMESPACE
-rw-r--r-- root/root 8496 2013-12-12 08:15 ./usr/lib/R/site-library/Rsamtools/NEWS
-rw-r--r-- root/root 1259 2013-12-12 08:15 ./usr/lib/R/site-library/Rsamtools/DESCRIPTION
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/Meta/
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-rw-r--r-- root/root 2243 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/Meta/links.rds
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-rw-r--r-- root/root 756 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/Meta/nsInfo.rds
drwxr-xr-x root/root 0 2013-12-12 08:19 ./usr/lib/R/site-library/Rsamtools/libs/
-rw-r--r-- root/root 347936 2013-12-12 08:19 ./usr/lib/R/site-library/Rsamtools/libs/Rsamtools.so
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/usretc/
-rw-r--r-- root/root 386 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/usretc/Rsamtools.mk
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/
-rw-r--r-- root/root 7226 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/bcf.h
-rw-r--r-- root/root 1457 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/prob1.h
-rw-r--r-- root/root 25788 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/bam.h
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-rw-r--r-- root/root 6326 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/bgzf.h
-rw-r--r-- root/root 3188 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/faidx.h
-rw-r--r-- root/root 2072 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/kaln.h
-rw-r--r-- root/root 17815 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/khash.h
-rw-r--r-- root/root 1750 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/knetfile.h
-rw-r--r-- root/root 1568 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/kprobaln.h
-rw-r--r-- root/root 8811 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/kseq.h
-rw-r--r-- root/root 10304 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/ksort.h
-rw-r--r-- root/root 4459 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/kstring.h
-rw-r--r-- root/root 4137 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/razf.h
-rw-r--r-- root/root 2688 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/sam.h
-rw-r--r-- root/root 1597 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/samtools/sam_header.h
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/tabix/
-rw-r--r-- root/root 4712 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/tabix/tabix.h
-rw-r--r-- root/root 6326 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/tabix/bgzf.h
-rw-r--r-- root/root 4459 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/tabix/kstring.h
-rw-r--r-- root/root 1750 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/include/tabix/knetfile.h
drwxr-xr-x root/root 0 2013-12-12 08:19 ./usr/lib/R/site-library/Rsamtools/usrlib/
-rw-r--r-- root/root 220494 2013-12-12 08:19 ./usr/lib/R/site-library/Rsamtools/usrlib/libbam.a
-rw-r--r-- root/root 89238 2013-12-12 08:19 ./usr/lib/R/site-library/Rsamtools/usrlib/libbcf.a
-rw-r--r-- root/root 70228 2013-12-12 08:19 ./usr/lib/R/site-library/Rsamtools/usrlib/libtabix.a
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/R/
-rw-r--r-- root/root 1056 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools
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drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/doc/
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-rw-r--r-- root/root 20107 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.Rnw
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-rw-r--r-- root/root 1741 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/doc/index.html
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/
-rw-r--r-- root/root 36 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/README
-rw-r--r-- root/root 36039 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/accepted_hits.sam
-rw-r--r-- root/root 4381 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/coverage.wig
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-rw-r--r-- root/root 20480 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/CaffeineTxdb.sqlite
-rw-r--r-- root/root 176 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa
-rw-r--r-- root/root 112 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa.fai
-rw-r--r-- root/root 126539 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam
-rw-r--r-- root/root 72 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam.bai
-rw-r--r-- root/root 74700 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf
-rw-r--r-- root/root 77 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.bci
-rw-r--r-- root/root 559422 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.sam
-rw-r--r-- root/root 3778 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz
-rw-r--r-- root/root 259 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz.tbi
-rw-r--r-- root/root 333 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam
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-rw-r--r-- root/root 322 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.sam
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-rw-r--r-- root/root 138598 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/pileup.txt
-rw-r--r-- root/root 31 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/samtools-github.txt
-rw-r--r-- root/root 2808 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/extdata/slxMaq09_urls.txt
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/scripts/
-rw-r--r-- root/root 2991 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/scripts/BamViews-1000g.R
-rw-r--r-- root/root 998 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/scripts/features.R
-rw-r--r-- root/root 3386 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/scripts/readAligned_prototype.R
-rw-r--r-- root/root 763 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/scripts/remote_test.R
-rwxr-xr-x root/root 997 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/scripts/update-samtools.sh
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/unitTests/
drwxr-xr-x root/root 0 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/unitTests/cases/
-rw-r--r-- root/root 114590 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/unitTests/cases/ex1.sam.gz
-rw-r--r-- root/root 126539 2013-12-12 08:18 ./usr/lib/R/site-library/Rsamtools/unitTests/cases/ex1_noindex.bam
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┌──────────────────────────────────────────────────────────────────────────────┐
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┌──────────────────────────────────────────────────────────────────────────────┐
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Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 16036
Build-Time: 247
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 448
Job: r-bioc-rsamtools_1.14.2-1
Machine Architecture: armhf
Package: r-bioc-rsamtools
Package-Time: 761
Source-Version: 1.14.2-1
Space: 16036
Status: successful
Version: 1.14.2-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20131212-0819
Build needed 00:12:41, 16036k disc space