r-bioc-variantannotation →
1.10.5-1 →
armhf → 2014-08-14 07:04:49
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-04
╔══════════════════════════════════════════════════════════════════════════════╗
║ r-bioc-variantannotation 1.10.5-1 (armhf) 14 Aug 2014 06:49 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: r-bioc-variantannotation
Version: 1.10.5-1
Source Version: 1.10.5-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/r-bioc-variantannotation-UZKW7z/r-bioc-variantannotation-1.10.5' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/r-bioc-variantannotation-UZKW7z' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-3c8e6ecd-f8db-439d-8414-128015f82aac' 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 [7461 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8505 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-variantannotation' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-variantannotation/trunk/
Need to get 1310 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main r-bioc-variantannotation 1.10.5-1 (dsc) [2358 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main r-bioc-variantannotation 1.10.5-1 (tar) [1300 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main r-bioc-variantannotation 1.10.5-1 (diff) [6924 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-lc6OSf/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 59 not upgraded.
Need to get 0 B/818 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-bioc-biocgenerics, r-bioc-genomicranges, r-bioc-rsamtools (>= 1.15.5), r-bioc-iranges, r-bioc-annotationdbi, r-bioc-genomicfeatures (>= 1.15.15)
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-bioc-biocgenerics, r-bioc-genomicranges, r-bioc-rsamtools (>= 1.15.5), r-bioc-iranges, r-bioc-annotationdbi, r-bioc-genomicfeatures (>= 1.15.15)
dpkg-deb: building package `sbuild-build-depends-r-bioc-variantannotation-dummy' in `/«BUILDDIR»/resolver-qAEjTn/apt_archive/sbuild-build-depends-r-bioc-variantannotation-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install r-bioc-variantannotation 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 bzip2 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 libbz2-1.0 libbz2-dev
libcairo2 libcroco3 libcurl3-nss libdatrie1 libdrm2 libexpat1 libffi6
libfontconfig1 libfreetype6 libgcc-4.9-dev libgcc1 libgcrypt11 libgcrypt20
libgfortran-4.9-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0
libgnutls-deb0-28 libgnutls26 libgomp1 libgpg-error0 libgraphite2-3
libgssapi-krb5-2 libharfbuzz0b libhogweed2 libice6 libidn11 libjbig0
libjpeg8 libjpeg8-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblapack-dev liblapack3 libldap-2.4-2 liblzma-dev libmagic1 libncurses5
libncurses5-dev libncursesw5 libnettle4 libnspr4 libnss3 libp11-kit0
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 libreadline6-dev
librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1
libstdc++-4.9-dev libstdc++6 libtasn1-6 libtcl8.5 libthai-data libthai0
libtiff5 libtinfo-dev libtinfo5 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 man-db ncurses-bin po-debconf r-base-core
r-base-dev r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics
r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-genomeinfodb
r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools
r-bioc-rtracklayer r-bioc-xvector r-cran-bitops r-cran-dbi r-cran-rcurl
r-cran-rsqlite r-cran-xml ucf unzip x11-common xdg-utils zip zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation bzip2-doc 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 rng-tools
gnutls-bin krb5-doc krb5-user liblzma-doc ncurses-doc ttf-baekmuk
ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp
ttf-arphic-bkai00mp readline-doc libstdc++-4.9-doc tcl8.5 tk8.5 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-runit gvfs-bin
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
ca-certificates libgl1-mesa-dri libglib2.0-data shared-mime-info
krb5-locales libgpm2 libsasl2-modules xml-core libmail-sendmail-perl
r-recommended r-doc-html r-bioc-shortread 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 libcurl3-nss libdatrie1 libdrm2 libexpat1 libffi6 libfontconfig1
libfreetype6 libgcrypt11 libgcrypt20 libgfortran-4.9-dev libgfortran3
libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgnutls-deb0-28 libgnutls26
libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed2
libice6 libidn11 libjbig0 libjpeg8 libjpeg8-dev libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 liblzma-dev
libmagic1 libncurses5-dev libnettle4 libnspr4 libnss3 libp11-kit0
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 librtmp1 libsasl2-2
libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libtasn1-6 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 man-db po-debconf r-base-core r-base-dev
r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biomart
r-bioc-biostrings r-bioc-bsgenome r-bioc-genomeinfodb r-bioc-genomicfeatures
r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-rtracklayer
r-bioc-xvector r-cran-bitops r-cran-dbi r-cran-rcurl r-cran-rsqlite
r-cran-xml sbuild-build-depends-r-bioc-variantannotation-dummy ucf unzip
x11-common xdg-utils zip zlib1g-dev
The following packages will be upgraded:
bzip2 cpp cpp-4.9 g++-4.9 gcc gcc-4.9 gcc-4.9-base libasan1 libatomic1
libbz2-1.0 libgcc-4.9-dev libgcc1 libgomp1 libncurses5 libncursesw5 libpcre3
libreadline6 libstdc++-4.9-dev libstdc++6 libtinfo5 libubsan0 ncurses-bin
22 upgraded, 138 newly installed, 0 to remove and 37 not upgraded.
Need to get 95.2 MB/95.2 MB of archives.
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Get:6 http://172.17.0.1/private/ jessie-staging/main libtinfo5 armhf 5.9+20140712-2 [269 kB]
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Get:9 http://172.17.0.1/private/ jessie-staging/main libgomp1 armhf 4.9.1-4 [33.3 kB]
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Get:36 http://172.17.0.1/private/ jessie-staging/main libkeyutils1 armhf 1.5.9-5 [10.9 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main libkrb5support0 armhf 1.12.1+dfsg-7 [53.2 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main libk5crypto3 armhf 1.12.1+dfsg-7 [105 kB]
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Get:41 http://172.17.0.1/private/ jessie-staging/main libidn11 armhf 1.28-2 [154 kB]
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Get:83 http://172.17.0.1/private/ jessie-staging/main librtmp1 armhf 2.4+20131018.git79459a2-4 [53.1 kB]
Get:84 http://172.17.0.1/private/ jessie-staging/main libssh2-1 armhf 1.4.3-3 [114 kB]
Get:85 http://172.17.0.1/private/ jessie-staging/main libcurl3-nss armhf 7.37.1-1 [229 kB]
Get:86 http://172.17.0.1/private/ jessie-staging/main libdatrie1 armhf 0.2.8-1 [29.1 kB]
Get:87 http://172.17.0.1/private/ jessie-staging/main libgfortran3 armhf 4.9.1-4 [154 kB]
Get:88 http://172.17.0.1/private/ jessie-staging/main libgraphite2-3 armhf 1.2.4-3 [48.2 kB]
Get:89 http://172.17.0.1/private/ jessie-staging/main libharfbuzz0b armhf 0.9.33-1 [453 kB]
Get:90 http://172.17.0.1/private/ jessie-staging/main x11-common all 1:7.7+7 [287 kB]
Get:91 http://172.17.0.1/private/ jessie-staging/main libice6 armhf 2:1.0.9-1 [51.2 kB]
Get:92 http://172.17.0.1/private/ jessie-staging/main libjbig0 armhf 2.1-3 [27.3 kB]
Get:93 http://172.17.0.1/private/ jessie-staging/main libjpeg8 armhf 8d1-1 [108 kB]
Get:94 http://172.17.0.1/private/ jessie-staging/main libthai-data all 0.1.20-3 [157 kB]
Get:95 http://172.17.0.1/private/ jessie-staging/main libthai0 armhf 0.1.20-3 [41.6 kB]
Get:96 http://172.17.0.1/private/ jessie-staging/main fontconfig armhf 2.11.0-5 [401 kB]
Get:97 http://172.17.0.1/private/ jessie-staging/main libpango-1.0-0 armhf 1.36.3-1 [265 kB]
Get:98 http://172.17.0.1/private/ jessie-staging/main libpangoft2-1.0-0 armhf 1.36.3-1 [199 kB]
Get:99 http://172.17.0.1/private/ jessie-staging/main libpangocairo-1.0-0 armhf 1.36.3-1 [189 kB]
Get:100 http://172.17.0.1/private/ jessie-staging/main libpaper1 armhf 1.1.24+nmu3 [20.7 kB]
Get:101 http://172.17.0.1/private/ jessie-staging/main libpcrecpp0 armhf 1:8.35-3 [138 kB]
Get:102 http://172.17.0.1/private/ jessie-staging/main libsm6 armhf 2:1.2.2-1 [31.2 kB]
Get:103 http://172.17.0.1/private/ jessie-staging/main libtcl8.5 armhf 8.5.15-4 [649 kB]
Get:104 http://172.17.0.1/private/ jessie-staging/main libtiff5 armhf 4.0.3-9 [191 kB]
Get:105 http://172.17.0.1/private/ jessie-staging/main libxft2 armhf 2.3.2-1 [48.3 kB]
Get:106 http://172.17.0.1/private/ jessie-staging/main libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:107 http://172.17.0.1/private/ jessie-staging/main libtk8.5 armhf 8.5.15-4 [646 kB]
Get:108 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:109 http://172.17.0.1/private/ jessie-staging/main libxt6 armhf 1:1.1.4-1 [183 kB]
Get:110 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.19-1 [57.7 kB]
Get:111 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.19.2-1 [116 kB]
Get:112 http://172.17.0.1/private/ jessie-staging/main cdbs all 0.4.125 [75.3 kB]
Get:113 http://172.17.0.1/private/ jessie-staging/main cpp armhf 4:4.9.1-1 [17.0 kB]
Get:114 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.19.2-1 [1160 kB]
Get:115 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:116 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu3 [220 kB]
Get:117 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140613 [692 kB]
Get:118 http://172.17.0.1/private/ jessie-staging/main gcc armhf 4:4.9.1-1 [5134 B]
Get:119 http://172.17.0.1/private/ jessie-staging/main libgfortran-4.9-dev armhf 4.9.1-4 [181 kB]
Get:120 http://172.17.0.1/private/ jessie-staging/main gfortran-4.9 armhf 4.9.1-4 [4507 kB]
Get:121 http://172.17.0.1/private/ jessie-staging/main gfortran armhf 4:4.9.1-1 [1288 B]
Get:122 http://172.17.0.1/private/ jessie-staging/main libblas3 armhf 1.2.20110419-7 [186 kB]
Get:123 http://172.17.0.1/private/ jessie-staging/main libblas-dev armhf 1.2.20110419-7 [201 kB]
Get:124 http://172.17.0.1/private/ jessie-staging/main libbz2-dev armhf 1.0.6-7 [27.5 kB]
Get:125 http://172.17.0.1/private/ jessie-staging/main libjpeg8-dev armhf 8d1-1 [205 kB]
Get:126 http://172.17.0.1/private/ jessie-staging/main liblapack3 armhf 3.5.0-3 [1277 kB]
Get:127 http://172.17.0.1/private/ jessie-staging/main liblapack-dev armhf 3.5.0-3 [1325 kB]
Get:128 http://172.17.0.1/private/ jessie-staging/main liblzma-dev armhf 5.1.1alpha+20120614-2 [272 kB]
Get:129 http://172.17.0.1/private/ jessie-staging/main libtinfo-dev armhf 5.9+20140712-2 [65.4 kB]
Get:130 http://172.17.0.1/private/ jessie-staging/main libncurses5-dev armhf 5.9+20140712-2 [153 kB]
Get:131 http://172.17.0.1/private/ jessie-staging/main libpaper-utils armhf 1.1.24+nmu3 [17.0 kB]
Get:132 http://172.17.0.1/private/ jessie-staging/main libpcre3-dev armhf 1:8.35-3 [407 kB]
Get:133 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1+rpi1 [192 kB]
Get:134 http://172.17.0.1/private/ jessie-staging/main libpng12-dev armhf 1.2.50-2 [236 kB]
Get:135 http://172.17.0.1/private/ jessie-staging/main libreadline6-dev armhf 6.3-8 [105 kB]
Get:136 http://172.17.0.1/private/ jessie-staging/main libreadline-dev armhf 6.3-8 [994 B]
Get:137 http://172.17.0.1/private/ jessie-staging/main zip armhf 3.0-8 [326 kB]
Get:138 http://172.17.0.1/private/ jessie-staging/main unzip armhf 6.0-12 [152 kB]
Get:139 http://172.17.0.1/private/ jessie-staging/main xdg-utils all 1.1.0~rc1+git20111210-7.1 [64.6 kB]
Get:140 http://172.17.0.1/private/ jessie-staging/main r-base-core armhf 3.1.1-1 [19.5 MB]
Get:141 http://172.17.0.1/private/ jessie-staging/main r-base-dev all 3.1.1-1 [4018 B]
Get:142 http://172.17.0.1/private/ jessie-staging/main r-cran-dbi armhf 0.2-7-1 [274 kB]
Get:143 http://172.17.0.1/private/ jessie-staging/main r-cran-rsqlite armhf 0.11.4-1 [300 kB]
Get:144 http://172.17.0.1/private/ jessie-staging/main r-bioc-biocgenerics all 0.10.0-1 [397 kB]
Get:145 http://172.17.0.1/private/ jessie-staging/main r-bioc-biobase armhf 2.24.0-1 [2201 kB]
Get:146 http://172.17.0.1/private/ jessie-staging/main r-bioc-iranges armhf 1.22.8-1 [1807 kB]
Get:147 http://172.17.0.1/private/ jessie-staging/main r-bioc-genomeinfodb all 1.0.2-1 [221 kB]
Get:148 http://172.17.0.1/private/ jessie-staging/main r-bioc-annotationdbi all 1.26.0-1 [4177 kB]
Get:149 http://172.17.0.1/private/ jessie-staging/main r-cran-xml armhf 3.98-1.1-1 [1800 kB]
Get:150 http://172.17.0.1/private/ jessie-staging/main r-cran-bitops armhf 1.0-6-1 [23.6 kB]
Get:151 http://172.17.0.1/private/ jessie-staging/main r-cran-rcurl armhf 1.95-4.1-1 [532 kB]
Get:152 http://172.17.0.1/private/ jessie-staging/main r-bioc-biomart all 2.20.0-1 [365 kB]
Get:153 http://172.17.0.1/private/ jessie-staging/main r-bioc-xvector armhf 0.4.0-1 [328 kB]
Get:154 http://172.17.0.1/private/ jessie-staging/main r-bioc-biostrings armhf 2.32.0-1 [2235 kB]
Get:155 http://172.17.0.1/private/ jessie-staging/main r-bioc-genomicranges armhf 1.16.3-1 [1097 kB]
Get:156 http://172.17.0.1/private/ jessie-staging/main r-bioc-rsamtools armhf 1.16.1-2 [3091 kB]
Get:157 http://172.17.0.1/private/ jessie-staging/main r-bioc-bsgenome all 1.32.0-1 [763 kB]
Get:158 http://172.17.0.1/private/ jessie-staging/main r-bioc-rtracklayer armhf 1.22.0-1 [1727 kB]
Get:159 http://172.17.0.1/private/ jessie-staging/main r-bioc-genomicfeatures all 1.16.2-1 [887 kB]
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No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libnspr4:armhf (2:4.10.6-1) ...
Setting up libnss3:armhf (2:3.16.3-1) ...
Setting up librtmp1:armhf (2.4+20131018.git79459a2-4) ...
Setting up libssh2-1:armhf (1.4.3-3) ...
Setting up libcurl3-nss:armhf (7.37.1-1) ...
Setting up libdatrie1:armhf (0.2.8-1) ...
Setting up libgfortran3:armhf (4.9.1-4) ...
Setting up libgraphite2-3:armhf (1.2.4-3) ...
Setting up libharfbuzz0b:armhf (0.9.33-1) ...
Setting up x11-common (1:7.7+7) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.9-1) ...
Setting up libjbig0:armhf (2.1-3) ...
Setting up libjpeg8:armhf (8d1-1) ...
Setting up libthai-data (0.1.20-3) ...
Setting up libthai0:armhf (0.1.20-3) ...
Setting up fontconfig (2.11.0-5) ...
Regenerating fonts cache... done.
Setting up libpango-1.0-0:armhf (1.36.3-1) ...
Setting up libpangoft2-1.0-0:armhf (1.36.3-1) ...
Setting up libpangocairo-1.0-0:armhf (1.36.3-1) ...
Setting up libpaper1:armhf (1.1.24+nmu3) ...
Creating config file /etc/papersize with new version
Setting up libpcrecpp0:armhf (1:8.35-3) ...
Setting up libsm6:armhf (2:1.2.2-1) ...
Setting up libtcl8.5:armhf (8.5.15-4) ...
Setting up libtiff5:armhf (4.0.3-9) ...
Setting up libxft2:armhf (2.3.2-1) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libtk8.5:armhf (8.5.15-4) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libxt6:armhf (1:1.1.4-1) ...
Setting up file (1:5.19-1) ...
Setting up gettext-base (0.19.2-1) ...
Setting up cdbs (0.4.125) ...
Setting up cpp (4:4.9.1-1) ...
Setting up gettext (0.19.2-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu3) ...
Setting up debhelper (9.20140613) ...
Setting up gcc (4:4.9.1-1) ...
Setting up libgfortran-4.9-dev:armhf (4.9.1-4) ...
Setting up gfortran-4.9 (4.9.1-4) ...
Setting up gfortran (4:4.9.1-1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libblas3 (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libblas-dev (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libbz2-dev:armhf (1.0.6-7) ...
Setting up libjpeg8-dev:armhf (8d1-1) ...
Setting up liblapack3 (3.5.0-3) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up liblapack-dev (3.5.0-3) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up liblzma-dev:armhf (5.1.1alpha+20120614-2) ...
Setting up libtinfo-dev:armhf (5.9+20140712-2) ...
Setting up libncurses5-dev:armhf (5.9+20140712-2) ...
Setting up libpaper-utils (1.1.24+nmu3) ...
Setting up libpcre3-dev:armhf (1:8.35-3) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1+rpi1) ...
Setting up libpng12-dev:armhf (1.2.50-2) ...
Setting up libreadline6-dev:armhf (6.3-8) ...
Setting up libreadline-dev:armhf (6.3-8) ...
Setting up zip (3.0-8) ...
Setting up unzip (6.0-12) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-7.1) ...
Setting up r-base-core (3.1.1-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.1.1-1) ...
Setting up r-cran-dbi (0.2-7-1) ...
Setting up r-cran-rsqlite (0.11.4-1) ...
Setting up r-bioc-biocgenerics (0.10.0-1) ...
Setting up r-bioc-biobase (2.24.0-1) ...
Setting up r-bioc-iranges (1.22.8-1) ...
Setting up r-bioc-genomeinfodb (1.0.2-1) ...
Setting up r-bioc-annotationdbi (1.26.0-1) ...
Setting up r-cran-xml (3.98-1.1-1) ...
Setting up r-cran-bitops (1.0-6-1) ...
Setting up r-cran-rcurl (1.95-4.1-1) ...
Setting up r-bioc-biomart (2.20.0-1) ...
Setting up r-bioc-xvector (0.4.0-1) ...
Setting up r-bioc-biostrings (2.32.0-1) ...
Setting up r-bioc-genomicranges (1.16.3-1) ...
Setting up r-bioc-rsamtools (1.16.1-2) ...
Setting up r-bioc-bsgenome (1.32.0-1) ...
Setting up r-bioc-rtracklayer (1.22.0-1) ...
Setting up r-bioc-genomicfeatures (1.16.2-1) ...
Setting up sbuild-build-depends-r-bioc-variantannotation-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-7) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.16-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140617-1 dpkg-dev_1.17.10 g++-4.9_4.9.1-4 gcc-4.8_4.8.3-4 gcc-4.9_4.9.1-4 libc6-dev_2.19-7 libstdc++-4.9-dev_4.9.1-4 libstdc++6_4.9.1-4 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_1.0.6-7 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_4.9.1-4 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_4.9.1-4 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_4.9.1-4 gcc-4.9-base_4.9.1-4 gettext_0.19.2-1 gettext-base_0.19.2-1 gfortran_4:4.9.1-1 gfortran-4.9_4.9.1-4 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_4.9.1-4 libasprintf0c2_0.19.2-1 libatomic1_4.9.1-4 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_1.0.6-7 libbz2-dev_1.0.6-7 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 libcurl3-nss_7.37.1-1 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_2.5.2-1.1 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.3-4 libgcc-4.9-dev_4.9.1-4 libgcc1_1:4.9.1-4 libgcrypt11_1.5.3-5 libgcrypt20_1.6.1-2 libgdbm3_1.8.3-12 libgfortran-4.9-dev_4.9.1-4 libgfortran3_4.9.1-4 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 libgnutls-deb0-28_3.2.16-1 libgnutls26_2.12.23-17 libgomp1_4.9.1-4 libgpg-error0_1.13-3 libgraphite2-3_1.2.4-3 libgssapi-krb5-2_1.12.1+dfsg-7 libharfbuzz0b_0.9.33-1 libhogweed2_2.7.1-3 libice6_2:1.0.9-1 libidn11_1.28-2 libisl10_0.12.2-2 libjbig0_2.1-3 libjpeg8_8d1-1 libjpeg8-dev_8d1-1 libk5crypto3_1.12.1+dfsg-7 libkeyutils1_1.5.9-5 libklibc_2.0.3-1+rpi1 libkmod2_16-2 libkrb5-3_1.12.1+dfsg-7 libkrb5support0_1.12.1+dfsg-7 liblapack-dev_3.5.0-3 liblapack3_3.5.0-3 libldap-2.4-2_2.4.39-1+rpi1 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+20140712-2 libncurses5-dev_5.9+20140712-2 libncursesw5_5.9+20140712-2 libnettle4_2.7.1-3 libnspr4_2:4.10.6-1 libnss3_2:3.16.3-1 libp11-kit0_0.20.2-5 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_1.2.50-2 libpng12-dev_1.2.50-2 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-5 libreadline-dev_6.3-8 libreadline6_6.3-8 libreadline6-dev_6.3-8 librtmp1_2.4+20131018.git79459a2-4 libsasl2-2_2.1.26.dfsg1-11 libsasl2-modules-db_2.1.26.dfsg1-11 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 libssh2-1_1.4.3-3 libstdc++-4.9-dev_4.9.1-4 libstdc++6_4.9.1-4 libtasn1-6_4.0-2 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+20140712-2 libtinfo5_5.9+20140712-2 libtk8.5_8.5.15-4 libubsan0_4.9.1-4 libudev1_204-14 libunistring0_0.9.3-5.2 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 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+20140712-2 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-annotationdbi_1.26.0-1 r-bioc-biobase_2.24.0-1 r-bioc-biocgenerics_0.10.0-1 r-bioc-biomart_2.20.0-1 r-bioc-biostrings_2.32.0-1 r-bioc-bsgenome_1.32.0-1 r-bioc-genomeinfodb_1.0.2-1 r-bioc-genomicfeatures_1.16.2-1 r-bioc-genomicranges_1.16.3-1 r-bioc-iranges_1.22.8-1 r-bioc-rsamtools_1.16.1-2 r-bioc-rtracklayer_1.22.0-1 r-bioc-xvector_0.4.0-1 r-cran-bitops_1.0-6-1 r-cran-dbi_0.2-7-1 r-cran-rcurl_1.95-4.1-1 r-cran-rsqlite_0.11.4-1 r-cran-xml_3.98-1.1-1 raspbian-archive-keyring_20120528.2 readline-common_6.3-6 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-variantannotation-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 Fri Aug 8 12:44:34 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-variantannotation_1.10.5-1.dsc
dpkg-source: info: extracting r-bioc-variantannotation in r-bioc-variantannotation-1.10.5
dpkg-source: info: unpacking r-bioc-variantannotation_1.10.5.orig.tar.gz
dpkg-source: info: unpacking r-bioc-variantannotation_1.10.5-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch
dpkg-source: info: applying drop_tests_requiring_large_data_sets.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-3c8e6ecd-f8db-439d-8414-128015f82aac
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-variantannotation
dpkg-buildpackage: source version 1.10.5-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build r-bioc-variantannotation-1.10.5
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-variantannotation.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-variantannotation/usr/lib/R/site-library --clean \
. ; \
else \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-variantannotation/usr/lib/R/site-library \
--clean . ;\
fi
* installing *source* package 'VariantAnnotation' ...
** libs
make[1]: Entering directory '/«PKGBUILDDIR»/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dna_hash.c -o dna_hash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rle.c -o rle.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c strhash.c -o strhash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c utilities.c -o utilities.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c vcffile.c -o vcffile.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c vcftype.c -o vcftype.o
gcc -std=gnu99 -shared -Wl,-z,relro -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o /usr/lib/R/site-library/Rsamtools/usrlib//libbam.a /usr/lib/R/site-library/Rsamtools/usrlib//libbcf.a /usr/lib/R/site-library/Rsamtools/usrlib//libtabix.a -lz -pthread -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-variantannotation/usr/lib/R/site-library/VariantAnnotation/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'tabulate' in package 'VariantAnnotation'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VariantAnnotation)
rm -vf /«PKGBUILDDIR»/debian/r-bioc-variantannotation/usr/lib/R/site-library/R.css \
/«PKGBUILDDIR»/debian/r-bioc-variantannotation/usr/lib/R/site-library/VariantAnnotation/COPYING \
/«PKGBUILDDIR»/debian/r-bioc-variantannotation/usr/lib/R/site-library/VariantAnnotation/LICENSE.txt
if test -f debian/overrides; then \
install -d /«PKGBUILDDIR»/debian/r-bioc-variantannotation/usr/share/lintian/overrides ; \
install -m 0644 debian/overrides \
/«PKGBUILDDIR»/debian/r-bioc-variantannotation/usr/share/lintian/overrides/r-bioc-variantannotation; \
fi
Adding cdbs dependencies to debian/r-bioc-variantannotation.substvars
dh_installdirs -pr-bioc-variantannotation
dh_installdocs -pr-bioc-variantannotation ./NEWS
dh_installexamples -pr-bioc-variantannotation
dh_installman -pr-bioc-variantannotation
dh_installinfo -pr-bioc-variantannotation
dh_installmenu -pr-bioc-variantannotation
dh_installcron -pr-bioc-variantannotation
dh_installinit -pr-bioc-variantannotation
dh_installdebconf -pr-bioc-variantannotation
dh_installemacsen -pr-bioc-variantannotation
dh_installcatalogs -pr-bioc-variantannotation
dh_installpam -pr-bioc-variantannotation
dh_installlogrotate -pr-bioc-variantannotation
dh_installlogcheck -pr-bioc-variantannotation
dh_installchangelogs -pr-bioc-variantannotation
dh_installudev -pr-bioc-variantannotation
dh_lintian -pr-bioc-variantannotation
dh_bugfiles -pr-bioc-variantannotation
dh_install -pr-bioc-variantannotation
dh_link -pr-bioc-variantannotation
dh_installmime -pr-bioc-variantannotation
dh_installgsettings -pr-bioc-variantannotation
dh_strip -pr-bioc-variantannotation
dh_compress -pr-bioc-variantannotation
dh_fixperms -pr-bioc-variantannotation
dh_makeshlibs -pr-bioc-variantannotation
dh_installdeb -pr-bioc-variantannotation
dh_perl -pr-bioc-variantannotation
dh_shlibdeps -pr-bioc-variantannotation
dh_gencontrol -pr-bioc-variantannotation
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -pr-bioc-variantannotation
dh_builddeb -pr-bioc-variantannotation
dpkg-deb: building package `r-bioc-variantannotation' in `../r-bioc-variantannotation_1.10.5-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-variantannotation_1.10.5-1_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-variantannotation-1.10.5
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140814-0704
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-variantannotation_1.10.5-1_armhf.changes:
────────────────────────────────────────────────
Format: 1.8
Date: Fri, 08 Aug 2014 14:36:50 +0200
Source: r-bioc-variantannotation
Binary: r-bioc-variantannotation
Architecture: armhf
Version: 1.10.5-1
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-variantannotation - BioConductor annotation of genetic variants
Changes:
r-bioc-variantannotation (1.10.5-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
850ad6da43606a26eb97434540ea61988f56edcf 1780136 r-bioc-variantannotation_1.10.5-1_armhf.deb
Checksums-Sha256:
fa6eb4d7e8e9fd1b61296556610f8a26c1b2bb94dac059d8a9f3d2467c4e4138 1780136 r-bioc-variantannotation_1.10.5-1_armhf.deb
Files:
e28b2da3e346f70944d50230f83ac29e 1780136 gnu-r optional r-bioc-variantannotation_1.10.5-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-variantannotation_1.10.5-1_armhf.deb
───────────────────────────────────────────
new debian package, version 2.0.
size 1780136 bytes: control archive=2775 bytes.
739 bytes, 13 lines control
6454 bytes, 65 lines md5sums
Package: r-bioc-variantannotation
Version: 1.10.5-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2250
Depends: r-base-core (>= 3.1.1-1), libc6 (>= 2.15), zlib1g (>= 1:1.2.3.3), r-bioc-biocgenerics, r-bioc-genomicranges, r-bioc-rsamtools (>= 1.15.5), r-bioc-iranges, r-bioc-annotationdbi, r-bioc-genomicfeatures (>= 1.15.15)
Suggests: r-bioc-snpstats
Section: gnu-r
Priority: optional
Homepage: http://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html
Description: BioConductor annotation of genetic variants
This BioConductor package provides R functions to annotate variants,
compute amino acid coding changess and to predict coding outcomes.
drwxr-xr-x root/root 0 2014-08-14 07:04 ./
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drwxr-xr-x root/root 0 2014-08-14 07:01 ./usr/lib/
drwxr-xr-x root/root 0 2014-08-14 07:01 ./usr/lib/R/
drwxr-xr-x root/root 0 2014-08-14 07:04 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2014-08-14 07:03 ./usr/lib/R/site-library/VariantAnnotation/
-rw-r--r-- root/root 3943 2014-08-14 07:01 ./usr/lib/R/site-library/VariantAnnotation/NAMESPACE
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-rw-r--r-- root/root 1203 2014-08-14 07:01 ./usr/lib/R/site-library/VariantAnnotation/DESCRIPTION
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-rw-r--r-- root/root 204915 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/doc/VariantAnnotation.pdf
-rw-r--r-- root/root 3547 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/doc/filterVcf.R
-rw-r--r-- root/root 14486 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/doc/filterVcf.Rnw
-rw-r--r-- root/root 198418 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/doc/filterVcf.pdf
-rw-r--r-- root/root 1741 2014-08-14 07:03 ./usr/lib/R/site-library/VariantAnnotation/doc/index.html
drwxr-xr-x root/root 0 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/extdata/
-rw-r--r-- root/root 561698 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/extdata/chr22.vcf.gz
-rw-r--r-- root/root 655 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/extdata/chr22.vcf.gz.tbi
-rw-r--r-- root/root 113168 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/extdata/chr7-sub.vcf.gz
-rw-r--r-- root/root 744 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/extdata/chr7-sub.vcf.gz.tbi
-rw-r--r-- root/root 1645 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/extdata/ex2.vcf
-rw-r--r-- root/root 24819 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/extdata/gl_chr1.vcf
-rw-r--r-- root/root 124778 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/extdata/h1187-10k.vcf.gz
-rw-r--r-- root/root 441 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/extdata/h1187-10k.vcf.gz.tbi
-rw-r--r-- root/root 3060 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/extdata/structural.vcf
drwxr-xr-x root/root 0 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/scripts/
-rw-r--r-- root/root 10910 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/scripts/test_Rplinkseq.R
drwxr-xr-x root/root 0 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/
drwxr-xr-x root/root 0 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/
-rw-r--r-- root/root 602 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/FORMAT_header_no_SAMPLEs.vcf
-rw-r--r-- root/root 3074 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/VarScan_header.vcf
-rw-r--r-- root/root 1836 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/expand.vcf
-rw-r--r-- root/root 614 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/fewer-FORMAT-than-GENO.vcf
-rw-r--r-- root/root 553 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/missing-FORMAT-metadata-elt.vcf
-rw-r--r-- root/root 2970 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/mixedStructural.vcf
-rw-r--r-- root/root 3044 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/negative_FORMAT_Number.vcf
-rw-r--r-- root/root 287 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/no_FORMAT_column.vcf
-rw-r--r-- root/root 573 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/no_GENO_row.vcf
-rw-r--r-- root/root 300 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/no_INFO_header.vcf
-rw-r--r-- root/root 1679 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/unspecified_INFO_FORMAT_fields.vcf
-rw-r--r-- root/root 2874 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/test_ScanVcfParam-class.R
-rw-r--r-- root/root 9596 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/test_VCF-class.R
-rw-r--r-- root/root 11019 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/test_VRanges-class.R
-rw-r--r-- root/root 1130 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/test_expand-methods.R
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-rw-r--r-- root/root 6080 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/test_genotypeToSnpMatrix.R
-rw-r--r-- root/root 2914 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/test_isSNV.R
-rw-r--r-- root/root 8821 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/test_readVcf-methods.R
-rw-r--r-- root/root 3800 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/test_scanVcf.R
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-rw-r--r-- root/root 636 2014-08-14 07:02 ./usr/lib/R/site-library/VariantAnnotation/unitTests/test_summarizeVariants-methods.R
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drwxr-xr-x root/root 0 2014-08-14 07:03 ./usr/lib/R/site-library/VariantAnnotation/help/
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drwxr-xr-x root/root 0 2014-08-14 07:04 ./usr/share/doc/r-bioc-variantannotation/
-rw-r--r-- root/root 1506 2014-07-24 07:42 ./usr/share/doc/r-bioc-variantannotation/README.test
-rw-r--r-- root/root 5411 2014-07-24 09:00 ./usr/share/doc/r-bioc-variantannotation/copyright
-rw-r--r-- root/root 3177 2014-04-11 22:35 ./usr/share/doc/r-bioc-variantannotation/NEWS.gz
-rw-r--r-- root/root 215 2014-08-08 12:37 ./usr/share/doc/r-bioc-variantannotation/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 6304
Build-Time: 207
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 674
Job: r-bioc-variantannotation_1.10.5-1
Machine Architecture: armhf
Package: r-bioc-variantannotation
Package-Time: 933
Source-Version: 1.10.5-1
Space: 6304
Status: successful
Version: 1.10.5-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140814-0704
Build needed 00:15:33, 6304k disc space