r-bioc-variantannotation →
1.14.13-1 →
armhf → 2015-09-30 06:08:18
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-01
╔══════════════════════════════════════════════════════════════════════════════╗
║ r-bioc-variantannotation 1.14.13-1 (armhf) 30 Sep 2015 05:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: r-bioc-variantannotation
Version: 1.14.13-1
Source Version: 1.14.13-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/r-bioc-variantannotation-w3BGsh/r-bioc-variantannotation-1.14.13' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/r-bioc-variantannotation-w3BGsh' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-2b30b98d-3bb6-4ca5-aa79-ad30d04f9b69' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
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Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8337 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.2 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Reading package lists...
Building dependency tree...
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 1326 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main r-bioc-variantannotation 1.14.13-1 (dsc) [2282 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main r-bioc-variantannotation 1.14.13-1 (tar) [1316 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main r-bioc-variantannotation 1.14.13-1 (diff) [7240 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-OdyxWc/apt_archive/sbuild-build-depends-core-dummy.deb'.
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Get:1 file: ./ Release.gpg [299 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
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 27 not upgraded.
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Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), cdbs, r-base-dev, r-bioc-genomicfeatures (>= 1.20.1), r-bioc-bsgenome (>= 1.36.1)
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), cdbs, r-base-dev, r-bioc-genomicfeatures (>= 1.20.1), r-bioc-bsgenome (>= 1.36.1)
dpkg-deb: building package 'sbuild-build-depends-r-bioc-variantannotation-dummy' in '/«BUILDDIR»/resolver-UJQitG/apt_archive/sbuild-build-depends-r-bioc-variantannotation-dummy.deb'.
OK
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Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
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 ca-certificates cdbs debhelper file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-5
groff-base intltool-debian libblas-common libblas-dev libblas3 libbz2-dev
libcairo2 libcroco3 libcurl3 libdatrie1 libexpat1 libffi6 libfontconfig1
libfreetype6 libgfortran-5-dev libgfortran3 libglib2.0-0 libgnutls-deb0-28
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed4 libice6 libicu55
libidn11 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libldap-2.4-2 liblzma-dev libmagic1 libncurses5-dev libnettle6 libp11-kit0
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpcre16-3 libpcre3 libpcre3-dev libpcre32-3 libpcrecpp0v5
libpipeline1 libpixman-1-0 libpng12-dev libreadline-dev libreadline6-dev
librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1
libssl1.0.0 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff5 libtinfo-dev
libtk8.6 libunistring0 libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1
libxt6 littler man-db openssl po-debconf r-base-core r-base-dev
r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel
r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-genomeinfodb
r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges
r-bioc-iranges r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors
r-bioc-xvector r-cran-base64enc r-cran-batchjobs r-cran-bbmisc r-cran-bitops
r-cran-brew r-cran-checkmate r-cran-codetools r-cran-dbi r-cran-digest
r-cran-fail r-cran-foreach r-cran-futile.logger r-cran-futile.options
r-cran-iterators r-cran-lambda.r r-cran-pkgkitten r-cran-plyr r-cran-rcpp
r-cran-rcurl r-cran-rsqlite r-cran-sendmailr r-cran-snow r-cran-stringr
r-cran-xml ucf unzip x11-common xdg-utils zip zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc autopoint
libasprintf-dev libgettextpo-dev gfortran-doc gfortran-5-doc
libgfortran3-dbg groff gnutls-bin krb5-doc krb5-user liblzma-doc ncurses-doc
readline-doc tcl8.6 tk8.6 r-cran-getopt less www-browser libmail-box-perl
r-doc-info r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base
texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra
texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo
r-cran-mpi r-cran-rmysql r-cran-inline r-cran-runit r-cran-rmpi
r-cran-rsprng r-cran-rlecuyer gvfs-bin
Recommended packages:
autotools-dev curl wget lynx-cur bzip2-doc libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libsasl2-modules xml-core libmail-sendmail-perl
r-recommended r-doc-html r-cran-doparallel r-bioc-shortread r-cran-mass
r-cran-domc r-cran-abind libfile-mimeinfo-perl libnet-dbus-perl
libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
bsdmainutils ca-certificates cdbs debhelper file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-5
groff-base intltool-debian libblas-common libblas-dev libblas3 libbz2-dev
libcairo2 libcroco3 libcurl3 libdatrie1 libexpat1 libffi6 libfontconfig1
libfreetype6 libgfortran-5-dev libgfortran3 libglib2.0-0 libgnutls-deb0-28
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed4 libice6 libicu55
libidn11 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libldap-2.4-2 liblzma-dev libmagic1 libncurses5-dev libnettle6 libp11-kit0
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1
libpixman-1-0 libpng12-dev libreadline-dev libreadline6-dev librtmp1
libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libssl1.0.0
libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff5 libtinfo-dev libtk8.6
libunistring0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0
libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6
littler man-db openssl po-debconf r-base-core r-base-dev
r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel
r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-genomeinfodb
r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges
r-bioc-iranges r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors
r-bioc-xvector r-cran-base64enc r-cran-batchjobs r-cran-bbmisc r-cran-bitops
r-cran-brew r-cran-checkmate r-cran-codetools r-cran-dbi r-cran-digest
r-cran-fail r-cran-foreach r-cran-futile.logger r-cran-futile.options
r-cran-iterators r-cran-lambda.r r-cran-pkgkitten r-cran-plyr r-cran-rcpp
r-cran-rcurl r-cran-rsqlite r-cran-sendmailr r-cran-snow r-cran-stringr
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:
libpcre3
1 upgraded, 148 newly installed, 0 to remove and 26 not upgraded.
Need to get 127 MB/127 MB of archives.
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Get:3 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.3-1 [975 kB]
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Get:9 http://172.17.0.1/private/ stretch-staging/main ucf all 3.0030 [69.7 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main fonts-dejavu-core all 2.35-1 [1064 kB]
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Get:17 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.2+zdfsg1-4 [797 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libgfortran3 armhf 5.2.1-17+rpi1 [154 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libthai-data all 0.1.22-2 [161 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libdatrie1 armhf 0.2.9-2 [31.5 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libthai0 armhf 0.1.22-2 [44.8 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main libpango-1.0-0 armhf 1.36.8-3 [274 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main libpixman-1-0 armhf 0.33.2-2 [444 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libxdmcp6 armhf 1:1.1.2-1 [25.0 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main libxcb1 armhf 1.10-3+b1 [40.6 kB]
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Get:32 http://172.17.0.1/private/ stretch-staging/main libxcb-shm0 armhf 1.10-3+b1 [11.4 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main libxrender1 armhf 1:0.9.8-1+b1 [28.4 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main libcairo2 armhf 1.14.2-2 [672 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libgraphite2-3 armhf 1.3.3-1 [61.1 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libharfbuzz0b armhf 1.0.1-1+b1 [501 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libpangoft2-1.0-0 armhf 1.36.8-3 [207 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libpangocairo-1.0-0 armhf 1.36.8-3 [197 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main libpcrecpp0v5 armhf 2:8.35-7.2 [141 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main libssh2-1 armhf 1.5.0-2 [122 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libtcl8.6 armhf 8.6.4+dfsg-2 [866 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main libxft2 armhf 2.3.2-1 [48.3 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main x11-common all 1:7.7+9 [287 kB]
Get:46 http://172.17.0.1/private/ stretch-staging/main libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main libtk8.6 armhf 8.6.4+dfsg-2 [664 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
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Get:50 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.25-2 [250 kB]
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Get:57 http://172.17.0.1/private/ stretch-staging/main libkeyutils1 armhf 1.5.9-7 [11.5 kB]
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Get:59 http://172.17.0.1/private/ stretch-staging/main libk5crypto3 armhf 1.13.2+dfsg-2 [109 kB]
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Get:71 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:73 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150811 [817 kB]
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Get:90 http://172.17.0.1/private/ stretch-staging/main libtinfo-dev armhf 6.0+20150810-1 [65.8 kB]
Get:91 http://172.17.0.1/private/ stretch-staging/main libncurses5-dev armhf 6.0+20150810-1 [154 kB]
Get:92 http://172.17.0.1/private/ stretch-staging/main libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:93 http://172.17.0.1/private/ stretch-staging/main libpcre16-3 armhf 2:8.35-7.2 [221 kB]
Get:94 http://172.17.0.1/private/ stretch-staging/main libpcre32-3 armhf 2:8.35-7.2 [214 kB]
Get:95 http://172.17.0.1/private/ stretch-staging/main libpcre3-dev armhf 2:8.35-7.2 [546 kB]
Get:96 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:97 http://172.17.0.1/private/ stretch-staging/main libpng12-dev armhf 1.2.50-2+b2 [236 kB]
Get:98 http://172.17.0.1/private/ stretch-staging/main libreadline6-dev armhf 6.3-8+b3 [105 kB]
Get:99 http://172.17.0.1/private/ stretch-staging/main libreadline-dev armhf 6.3-8+b3 [958 B]
Get:100 http://172.17.0.1/private/ stretch-staging/main libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
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Get:102 http://172.17.0.1/private/ stretch-staging/main libxt6 armhf 1:1.1.4-1+b1 [154 kB]
Get:103 http://172.17.0.1/private/ stretch-staging/main zip armhf 3.0-11 [212 kB]
Get:104 http://172.17.0.1/private/ stretch-staging/main unzip armhf 6.0-18 [142 kB]
Get:105 http://172.17.0.1/private/ stretch-staging/main xdg-utils all 1.1.0~rc3+git20150922-1 [69.2 kB]
Get:106 http://172.17.0.1/private/ stretch-staging/main r-base-core armhf 3.2.2-1 [20.2 MB]
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Get:109 http://172.17.0.1/private/ stretch-staging/main r-cran-dbi armhf 0.3.1-1 [156 kB]
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Get:111 http://172.17.0.1/private/ stretch-staging/main r-bioc-biocgenerics all 0.14.0-1 [440 kB]
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Get:115 http://172.17.0.1/private/ stretch-staging/main r-bioc-genomeinfodb all 1.4.3-1 [438 kB]
Get:116 http://172.17.0.1/private/ stretch-staging/main r-bioc-annotationdbi all 1.30.1-1 [4177 kB]
Get:117 http://172.17.0.1/private/ stretch-staging/main r-cran-checkmate armhf 1.6.0-1 [268 kB]
Get:118 http://172.17.0.1/private/ stretch-staging/main r-cran-bbmisc armhf 1.9-1 [279 kB]
Get:119 http://172.17.0.1/private/ stretch-staging/main r-cran-brew armhf 1.0-6-1 [61.3 kB]
Get:120 http://172.17.0.1/private/ stretch-staging/main r-cran-digest armhf 0.6.8-1 [89.7 kB]
Get:121 http://172.17.0.1/private/ stretch-staging/main r-cran-pkgkitten all 0.1.3-1 [18.3 kB]
Get:122 http://172.17.0.1/private/ stretch-staging/main r-cran-rcpp armhf 0.12.1-1 [2118 kB]
Get:123 http://172.17.0.1/private/ stretch-staging/main r-cran-plyr armhf 1.8.3-1 [728 kB]
Get:124 http://172.17.0.1/private/ stretch-staging/main r-cran-stringr all 0.6.2-2 [71.8 kB]
Get:125 http://172.17.0.1/private/ stretch-staging/main r-cran-base64enc armhf 0.1-2-1 [19.6 kB]
Get:126 http://172.17.0.1/private/ stretch-staging/main r-cran-sendmailr armhf 1.2-1-1 [29.0 kB]
Get:127 http://172.17.0.1/private/ stretch-staging/main r-cran-fail armhf 1.2-1 [42.6 kB]
Get:128 http://172.17.0.1/private/ stretch-staging/main r-cran-batchjobs armhf 1.6-1 [422 kB]
Get:129 http://172.17.0.1/private/ stretch-staging/main r-cran-codetools all 0.2-14-1 [46.5 kB]
Get:130 http://172.17.0.1/private/ stretch-staging/main r-cran-iterators all 1.0.7-1 [306 kB]
Get:131 http://172.17.0.1/private/ stretch-staging/main r-cran-foreach all 1.4.2-1 [371 kB]
Get:132 http://172.17.0.1/private/ stretch-staging/main r-cran-lambda.r all 1.1.7-2 [66.3 kB]
Get:133 http://172.17.0.1/private/ stretch-staging/main r-cran-futile.options all 1.0.0-2 [15.4 kB]
Get:134 http://172.17.0.1/private/ stretch-staging/main r-cran-futile.logger all 1.4.1-1 [84.4 kB]
Get:135 http://172.17.0.1/private/ stretch-staging/main r-cran-snow all 1:0.3.13-1 [66.7 kB]
Get:136 http://172.17.0.1/private/ stretch-staging/main r-bioc-biocparallel all 1.2.6-1 [600 kB]
Get:137 http://172.17.0.1/private/ stretch-staging/main r-cran-xml armhf 3.98-1.3-1 [1643 kB]
Get:138 http://172.17.0.1/private/ stretch-staging/main r-cran-bitops armhf 1.0-6-1 [23.6 kB]
Get:139 http://172.17.0.1/private/ stretch-staging/main r-cran-rcurl armhf 1.95-4.3-2 [525 kB]
Get:140 http://172.17.0.1/private/ stretch-staging/main r-bioc-biomart all 2.24.1-1 [388 kB]
Get:141 http://172.17.0.1/private/ stretch-staging/main r-bioc-xvector armhf 0.8.0-1 [318 kB]
Get:142 http://172.17.0.1/private/ stretch-staging/main r-bioc-biostrings armhf 2.36.1-1 [13.5 MB]
Get:143 http://172.17.0.1/private/ stretch-staging/main r-bioc-genomicranges armhf 1.20.5-1 [1428 kB]
Get:144 http://172.17.0.1/private/ stretch-staging/main r-bioc-rsamtools armhf 1.20.4-1 [3171 kB]
Get:145 http://172.17.0.1/private/ stretch-staging/main r-bioc-genomicalignments armhf 1.4.1-1 [1274 kB]
Get:146 http://172.17.0.1/private/ stretch-staging/main r-bioc-rtracklayer armhf 1.28.10-1 [1753 kB]
Get:147 http://172.17.0.1/private/ stretch-staging/main r-bioc-bsgenome all 1.36.3-1 [6461 kB]
Get:148 http://172.17.0.1/private/ stretch-staging/main r-bioc-genomicfeatures all 1.20.5-1 [999 kB]
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Setting up r-cran-bbmisc (1.9-1) ...
Setting up r-cran-brew (1.0-6-1) ...
Setting up r-cran-digest (0.6.8-1) ...
Setting up r-cran-pkgkitten (0.1.3-1) ...
Setting up r-cran-rcpp (0.12.1-1) ...
Setting up r-cran-plyr (1.8.3-1) ...
Setting up r-cran-stringr (0.6.2-2) ...
Setting up r-cran-base64enc (0.1-2-1) ...
Setting up r-cran-sendmailr (1.2-1-1) ...
Setting up r-cran-fail (1.2-1) ...
Setting up r-cran-batchjobs (1.6-1) ...
Setting up r-cran-codetools (0.2-14-1) ...
Setting up r-cran-iterators (1.0.7-1) ...
Setting up r-cran-foreach (1.4.2-1) ...
Setting up r-cran-lambda.r (1.1.7-2) ...
Setting up r-cran-futile.options (1.0.0-2) ...
Setting up r-cran-futile.logger (1.4.1-1) ...
Setting up r-cran-snow (1:0.3.13-1) ...
Setting up r-bioc-biocparallel (1.2.6-1) ...
Setting up r-cran-xml (3.98-1.3-1) ...
Setting up r-cran-bitops (1.0-6-1) ...
Setting up r-cran-rcurl (1.95-4.3-2) ...
Setting up r-bioc-biomart (2.24.1-1) ...
Setting up r-bioc-xvector (0.8.0-1) ...
Setting up r-bioc-biostrings (2.36.1-1) ...
Setting up r-bioc-genomicranges (1.20.5-1) ...
Setting up r-bioc-rsamtools (1.20.4-1) ...
Setting up r-bioc-genomicalignments (1.4.1-1) ...
Setting up r-bioc-rtracklayer (1.28.10-1) ...
Setting up r-bioc-bsgenome (1.36.3-1) ...
Setting up r-bioc-genomicfeatures (1.20.5-1) ...
Setting up sbuild-build-depends-r-bioc-variantannotation-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-19) ...
Processing triggers for systemd (225-1) ...
Processing triggers for ca-certificates (20150426) ...
Updating certificates in /etc/ssl/certs...
180 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-5_5.2.1-17+rpi1 gcc-5_5.2.1-17+rpi1 libc6-dev_2.19-19 libstdc++-5-dev_5.2.1-17+rpi1 libstdc++6_5.2.1-17+rpi1 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2
Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.26.2-9 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20150426 cdbs_0.4.130 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-5_5.2.1-17+rpi1 dash_0.5.7-4 debconf_1.5.57 debconf-i18n_1.5.57 debfoster_2.7-2 debhelper_9.20150811 debianutils_4.5.1 diffutils_1:3.3-1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-9 fontconfig_2.11.0-6.3 fontconfig-config_2.11.0-6.3 fonts-dejavu-core_2.35-1 g++_4:5.2.1-4+rpi2 g++-5_5.2.1-17+rpi1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-4 gcc-4.9-base_4.9.3-4 gcc-5_5.2.1-17+rpi1 gcc-5-base_5.2.1-17+rpi1 gettext_0.19.6-1 gettext-base_0.19.6-1 gfortran_4:5.2.1-4+rpi2 gfortran-5_5.2.1-17+rpi1 gnupg_1.4.19-5 gpgv_1.4.19-5 grep_2.21-2 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.16 init_1.23 init-system-helpers_1.23 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.9.2-3 libapt-pkg4.16_1.0.10.2 libasan2_5.2.1-17+rpi1 libatomic1_5.2.1-17+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-1 libaudit1_1:2.4.4-1 libblas-common_1.2.20110419-10 libblas-dev_1.2.20110419-10 libblas3_1.2.20110419-10 libblkid1_2.26.2-9 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.19-19 libc-dev-bin_2.19-19 libc6_2.19-19 libc6-dev_2.19-19 libcairo2_1.14.2-2 libcap2_1:2.24-11 libcap2-bin_1:2.24-11 libcc1-0_5.2.1-17+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libcurl3_7.44.0-2 libdatrie1_0.2.9-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.0-2 libdebconfclient0_0.195 libdevmapper1.02.1_2:1.02.104-1 libdpkg-perl_1.18.2 libdrm2_2.4.64-1 libexpat1_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.26.2-9 libffi6_3.2.1-3 libfontconfig1_2.11.0-6.3 libfreetype6_2.6-2 libgc1c2_1:7.2d-6.4 libgcc-5-dev_5.2.1-17+rpi1 libgcc1_1:5.2.1-17+rpi1 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libgfortran-5-dev_5.2.1-17+rpi1 libgfortran3_5.2.1-17+rpi1 libglib2.0-0_2.44.1-1.1 libgmp10_2:6.0.0+dfsg-7+rpi1 libgnutls-deb0-28_3.3.17-1 libgomp1_5.2.1-17+rpi1 libgpg-error0_1.20-1 libgraphite2-3_1.3.3-1 libgssapi-krb5-2_1.13.2+dfsg-2 libharfbuzz0b_1.0.1-1+b1 libhogweed4_3.1.1-4 libice6_2:1.0.9-1+b1 libicu55_55.1-5 libidn11_1.32-1 libisl13_0.14-2 libjbig0_2.1-3.1 libjpeg-dev_1:1.4.1-2 libjpeg62-turbo_1:1.4.1-2 libjpeg62-turbo-dev_1:1.4.1-2 libk5crypto3_1.13.2+dfsg-2 libkeyutils1_1.5.9-7 libklibc_2.0.4-2+rpi1 libkmod2_21-1 libkrb5-3_1.13.2+dfsg-2 libkrb5support0_1.13.2+dfsg-2 liblapack-dev_3.5.0-4 liblapack3_3.5.0-4 libldap-2.4-2_2.4.42+dfsg-2+rpi1 liblocale-gettext-perl_1.05-9 liblzma-dev_5.1.1alpha+20120614-2.1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.26.2-9 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20150810-1 libncurses5-dev_6.0+20150810-1 libncursesw5_6.0+20150810-1 libnettle6_3.1.1-4 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libp11-kit0_0.23.1-3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpango-1.0-0_1.36.8-3 libpangocairo-1.0-0_1.36.8-3 libpangoft2-1.0-0_1.36.8-3 libpaper-utils_1.1.24+nmu4 libpaper1_1.1.24+nmu4 libpcre16-3_2:8.35-7.2 libpcre3_2:8.35-7.2 libpcre3-dev_2:8.35-7.2 libpcre32-3_2:8.35-7.2 libpcrecpp0v5_2:8.35-7.2 libpipeline1_1.4.1-1 libpixman-1-0_0.33.2-2 libpng12-0_1.2.50-2+b2 libpng12-dev_1.2.50-2+b2 libprocps4_2:3.3.10-2 libreadline-dev_6.3-8+b3 libreadline6_6.3-8+b3 libreadline6-dev_6.3-8+b3 librtmp1_2.4+20150115.gita107cef-1+b1 libsasl2-2_2.1.26.dfsg1-14 libsasl2-modules-db_2.1.26.dfsg1-14 libseccomp2_2.2.3-2 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libsm6_2:1.2.2-1+b1 libsmartcols1_2.26.2-9 libsqlite3-0_3.8.11.1-1 libss2_1.42.13-1 libssh2-1_1.5.0-2 libssl1.0.0_1.0.2d-1 libstdc++-5-dev_5.2.1-17+rpi1 libstdc++6_5.2.1-17+rpi1 libsystemd0_225-1 libtasn1-6_4.5-2 libtcl8.6_8.6.4+dfsg-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.22-2 libthai0_0.1.22-2 libtiff5_4.0.5-1 libtinfo-dev_6.0+20150810-1 libtinfo5_6.0+20150810-1 libtk8.6_8.6.4+dfsg-2 libubsan0_5.2.1-17+rpi1 libudev1_225-1 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.26.2-9 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxcb-render0_1.10-3+b1 libxcb-shm0_1.10-3+b1 libxcb1_1.10-3+b1 libxdmcp6_1:1.1.2-1 libxext6_2:1.3.3-1 libxft2_2.3.2-1 libxml2_2.9.2+zdfsg1-4 libxrender1_1:0.9.8-1+b1 libxss1_1:1.2.2-1 libxt6_1:1.1.4-1+b1 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2 littler_0.2.3-2 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.3-1 mawk_1.3.3-17 mount_2.26.2-9 mountall_2.54 multiarch-support_2.19-19 ncurses-base_6.0+20150810-1 ncurses-bin_6.0+20150810-1 openssl_1.0.2d-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.10-2 r-base-core_3.2.2-1 r-base-dev_3.2.2-1 r-bioc-annotationdbi_1.30.1-1 r-bioc-biobase_2.28.0-1 r-bioc-biocgenerics_0.14.0-1 r-bioc-biocparallel_1.2.6-1 r-bioc-biomart_2.24.1-1 r-bioc-biostrings_2.36.1-1 r-bioc-bsgenome_1.36.3-1 r-bioc-genomeinfodb_1.4.3-1 r-bioc-genomicalignments_1.4.1-1 r-bioc-genomicfeatures_1.20.5-1 r-bioc-genomicranges_1.20.5-1 r-bioc-iranges_2.2.5-1 r-bioc-rsamtools_1.20.4-1 r-bioc-rtracklayer_1.28.10-1 r-bioc-s4vectors_0.6.2-1 r-bioc-xvector_0.8.0-1 r-cran-base64enc_0.1-2-1 r-cran-batchjobs_1.6-1 r-cran-bbmisc_1.9-1 r-cran-bitops_1.0-6-1 r-cran-brew_1.0-6-1 r-cran-checkmate_1.6.0-1 r-cran-codetools_0.2-14-1 r-cran-dbi_0.3.1-1 r-cran-digest_0.6.8-1 r-cran-fail_1.2-1 r-cran-foreach_1.4.2-1 r-cran-futile.logger_1.4.1-1 r-cran-futile.options_1.0.0-2 r-cran-iterators_1.0.7-1 r-cran-lambda.r_1.1.7-2 r-cran-pkgkitten_0.1.3-1 r-cran-plyr_1.8.3-1 r-cran-rcpp_0.12.1-1 r-cran-rcurl_1.95-4.3-2 r-cran-rsqlite_1.0.0-1 r-cran-sendmailr_1.2-1-1 r-cran-snow_1:0.3.13-1 r-cran-stringr_0.6.2-2 r-cran-xml_3.98-1.3-1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-variantannotation-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_225-1 systemd-sysv_225-1 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-1 tzdata_2015f-1 ucf_3.0030 udev_225-1 unzip_6.0-18 util-linux_2.26.2-9 x11-common_1:7.7+9 xdg-utils_1.1.0~rc3+git20150922-1 xz-utils_5.1.1alpha+20120614-2.1 zip_3.0-11 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Sep 24 19:51:25 2015 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_1.14.13-1.dsc
dpkg-source: info: extracting r-bioc-variantannotation in r-bioc-variantannotation-1.14.13
dpkg-source: info: unpacking r-bioc-variantannotation_1.14.13.orig.tar.gz
dpkg-source: info: unpacking r-bioc-variantannotation_1.14.13-1.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
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-2b30b98d-3bb6-4ca5-aa79-ad30d04f9b69
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=vt102
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package r-bioc-variantannotation
dpkg-buildpackage: source version 1.14.13-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build r-bioc-variantannotation-1.14.13
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 (>= 3.2.2-1), r-api-3" >> 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 \
. \
"--built-timestamp=\"Thu, 24 Sep 2015 21:49:23 +0200\"" \
; \
else \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-variantannotation/usr/lib/R/site-library \
--clean . \
"--built-timestamp=\"Thu, 24 Sep 2015 21:49:23 +0200\"" \
; \
fi
* installing *source* package 'VariantAnnotation' ...
** libs
make[1]: Entering directory '/«PKGBUILDDIR»/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -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 -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -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 -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -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 -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -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 -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -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 -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -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 -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -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 -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -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 -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -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 -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c vcftype.c -o vcftype.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c writevcf.c -o writevcf.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -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 writevcf.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 generic function for 'nchar' from package 'base' in package 'S4Vectors'
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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* 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_1.14.13-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-variantannotation_1.14.13-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-variantannotation-1.14.13
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150930-0607
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-variantannotation_1.14.13-1_armhf.changes:
─────────────────────────────────────────────────
Format: 1.8
Date: Thu, 24 Sep 2015 21:49:23 +0200
Source: r-bioc-variantannotation
Binary: r-bioc-variantannotation
Architecture: armhf
Version: 1.14.13-1
Distribution: stretch-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 (1.14.13-1) unstable; urgency=medium
.
* New upstream version
* Fixed watch file
Checksums-Sha1:
dd348e91267b09c0e7abf1669cdb0e447e19a2c6 1865574 r-bioc-variantannotation_1.14.13-1_armhf.deb
Checksums-Sha256:
8510e528c63f000490afb25575f41ba28183a4024074c92a03087162594fdfea 1865574 r-bioc-variantannotation_1.14.13-1_armhf.deb
Files:
043d1a239ed25f805104b060c4023898 1865574 gnu-r optional r-bioc-variantannotation_1.14.13-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-variantannotation_1.14.13-1_armhf.deb
────────────────────────────────────────────
new debian package, version 2.0.
size 1865574 bytes: control archive=2750 bytes.
666 bytes, 13 lines control
6761 bytes, 68 lines md5sums
Package: r-bioc-variantannotation
Version: 1.14.13-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2404
Depends: r-base-core (>= 3.2.2-1), r-api-3, libc6 (>= 2.15), zlib1g (>= 1:1.2.3.3), r-bioc-genomicfeatures (>= 1.18.0), r-bioc-bsgenome (>= 1.34.0)
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 2015-09-30 06:07 ./
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drwxr-xr-x root/root 0 2015-09-30 06:04 ./usr/lib/R/
drwxr-xr-x root/root 0 2015-09-30 06:07 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2015-09-30 06:06 ./usr/lib/R/site-library/VariantAnnotation/
-rw-r--r-- root/root 1636 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/CITATION
-rw-r--r-- root/root 1665 2015-09-30 06:04 ./usr/lib/R/site-library/VariantAnnotation/DESCRIPTION
-rw-r--r-- root/root 1563 2015-09-30 06:06 ./usr/lib/R/site-library/VariantAnnotation/INDEX
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-rw-r--r-- root/root 208403 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/doc/VariantAnnotation.pdf
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-rw-r--r-- root/root 199911 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/doc/filterVcf.pdf
-rw-r--r-- root/root 1975 2015-09-30 06:06 ./usr/lib/R/site-library/VariantAnnotation/doc/index.html
drwxr-xr-x root/root 0 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/extdata/
-rw-r--r-- root/root 561698 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/extdata/chr22.vcf.gz
-rw-r--r-- root/root 655 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/extdata/chr22.vcf.gz.tbi
-rw-r--r-- root/root 113168 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/extdata/chr7-sub.vcf.gz
-rw-r--r-- root/root 744 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/extdata/chr7-sub.vcf.gz.tbi
-rw-r--r-- root/root 1892 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/extdata/ex2.vcf
-rw-r--r-- root/root 24819 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/extdata/gl_chr1.vcf
-rw-r--r-- root/root 124778 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/extdata/h1187-10k.vcf.gz
-rw-r--r-- root/root 441 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/extdata/h1187-10k.vcf.gz.tbi
-rw-r--r-- root/root 3060 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/extdata/structural.vcf
drwxr-xr-x root/root 0 2015-09-30 06:06 ./usr/lib/R/site-library/VariantAnnotation/help/
-rw-r--r-- root/root 15115 2015-09-30 06:06 ./usr/lib/R/site-library/VariantAnnotation/help/AnIndex
-rw-r--r-- root/root 179981 2015-09-30 06:06 ./usr/lib/R/site-library/VariantAnnotation/help/VariantAnnotation.rdb
-rw-r--r-- root/root 796 2015-09-30 06:06 ./usr/lib/R/site-library/VariantAnnotation/help/VariantAnnotation.rdx
-rw-r--r-- root/root 2907 2015-09-30 06:06 ./usr/lib/R/site-library/VariantAnnotation/help/aliases.rds
-rw-r--r-- root/root 410 2015-09-30 06:06 ./usr/lib/R/site-library/VariantAnnotation/help/paths.rds
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-rw-r--r-- root/root 1319 2015-09-30 06:06 ./usr/lib/R/site-library/VariantAnnotation/html/R.css
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-rw-r--r-- root/root 104636 2015-09-30 06:07 ./usr/lib/R/site-library/VariantAnnotation/libs/VariantAnnotation.so
drwxr-xr-x root/root 0 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/scripts/
-rw-r--r-- root/root 10914 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/scripts/test_Rplinkseq.R
drwxr-xr-x root/root 0 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/
drwxr-xr-x root/root 0 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/
-rw-r--r-- root/root 602 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/FORMAT_header_no_SAMPLEs.vcf
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-rw-r--r-- root/root 3700 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/banded_gvcf.vcf
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-rw-r--r-- root/root 614 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/fewer-FORMAT-than-GENO.vcf
-rw-r--r-- root/root 553 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/missing-FORMAT-metadata-elt.vcf
-rw-r--r-- root/root 2970 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/mixedStructural.vcf
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-rw-r--r-- root/root 287 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/no_FORMAT_column.vcf
-rw-r--r-- root/root 573 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/no_GENO_row.vcf
-rw-r--r-- root/root 300 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/no_INFO_header.vcf
-rw-r--r-- root/root 1679 2015-09-30 06:05 ./usr/lib/R/site-library/VariantAnnotation/unitTests/cases/unspecified_INFO_FORMAT_fields.vcf
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drwxr-xr-x root/root 0 2015-09-30 06:07 ./usr/share/
drwxr-xr-x root/root 0 2015-09-30 06:07 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-09-30 06:07 ./usr/share/doc/r-bioc-variantannotation/
-rw-r--r-- root/root 4395 2015-04-16 20:14 ./usr/share/doc/r-bioc-variantannotation/NEWS.gz
-rw-r--r-- root/root 1506 2014-07-24 07:42 ./usr/share/doc/r-bioc-variantannotation/README.test
-rw-r--r-- root/root 355 2015-09-24 19:49 ./usr/share/doc/r-bioc-variantannotation/changelog.Debian.gz
-rw-r--r-- root/root 5411 2014-07-24 09:00 ./usr/share/doc/r-bioc-variantannotation/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 6548
Build-Time: 205
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 658
Job: r-bioc-variantannotation_1.14.13-1
Machine Architecture: armhf
Package: r-bioc-variantannotation
Package-Time: 920
Source-Version: 1.14.13-1
Space: 6548
Status: successful
Version: 1.14.13-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20150930-0607
Build needed 00:15:20, 6548k disc space