r-bioc-rsamtools →
1.20.4-1 →
armhf → 2015-07-14 11:38:00
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on testwandboard
╔══════════════════════════════════════════════════════════════════════════════╗
║ r-bioc-rsamtools 1.20.4-1 (armhf) 14 Jul 2015 11:19 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: r-bioc-rsamtools
Version: 1.20.4-1
Source Version: 1.20.4-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-Gzha2s/r-bioc-rsamtools-1.20.4' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-Gzha2s' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-8f601c43-c5e7-4561-a4e9-8753addabca7' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8089 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [9947 kB]
Ign http://172.17.0.1 stretch-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...
NOTICE: 'r-bioc-rsamtools' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
Need to get 2986 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main r-bioc-rsamtools 1.20.4-1 (dsc) [2210 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main r-bioc-rsamtools 1.20.4-1 (tar) [2977 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main r-bioc-rsamtools 1.20.4-1 (diff) [6620 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-wByV0A/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
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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 81 not upgraded.
Need to get 0 B/816 B of archives.
After this operation, 0 B of additional disk space will be used.
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(Reading database ... 11998 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: 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-cran-bitops, r-bioc-biostrings (>= 2.34.0), r-bioc-genomicranges (>= 1.18.0), libbam-dev
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-cran-bitops, r-bioc-biostrings (>= 2.34.0), r-bioc-genomicranges (>= 1.18.0), libbam-dev
dpkg-deb: building package `sbuild-build-depends-r-bioc-rsamtools-dummy' in `/«BUILDDIR»/resolver-JXbyD9/apt_archive/sbuild-build-depends-r-bioc-rsamtools-dummy.deb'.
OK
Ign file: ./ InRelease
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-rsamtools build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils bzip2 ca-certificates cdbs cpp cpp-4.9 debhelper file
fontconfig fontconfig-config fonts-dejavu-core g++-4.9 gcc gcc-4.9
gcc-4.9-base gcc-5-base gettext gettext-base gfortran gfortran-4.9
groff-base intltool-debian libasan1 libasprintf0c2 libatomic1 libbam-dev
libblas-common libblas-dev libblas3 libbz2-1.0 libbz2-dev libcairo2
libcroco3 libcurl3 libdatrie1 libexpat1 libffi6 libfontconfig1 libfreetype6
libgcc-4.9-dev libgcc1 libgfortran-4.9-dev libgfortran3 libglib2.0-0
libgnutls-deb0-28 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b
libhogweed4 libice6 libidn11 libisl13 libjbig0 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblapack-dev liblapack3 libldap-2.4-2 liblzma-dev liblzma5 libmagic1
libmpfr4 libncurses5 libncurses5-dev libncursesw5 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 libpcrecpp0
libpipeline1 libpixman-1-0 libpng12-dev libreadline-dev libreadline6-dev
librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libssl1.0.0
libstdc++-4.9-dev libstdc++6 libtasn1-6 libtcl8.6 libthai-data libthai0
libtiff5 libtinfo-dev libtinfo5 libtk8.6 libubsan0 libunistring0 libx11-6
libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6
libxft2 libxml2 libxrender1 libxss1 libxt6 man-db ncurses-bin openssl
po-debconf r-base-core r-base-dev r-bioc-biocgenerics r-bioc-biostrings
r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors
r-bioc-xvector r-cran-bitops 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 libcilkrts5-dbg libquadmath-dbg gettext-doc
gfortran-doc gfortran-4.9-doc libgfortran3-dbg groff gnutls-bin krb5-doc
krb5-user liblzma-doc ncurses-doc readline-doc libstdc++-4.9-doc tcl8.6
tk8.6 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 gvfs-bin
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2
libsasl2-modules xml-core libmail-sendmail-perl r-recommended r-doc-html
r-cran-digest 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 gcc-5-base gettext gettext-base gfortran
gfortran-4.9 groff-base intltool-debian libasprintf0c2 libbam-dev
libblas-common libblas-dev libblas3 libbz2-dev libcairo2 libcroco3 libcurl3
libdatrie1 libexpat1 libffi6 libfontconfig1 libfreetype6 libgfortran-4.9-dev
libgfortran3 libglib2.0-0 libgnutls-deb0-28 libgraphite2-3 libgssapi-krb5-2
libharfbuzz0b libhogweed4 libice6 libidn11 libisl13 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 libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-dev
libreadline-dev libreadline6-dev librtmp1 libsasl2-2 libsasl2-modules-db
libsm6 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 man-db openssl po-debconf r-base-core r-base-dev
r-bioc-biocgenerics r-bioc-biostrings r-bioc-genomeinfodb
r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors r-bioc-xvector
r-cran-bitops sbuild-build-depends-r-bioc-rsamtools-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 liblzma5 libmpfr4 libncurses5
libncursesw5 libpcre3 libstdc++-4.9-dev libstdc++6 libtinfo5 libubsan0
ncurses-bin
23 upgraded, 117 newly installed, 0 to remove and 58 not upgraded.
Need to get 96.2 MB/96.2 MB of archives.
After this operation, 151 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main ncurses-bin armhf 5.9+20150516-2 [346 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main libpcre3 armhf 2:8.35-7 [299 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main gcc-5-base armhf 5.1.1-12+rpi1 [165 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main libgcc1 armhf 1:5.1.1-12+rpi1 [38.5 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libstdc++6 armhf 5.1.1-12+rpi1 [249 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.0-1 [24.0 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main libtinfo5 armhf 5.9+20150516-2 [275 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libncurses5 armhf 5.9+20150516-2 [76.6 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libncursesw5 armhf 5.9+20150516-2 [99.3 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.0.2-5 [972 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libasprintf0c2 armhf 0.19.4-1 [31.5 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libkeyutils1 armhf 1.5.9-5 [10.9 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libkrb5support0 armhf 1.12.1+dfsg-20 [54.9 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main libk5crypto3 armhf 1.12.1+dfsg-20 [108 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libkrb5-3 armhf 1.12.1+dfsg-20 [258 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libgssapi-krb5-2 armhf 1.12.1+dfsg-20 [128 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libidn11 armhf 1.30-1 [166 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main libnettle6 armhf 3.1.1-3 [200 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libhogweed4 armhf 3.1.1-3 [126 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libp11-kit0 armhf 0.23.1-2 [94.1 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main libtasn1-6 armhf 4.5-2 [43.9 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main libgnutls-deb0-28 armhf 3.3.15-7 [645 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libsasl2-modules-db armhf 2.1.26.dfsg1-13 [65.5 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libsasl2-2 armhf 2.1.26.dfsg1-13 [97.2 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main libldap-2.4-2 armhf 2.4.40+dfsg-2+rpi1 [196 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main liblzma5 armhf 5.1.1alpha+20120614-2.1 [186 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-6 [60.2 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main libfreetype6 armhf 2.5.2-4 [412 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main ucf all 3.0030 [69.7 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main fonts-dejavu-core all 2.35-1 [1064 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main fontconfig-config all 2.11.0-6.3 [273 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main fontconfig armhf 2.11.0-6.3 [402 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libisl13 armhf 0.14-2 [353 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main libmpfr4 armhf 3.1.3-1 [517 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main g++-4.9 armhf 4.9.3-1 [11.9 MB]
Get:42 http://172.17.0.1/private/ stretch-staging/main gcc-4.9 armhf 4.9.3-1 [4470 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main cpp-4.9 armhf 4.9.3-1 [4275 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main libgomp1 armhf 5.1.1-12+rpi1 [47.4 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main libatomic1 armhf 5.1.1-12+rpi1 [6720 B]
Get:46 http://172.17.0.1/private/ stretch-staging/main libubsan0 armhf 5.1.1-12+rpi1 [84.3 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main libstdc++-4.9-dev armhf 4.9.3-1 [1127 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main libgcc-4.9-dev armhf 4.9.3-1 [355 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main libasan1 armhf 4.9.3-1 [165 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main gcc-4.9-base armhf 4.9.3-1 [162 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1.1 [2312 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main libgfortran3 armhf 5.1.1-12+rpi1 [154 kB]
Get:54 http://172.17.0.1/private/ stretch-staging/main libgraphite2-3 armhf 1.2.4-3 [48.2 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main x11-common all 1:7.7+9 [287 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main libice6 armhf 2:1.0.9-1 [51.2 kB]
Get:57 http://172.17.0.1/private/ stretch-staging/main libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:58 http://172.17.0.1/private/ stretch-staging/main libthai-data all 0.1.22-2 [161 kB]
Get:59 http://172.17.0.1/private/ stretch-staging/main libdatrie1 armhf 0.2.9-2 [31.5 kB]
Get:60 http://172.17.0.1/private/ stretch-staging/main libthai0 armhf 0.1.22-2 [44.8 kB]
Get:61 http://172.17.0.1/private/ stretch-staging/main libpango-1.0-0 armhf 1.36.8-3 [274 kB]
Get:62 http://172.17.0.1/private/ stretch-staging/main libpixman-1-0 armhf 0.32.6-3 [422 kB]
Get:63 http://172.17.0.1/private/ stretch-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main libxdmcp6 armhf 1:1.1.2-1 [25.0 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main libxcb1 armhf 1.10-3 [38.1 kB]
Get:66 http://172.17.0.1/private/ stretch-staging/main libx11-data all 2:1.6.3-1 [128 kB]
Get:67 http://172.17.0.1/private/ stretch-staging/main libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:68 http://172.17.0.1/private/ stretch-staging/main libxcb-render0 armhf 1.10-3 [16.0 kB]
Get:69 http://172.17.0.1/private/ stretch-staging/main libxcb-shm0 armhf 1.10-3 [11.0 kB]
Get:70 http://172.17.0.1/private/ stretch-staging/main libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:71 http://172.17.0.1/private/ stretch-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main libcairo2 armhf 1.14.2-2 [672 kB]
Get:73 http://172.17.0.1/private/ stretch-staging/main libharfbuzz0b armhf 0.9.41-1 [488 kB]
Get:74 http://172.17.0.1/private/ stretch-staging/main libpangoft2-1.0-0 armhf 1.36.8-3 [207 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main libpangocairo-1.0-0 armhf 1.36.8-3 [197 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:77 http://172.17.0.1/private/ stretch-staging/main libpcrecpp0 armhf 2:8.35-7 [139 kB]
Get:78 http://172.17.0.1/private/ stretch-staging/main libsm6 armhf 2:1.2.2-1 [31.2 kB]
Get:79 http://172.17.0.1/private/ stretch-staging/main libssh2-1 armhf 1.5.0-2 [122 kB]
Get:80 http://172.17.0.1/private/ stretch-staging/main libtcl8.6 armhf 8.6.4+dfsg-2 [866 kB]
Get:81 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo armhf 1:1.4.0-7 [102 kB]
Get:82 http://172.17.0.1/private/ stretch-staging/main libtiff5 armhf 4.0.3-13 [193 kB]
Get:83 http://172.17.0.1/private/ stretch-staging/main libxft2 armhf 2.3.2-1 [48.3 kB]
Get:84 http://172.17.0.1/private/ stretch-staging/main libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:85 http://172.17.0.1/private/ stretch-staging/main libtk8.6 armhf 8.6.4+dfsg-2 [664 kB]
Get:86 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:87 http://172.17.0.1/private/ stretch-staging/main libxt6 armhf 1:1.1.4-1 [183 kB]
Get:88 http://172.17.0.1/private/ stretch-staging/main bzip2 armhf 1.0.6-8 [45.1 kB]
Get:89 http://172.17.0.1/private/ stretch-staging/main libbz2-1.0 armhf 1.0.6-8 [42.0 kB]
Get:90 http://172.17.0.1/private/ stretch-staging/main libssl1.0.0 armhf 1.0.2d-1 [882 kB]
Get:91 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:92 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.4-1 [117 kB]
Get:93 http://172.17.0.1/private/ stretch-staging/main openssl armhf 1.0.2d-1 [683 kB]
Get:94 http://172.17.0.1/private/ stretch-staging/main ca-certificates all 20150426 [208 kB]
Get:95 http://172.17.0.1/private/ stretch-staging/main cdbs all 0.4.130 [76.4 kB]
Get:96 http://172.17.0.1/private/ stretch-staging/main cpp armhf 4:4.9.2-4+rpi1 [17.8 kB]
Get:97 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.4-1 [1168 kB]
Get:98 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:99 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:100 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150628 [817 kB]
Get:101 http://172.17.0.1/private/ stretch-staging/main gcc armhf 4:4.9.2-4+rpi1 [5134 B]
Get:102 http://172.17.0.1/private/ stretch-staging/main libgfortran-4.9-dev armhf 4.9.3-1 [179 kB]
Get:103 http://172.17.0.1/private/ stretch-staging/main gfortran-4.9 armhf 4.9.3-1 [4528 kB]
Get:104 http://172.17.0.1/private/ stretch-staging/main gfortran armhf 4:4.9.2-4+rpi1 [1290 B]
Get:105 http://172.17.0.1/private/ stretch-staging/main libbam-dev armhf 0.1.19-2 [109 kB]
Get:106 http://172.17.0.1/private/ stretch-staging/main libblas-common armhf 1.2.20110419-10 [8494 B]
Get:107 http://172.17.0.1/private/ stretch-staging/main libblas3 armhf 1.2.20110419-10 [120 kB]
Get:108 http://172.17.0.1/private/ stretch-staging/main libblas-dev armhf 1.2.20110419-10 [117 kB]
Get:109 http://172.17.0.1/private/ stretch-staging/main libbz2-dev armhf 1.0.6-8 [27.8 kB]
Get:110 http://172.17.0.1/private/ stretch-staging/main librtmp1 armhf 2.4+20150115.gita107cef-1+b1 [54.5 kB]
Get:111 http://172.17.0.1/private/ stretch-staging/main libcurl3 armhf 7.43.0-1 [238 kB]
Get:112 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo-dev armhf 1:1.4.0-7 [414 kB]
Get:113 http://172.17.0.1/private/ stretch-staging/main libjpeg-dev all 1:1.4.0-7 [50.8 kB]
Get:114 http://172.17.0.1/private/ stretch-staging/main liblapack3 armhf 3.5.0-4 [1316 kB]
Get:115 http://172.17.0.1/private/ stretch-staging/main liblapack-dev armhf 3.5.0-4 [1364 kB]
Get:116 http://172.17.0.1/private/ stretch-staging/main liblzma-dev armhf 5.1.1alpha+20120614-2.1 [248 kB]
Get:117 http://172.17.0.1/private/ stretch-staging/main libtinfo-dev armhf 5.9+20150516-2 [66.0 kB]
Get:118 http://172.17.0.1/private/ stretch-staging/main libncurses5-dev armhf 5.9+20150516-2 [154 kB]
Get:119 http://172.17.0.1/private/ stretch-staging/main libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:120 http://172.17.0.1/private/ stretch-staging/main libpcre16-3 armhf 2:8.35-7 [221 kB]
Get:121 http://172.17.0.1/private/ stretch-staging/main libpcre32-3 armhf 2:8.35-7 [214 kB]
Get:122 http://172.17.0.1/private/ stretch-staging/main libpcre3-dev armhf 2:8.35-7 [550 kB]
Get:123 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2 [199 kB]
Get:124 http://172.17.0.1/private/ stretch-staging/main libpng12-dev armhf 1.2.50-2 [236 kB]
Get:125 http://172.17.0.1/private/ stretch-staging/main libreadline6-dev armhf 6.3-8 [105 kB]
Get:126 http://172.17.0.1/private/ stretch-staging/main libreadline-dev armhf 6.3-8 [994 B]
Get:127 http://172.17.0.1/private/ stretch-staging/main zip armhf 3.0-10 [212 kB]
Get:128 http://172.17.0.1/private/ stretch-staging/main unzip armhf 6.0-17 [143 kB]
Get:129 http://172.17.0.1/private/ stretch-staging/main xdg-utils all 1.1.0~rc1+git20111210-7.4 [65.0 kB]
Get:130 http://172.17.0.1/private/ stretch-staging/main r-base-core armhf 3.2.1-4 [20.1 MB]
Get:131 http://172.17.0.1/private/ stretch-staging/main r-base-dev all 3.2.1-4 [4288 B]
Get:132 http://172.17.0.1/private/ stretch-staging/main r-bioc-biocgenerics all 0.14.0-1 [440 kB]
Get:133 http://172.17.0.1/private/ stretch-staging/main r-bioc-s4vectors armhf 0.6.0-1 [734 kB]
Get:134 http://172.17.0.1/private/ stretch-staging/main r-bioc-iranges armhf 2.2.1-1 [1528 kB]
Get:135 http://172.17.0.1/private/ stretch-staging/main r-bioc-xvector armhf 0.8.0-1 [318 kB]
Get:136 http://172.17.0.1/private/ stretch-staging/main r-bioc-biostrings armhf 2.36.1-1 [13.5 MB]
Get:137 http://172.17.0.1/private/ stretch-staging/main r-bioc-genomeinfodb all 1.4.1-1 [431 kB]
Get:138 http://172.17.0.1/private/ stretch-staging/main r-bioc-genomicranges armhf 1.20.3-1 [1425 kB]
Get:139 http://172.17.0.1/private/ stretch-staging/main r-cran-bitops armhf 1.0-6-1 [23.6 kB]
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update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
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Creating config file /etc/papersize with new version
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Setting up libbz2-dev:armhf (1.0.6-8) ...
Setting up librtmp1:armhf (2.4+20150115.gita107cef-1+b1) ...
Setting up libcurl3:armhf (7.43.0-1) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.4.0-7) ...
Setting up libjpeg-dev (1:1.4.0-7) ...
Setting up liblapack3 (3.5.0-4) ...
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 (3.5.0-4) ...
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+20120614-2.1) ...
Setting up libtinfo-dev:armhf (5.9+20150516-2) ...
Setting up libncurses5-dev:armhf (5.9+20150516-2) ...
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libpcre16-3:armhf (2:8.35-7) ...
Setting up libpcre32-3:armhf (2:8.35-7) ...
Setting up libpcre3-dev:armhf (2:8.35-7) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2) ...
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 (3.0-10) ...
Setting up unzip (6.0-17) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-7.4) ...
Setting up r-base-core (3.2.1-4) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.2.1-4) ...
Setting up r-bioc-biocgenerics (0.14.0-1) ...
Setting up r-bioc-s4vectors (0.6.0-1) ...
Setting up r-bioc-iranges (2.2.1-1) ...
Setting up r-bioc-xvector (0.8.0-1) ...
Setting up r-bioc-biostrings (2.36.1-1) ...
Setting up r-bioc-genomeinfodb (1.4.1-1) ...
Setting up r-bioc-genomicranges (1.20.3-1) ...
Setting up r-cran-bitops (1.0-6-1) ...
Setting up sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-18) ...
Processing triggers for systemd (215-17) ...
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_2.25-5 dpkg-dev_1.17.25 g++-4.9_4.9.3-1 gcc-4.9_4.9.3-1 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.3-1 libstdc++6_5.1.1-12+rpi1 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 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_4:4.9.2-4+rpi1 cpp-4.9_4.9.3-1 dash_0.5.7-4 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150628 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 dpkg_1.17.25 dpkg-dev_1.17.25 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 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++_4:4.9.2-2 g++-4.9_4.9.3-1 gcc_4:4.9.2-4+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.3-1 gcc-4.9-base_4.9.3-1 gcc-5-base_5.1.1-12+rpi1 gettext_0.19.4-1 gettext-base_0.19.4-1 gfortran_4:4.9.2-4+rpi1 gfortran-4.9_4.9.3-1 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 init_1.22 init-system-helpers_1.22 initramfs-tools_0.120 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8 libasan1_4.9.3-1 libasprintf0c2_0.19.4-1 libatomic1_5.1.1-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libbam-dev_0.1.19-2 libblas-common_1.2.20110419-10 libblas-dev_1.2.20110419-10 libblas3_1.2.20110419-10 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.19-18 libc-dev-bin_2.19-18 libc6_2.19-18 libc6-dev_2.19-18 libcairo2_1.14.2-2 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libcurl3_7.43.0-1 libdatrie1_0.2.9-2 libdb5.3_5.3.28-9 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.25 libdrm2_2.4.58-2 libexpat1_2.1.0-6 libfakeroot_1.20.2-1 libffi6_3.1-2 libfontconfig1_2.11.0-6.3 libfreetype6_2.5.2-4 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.3-1 libgcc1_1:5.1.1-12+rpi1 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libgfortran-4.9-dev_4.9.3-1 libgfortran3_5.1.1-12+rpi1 libglib2.0-0_2.44.1-1.1 libgmp10_2:6.0.0+dfsg-6+rpi1 libgnutls-deb0-28_3.3.15-7 libgomp1_5.1.1-12+rpi1 libgpg-error0_1.17-3 libgraphite2-3_1.2.4-3 libgssapi-krb5-2_1.12.1+dfsg-20 libharfbuzz0b_0.9.41-1 libhogweed4_3.1.1-3 libice6_2:1.0.9-1 libidn11_1.30-1 libisl10_0.12.2-2 libisl13_0.14-2 libjbig0_2.1-3.1 libjpeg-dev_1:1.4.0-7 libjpeg62-turbo_1:1.4.0-7 libjpeg62-turbo-dev_1:1.4.0-7 libk5crypto3_1.12.1+dfsg-20 libkeyutils1_1.5.9-5 libklibc_2.0.4-2+rpi1 libkmod2_18-3 libkrb5-3_1.12.1+dfsg-20 libkrb5support0_1.12.1+dfsg-20 liblapack-dev_3.5.0-4 liblapack3_3.5.0-4 libldap-2.4-2_2.4.40+dfsg-2+rpi1 liblocale-gettext-perl_1.05-8+b1 liblzma-dev_5.1.1alpha+20120614-2.1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.22+15-2 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.3-1 libncurses5_5.9+20150516-2 libncurses5-dev_5.9+20150516-2 libncursesw5_5.9+20150516-2 libnettle6_3.1.1-3 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libp11-kit0_0.23.1-2 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 libpcre3_2:8.35-7 libpcre3-dev_2:8.35-7 libpcre32-3_2:8.35-7 libpcrecpp0_2:8.35-7 libpipeline1_1.4.0-1 libpixman-1-0_0.32.6-3 libpng12-0_1.2.50-2 libpng12-dev_1.2.50-2 libprocps3_2:3.3.9-9 libreadline-dev_6.3-8 libreadline6_6.3-8 libreadline6-dev_6.3-8 librtmp1_2.4+20150115.gita107cef-1+b1 libsasl2-2_2.1.26.dfsg1-13 libsasl2-modules-db_2.1.26.dfsg1-13 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsm6_2:1.2.2-1 libsmartcols1_2.25.2-6 libss2_1.42.12-1.1 libssh2-1_1.5.0-2 libssl1.0.0_1.0.2d-1 libstdc++-4.9-dev_4.9.3-1 libstdc++6_5.1.1-12+rpi1 libsystemd0_215-17 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 libthai-data_0.1.22-2 libthai0_0.1.22-2 libtiff5_4.0.3-13 libtimedate-perl_2.3000-2 libtinfo-dev_5.9+20150516-2 libtinfo5_5.9+20150516-2 libtk8.6_8.6.4+dfsg-2 libubsan0_5.1.1-12+rpi1 libudev1_215-17 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.25.2-6 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 libxcb-shm0_1.10-3 libxcb1_1.10-3 libxdmcp6_1:1.1.2-1 libxext6_2:1.3.3-1 libxft2_2.3.2-1 libxml2_2.9.1+dfsg1-5 libxrender1_1:0.9.8-1 libxss1_1:1.2.2-1 libxt6_1:1.1.4-1 linux-libc-dev_3.16.7-ckt4-1+rpi1 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-6 mountall_2.54 multiarch-support_2.19-18 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20150516-2 openssl_1.0.2d-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-3 perl-base_5.20.2-3 perl-modules_5.20.2-3 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.9-9 r-base-core_3.2.1-4 r-base-dev_3.2.1-4 r-bioc-biocgenerics_0.14.0-1 r-bioc-biostrings_2.36.1-1 r-bioc-genomeinfodb_1.4.1-1 r-bioc-genomicranges_1.20.3-1 r-bioc-iranges_2.2.1-1 r-bioc-s4vectors_0.6.0-1 r-bioc-xvector_0.8.0-1 r-cran-bitops_1.0-6-1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rsamtools-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 systemd_215-17 systemd-sysv_215-17 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2 tzdata_2015c-1 ucf_3.0030 udev_215-17 unzip_6.0-17 util-linux_2.25.2-6 x11-common_1:7.7+9 xdg-utils_1.1.0~rc1+git20111210-7.4 xz-utils_5.1.1alpha+20120614-2 zip_3.0-10 zlib1g_1:1.2.8.dfsg-2 zlib1g-dev_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Jun 27 14:21:52 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-rsamtools_1.20.4-1.dsc
dpkg-source: info: extracting r-bioc-rsamtools in r-bioc-rsamtools-1.20.4
dpkg-source: info: unpacking r-bioc-rsamtools_1.20.4.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rsamtools_1.20.4-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
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-8f601c43-c5e7-4561-a4e9-8753addabca7
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package r-bioc-rsamtools
dpkg-buildpackage: source version 1.20.4-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build r-bioc-rsamtools-1.20.4
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
test -x debian/rules
dh_clean
if test -d src; then \
find src -regex ".*\.o" | \
xargs --no-run-if-empty -r rm; \
fi
rm -f config.log config.status
dh_clean
rm -f src/*.a
debian/rules build-arch
test -x debian/rules
mkdir -p "."
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
dh_installdirs usr/lib/R/site-library
echo "R:Depends=r-base-core (>= 3.2.1-4), r-api-3" >> debian/r-bioc-rsamtools.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean \
. \
"--built-timestamp=\"Sat, 27 Jun 2015 16:20:16 +0200\"" \
; \
else \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library \
--clean . \
"--built-timestamp=\"Sat, 27 Jun 2015 16:20:16 +0200\"" \
; \
fi
* installing *source* package 'Rsamtools' ...
** libs
make[1]: Entering directory '/«PKGBUILDDIR»/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -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 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c PileupBuffer.cpp -o PileupBuffer.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c PosCacheColl.cpp -o PosCacheColl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ResultManager.cpp -o ResultManager.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -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 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c as_bam.c -o as_bam.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bam_data.c -o bam_data.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bam_mate_iter.cpp -o bam_mate_iter.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bambuffer.c -o bambuffer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bamfile.c -o bamfile.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bcffile.c -o bcffile.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c encode.c -o encode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fafile.c -o fafile.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c io_sam.c -o io_sam.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pileup.cpp -o pileup.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pileupbam.c -o pileupbam.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools_patch.c -o samtools_patch.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scan_bam_data.c -o scan_bam_data.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tabixfile.c -o tabixfile.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tagfilter.c -o tagfilter.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -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 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c zip_compression.c -o zip_compression.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bgzf.c -o samtools/bgzf.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/kstring.c -o samtools/kstring.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam.c -o samtools/bam.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_import.c -o samtools/bam_import.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/sam.c -o samtools/sam.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function 'bam_index_load_core':
samtools/bam_index.c:335:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic, 1, 4, fp);
^
samtools/bam_index.c:342:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&idx->n, 4, 1, fp);
^
samtools/bam_index.c:355:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&size, 4, 1, fp);
^
samtools/bam_index.c:358:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&key, 4, 1, fp);
^
samtools/bam_index.c:362:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&p->n, 4, 1, fp);
^
samtools/bam_index.c:366:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(p->list, 16, p->n, fp);
^
samtools/bam_index.c:376:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&index2->n, 4, 1, fp);
^
samtools/bam_index.c:380:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(index2->offset, index2->n, 8, fp);
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_md.c -o samtools/bam_md.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function 'razf_flush':
samtools/razf.c:221:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
samtools/razf.c:234:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
samtools/razf.c: In function '_razf_write':
samtools/razf.c:201:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
samtools/razf.c: In function 'razf_close':
samtools/razf.c:810:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &rz->in, sizeof(int64_t));
^
samtools/razf.c:811:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &rz->out, sizeof(int64_t));
^
samtools/razf.c:814:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &v64, sizeof(int64_t));
^
samtools/razf.c:816:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &v64, sizeof(int64_t));
^
samtools/razf.c: In function 'razf_end_flush':
samtools/razf.c:258:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
samtools/razf.c: In function 'save_zindex':
samtools/razf.c:96:12: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
if(is_be) write(fd, &rz->index->size, sizeof(int));
^
samtools/razf.c:99:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, &v32, sizeof(uint32_t));
^
samtools/razf.c:106:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
^
samtools/razf.c:107:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/faidx.c -o samtools/faidx.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/knetfile.c -o samtools/knetfile.o
In file included from samtools/knetfile.c:49:0:
samtools/knetfile.c: In function 'kftp_send_cmd':
samtools/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^
samtools/knetfile.c:239:2: note: in expansion of macro 'netwrite'
netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
^
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^
samtools/knetfile.c:418:2: note: in expansion of macro 'netwrite'
netwrite(fp->fd, buf, l);
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_sort.c -o samtools/bam_sort.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/sam_header.c -o samtools/sam_header.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_reheader.c -o samtools/bam_reheader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/kprobaln.c -o samtools/kprobaln.o
ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tabix/index.c -o tabix/index.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools"
mkdir -p "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix"
cp samtools/*.h "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/"
mkdir -p "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib"
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbam.a /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbcf.a /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libtabix.a -lz -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/«PKGBUILDDIR»/src'
make[1]: Entering directory '/«PKGBUILDDIR»/src'
make[1]: Leaving directory '/«PKGBUILDDIR»/src'
installing to /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsamtools)
rm -vf /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/R.css \
/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/COPYING \
/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE.txt
if test -f debian/overrides; then \
install -d /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/share/lintian/overrides ; \
install -m 0644 debian/overrides \
/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/share/lintian/overrides/r-bioc-rsamtools; \
fi
Adding cdbs dependencies to debian/r-bioc-rsamtools.substvars
dh_installdirs -pr-bioc-rsamtools
rm -rf debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE
dh_installdocs -pr-bioc-rsamtools ./NEWS
dh_installexamples -pr-bioc-rsamtools
dh_installman -pr-bioc-rsamtools
dh_installinfo -pr-bioc-rsamtools
dh_installmenu -pr-bioc-rsamtools
dh_installcron -pr-bioc-rsamtools
dh_installinit -pr-bioc-rsamtools
dh_installdebconf -pr-bioc-rsamtools
dh_installemacsen -pr-bioc-rsamtools
dh_installcatalogs -pr-bioc-rsamtools
dh_installpam -pr-bioc-rsamtools
dh_installlogrotate -pr-bioc-rsamtools
dh_installlogcheck -pr-bioc-rsamtools
dh_installchangelogs -pr-bioc-rsamtools
dh_installudev -pr-bioc-rsamtools
dh_lintian -pr-bioc-rsamtools
dh_bugfiles -pr-bioc-rsamtools
dh_install -pr-bioc-rsamtools
dh_link -pr-bioc-rsamtools
dh_installmime -pr-bioc-rsamtools
dh_installgsettings -pr-bioc-rsamtools
dh_strip -pr-bioc-rsamtools
dh_compress -pr-bioc-rsamtools
dh_fixperms -pr-bioc-rsamtools
dh_makeshlibs -pr-bioc-rsamtools
dh_installdeb -pr-bioc-rsamtools
dh_perl -pr-bioc-rsamtools
dh_shlibdeps -pr-bioc-rsamtools
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/libs/Rsamtools.so was not linked against libgomp.so.1 (it uses none of the library's symbols)
dh_gencontrol -pr-bioc-rsamtools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -pr-bioc-rsamtools
dh_builddeb -pr-bioc-rsamtools
dpkg-deb: building package `r-bioc-rsamtools' in `../r-bioc-rsamtools_1.20.4-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-rsamtools_1.20.4-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-rsamtools-1.20.4
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150714-1137
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-rsamtools_1.20.4-1_armhf.changes:
────────────────────────────────────────
Format: 1.8
Date: Sat, 27 Jun 2015 16:20:16 +0200
Source: r-bioc-rsamtools
Binary: r-bioc-rsamtools
Architecture: armhf
Version: 1.20.4-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix file i
Changes:
r-bioc-rsamtools (1.20.4-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
d69d067e38556b0292d476832ccdff1a64337cfb 3171000 r-bioc-rsamtools_1.20.4-1_armhf.deb
Checksums-Sha256:
383ff94e9afa7da91a2ec3d64cc1a4946d362ac26947c698ca24f18eccb7cec0 3171000 r-bioc-rsamtools_1.20.4-1_armhf.deb
Files:
b0c6e20b67550cb99dfc9c323076eb17 3171000 gnu-r optional r-bioc-rsamtools_1.20.4-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-rsamtools_1.20.4-1_armhf.deb
───────────────────────────────────
new debian package, version 2.0.
size 3171000 bytes: control archive=4544 bytes.
843 bytes, 15 lines control
11041 bytes, 121 lines md5sums
Package: r-bioc-rsamtools
Version: 1.20.4-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4898
Depends: r-base-core (>= 3.2.1-4), r-api-3, libc6 (>= 2.15), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 4.9), zlib1g (>= 1:1.2.3.3), r-cran-bitops, r-bioc-biostrings (>= 2.34.0), r-bioc-genomicranges (>= 1.18.0)
Recommends: r-bioc-shortread
Section: gnu-r
Priority: optional
Homepage: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html
Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
This package provides an interface to the 'samtools', 'bcftools', and
'tabix' utilities for manipulating SAM (Sequence Alignment / Map),
binary variant call (BCF) and compressed indexed tab-delimited (tabix)
files.
drwxr-xr-x root/root 0 2015-07-14 11:37 ./
drwxr-xr-x root/root 0 2015-07-14 11:37 ./usr/
drwxr-xr-x root/root 0 2015-07-14 11:32 ./usr/lib/
drwxr-xr-x root/root 0 2015-07-14 11:32 ./usr/lib/R/
drwxr-xr-x root/root 0 2015-07-14 11:37 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2015-07-14 11:37 ./usr/lib/R/site-library/Rsamtools/
-rw-r--r-- root/root 1548 2015-07-14 11:32 ./usr/lib/R/site-library/Rsamtools/DESCRIPTION
-rw-r--r-- root/root 2136 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/INDEX
drwxr-xr-x root/root 0 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/Meta/
-rw-r--r-- root/root 3124 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/Meta/Rd.rds
-rw-r--r-- root/root 3253 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/Meta/hsearch.rds
-rw-r--r-- root/root 2365 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/Meta/links.rds
-rw-r--r-- root/root 718 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/Meta/nsInfo.rds
-rw-r--r-- root/root 1567 2015-07-14 11:32 ./usr/lib/R/site-library/Rsamtools/Meta/package.rds
-rw-r--r-- root/root 283 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/Meta/vignette.rds
-rw-r--r-- root/root 1307 2015-07-14 11:32 ./usr/lib/R/site-library/Rsamtools/NAMESPACE
-rw-r--r-- root/root 11948 2015-07-14 11:32 ./usr/lib/R/site-library/Rsamtools/NEWS
drwxr-xr-x root/root 0 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/R/
-rw-r--r-- root/root 1056 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools
-rw-r--r-- root/root 382928 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdb
-rw-r--r-- root/root 6159 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdx
drwxr-xr-x root/root 0 2015-07-14 11:36 ./usr/lib/R/site-library/Rsamtools/doc/
-rw-r--r-- root/root 9643 2015-07-14 11:35 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.R
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Build Architecture: armhf
Build-Space: 15928
Build-Time: 359
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 640
Job: r-bioc-rsamtools_1.20.4-1
Machine Architecture: armhf
Package: r-bioc-rsamtools
Package-Time: 1089
Source-Version: 1.20.4-1
Space: 15928
Status: successful
Version: 1.20.4-1
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Finished at 20150714-1137
Build needed 00:18:09, 15928k disc space