r-bioc-rsamtools →
1.22.0-1 →
armhf → 2016-03-02 23:58:24
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-03
+==============================================================================+
| r-bioc-rsamtools 1.22.0-1 (armhf) 02 Mar 2016 23:40 |
+==============================================================================+
Package: r-bioc-rsamtools
Version: 1.22.0-1
Source Version: 1.22.0-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-EmX7hU/r-bioc-rsamtools-1.22.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-EmX7hU' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-27296767-1a66-4c57-b013-18db5facb047' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8771 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.9 MB]
Fetched 19.6 MB in 21s (911 kB/s)
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
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 2991 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main r-bioc-rsamtools 1.22.0-1 (dsc) [2231 B]
Get:2 http://172.17.0.1/private stretch-staging/main r-bioc-rsamtools 1.22.0-1 (tar) [2982 kB]
Get:3 http://172.17.0.1/private stretch-staging/main r-bioc-rsamtools 1.22.0-1 (diff) [6820 B]
Fetched 2991 kB in 0s (8259 kB/s)
Download complete and in download only mode
Check architectures
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Check dependencies
------------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-y_Umzb/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-y_Umzb/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-y_Umzb/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-y_Umzb/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-y_Umzb/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-y_Umzb/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-y_Umzb/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-y_Umzb/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-y_Umzb/apt_archive ./ Packages [526 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 40 not upgraded.
Need to get 0 B/762 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-y_Umzb/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [762 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 12651 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) ...
W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-cran-bitops, r-bioc-biostrings (>= 2.38.0), r-bioc-genomicranges (>= 1.22.0), r-bioc-biocparallel, libbam-dev
Filtered Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-cran-bitops, r-bioc-biostrings (>= 2.38.0), r-bioc-genomicranges (>= 1.22.0), r-bioc-biocparallel, libbam-dev
dpkg-deb: building package 'sbuild-build-depends-r-bioc-rsamtools-dummy' in '/<<BUILDDIR>>/resolver-L46BnR/apt_archive/sbuild-build-depends-r-bioc-rsamtools-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-L46BnR/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-L46BnR/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-L46BnR/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-L46BnR/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-L46BnR/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-L46BnR/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-L46BnR/apt_archive ./ Sources [281 B]
Get:5 file:/<<BUILDDIR>>/resolver-L46BnR/apt_archive ./ Packages [599 B]
Reading package lists...
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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 additional packages will be installed:
autotools-dev bsdmainutils ca-certificates cdbs debhelper
dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core
gettext gettext-base gfortran gfortran-5 groff-base intltool-debian
libarchive-zip-perl libbam-dev libblas-common libblas-dev libblas3
libbz2-dev libcairo2 libcroco3 libcurl3 libdatrie1 libexpat1 libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran-5-dev libgfortran3 libglib2.0-0 libgnutls30 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 libncurses5-dev libncursesw5
libnettle6 libnghttp2-14 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 libpng12-0 libpng12-dev
libreadline-dev libreadline6-dev librtmp1 libsasl2-2 libsasl2-modules-db
libsm6 libsqlite3-0 libssh2-1 libssl1.0.2 libtasn1-6 libtcl8.6 libthai-data
libthai0 libtiff5 libtimedate-perl libtinfo-dev libtinfo5 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-biocgenerics
r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb
r-bioc-genomicranges r-bioc-iranges 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-littler r-cran-magrittr r-cran-pkgkitten r-cran-plyr
r-cran-rcpp r-cran-rsqlite r-cran-sendmailr r-cran-snow r-cran-stringi
r-cran-stringr 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 liblapack-doc-man liblapack-doc gnutls-bin krb5-doc
krb5-user liblzma-doc ncurses-doc readline-doc tcl8.6 tk8.6 less www-browser
libmail-box-perl ess 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-getopt r-cran-inline r-cran-runit r-cran-rmpi
r-cran-rsprng r-cran-rlecuyer gvfs-bin
Recommended packages:
curl | wget | lynx-cur bzip2-doc 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-doparallel r-cran-mass
r-cran-crayon 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:
autotools-dev bsdmainutils ca-certificates cdbs debhelper
dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core
gettext gettext-base gfortran gfortran-5 groff-base intltool-debian
libarchive-zip-perl libbam-dev libblas-common libblas-dev libblas3
libbz2-dev libcairo2 libcroco3 libcurl3 libdatrie1 libexpat1 libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran-5-dev libgfortran3 libglib2.0-0 libgnutls30 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 libnghttp2-14
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
libssl1.0.2 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff5
libtimedate-perl 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-biocgenerics r-bioc-biocparallel
r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-iranges
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-littler
r-cran-magrittr r-cran-pkgkitten r-cran-plyr r-cran-rcpp r-cran-rsqlite
r-cran-sendmailr r-cran-snow r-cran-stringi r-cran-stringr
sbuild-build-depends-r-bioc-rsamtools-dummy ucf unzip x11-common xdg-utils
zip zlib1g-dev
The following packages will be upgraded:
libncurses5 libncursesw5 libpng12-0 libtinfo5
4 upgraded, 148 newly installed, 0 to remove and 36 not upgraded.
Need to get 125 MB/125 MB of archives.
After this operation, 309 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-L46BnR/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [838 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libtinfo5 armhf 6.0+20160213-1 [281 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libncurses5 armhf 6.0+20160213-1 [74.8 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libncursesw5 armhf 6.0+20160213-1 [93.3 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.6 [177 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libpng12-0 armhf 1.2.54-3 [160 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.1-0.1 [411 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0035 [68.5 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.35-1 [1064 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.3 [273 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf fontconfig armhf 2.11.0-6.3 [402 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libpcrecpp0v5 armhf 2:8.38-1 [148 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.5.0-2 [122 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1 [40.9 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libxft2 armhf 2.3.2-1 [48.3 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+13 [251 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2f-2 [883 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libnettle6 armhf 3.2-1 [202 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libhogweed4 armhf 3.2-1 [126 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libidn11 armhf 1.32-3 [110 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.2-3 [93.3 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.7-3 [44.4 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.4.9-2 [711 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-8 [11.5 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.13.2+dfsg-5 [56.6 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.13.2+dfsg-5 [110 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.13.2+dfsg-5 [259 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.13.2+dfsg-5 [130 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.26.dfsg1-14+b1 [65.8 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.26.dfsg1-14+b1 [97.1 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.42+dfsg-2+rpi1+b2 [198 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.10.2-1 [408 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2f-2 [663 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf cdbs all 0.4.130 [76.4 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-3 [2482 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.015-1 [6810 B]
Get:67 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160115 [827 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 5.3.1-8+rpi1 [153 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libgfortran-5-dev armhf 5.3.1-8+rpi1 [183 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf gfortran-5 armhf 5.3.1-8+rpi1 [23.7 MB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:5.3.1-1+rpi1 [1362 B]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.0-2 [13.5 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.0-2 [110 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.0-2 [116 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libbz2-dev armhf 1.0.6-8 [27.8 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-0 armhf 0.33.6-1 [454 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0 armhf 1.11.1-1 [17.0 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0 armhf 1.11.1-1 [11.5 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libcairo2 armhf 1.14.6-1 [688 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.7.1-2 [63.2 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d-1+b1 [54.4 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf libcurl3 armhf 7.47.0-1 [247 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf libdatrie1 armhf 0.2.10-2 [32.5 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libgraphite2-3 armhf 1.3.5-1 [61.5 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz0b armhf 1.0.1-1+b1 [501 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.4.2-2 [104 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.4.2-2 [413 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.4.2-2 [51.7 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.0-2 [1382 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.0-2 [1355 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf liblzma-dev armhf 5.1.1alpha+20120614-2.1 [248 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20160213-1 [66.0 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf libncurses5-dev armhf 6.0+20160213-1 [154 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf libthai-data all 0.1.24-2 [163 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf libthai0 armhf 0.1.24-2 [46.6 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf libpango-1.0-0 armhf 1.38.1-1 [292 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf libpangoft2-1.0-0 armhf 1.38.1-1 [229 kB]
Get:100 http://172.17.0.1/private stretch-staging/main armhf libpangocairo-1.0-0 armhf 1.38.1-1 [218 kB]
Get:101 http://172.17.0.1/private stretch-staging/main armhf libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:102 http://172.17.0.1/private stretch-staging/main armhf libpcre16-3 armhf 2:8.38-1 [229 kB]
Get:103 http://172.17.0.1/private stretch-staging/main armhf libpcre32-3 armhf 2:8.38-1 [222 kB]
Get:104 http://172.17.0.1/private stretch-staging/main armhf libpcre3-dev armhf 2:8.38-1 [556 kB]
Get:105 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:106 http://172.17.0.1/private stretch-staging/main armhf libpng12-dev armhf 1.2.54-3 [233 kB]
Get:107 http://172.17.0.1/private stretch-staging/main armhf libreadline6-dev armhf 6.3-8+b3 [105 kB]
Get:108 http://172.17.0.1/private stretch-staging/main armhf libreadline-dev armhf 6.3-8+b3 [958 B]
Get:109 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:110 http://172.17.0.1/private stretch-staging/main armhf libtcl8.6 armhf 8.6.4+dfsg-3 [855 kB]
Get:111 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.6-1 [201 kB]
Get:112 http://172.17.0.1/private stretch-staging/main armhf libtk8.6 armhf 8.6.4+dfsg-3 [664 kB]
Get:113 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:114 http://172.17.0.1/private stretch-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:115 http://172.17.0.1/private stretch-staging/main armhf unzip armhf 6.0-20 [142 kB]
Get:116 http://172.17.0.1/private stretch-staging/main armhf xdg-utils all 1.1.1-1 [71.1 kB]
Get:117 http://172.17.0.1/private stretch-staging/main armhf r-base-core armhf 3.2.3-6 [20.2 MB]
Get:118 http://172.17.0.1/private stretch-staging/main armhf r-cran-littler armhf 0.3.0-2 [64.7 kB]
Get:119 http://172.17.0.1/private stretch-staging/main armhf littler all 0.3.0-2 [11.0 kB]
Get:120 http://172.17.0.1/private stretch-staging/main armhf r-base-dev all 3.2.3-6 [4292 B]
Get:121 http://172.17.0.1/private stretch-staging/main armhf r-bioc-biocgenerics all 0.16.0-1 [474 kB]
Get:122 http://172.17.0.1/private stretch-staging/main armhf r-cran-checkmate armhf 1.6.0-1 [268 kB]
Get:123 http://172.17.0.1/private stretch-staging/main armhf r-cran-bbmisc armhf 1.9-1 [279 kB]
Get:124 http://172.17.0.1/private stretch-staging/main armhf r-cran-brew armhf 1.0-6-1 [61.3 kB]
Get:125 http://172.17.0.1/private stretch-staging/main armhf r-cran-digest armhf 0.6.9-1 [103 kB]
Get:126 http://172.17.0.1/private stretch-staging/main armhf r-cran-dbi armhf 0.3.1-1 [156 kB]
Get:127 http://172.17.0.1/private stretch-staging/main armhf r-cran-rsqlite armhf 1.0.0-2 [302 kB]
Get:128 http://172.17.0.1/private stretch-staging/main armhf r-cran-pkgkitten all 0.1.3-1 [18.3 kB]
Get:129 http://172.17.0.1/private stretch-staging/main armhf r-cran-rcpp armhf 0.12.3-1 [2123 kB]
Get:130 http://172.17.0.1/private stretch-staging/main armhf r-cran-plyr armhf 1.8.3-1 [728 kB]
Get:131 http://172.17.0.1/private stretch-staging/main armhf r-cran-magrittr armhf 1.5-1 [147 kB]
Get:132 http://172.17.0.1/private stretch-staging/main armhf r-cran-stringi armhf 1.0-1-1 [623 kB]
Get:133 http://172.17.0.1/private stretch-staging/main armhf r-cran-stringr all 1.0.0-1 [76.6 kB]
Get:134 http://172.17.0.1/private stretch-staging/main armhf r-cran-base64enc armhf 0.1-2-1 [19.6 kB]
Get:135 http://172.17.0.1/private stretch-staging/main armhf r-cran-sendmailr armhf 1.2-1-1 [29.0 kB]
Get:136 http://172.17.0.1/private stretch-staging/main armhf r-cran-fail armhf 1.3-1 [43.2 kB]
Get:137 http://172.17.0.1/private stretch-staging/main armhf r-cran-batchjobs armhf 1.6-1 [422 kB]
Get:138 http://172.17.0.1/private stretch-staging/main armhf r-cran-codetools all 0.2-14-1 [46.5 kB]
Get:139 http://172.17.0.1/private stretch-staging/main armhf r-cran-iterators all 1.0.8-1 [306 kB]
Get:140 http://172.17.0.1/private stretch-staging/main armhf r-cran-foreach all 1.4.3-1 [371 kB]
Get:141 http://172.17.0.1/private stretch-staging/main armhf r-cran-lambda.r all 1.1.7-2 [66.3 kB]
Get:142 http://172.17.0.1/private stretch-staging/main armhf r-cran-futile.options all 1.0.0-2 [15.4 kB]
Get:143 http://172.17.0.1/private stretch-staging/main armhf r-cran-futile.logger all 1.4.1-1 [84.4 kB]
Get:144 http://172.17.0.1/private stretch-staging/main armhf r-cran-snow all 1:0.4.1-1 [64.9 kB]
Get:145 http://172.17.0.1/private stretch-staging/main armhf r-bioc-biocparallel all 1.4.0-1 [627 kB]
Get:146 http://172.17.0.1/private stretch-staging/main armhf r-bioc-s4vectors armhf 0.8.11-1 [809 kB]
Get:147 http://172.17.0.1/private stretch-staging/main armhf r-bioc-iranges armhf 2.4.7-1 [1470 kB]
Get:148 http://172.17.0.1/private stretch-staging/main armhf r-bioc-xvector armhf 0.10.0-1 [327 kB]
Get:149 http://172.17.0.1/private stretch-staging/main armhf r-bioc-biostrings armhf 2.38.4-1 [13.5 MB]
Get:150 http://172.17.0.1/private stretch-staging/main armhf r-bioc-genomeinfodb all 1.6.0-1 [19.1 MB]
Get:151 http://172.17.0.1/private stretch-staging/main armhf r-bioc-genomicranges armhf 1.22.0-1 [1476 kB]
Get:152 http://172.17.0.1/private stretch-staging/main armhf r-cran-bitops armhf 1.0-6-1 [23.6 kB]
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update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libblas-dev (3.6.0-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libbz2-dev:armhf (1.0.6-8) ...
Setting up libpixman-1-0:armhf (0.33.6-1) ...
Setting up libxcb-render0:armhf (1.11.1-1) ...
Setting up libxcb-shm0:armhf (1.11.1-1) ...
Setting up libcairo2:armhf (1.14.6-1) ...
Setting up libnghttp2-14:armhf (1.7.1-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d-1+b1) ...
Setting up libcurl3:armhf (7.47.0-1) ...
Setting up libdatrie1:armhf (0.2.10-2) ...
Setting up libgraphite2-3:armhf (1.3.5-1) ...
Setting up libharfbuzz0b:armhf (1.0.1-1+b1) ...
Setting up libice6:armhf (2:1.0.9-1+b1) ...
Setting up libjpeg62-turbo:armhf (1:1.4.2-2) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.4.2-2) ...
Setting up libjpeg-dev (1:1.4.2-2) ...
Setting up liblapack3 (3.6.0-2) ...
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 (3.6.0-2) ...
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 (6.0+20160213-1) ...
Setting up libncurses5-dev:armhf (6.0+20160213-1) ...
Setting up libthai-data (0.1.24-2) ...
Setting up libthai0:armhf (0.1.24-2) ...
Setting up libpango-1.0-0:armhf (1.38.1-1) ...
Setting up libpangoft2-1.0-0:armhf (1.38.1-1) ...
Setting up libpangocairo-1.0-0:armhf (1.38.1-1) ...
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libpcre16-3:armhf (2:8.38-1) ...
Setting up libpcre32-3:armhf (2:8.38-1) ...
Setting up libpcre3-dev:armhf (2:8.38-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libpng12-dev:armhf (1.2.54-3) ...
Setting up libreadline6-dev:armhf (6.3-8+b3) ...
Setting up libreadline-dev:armhf (6.3-8+b3) ...
Setting up libsm6:armhf (2:1.2.2-1+b1) ...
Setting up libtcl8.6:armhf (8.6.4+dfsg-3) ...
Setting up libtiff5:armhf (4.0.6-1) ...
Setting up libtk8.6:armhf (8.6.4+dfsg-3) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up zip (3.0-11) ...
Setting up unzip (6.0-20) ...
Setting up xdg-utils (1.1.1-1) ...
Setting up r-base-core (3.2.3-6) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-littler (0.3.0-2) ...
Setting up littler (0.3.0-2) ...
Setting up r-base-dev (3.2.3-6) ...
Setting up r-bioc-biocgenerics (0.16.0-1) ...
Setting up r-cran-checkmate (1.6.0-1) ...
Setting up r-cran-bbmisc (1.9-1) ...
Setting up r-cran-brew (1.0-6-1) ...
Setting up r-cran-digest (0.6.9-1) ...
Setting up r-cran-dbi (0.3.1-1) ...
Setting up r-cran-rsqlite (1.0.0-2) ...
Setting up r-cran-pkgkitten (0.1.3-1) ...
Setting up r-cran-rcpp (0.12.3-1) ...
Setting up r-cran-plyr (1.8.3-1) ...
Setting up r-cran-magrittr (1.5-1) ...
Setting up r-cran-stringi (1.0-1-1) ...
Setting up r-cran-stringr (1.0.0-1) ...
Setting up r-cran-base64enc (0.1-2-1) ...
Setting up r-cran-sendmailr (1.2-1-1) ...
Setting up r-cran-fail (1.3-1) ...
Setting up r-cran-batchjobs (1.6-1) ...
Setting up r-cran-codetools (0.2-14-1) ...
Setting up r-cran-iterators (1.0.8-1) ...
Setting up r-cran-foreach (1.4.3-1) ...
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 (1:0.4.1-1) ...
Setting up r-bioc-biocparallel (1.4.0-1) ...
Setting up r-bioc-s4vectors (0.8.11-1) ...
Setting up r-bioc-iranges (2.4.7-1) ...
Setting up r-bioc-xvector (0.10.0-1) ...
Setting up r-bioc-biostrings (2.38.4-1) ...
Setting up r-bioc-genomeinfodb (1.6.0-1) ...
Setting up r-bioc-genomicranges (1.22.0-1) ...
Setting up r-cran-bitops (1.0-6-1) ...
Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.015-1) ...
Processing triggers for libc-bin (2.21-7) ...
Processing triggers for systemd (228-6) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-3 dpkg-dev_1.18.4 g++-5_5.3.1-8+rpi1 gcc-5_5.3.1-8+rpi1 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-8+rpi1 libstdc++6_5.3.1-8+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.113+nmu3 apt_1.2.3 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-3 bsdmainutils_9.0.6 bsdutils_1:2.27.1-3 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20160104 cdbs_0.4.130 coreutils_8.24-1 cpio_2.11+dfsg-4.1 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-8+rpi1 dash_0.5.8-2.1 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20160115 debianutils_4.7 dh-strip-nondeterminism_0.015-1 diffutils_1:3.3-3 dmsetup_2:1.02.115-2 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 fontconfig_2.11.0-6.3 fontconfig-config_2.11.0-6.3 fonts-dejavu-core_2.35-1 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-8+rpi1 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-10 gcc-5_5.3.1-8+rpi1 gcc-5-base_5.3.1-8+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gfortran_4:5.3.1-1+rpi1 gfortran-5_5.3.1-8+rpi1 gnupg_1.4.20-1 gpgv_1.4.20-1 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5.2 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-7+rpi1 kmod_22-1 libacl1_2.2.52-3 libapparmor1_2.10-3 libapt-pkg5.0_1.2.3 libarchive-zip-perl_1.56-2 libasan2_5.3.1-8+rpi1 libatomic1_5.3.1-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libbam-dev_0.1.19-2 libblas-common_3.6.0-2 libblas-dev_3.6.0-2 libblas3_3.6.0-2 libblkid1_2.27.1-3 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.21-7 libc-dev-bin_2.21-7 libc6_2.21-7 libc6-dev_2.21-7 libcairo2_1.14.6-1 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-8+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libcurl3_7.47.0-1 libdatrie1_0.2.10-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1 libdebconfclient0_0.204 libdevmapper1.02.1_2:1.02.115-2 libdpkg-perl_1.18.4 libdrm2_2.4.66-2 libexpat1_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.27.1-3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.015-1 libfontconfig1_2.11.0-6.3 libfreetype6_2.6.1-0.1 libgc1c2_1:7.4.2-7.3 libgcc-5-dev_5.3.1-8+rpi1 libgcc1_1:5.3.1-8+rpi1 libgcrypt20_1.6.4-5 libgdbm3_1.8.3-13.1 libgfortran-5-dev_5.3.1-8+rpi1 libgfortran3_5.3.1-8+rpi1 libglib2.0-0_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.9-2 libgomp1_5.3.1-8+rpi1 libgpg-error0_1.21-1 libgraphite2-3_1.3.5-1 libgssapi-krb5-2_1.13.2+dfsg-5 libharfbuzz0b_1.0.1-1+b1 libhogweed4_3.2-1 libice6_2:1.0.9-1+b1 libicu55_55.1-7 libidn11_1.32-3 libisl15_0.16.1-1 libjbig0_2.1-3.1 libjpeg-dev_1:1.4.2-2 libjpeg62-turbo_1:1.4.2-2 libjpeg62-turbo-dev_1:1.4.2-2 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-8 libklibc_2.0.4-7+rpi1 libkmod2_22-1 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 liblapack-dev_3.6.0-2 liblapack3_3.6.0-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 liblz4-1_0.0~r131-1 liblzma-dev_5.1.1alpha+20120614-2.1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-3 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20160213-1 libncurses5-dev_6.0+20160213-1 libncursesw5_6.0+20160213-1 libnettle6_3.2-1 libnghttp2-14_1.7.1-2 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpango-1.0-0_1.38.1-1 libpangocairo-1.0-0_1.38.1-1 libpangoft2-1.0-0_1.38.1-1 libpaper-utils_1.1.24+nmu4 libpaper1_1.1.24+nmu4 libpcre16-3_2:8.38-1 libpcre3_2:8.38-1 libpcre3-dev_2:8.38-1 libpcre32-3_2:8.38-1 libpcrecpp0v5_2:8.38-1 libperl5.22_5.22.1-5 libpipeline1_1.4.1-2 libpixman-1-0_0.33.6-1 libplymouth4_0.9.2-3 libpng12-0_1.2.54-3 libpng12-dev_1.2.54-3 libprocps5_2:3.3.11-3 libreadline-dev_6.3-8+b3 libreadline6_6.3-8+b3 libreadline6-dev_6.3-8+b3 librtmp1_2.4+20151223.gitfa8646d-1+b1 libsasl2-2_2.1.26.dfsg1-14+b1 libsasl2-modules-db_2.1.26.dfsg1-14+b1 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsm6_2:1.2.2-1+b1 libsmartcols1_2.27.1-3 libsqlite3-0_3.10.2-1 libss2_1.42.13-1 libssh2-1_1.5.0-2 libssl1.0.2_1.0.2f-2 libstdc++-5-dev_5.3.1-8+rpi1 libstdc++6_5.3.1-8+rpi1 libsystemd0_228-6 libtasn1-6_4.7-3 libtcl8.6_8.6.4+dfsg-3 libthai-data_0.1.24-2 libthai0_0.1.24-2 libtiff5_4.0.6-1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20160213-1 libtinfo5_6.0+20160213-1 libtk8.6_8.6.4+dfsg-3 libubsan0_5.3.1-8+rpi1 libudev1_228-6 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-3 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxcb-render0_1.11.1-1 libxcb-shm0_1.11.1-1 libxcb1_1.11.1-1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxft2_2.3.2-1 libxml2_2.9.3+dfsg1-1 libxrender1_1:0.9.9-2 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch littler_0.3.0-2 login_1:4.2-3.1 lsb-base_9.20160110+rpi1 make_4.1-5 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-1 mawk_1.3.3-17 mount_2.27.1-3 multiarch-support_2.21-7 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 openssl_1.0.2f-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-5 perl-base_5.22.1-5 perl-modules-5.22_5.22.1-7 plymouth_0.9.2-3 po-debconf_1.0.19 procps_2:3.3.11-3 r-base-core_3.2.3-6 r-base-dev_3.2.3-6 r-bioc-biocgenerics_0.16.0-1 r-bioc-biocparallel_1.4.0-1 r-bioc-biostrings_2.38.4-1 r-bioc-genomeinfodb_1.6.0-1 r-bioc-genomicranges_1.22.0-1 r-bioc-iranges_2.4.7-1 r-bioc-s4vectors_0.8.11-1 r-bioc-xvector_0.10.0-1 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_0.6.9-1 r-cran-fail_1.3-1 r-cran-foreach_1.4.3-1 r-cran-futile.logger_1.4.1-1 r-cran-futile.options_1.0.0-2 r-cran-iterators_1.0.8-1 r-cran-lambda.r_1.1.7-2 r-cran-littler_0.3.0-2 r-cran-magrittr_1.5-1 r-cran-pkgkitten_0.1.3-1 r-cran-plyr_1.8.3-1 r-cran-rcpp_0.12.3-1 r-cran-rsqlite_1.0.0-2 r-cran-sendmailr_1.2-1-1 r-cran-snow_1:0.4.1-1 r-cran-stringi_1.0-1-1 r-cran-stringr_1.0.0-1 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_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_228-6 systemd-sysv_228-6 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2016a-1 ucf_3.0035 udev_228-6 unzip_6.0-20 util-linux_2.27.1-3 x11-common_1:7.7+13 xdg-utils_1.1.1-1 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 Fri Oct 30 15:09:51 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_1.22.0-1.dsc
dpkg-source: info: extracting r-bioc-rsamtools in r-bioc-rsamtools-1.22.0
dpkg-source: info: unpacking r-bioc-rsamtools_1.22.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rsamtools_1.22.0-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
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-27296767-1a66-4c57-b013-18db5facb047
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package r-bioc-rsamtools
dpkg-buildpackage: source version 1.22.0-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build r-bioc-rsamtools-1.22.0
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
test -x debian/rules
dh_clean
if test -d src; then \
find src -regex ".*\.o" | \
xargs --no-run-if-empty -r rm; \
fi
rm -f config.log config.status
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 (>= 3.2.3-6), 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=\"Fri, 30 Oct 2015 14:05:41 +0100\"" \
; \
else \
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library \
--clean . \
"--built-timestamp=\"Fri, 30 Oct 2015 14:05:41 +0100\"" \
; \
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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_import.c -o samtools/bam_import.o
In file included from /usr/include/limits.h:25:0,
from /usr/lib/gcc/arm-linux-gnueabihf/5/include-fixed/limits.h:168,
from /usr/lib/gcc/arm-linux-gnueabihf/5/include-fixed/syslimits.h:7,
from /usr/lib/gcc/arm-linux-gnueabihf/5/include-fixed/limits.h:34,
from /usr/include/arm-linux-gnueabihf/zconf.h:395,
from /usr/include/zlib.h:34,
from samtools/bam_import.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/sam.c -o samtools/sam.o
In file included from /usr/include/string.h:25:0,
from samtools/sam.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/knetfile.c -o samtools/knetfile.o
In file included from /usr/include/time.h:27:0,
from samtools/knetfile.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_sort.c -o samtools/bam_sort.o
In file included from /usr/include/stdlib.h:24:0,
from samtools/bam_sort.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/sam_header.c -o samtools/sam_header.o
In file included from /usr/include/stdio.h:27:0,
from samtools/sam_header.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
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 -Wdate-time -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 -Wdate-time -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
ar: `u' modifier ignored since `D' is the default (see `U')
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 -Wdate-time -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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
In file included from /usr/include/limits.h:25:0,
from /usr/lib/gcc/arm-linux-gnueabihf/5/include-fixed/limits.h:168,
from /usr/lib/gcc/arm-linux-gnueabihf/5/include-fixed/syslimits.h:7,
from /usr/lib/gcc/arm-linux-gnueabihf/5/include-fixed/limits.h:34,
from /usr/include/arm-linux-gnueabihf/zconf.h:395,
from /usr/include/zlib.h:34,
from samtools/bcftools/vcf.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
In file included from /usr/include/alloca.h:21:0,
from samtools/bcftools/bcfutils.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
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 -Wdate-time -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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/index.c -o samtools/bcftools/index.o
In file included from /usr/include/assert.h:35:0,
from samtools/bcftools/index.c:2:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
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 -Wdate-time -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 -Wdate-time -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
ar: `u' modifier ignored since `D' is the default (see `U')
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 -Wdate-time -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 -Wdate-time -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
ar: `u' modifier ignored since `D' is the default (see `U')
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
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-dbgsym' in '../r-bioc-rsamtools-dbgsym_1.22.0-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-rsamtools' in '../r-bioc-rsamtools_1.22.0-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-rsamtools_1.22.0-1_armhf.changes
dpkg-genchanges: warning: package r-bioc-rsamtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-rsamtools-1.22.0
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160302-2357
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-rsamtools_1.22.0-1_armhf.changes:
----------------------------------------
Format: 1.8
Date: Fri, 30 Oct 2015 14:05:41 +0100
Source: r-bioc-rsamtools
Binary: r-bioc-rsamtools
Architecture: armhf
Version: 1.22.0-1
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 (1.22.0-1) unstable; urgency=medium
.
* New upstream version
* (Build-)Depends: r-bioc-biocparallel
* Add lintian-override for false positive
Checksums-Sha1:
198f3b4389114c9eac19d8aff04a584eba029fbf 730548 r-bioc-rsamtools-dbgsym_1.22.0-1_armhf.deb
6b7df0e5223fa1aeb75e5c55b502fad4334bec39 3196462 r-bioc-rsamtools_1.22.0-1_armhf.deb
Checksums-Sha256:
cd153a277d6f6f4b7fb7dc113697ee3baf0b82cf449b31b244b9eaea80ecd3d7 730548 r-bioc-rsamtools-dbgsym_1.22.0-1_armhf.deb
da49e700e8efc2917502b308cc0723cd9eb0397d9433dba7fdceec083c090acd 3196462 r-bioc-rsamtools_1.22.0-1_armhf.deb
Files:
ef625bd2baf334c512305eb5fa1d8db1 730548 debug extra r-bioc-rsamtools-dbgsym_1.22.0-1_armhf.deb
5183d4a6a4b713a7a7a3e0453c0d8106 3196462 gnu-r optional r-bioc-rsamtools_1.22.0-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-rsamtools-dbgsym_1.22.0-1_armhf.deb
------------------------------------------
new debian package, version 2.0.
size 730548 bytes: control archive=516 bytes.
485 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-rsamtools-dbgsym
Source: r-bioc-rsamtools
Version: 1.22.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 778
Depends: r-bioc-rsamtools (= 1.22.0-1)
Section: debug
Priority: extra
Homepage: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html
Description: Debug symbols for r-bioc-rsamtools
Auto-Built-Package: debug-symbols
Build-Ids: a67c62a54afaa83f062db6da3f59b24340879679
drwxr-xr-x root/root 0 2016-03-02 23:57 ./
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/debug/.build-id/a6/
-rw-r--r-- root/root 785420 2016-03-02 23:56 ./usr/lib/debug/.build-id/a6/7c62a54afaa83f062db6da3f59b24340879679.debug
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/share/
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-03-02 23:56 ./usr/share/doc/r-bioc-rsamtools-dbgsym -> r-bioc-rsamtools
r-bioc-rsamtools_1.22.0-1_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 3196462 bytes: control archive=4486 bytes.
862 bytes, 15 lines control
11951 bytes, 131 lines md5sums
Package: r-bioc-rsamtools
Version: 1.22.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5037
Depends: r-base-core (>= 3.2.3-6), r-api-3, libc6 (>= 2.15), libgcc1 (>= 1:3.5), libgomp1 (>= 4.2.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), r-cran-bitops, r-bioc-biostrings (>= 2.34.0), r-bioc-genomicranges (>= 1.18.0), r-bioc-biocparallel
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 2016-03-02 23:56 ./
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/
drwxr-xr-x root/root 0 2016-03-02 23:52 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-02 23:52 ./usr/lib/R/
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/
-rw-r--r-- root/root 1558 2016-03-02 23:52 ./usr/lib/R/site-library/Rsamtools/DESCRIPTION
-rw-r--r-- root/root 2136 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/INDEX
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/Meta/
-rw-r--r-- root/root 3150 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/Meta/Rd.rds
-rw-r--r-- root/root 3271 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/Meta/hsearch.rds
-rw-r--r-- root/root 2389 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/Meta/links.rds
-rw-r--r-- root/root 738 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/Meta/nsInfo.rds
-rw-r--r-- root/root 1577 2016-03-02 23:52 ./usr/lib/R/site-library/Rsamtools/Meta/package.rds
-rw-r--r-- root/root 284 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/Meta/vignette.rds
-rw-r--r-- root/root 1369 2016-03-02 23:52 ./usr/lib/R/site-library/Rsamtools/NAMESPACE
-rw-r--r-- root/root 12612 2016-03-02 23:52 ./usr/lib/R/site-library/Rsamtools/NEWS
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/R/
-rw-r--r-- root/root 1056 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools
-rw-r--r-- root/root 391785 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdb
-rw-r--r-- root/root 6180 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdx
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/doc/
-rw-r--r-- root/root 9643 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.R
-rw-r--r-- root/root 19840 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.Rnw
-rw-r--r-- root/root 140911 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.pdf
-rw-r--r-- root/root 221 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.R
-rw-r--r-- root/root 3994 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.Rnw
-rw-r--r-- root/root 86258 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.pdf
-rw-r--r-- root/root 1975 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/doc/index.html
drwxr-xr-x root/root 0 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/
-rw-r--r-- root/root 176 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa
-rw-r--r-- root/root 112 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa.fai
-rw-r--r-- root/root 126539 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam
-rw-r--r-- root/root 176 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam.bai
-rw-r--r-- root/root 74700 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf
-rw-r--r-- root/root 77 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.bci
-rw-r--r-- root/root 559422 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.sam
-rw-r--r-- root/root 3778 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz
-rw-r--r-- root/root 259 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz.tbi
-rw-r--r-- root/root 348 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam
-rw-r--r-- root/root 96 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam.bai
-rw-r--r-- root/root 368 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.sam
-rw-r--r-- root/root 203 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam
-rw-r--r-- root/root 176 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam.bai
-rw-r--r-- root/root 240 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.sam
-rw-r--r-- root/root 198 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam
-rw-r--r-- root/root 176 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam.bai
-rw-r--r-- root/root 168 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.sam
-rw-r--r-- root/root 1663363 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/olaps.Rda
-rw-r--r-- root/root 138598 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/pileup.txt
-rw-r--r-- root/root 181 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam
-rw-r--r-- root/root 96 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam.bai
-rw-r--r-- root/root 117 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.sam
-rw-r--r-- root/root 381 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam
-rw-r--r-- root/root 416 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam.bai
-rw-r--r-- root/root 770 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.sam
-rw-r--r-- root/root 31 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/samtools-github.txt
-rw-r--r-- root/root 2808 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/slxMaq09_urls.txt
-rw-r--r-- root/root 333 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam
-rw-r--r-- root/root 656 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam.bai
-rw-r--r-- root/root 804 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.sam
-rw-r--r-- root/root 1167 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam
-rw-r--r-- root/root 2336 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam.bai
-rw-r--r-- root/root 4102 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.sam
drwxr-xr-x root/root 0 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/
-rw-r--r-- root/root 36 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/README
-rw-r--r-- root/root 36039 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/accepted_hits.sam
-rw-r--r-- root/root 4381 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/coverage.wig
-rw-r--r-- root/root 196 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/junctions.bed
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/help/
-rw-r--r-- root/root 11330 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/help/AnIndex
-rw-r--r-- root/root 170994 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/help/Rsamtools.rdb
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-rw-r--r-- root/root 2433 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/help/aliases.rds
-rw-r--r-- root/root 369 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/help/paths.rds
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/html/
-rw-r--r-- root/root 40859 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/html/00Index.html
-rw-r--r-- root/root 1319 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/html/R.css
drwxr-xr-x root/root 0 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/
drwxr-xr-x root/root 0 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/samtools/
-rw-r--r-- root/root 25788 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/samtools/bam.h
-rw-r--r-- root/root 1064 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/samtools/bam_endian.h
drwxr-xr-x root/root 0 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/
-rw-r--r-- root/root 7226 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/bcf.h
-rw-r--r-- root/root 1457 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/prob1.h
-rw-r--r-- root/root 6326 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/samtools/bgzf.h
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drwxr-xr-x root/root 0 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/tabix/
-rw-r--r-- root/root 6326 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/tabix/bgzf.h
-rw-r--r-- root/root 1750 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/tabix/knetfile.h
-rw-r--r-- root/root 4459 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/tabix/kstring.h
-rw-r--r-- root/root 4712 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/include/tabix/tabix.h
drwxr-xr-x root/root 0 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/libs/
-rw-r--r-- root/root 406300 2016-03-02 23:56 ./usr/lib/R/site-library/Rsamtools/libs/Rsamtools.so
drwxr-xr-x root/root 0 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/scripts/
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drwxr-xr-x root/root 0 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/unitTests/
drwxr-xr-x root/root 0 2016-03-02 23:55 ./usr/lib/R/site-library/Rsamtools/unitTests/cases/
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Build Architecture: armhf
Build-Space: 17552
Build-Time: 330
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 618
Job: r-bioc-rsamtools_1.22.0-1
Machine Architecture: armhf
Package: r-bioc-rsamtools
Package-Time: 988
Source-Version: 1.22.0-1
Space: 17552
Status: successful
Version: 1.22.0-1
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Finished at 20160302-2357
Build needed 00:16:28, 17552k disc space