r-bioc-rsamtools →
1.28.0-2 →
armhf → 2017-10-13 16:47:33
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| r-bioc-rsamtools 1.28.0-2 (armhf) Fri, 13 Oct 2017 16:35:25 +0000 |
+==============================================================================+
Package: r-bioc-rsamtools
Version: 1.28.0-2
Source Version: 1.28.0-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-08f653e7-3f3e-4569-93db-66374b51dc54' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.1 MB]
Fetched 22.4 MB in 8s (2783 kB/s)
Reading package lists...
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 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/r-bioc-rsamtools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/r-bioc-rsamtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2993 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-rsamtools 1.28.0-2 (dsc) [2258 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-rsamtools 1.28.0-2 (tar) [2985 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-rsamtools 1.28.0-2 (diff) [5936 B]
Fetched 2993 kB in 0s (3904 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-CWDdG6/r-bioc-rsamtools-1.28.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-CWDdG6' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-mk1mEh/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-mk1mEh/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-mk1mEh/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (8370 B/s)
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 packages were automatically installed and are no longer required:
ca-certificates libreadline5 libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 35 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15082 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.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
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), dh-r, r-base-dev, r-cran-bitops, r-bioc-biostrings (>= 2.40.0), r-bioc-genomicranges (>= 1.24.0), r-bioc-biocparallel, libbam-dev
Filtered Build-Depends: debhelper (>= 10), dh-r, r-base-dev, r-cran-bitops, r-bioc-biostrings (>= 2.40.0), r-bioc-genomicranges (>= 1.24.0), r-bioc-biocparallel, libbam-dev
dpkg-deb: building package 'sbuild-build-depends-r-bioc-rsamtools-dummy' in '/<<BUILDDIR>>/resolver-mk1mEh/apt_archive/sbuild-build-depends-r-bioc-rsamtools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-r-bioc-rsamtools-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ Sources [560 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ Packages [644 B]
Fetched 2537 B in 0s (9962 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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 packages were automatically installed and are no longer required:
libreadline5 libsasl2-modules
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cdbs cpp-7
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism file
fontconfig fontconfig-config fonts-dejavu-core g++-7 gcc-7 gcc-7-base
gettext gettext-base gfortran gfortran-7 groff-base icu-devtools
intltool-debian libarchive-zip-perl libasan4 libatomic1 libbam-dev
libblas-dev libblas3 libbsd0 libbz2-dev libcairo2 libcc1-0 libcilkrts5
libcroco3 libcurl3 libdatrie1 libexpat1 libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libgcc-7-dev libgcc1 libgfortran-7-dev
libgfortran4 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2
libharfbuzz0b libice6 libicu-dev libicu57 libjbig0 libjpeg-dev
libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 liblzma-dev libmagic-mgc libmagic1
libncurses5-dev libnghttp2-14 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 libpng-dev libpng16-16
libpsl5 libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.0.2
libstdc++-7-dev libstdc++6 libtcl8.6 libthai-data libthai0 libtiff5
libtimedate-perl libtinfo-dev libtk8.6 libtool libubsan0 libx11-6
libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6
libxft2 libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4 man-db pkg-config
po-debconf r-base-core r-base-dev r-bioc-biocgenerics r-bioc-biocparallel
r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomeinfodbdata
r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors r-bioc-xvector
r-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-lambda.r
r-cran-rcurl r-cran-snow ucf unzip x11-common xauth xdg-utils zip zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation devscripts gcc-7-locales debtags dh-make gcc-7-doc libstdc++6-7-dbg
libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan4-dbg
liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg
libquadmath0-dbg gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc
gfortran-7-doc libgfortran4-dbg libcoarrays-dev groff liblapack-doc krb5-doc
krb5-user icu-doc liblzma-doc ncurses-doc readline-doc libstdc++-7-doc
tcl8.6 tk8.6 libtool-doc gcj-jdk m4-doc 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-foreach r-cran-batchjobs r-cran-bbmisc
r-cran-doparallel r-cran-rmpi r-bioc-rsamtools r-bioc-genomicalignments
r-bioc-shortread r-cran-codetools r-cran-runit r-cran-knitr r-bioc-bsgenome
r-bioc-genomicfeatures r-bioc-affy r-bioc-biobase r-bioc-annotationdbi
r-bioc-annotate r-bioc-summarizedexperiment r-cran-matrix r-bioc-rtracklayer
r-bioc-gviz r-bioc-variantannotation r-bioc-annotationhub r-bioc-deseq2
r-bioc-edger r-cran-digest r-bioc-graph r-cran-data.table r-cran-testthat
r-cran-jsonlite r-cran-xml r-cran-rsprng r-cran-rlecuyer gvfs-bin
Recommended packages:
curl | wget | lynx-cur bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libpng-tools publicsuffix
libltdl-dev libmail-sendmail-perl r-recommended r-doc-html
libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cdbs dctrl-tools
debhelper dh-autoreconf dh-r dh-strip-nondeterminism file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-7
groff-base icu-devtools intltool-debian libarchive-zip-perl libbam-dev
libblas-dev libblas3 libbsd0 libbz2-dev libcairo2 libcroco3 libcurl3
libdatrie1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1
libfreetype6 libgfortran-7-dev libgfortran4 libglib2.0-0 libgraphite2-3
libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu57 libjbig0
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev libmagic-mgc
libmagic1 libncurses5-dev libnghttp2-14 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 libpng-dev libpsl5
libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.0.2 libtcl8.6
libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6
libtool libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4
man-db pkg-config po-debconf r-base-core r-base-dev r-bioc-biocgenerics
r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb
r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors
r-bioc-xvector r-cran-bitops r-cran-futile.logger r-cran-futile.options
r-cran-lambda.r r-cran-rcurl r-cran-snow
sbuild-build-depends-r-bioc-rsamtools-dummy ucf unzip x11-common xauth
xdg-utils zip zlib1g-dev
The following packages will be upgraded:
cpp-7 g++-7 gcc-7 gcc-7-base libasan4 libatomic1 libcc1-0 libcilkrts5
libgcc-7-dev libgcc1 libgomp1 libpng16-16 libstdc++-7-dev libstdc++6
libubsan0
15 upgraded, 130 newly installed, 0 to remove and 20 not upgraded.
Need to get 141 MB of archives.
After this operation, 16.0 MB disk space will be freed.
Get:1 copy:/<<BUILDDIR>>/resolver-mk1mEh/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [850 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 7.2.0-8 [63.5 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf gcc-7-base armhf 7.2.0-8 [181 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:7.2.0-8 [38.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 7.2.0-8 [6726 B]
Get:6 http://172.17.0.1/private buster-staging/main armhf libasan4 armhf 7.2.0-8 [302 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libubsan0 armhf 7.2.0-8 [106 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libcilkrts5 armhf 7.2.0-8 [35.4 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf cpp-7 armhf 7.2.0-8 [5136 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 7.2.0-8 [30.2 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-7 armhf 7.2.0-8 [5593 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf gcc-7 armhf 7.2.0-8 [5457 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-7-dev armhf 7.2.0-8 [670 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libstdc++-7-dev armhf 7.2.0-8 [1499 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 7.2.0-8 [335 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-2 [95.8 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.3-1 [67.1 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libpng16-16 armhf 1.6.34-1 [270 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8-0.2 [393 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.12.3-0.2 [304 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.12.3-0.2 [349 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.12.3-0.2 [435 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.12-1 [129 kB]
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Get:34 http://172.17.0.1/private buster-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf x11-common all 1:7.7+19 [251 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2l-2 [893 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.1-2 [58.4 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.15.1-2 [115 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.1-2 [265 kB]
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Get:47 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-4 [609 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf cdbs all 0.4.153 [83.0 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-2 [94.4 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
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Get:59 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
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Get:62 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.1-1 [2653 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.8 [973 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf unzip armhf 6.0-21 [149 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.24+nmu5 [20.8 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.2 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.1-1 [71.1 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.2.0-8 [191 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.7.1-4 [103 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libpixman-1-0 armhf 0.34.0-1 [451 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libxcb-render0 armhf 1.12-1 [104 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libxcb-shm0 armhf 1.12-1 [95.9 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.14.10-1 [692 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.26.0-1 [72.2 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.18.0-4 [42.4 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libcurl3 armhf 7.55.1-1 [264 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2 [110 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.7.1-4 [1508 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libthai-data all 0.1.26-3 [166 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.10-5 [33.0 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libthai0 armhf 0.1.26-3 [49.6 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.40.12-1 [179 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.10-5 [71.4 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.5.1-1 [661 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.40.12-1 [72.0 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.40.12-1 [61.2 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libsm6 armhf 2:1.2.2-1+b3 [31.2 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.7+dfsg-1 [869 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.8-5 [218 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-1+b2 [49.3 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.7-1 [660 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.4.2-1 [22.9 MB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.2.0-8 [231 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.2.0-8 [5442 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.2.0-1d1 [1352 B]
Get:108 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.7.1-4 [112 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.7.1-4 [1564 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libtinfo-dev armhf 6.0+20170902-1 [66.6 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.0+20170902-1 [151 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-3 [109 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2 [178 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-4 [235 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-4 [227 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-4 [149 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-4 [565 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf libpng-dev armhf 1.6.34-1 [274 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.2-1.3 [284 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 57.1-6 [156 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 57.1-6 [15.8 MB]
Get:125 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.9-1 [35.6 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf pkg-config armhf 0.29-4 [59.2 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.4.2-1 [4408 B]
Get:129 http://172.17.0.1/private buster-staging/main armhf dh-r all 20161219 [8794 B]
Get:130 http://172.17.0.1/private buster-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:131 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.22.0-2 [561 kB]
Get:132 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2-1 [86.3 kB]
Get:133 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.0-3 [15.6 kB]
Get:134 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-2 [93.8 kB]
Get:135 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.2-1.1 [65.4 kB]
Get:136 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel all 1.10.1-2 [656 kB]
Get:137 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.14.3-1 [1161 kB]
Get:138 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.10.2-1 [1442 kB]
Get:139 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.16.0-1 [364 kB]
Get:140 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.44.2-1 [13.6 MB]
Get:141 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-1 [23.6 kB]
Get:142 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.8-3 [616 kB]
Get:143 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 0.99.0-2 [16.2 MB]
Get:144 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.12.2-2 [3457 kB]
Get:145 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.28.5-1 [1465 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libstdc++6:armhf (7.2.0-8) ...
Selecting previously unselected package groff-base.
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Preparing to unpack .../000-groff-base_1.22.3-9_armhf.deb ...
Unpacking groff-base (1.22.3-9) ...
Selecting previously unselected package libbsd0:armhf.
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Unpacking libbsd0:armhf (0.8.6-2) ...
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Unpacking libpng16-16:armhf (1.6.34-1) over (1.6.32-3) ...
Selecting previously unselected package libfreetype6:armhf.
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Moving old data out of the way
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Selecting previously unselected package libssl1.0.2:armhf.
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No schema files found: doing nothing.
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Setting up libssh2-1:armhf (1.8.0-1) ...
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
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Creating config file /etc/papersize with new version
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Not building database; man-db/auto-update is not 'true'.
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
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update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
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Setting up fontconfig (2.12.3-0.2) ...
Regenerating fonts cache... done.
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Setting up libpango-1.0-0:armhf (1.40.12-1) ...
Setting up libcairo2:armhf (1.14.10-1) ...
Setting up libcurl3:armhf (7.55.1-1) ...
Setting up libtk8.6:armhf (8.6.7-1) ...
Setting up libpangoft2-1.0-0:armhf (1.40.12-1) ...
Setting up libpangocairo-1.0-0:armhf (1.40.12-1) ...
Setting up r-base-core (3.4.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.4.2-1) ...
Setting up r-bioc-biocgenerics (0.22.0-2) ...
Setting up r-cran-bitops (1.0-6-1) ...
Setting up r-cran-futile.options (1.0.0-3) ...
Setting up r-cran-rcurl (1.95-4.8-3) ...
Setting up r-cran-lambda.r (1.2-1) ...
Setting up r-cran-snow (1:0.4.2-1.1) ...
Setting up r-bioc-s4vectors (0.14.3-1) ...
Setting up r-bioc-genomeinfodbdata (0.99.0-2) ...
Setting up r-cran-futile.logger (1.4.3-2) ...
Setting up r-bioc-iranges (2.10.2-1) ...
Setting up r-bioc-biocparallel (1.10.1-2) ...
Setting up r-bioc-genomeinfodb (1.12.2-2) ...
Setting up r-bioc-xvector (0.16.0-1) ...
Setting up r-bioc-biostrings (2.44.2-1) ...
Setting up r-bioc-genomicranges (1.28.5-1) ...
Setting up dh-autoreconf (14) ...
Setting up dh-strip-nondeterminism (0.038-1) ...
Setting up debhelper (10.8) ...
Setting up dh-r (20161219) ...
Setting up sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-14) ...
Processing triggers for systemd (234-3) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-3+rpi1 dpkg-dev_1.18.24 g++-7_7.2.0-8 gcc-7_7.2.0-8 libc6-dev_2.24-14 libstdc++-7-dev_7.2.0-8 libstdc++6_7.2.0-8 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch
Package versions: adduser_3.116 apt_1.5 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-3+rpi1 binutils-arm-linux-gnueabihf_2.29.1-3+rpi1 binutils-common_2.29.1-3+rpi1 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 cdbs_0.4.153 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-8 dash_0.5.8-2.5 dctrl-tools_2.24-2 debconf_1.5.63 debhelper_10.8 debianutils_4.8.2 dh-autoreconf_14 dh-r_20161219 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dirmngr_2.2.1-1 dmsetup_2:1.02.142-1 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.6-1 e2fsprogs_1.43.6-1 fakeroot_1.22-1 fdisk_2.29.2-5 file_1:5.32-1 findutils_4.6.0+git+20170729-2 fontconfig_2.12.3-0.2 fontconfig-config_2.12.3-0.2 fonts-dejavu-core_2.37-1 g++_4:7.2.0-1d1 g++-7_7.2.0-8 gcc_4:7.2.0-1d1 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_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-8 gcc-7-base_7.2.0-8 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gfortran_4:7.2.0-1d1 gfortran-7_7.2.0-8 gnupg_2.2.1-1 gnupg-agent_2.2.1-1 gnupg-l10n_2.2.1-1 gnupg-utils_2.2.1-1 gpg_2.2.1-1 gpg-agent_2.2.1-1 gpg-wks-client_2.2.1-1 gpg-wks-server_2.2.1-1 gpgconf_2.2.1-1 gpgsm_2.2.1-1 gpgv_2.2.1-1 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-6 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-11 libapt-pkg5.0_1.5 libarchive-zip-perl_1.59-1 libasan4_7.2.0-8 libassuan0_2.4.3-3 libatomic1_7.2.0-8 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libbam-dev_0.1.19-2 libbinutils_2.29.1-3+rpi1 libblas-dev_3.7.1-4 libblas3_3.7.1-4 libblkid1_2.29.2-5 libbsd0_0.8.6-2 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.24-14 libc-dev-bin_2.24-14 libc6_2.24-14 libc6-dev_2.24-14 libcairo2_1.14.10-1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.2.0-8 libcilkrts5_7.2.0-8 libcomerr2_1.43.6-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libcurl3_7.55.1-1 libdatrie1_0.2.10-5 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.16+really1.10.22-1 libdebconfclient0_0.230 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.18.24 libdrm-common_2.4.82-1+rpi1 libdrm2_2.4.82-1+rpi1 libexpat1_2.2.3-1 libfakeroot_1.22-1 libfdisk1_2.29.2-5 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libfontconfig1_2.12.3-0.2 libfreetype6_2.8-0.2 libgcc-7-dev_7.2.0-8 libgcc1_1:7.2.0-8 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libgfortran-7-dev_7.2.0-8 libgfortran4_7.2.0-8 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.15-2 libgomp1_7.2.0-8 libgpg-error0_1.27-3 libgraphite2-3_1.3.10-5 libgssapi-krb5-2_1.15.1-2 libharfbuzz0b_1.5.1-1 libhogweed4_3.3-2 libice6_2:1.0.9-2 libicu-dev_57.1-6 libicu57_57.1-6 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2 libisl15_0.18-1 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2 libjpeg62-turbo-dev_1:1.5.2-2 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 liblapack-dev_3.7.1-4 liblapack3_3.7.1-4 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.29.2-5 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncurses5-dev_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnghttp2-14_1.26.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpango-1.0-0_1.40.12-1 libpangocairo-1.0-0_1.40.12-1 libpangoft2-1.0-0_1.40.12-1 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre16-3_2:8.39-4 libpcre3_2:8.39-4 libpcre3-dev_2:8.39-4 libpcre32-3_2:8.39-4 libpcrecpp0v5_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.0-8 libpipeline1_1.4.2-1 libpixman-1-0_0.34.0-1 libplymouth4_0.9.3-1 libpng-dev_1.6.34-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libpsl5_0.18.0-4 libreadline-dev_7.0-3 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsm6_2:1.2.2-1+b3 libsmartcols1_2.29.2-5 libsqlite3-0_3.20.1-1 libss2_1.43.6-1 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2l-2 libssl1.1_1.1.0f-5 libstdc++-7-dev_7.2.0-8 libstdc++6_7.2.0-8 libsystemd0_234-3 libtasn1-6_4.12-2.1 libtcl8.6_8.6.7+dfsg-1 libthai-data_0.1.26-3 libthai0_0.1.26-3 libtiff5_4.0.8-5 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20170902-1 libtinfo5_6.0+20170902-1 libtk8.6_8.6.7-1 libtool_2.4.6-2 libubsan0_7.2.0-8 libudev1_234-3 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-5 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1+b2 libxcb-render0_1.12-1 libxcb-shm0_1.12-1 libxcb1_1.12-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-1+b2 libxml2_2.9.4+dfsg1-4 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 linux-base_4.5 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch login_1:4.4-4.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-5 mountall_2.54 multiarch-support_2.24-14 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0f-5 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-8 perl-base_5.26.0-8 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-8 pinentry-curses_1.0.0-2 pkg-config_0.29-4 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 r-base-core_3.4.2-1 r-base-dev_3.4.2-1 r-bioc-biocgenerics_0.22.0-2 r-bioc-biocparallel_1.10.1-2 r-bioc-biostrings_2.44.2-1 r-bioc-genomeinfodb_1.12.2-2 r-bioc-genomeinfodbdata_0.99.0-2 r-bioc-genomicranges_1.28.5-1 r-bioc-iranges_2.10.2-1 r-bioc-s4vectors_0.14.3-1 r-bioc-xvector_0.16.0-1 r-cran-bitops_1.0-6-1 r-cran-futile.logger_1.4.3-2 r-cran-futile.options_1.0.0-3 r-cran-lambda.r_1.2-1 r-cran-rcurl_1.95-4.8-3 r-cran-snow_1:0.4.2-1.1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rsamtools-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-3 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017b-2 ucf_3.0036 udev_234-3 unzip_6.0-21 util-linux_2.29.2-5 x11-common_1:7.7+19 xauth_1:1.0.9-1 xdg-utils_1.1.1-1 xz-utils_5.2.2-1.3 zip_3.0-11 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Oct 2 14:21:31 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-rsamtools_1.28.0-2.dsc
dpkg-source: info: extracting r-bioc-rsamtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-rsamtools_1.28.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rsamtools_1.28.0-2.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch
dpkg-source: info: applying skip_test_requiring_network.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-08f653e7-3f3e-4569-93db-66374b51dc54
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-rsamtools
dpkg-buildpackage: info: source version 1.28.0-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build r-bioc-rsamtools-1.28.0
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem R
dh_testdir -O--buildsystem=R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules build-arch
dh build-arch --buildsystem R
dh_testdir -a -O--buildsystem=R
dh_update_autotools_config -a -O--buildsystem=R
dh_autoreconf -a -O--buildsystem=R
dh_auto_configure -a -O--buildsystem=R
dh_auto_build -a -O--buildsystem=R
dh_auto_test -a -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_installdirs -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R Package: Rsamtools Version: 1.28.0
I: Building using R version 3.4.2-1
I: R API version: r-api-3.4
I: Using built-time from d/changelog: Mon, 02 Oct 2017 16:06:17 +0200
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 02 Oct 2017 16:06:17 +0200'"
* 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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c idxstats.c -o idxstats.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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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/7/include-fixed/limits.h:194,
from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/syslimits.h:7,
from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/limits.h:34,
from /usr/include/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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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/7/include-fixed/limits.h:194,
from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/syslimits.h:7,
from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/limits.h:34,
from /usr/include/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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 -fdebug-prefix-map=/build/r-base-UavZkw/r-base-3.4.2=. -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 idxstats.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 -f /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE
I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.1.3)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.21.6)
I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.37.1)
I: Using r-bioc-genomicalignments for Suggests:GenomicAlignments
I: Using r-bioc-shortread for Suggests:ShortRead (>= 1.19.10)
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:TxDb.Dmelanogaster.UCSC.dm3.ensGene
W: Cannot find a debian package for Suggests:KEGG.db
W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg18.knownGene
W: Cannot find a debian package for Suggests:RNAseqData.HNRNPC.bam.chr14
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19
W: Cannot find a debian package for Suggests:pasillaBamSubset
I: Using r-cran-runit for Suggests:RUnit
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.1.3)
I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.13.8)
I: Using r-bioc-iranges for Imports:IRanges (>= 2.3.7)
I: Using r-bioc-xvector for Imports:XVector (>= 0.15.1)
I: Using r-cran-bitops for Imports:bitops
I: Using r-bioc-biocparallel for Imports:BiocParallel
dh_install -a -O--buildsystem=R
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
dh_installexamples -a -O--buildsystem=R
dh_installman -a -O--buildsystem=R
dh_installcatalogs -a -O--buildsystem=R
dh_installcron -a -O--buildsystem=R
dh_installdebconf -a -O--buildsystem=R
dh_installemacsen -a -O--buildsystem=R
dh_installifupdown -a -O--buildsystem=R
dh_installinfo -a -O--buildsystem=R
dh_systemd_enable -a -O--buildsystem=R
dh_installinit -a -O--buildsystem=R
dh_systemd_start -a -O--buildsystem=R
dh_installmenu -a -O--buildsystem=R
dh_installmime -a -O--buildsystem=R
dh_installmodules -a -O--buildsystem=R
dh_installlogcheck -a -O--buildsystem=R
dh_installlogrotate -a -O--buildsystem=R
dh_installpam -a -O--buildsystem=R
dh_installppp -a -O--buildsystem=R
dh_installudev -a -O--buildsystem=R
dh_installgsettings -a -O--buildsystem=R
dh_bugfiles -a -O--buildsystem=R
dh_ucf -a -O--buildsystem=R
dh_lintian -a -O--buildsystem=R
dh_gconf -a -O--buildsystem=R
dh_icons -a -O--buildsystem=R
dh_perl -a -O--buildsystem=R
dh_usrlocal -a -O--buildsystem=R
dh_link -a -O--buildsystem=R
dh_installwm -a -O--buildsystem=R
dh_installxfonts -a -O--buildsystem=R
dh_strip_nondeterminism -a -O--buildsystem=R
dh_compress -a -O--buildsystem=R
dh_fixperms -a -O--buildsystem=R
dh_missing -a -O--buildsystem=R
dh_strip -a -O--buildsystem=R
dh_makeshlibs -a -O--buildsystem=R
dh_shlibdeps -a -O--buildsystem=R
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_installdeb -a -O--buildsystem=R
dh_gencontrol -a -O--buildsystem=R
dh_md5sums -a -O--buildsystem=R
dh_builddeb -a -O--buildsystem=R
dpkg-deb: building package 'r-bioc-rsamtools-dbgsym' in '../r-bioc-rsamtools-dbgsym_1.28.0-2_armhf.deb'.
dpkg-deb: building package 'r-bioc-rsamtools' in '../r-bioc-rsamtools_1.28.0-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../r-bioc-rsamtools_1.28.0-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-rsamtools-1.28.0
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-10-13T16:47:30Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-rsamtools_1.28.0-2_armhf.changes:
----------------------------------------
Format: 1.8
Date: Mon, 02 Oct 2017 16:06:17 +0200
Source: r-bioc-rsamtools
Binary: r-bioc-rsamtools
Architecture: armhf
Version: 1.28.0-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <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 (1.28.0-2) unstable; urgency=medium
.
* Moved packaging from SVN to Git
* Standards-Version: 4.1.1
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e03607905fa95c1f3560c8b18567a2723c828650 3220492 r-bioc-rsamtools_1.28.0-2_armhf.deb
Checksums-Sha256:
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Files:
a0b5af78467a12c284a17e0306f84909 820442 debug optional r-bioc-rsamtools-dbgsym_1.28.0-2_armhf.deb
697d011ed42237ad57e534a300a404ba 7725 gnu-r optional r-bioc-rsamtools_1.28.0-2_armhf.buildinfo
27a515ae005c068a122f28bd39378c44 3220492 gnu-r optional r-bioc-rsamtools_1.28.0-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-rsamtools-dbgsym_1.28.0-2_armhf.deb
------------------------------------------
new debian package, version 2.0.
size 820442 bytes: control archive=461 bytes.
408 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-rsamtools-dbgsym
Source: r-bioc-rsamtools
Version: 1.28.0-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 867
Depends: r-bioc-rsamtools (= 1.28.0-2)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-rsamtools
Build-Ids: 01731f754de09fe2a14fd45cea1374887e4b9f2c
drwxr-xr-x root/root 0 2017-10-02 14:06 ./
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/debug/.build-id/01/
-rw-r--r-- root/root 876764 2017-10-02 14:06 ./usr/lib/debug/.build-id/01/731f754de09fe2a14fd45cea1374887e4b9f2c.debug
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/share/
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-10-02 14:06 ./usr/share/doc/r-bioc-rsamtools-dbgsym -> r-bioc-rsamtools
r-bioc-rsamtools_1.28.0-2_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 3220492 bytes: control archive=4564 bytes.
1063 bytes, 15 lines control
11990 bytes, 131 lines md5sums
Package: r-bioc-rsamtools
Version: 1.28.0-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5065
Depends: r-base-core (>= 3.4.2-1), r-api-3.4, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.21.6), r-bioc-biostrings (>= 2.37.1), r-bioc-biocgenerics (>= 0.1.3), r-bioc-s4vectors (>= 0.13.8), r-bioc-iranges (>= 2.3.7), r-bioc-xvector (>= 0.15.1), r-cran-bitops, r-bioc-biocparallel, libc6 (>= 2.15), libgcc1 (>= 1:3.5), libgomp1 (>= 4.2.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3)
Suggests: r-bioc-genomicalignments, r-bioc-shortread (>= 1.19.10), r-bioc-genomicfeatures, r-cran-runit
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/Rsamtools/
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 2017-10-02 14:06 ./
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/
-rw-r--r-- root/root 1559 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/DESCRIPTION
-rw-r--r-- root/root 2136 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/INDEX
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/Meta/
-rw-r--r-- root/root 3166 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/Meta/Rd.rds
-rw-r--r-- root/root 112 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/Meta/features.rds
-rw-r--r-- root/root 3295 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/Meta/hsearch.rds
-rw-r--r-- root/root 2417 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/Meta/links.rds
-rw-r--r-- root/root 765 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/Meta/nsInfo.rds
-rw-r--r-- root/root 1572 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/Meta/package.rds
-rw-r--r-- root/root 283 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/Meta/vignette.rds
-rw-r--r-- root/root 1407 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/NAMESPACE
-rw-r--r-- root/root 14084 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/NEWS
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/R/
-rw-r--r-- root/root 1056 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools
-rw-r--r-- root/root 426558 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdb
-rw-r--r-- root/root 6426 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdx
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/doc/
-rw-r--r-- root/root 9645 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.R
-rw-r--r-- root/root 19842 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.Rnw
-rw-r--r-- root/root 141091 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.pdf
-rw-r--r-- root/root 221 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.R
-rw-r--r-- root/root 3843 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.Rnw
-rw-r--r-- root/root 85276 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.pdf
-rw-r--r-- root/root 1976 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/doc/index.html
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/
-rw-r--r-- root/root 176 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa
-rw-r--r-- root/root 112 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa.fai
-rw-r--r-- root/root 126539 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam
-rw-r--r-- root/root 176 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam.bai
-rw-r--r-- root/root 74700 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf
-rw-r--r-- root/root 77 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.bci
-rw-r--r-- root/root 559422 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.sam
-rw-r--r-- root/root 3778 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz
-rw-r--r-- root/root 259 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz.tbi
-rw-r--r-- root/root 348 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam
-rw-r--r-- root/root 96 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam.bai
-rw-r--r-- root/root 368 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.sam
-rw-r--r-- root/root 203 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam
-rw-r--r-- root/root 176 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam.bai
-rw-r--r-- root/root 240 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.sam
-rw-r--r-- root/root 198 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam
-rw-r--r-- root/root 176 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam.bai
-rw-r--r-- root/root 168 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.sam
-rw-r--r-- root/root 1663363 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/olaps.Rda
-rw-r--r-- root/root 138598 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/pileup.txt
-rw-r--r-- root/root 181 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam
-rw-r--r-- root/root 96 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam.bai
-rw-r--r-- root/root 117 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.sam
-rw-r--r-- root/root 381 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam
-rw-r--r-- root/root 416 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam.bai
-rw-r--r-- root/root 770 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.sam
-rw-r--r-- root/root 31 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/samtools-github.txt
-rw-r--r-- root/root 2808 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/slxMaq09_urls.txt
-rw-r--r-- root/root 333 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam
-rw-r--r-- root/root 656 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam.bai
-rw-r--r-- root/root 804 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.sam
-rw-r--r-- root/root 1167 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam
-rw-r--r-- root/root 2336 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam.bai
-rw-r--r-- root/root 4102 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.sam
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/
-rw-r--r-- root/root 36 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/README
-rw-r--r-- root/root 36039 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/accepted_hits.sam
-rw-r--r-- root/root 4381 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/coverage.wig
-rw-r--r-- root/root 196 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/junctions.bed
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/help/
-rw-r--r-- root/root 11339 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/help/AnIndex
-rw-r--r-- root/root 174348 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/help/Rsamtools.rdb
-rw-r--r-- root/root 765 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/help/Rsamtools.rdx
-rw-r--r-- root/root 2458 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/help/aliases.rds
-rw-r--r-- root/root 372 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/help/paths.rds
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/html/
-rw-r--r-- root/root 42289 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/html/00Index.html
-rw-r--r-- root/root 1335 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/html/R.css
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/
-rw-r--r-- root/root 25788 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/bam.h
-rw-r--r-- root/root 1064 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/bam_endian.h
drwxr-xr-x root/root 0 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/
-rw-r--r-- root/root 7226 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/bcf.h
-rw-r--r-- root/root 1457 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/prob1.h
-rw-r--r-- root/root 6326 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/bgzf.h
-rw-r--r-- root/root 4115 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/faidx.h
-rw-r--r-- root/root 2072 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/kaln.h
-rw-r--r-- root/root 17844 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/khash.h
-rw-r--r-- root/root 1750 2017-10-02 14:06 ./usr/lib/R/site-library/Rsamtools/include/samtools/knetfile.h
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Purging /<<BUILDDIR>>
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| Summary |
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Build Architecture: armhf
Build-Space: 18108
Build-Time: 130
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 579
Job: r-bioc-rsamtools_1.28.0-2
Machine Architecture: armhf
Package: r-bioc-rsamtools
Package-Time: 725
Source-Version: 1.28.0-2
Space: 18108
Status: successful
Version: 1.28.0-2
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Finished at 2017-10-13T16:47:30Z
Build needed 00:12:05, 18108k disk space