r-bioc-shortread →
1.34.2-1 →
armhf → 2017-10-29 00:31:22
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| r-bioc-shortread 1.34.2-1 (armhf) Sun, 29 Oct 2017 00:19:25 +0000 |
+==============================================================================+
Package: r-bioc-shortread
Version: 1.34.2-1
Source Version: 1.34.2-1
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-408b1ea6-94fe-4607-9b1b-6e765dbd12e2' 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 7s (2806 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-shortread' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/r-bioc-shortread.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/r-bioc-shortread.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 5153 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-shortread 1.34.2-1 (dsc) [2259 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-shortread 1.34.2-1 (tar) [5145 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-shortread 1.34.2-1 (diff) [5248 B]
Fetched 5153 kB in 1s (4222 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-XHjvsZ/r-bioc-shortread-1.34.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-XHjvsZ' 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-BSLuAM/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-BSLuAM/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-BSLuAM/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-BSLuAM/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-BSLuAM/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-BSLuAM/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-BSLuAM/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-BSLuAM/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (7192 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 73 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-BSLuAM/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-bioc-biobase (>= 2.26.0), r-bioc-genomicalignments (>= 1.8.0), r-bioc-rsamtools (>= 1.28.0), r-cran-hwriter, r-cran-latticeextra
Filtered Build-Depends: debhelper (>= 10), dh-r, r-base-dev, r-bioc-biobase (>= 2.26.0), r-bioc-genomicalignments (>= 1.8.0), r-bioc-rsamtools (>= 1.28.0), r-cran-hwriter, r-cran-latticeextra
dpkg-deb: building package 'sbuild-build-depends-r-bioc-shortread-dummy' in '/<<BUILDDIR>>/resolver-BSLuAM/apt_archive/sbuild-build-depends-r-bioc-shortread-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-shortread-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-BSLuAM/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-BSLuAM/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-BSLuAM/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-BSLuAM/apt_archive ./ Sources [567 B]
Get:5 copy:/<<BUILDDIR>>/resolver-BSLuAM/apt_archive ./ Packages [647 B]
Fetched 2547 B in 0s (9559 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install r-bioc-shortread 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 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-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings
r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata
r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges
r-bioc-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector
r-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-hwriter
r-cran-lambda.r r-cran-lattice r-cran-latticeextra r-cran-matrix
r-cran-matrixstats r-cran-rcolorbrewer 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-shortread r-cran-codetools r-cran-runit
r-cran-knitr r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-affy
r-bioc-genefilter r-bioc-rtracklayer r-bioc-deseq2 r-bioc-edger
r-bioc-annotationdbi r-bioc-annotate r-bioc-gviz r-bioc-variantannotation
r-bioc-annotationhub r-cran-digest r-bioc-graph r-cran-data.table
r-cran-jsonlite r-cran-testthat r-cran-base64enc r-cran-ggplot2 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 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-biobase
r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings
r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata
r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges
r-bioc-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector
r-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-hwriter
r-cran-lambda.r r-cran-lattice r-cran-latticeextra r-cran-matrix
r-cran-matrixstats r-cran-rcolorbrewer r-cran-rcurl r-cran-snow
sbuild-build-depends-r-bioc-shortread-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, 140 newly installed, 0 to remove and 58 not upgraded.
Need to get 155 MB of archives.
After this operation, 6700 kB of additional disk space will be used.
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Get:2 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 7.2.0-11 [63.1 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf gcc-7-base armhf 7.2.0-11 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:7.2.0-11 [38.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 7.2.0-11 [6732 B]
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Get:7 http://172.17.0.1/private buster-staging/main armhf libubsan0 armhf 7.2.0-11 [106 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libcilkrts5 armhf 7.2.0-11 [35.3 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf cpp-7 armhf 7.2.0-11 [5136 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 7.2.0-11 [30.3 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-7 armhf 7.2.0-11 [5585 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf gcc-7 armhf 7.2.0-11 [5458 kB]
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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 9.0.14 [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]
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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]
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Get:38 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
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Get:40 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
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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]
Get:46 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [132 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-5 [609 kB]
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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+nmu1 [74.2 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 0.4.156 [83.1 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]
Get:58 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
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:61 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
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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 10.9.2 [979 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 7.2.0-11 [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 1.3.10-6 [71.5 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 7.2.0-11 [231 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.2.0-11 [5441 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 57.1-8 [156 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 57.1-8 [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 r-bioc-biocgenerics all 0.22.1-1 [564 kB]
Get:131 http://172.17.0.1/private buster-staging/main armhf r-bioc-biobase armhf 2.36.2-1 [2024 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 0.14.7-1 [1162 kB]
Get:138 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.10.5-1 [1441 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-matrixstats armhf 0.52.2-1 [552 kB]
Get:142 http://172.17.0.1/private buster-staging/main armhf r-bioc-delayedarray all 0.2.7-2 [378 kB]
Get:143 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-1 [23.6 kB]
Get:144 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.8-3 [616 kB]
Get:145 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 0.99.0-2 [16.2 MB]
Get:146 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.12.3-1 [3457 kB]
Get:147 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.28.6-1 [1465 kB]
Get:148 http://172.17.0.1/private buster-staging/main armhf r-cran-lattice armhf 0.20-35-1+b1 [723 kB]
Get:149 http://172.17.0.1/private buster-staging/main armhf r-cran-matrix armhf 1.2-11-1 [2330 kB]
Get:150 http://172.17.0.1/private buster-staging/main armhf r-bioc-summarizedexperiment all 1.6.5-1 [1399 kB]
Get:151 http://172.17.0.1/private buster-staging/main armhf r-bioc-rsamtools armhf 1.28.0-2 [3220 kB]
Get:152 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicalignments armhf 1.12.2-2 [1525 kB]
Get:153 http://172.17.0.1/private buster-staging/main armhf r-cran-hwriter all 1.3.2-2 [137 kB]
Get:154 http://172.17.0.1/private buster-staging/main armhf r-cran-rcolorbrewer all 1.1-2-1.1 [26.3 kB]
Get:155 http://172.17.0.1/private buster-staging/main armhf r-cran-latticeextra armhf 0.6-28-2+b1 [2059 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libstdc++6:armhf (7.2.0-11) ...
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Preparing to unpack .../000-groff-base_1.22.3-9_armhf.deb ...
Unpacking groff-base (1.22.3-9) ...
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Unpacking libbsd0:armhf (0.8.6-2) ...
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Moving old data out of the way
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Setting up libfile-stripnondeterminism-perl (0.039-1) ...
Setting up libpaper1:armhf (1.1.24+nmu5) ...
Creating config file /etc/papersize with new version
Setting up libpaper-utils (1.1.24+nmu5) ...
Setting up libpcre3-dev:armhf (2:8.39-4) ...
Setting up fontconfig-config (2.12.3-0.2) ...
Setting up gcc-7 (7.2.0-11) ...
Setting up gettext (0.19.8.1-4) ...
Setting up libblas-dev:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up g++-7 (7.2.0-11) ...
Setting up liblapack3:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libharfbuzz0b:armhf (1.5.1-1) ...
Setting up autoconf (2.69-11) ...
Setting up libthai0:armhf (0.1.26-3) ...
Setting up libicu-dev (57.1-8) ...
Setting up file (1:5.32-1) ...
Setting up libkrb5support0:armhf (1.15.1-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran-7 (7.2.0-11) ...
Setting up libpng-dev:armhf (1.6.34-1) ...
Setting up libxcb1:armhf (1.12-1) ...
Setting up liblapack-dev:armhf (3.7.1-4) ...
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
Setting up libtool (2.4.6-2) ...
Setting up gfortran (4:7.2.0-1d1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libfontconfig1:armhf (2.12.3-0.2) ...
Setting up libsm6:armhf (2:1.2.2-1+b3) ...
Setting up libk5crypto3:armhf (1.15.1-2) ...
Setting up libxcb-render0:armhf (1.12-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libx11-6:armhf (2:1.6.4-3) ...
Setting up libxmuu1:armhf (2:1.1.2-2) ...
Setting up libxcb-shm0:armhf (1.12-1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libkrb5-3:armhf (1.15.1-2) ...
Setting up libxft2:armhf (2.3.2-1+b2) ...
Setting up fontconfig (2.12.3-0.2) ...
Regenerating fonts cache... done.
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libgssapi-krb5-2:armhf (1.15.1-2) ...
Setting up xauth (1:1.0.9-1) ...
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 (0.22.1-1) ...
Setting up r-bioc-biobase (2.36.2-1) ...
Setting up r-cran-rcolorbrewer (1.1-2-1.1) ...
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-hwriter (1.3.2-2) ...
Setting up r-cran-lambda.r (1.2-1) ...
Setting up r-cran-matrixstats (0.52.2-1) ...
Setting up r-cran-snow (1:0.4.2-1.1) ...
Setting up r-bioc-s4vectors (0.14.7-1) ...
Setting up r-cran-lattice (0.20-35-1+b1) ...
Setting up r-cran-latticeextra (0.6-28-2+b1) ...
Setting up r-bioc-genomeinfodbdata (0.99.0-2) ...
Setting up r-cran-futile.logger (1.4.3-2) ...
Setting up r-bioc-iranges (2.10.5-1) ...
Setting up r-bioc-biocparallel (1.10.1-2) ...
Setting up r-cran-matrix (1.2-11-1) ...
Setting up r-bioc-delayedarray (0.2.7-2) ...
Setting up r-bioc-genomeinfodb (1.12.3-1) ...
Setting up r-bioc-xvector (0.16.0-1) ...
Setting up r-bioc-biostrings (2.44.2-1) ...
Setting up r-bioc-genomicranges (1.28.6-1) ...
Setting up r-bioc-summarizedexperiment (1.6.5-1) ...
Setting up r-bioc-rsamtools (1.28.0-2) ...
Setting up r-bioc-genomicalignments (1.12.2-2) ...
Setting up dh-autoreconf (14) ...
Setting up dh-strip-nondeterminism (0.039-1) ...
Setting up debhelper (10.9.2) ...
Setting up dh-r (20161219) ...
Setting up sbuild-build-depends-r-bioc-shortread-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_7.2.0-11 gcc-7_7.2.0-11 libc6-dev_2.24-14 libstdc++-7-dev_7.2.0-11 libstdc++6_7.2.0-11 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+nmu1 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_9.0.14 bsdutils_1:2.29.2-5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 cdbs_0.4.156 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-11 dash_0.5.8-2.5 dctrl-tools_2.24-2 debconf_1.5.63 debhelper_10.9.2 debianutils_4.8.2 dh-autoreconf_14 dh-r_20161219 dh-strip-nondeterminism_0.039-1 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_7.2.0-11 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_7.2.0-11 gcc-7-base_7.2.0-11 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gfortran_4:7.2.0-1d1 gfortran-7_7.2.0-11 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_57.1-8 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_7.2.0-11 libassuan0_2.4.3-3 libatomic1_7.2.0-11 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 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_7.2.0-11 libcilkrts5_7.2.0-11 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_0.039-1 libfontconfig1_2.12.3-0.2 libfreetype6_2.8-0.2 libgcc-7-dev_7.2.0-11 libgcc1_1:7.2.0-11 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libgfortran-7-dev_7.2.0-11 libgfortran4_7.2.0-11 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.15-2 libgomp1_7.2.0-11 libgpg-error0_1.27-3 libgraphite2-3_1.3.10-6 libgssapi-krb5-2_1.15.1-2 libharfbuzz0b_1.5.1-1 libhogweed4_3.3-2 libice6_2:1.0.9-2 libicu-dev_57.1-8 libicu57_57.1-8 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_7.2.0-11 libstdc++6_7.2.0-11 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_7.2.0-11 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+dfsg1-5 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-biobase_2.36.2-1 r-bioc-biocgenerics_0.22.1-1 r-bioc-biocparallel_1.10.1-2 r-bioc-biostrings_2.44.2-1 r-bioc-delayedarray_0.2.7-2 r-bioc-genomeinfodb_1.12.3-1 r-bioc-genomeinfodbdata_0.99.0-2 r-bioc-genomicalignments_1.12.2-2 r-bioc-genomicranges_1.28.6-1 r-bioc-iranges_2.10.5-1 r-bioc-rsamtools_1.28.0-2 r-bioc-s4vectors_0.14.7-1 r-bioc-summarizedexperiment_1.6.5-1 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-hwriter_1.3.2-2 r-cran-lambda.r_1.2-1 r-cran-lattice_0.20-35-1+b1 r-cran-latticeextra_0.6-28-2+b1 r-cran-matrix_1.2-11-1 r-cran-matrixstats_0.52.2-1 r-cran-rcolorbrewer_1.1-2-1.1 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-shortread-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 Sun Oct 22 17:32:45 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-shortread_1.34.2-1.dsc
dpkg-source: info: extracting r-bioc-shortread in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-shortread_1.34.2.orig.tar.gz
dpkg-source: info: unpacking r-bioc-shortread_1.34.2-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.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-408b1ea6-94fe-4607-9b1b-6e765dbd12e2
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-shortread
dpkg-buildpackage: info: source version 1.34.2-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build r-bioc-shortread-1.34.2
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: ShortRead Version: 1.34.2
I: Building using R version 3.4.2-1
I: R API version: r-api-3.4
I: Using built-time from d/changelog: Sun, 22 Oct 2017 19:30:51 +0200
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library --clean . "--built-timestamp='Sun, 22 Oct 2017 19:30:51 +0200'"
* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 4
configure: creating ./config.status
config.status: creating src/Makevars
** 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 -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 -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
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 -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_ShortRead.c -o R_init_ShortRead.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 -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 -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 -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 alphabet.c -o alphabet.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 -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.c -o io.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 -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_bowtie.c -o io_bowtie.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 -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_soap.c -o io_soap.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" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -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 readBfaToc.cc -o readBfaToc.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" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -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 read_maq_map.cc -o read_maq_map.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 -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 sampler.c -o sampler.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 -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 trim.c -o trim.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 -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 util.c -o util.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 -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 xsnap.c -o xsnap.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -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-shortread/usr/lib/R/site-library/ShortRead/libs
** R
** inst
** preparing package for lazy loading
code for methods in class "ShortReadFile" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqFileReader" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "QAData" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "Snapshot" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "SpTrellis" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqSampler" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqStreamer" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ShortRead)
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 286.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 287.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 290.
I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.22.1)
I: Using r-bioc-biocparallel for Depends:BiocParallel
I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.37.1)
I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.21.4)
I: Using r-bioc-genomicalignments for Depends:GenomicAlignments (>= 1.5.4)
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-cran-runit for Suggests:RUnit
I: Using r-bioc-biomart for Suggests:biomaRt
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:yeastNagalakshmi
I: Using r-bioc-biobase for Imports:Biobase
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-genomeinfodb for Imports:GenomeInfoDb (>= 1.1.19)
I: Using r-bioc-genomicranges for Imports:GenomicRanges (>= 1.21.6)
I: Using r-cran-hwriter for Imports:hwriter
I: Using r-cran-lattice for Imports:lattice
I: Using r-cran-latticeextra for Imports:latticeExtra
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-shortread/usr/lib/R/site-library/ShortRead/libs/ShortRead.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-shortread-dbgsym' in '../r-bioc-shortread-dbgsym_1.34.2-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-shortread' in '../r-bioc-shortread_1.34.2-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../r-bioc-shortread_1.34.2-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-shortread-1.34.2
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-10-29T00:31:20Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-shortread_1.34.2-1_armhf.changes:
----------------------------------------
Format: 1.8
Date: Sun, 22 Oct 2017 19:30:51 +0200
Source: r-bioc-shortread
Binary: r-bioc-shortread
Architecture: armhf
Version: 1.34.2-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-shortread - GNU R classes and methods for high-throughput short-read sequenci
Changes:
r-bioc-shortread (1.34.2-1) unstable; urgency=medium
.
* New upstream version
* Secure URI in watch file
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Files:
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c104435296c3627b37e59a2493e53265 8096 gnu-r optional r-bioc-shortread_1.34.2-1_armhf.buildinfo
119bd1b41af1952d768cc750d8f36608 4242534 gnu-r optional r-bioc-shortread_1.34.2-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-shortread-dbgsym_1.34.2-1_armhf.deb
------------------------------------------
new debian package, version 2.0.
size 138956 bytes: control archive=460 bytes.
408 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-shortread-dbgsym
Source: r-bioc-shortread
Version: 1.34.2-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 173
Depends: r-bioc-shortread (= 1.34.2-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-shortread
Build-Ids: 6df0ceca2b7cd9e2dfff2c4489506fa4e5e05b7b
drwxr-xr-x root/root 0 2017-10-22 17:30 ./
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/debug/.build-id/6d/
-rw-r--r-- root/root 166596 2017-10-22 17:30 ./usr/lib/debug/.build-id/6d/f0ceca2b7cd9e2dfff2c4489506fa4e5e05b7b.debug
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/share/
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-10-22 17:30 ./usr/share/doc/r-bioc-shortread-dbgsym -> r-bioc-shortread
r-bioc-shortread_1.34.2-1_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 4242534 bytes: control archive=4353 bytes.
1259 bytes, 17 lines control
10811 bytes, 113 lines md5sums
Package: r-bioc-shortread
Version: 1.34.2-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6022
Depends: r-base-core (>= 3.4.2-1), r-api-3.4, r-bioc-biocgenerics (>= 0.22.1), r-bioc-biocparallel, r-bioc-biostrings (>= 2.37.1), r-bioc-rsamtools (>= 1.21.4), r-bioc-genomicalignments (>= 1.5.4), r-bioc-biobase, r-bioc-s4vectors (>= 0.13.8), r-bioc-iranges (>= 2.3.7), r-bioc-genomeinfodb (>= 1.1.19), r-bioc-genomicranges (>= 1.21.6), r-cran-hwriter, r-cran-lattice, r-cran-latticeextra, libc6 (>= 2.7), libgcc1 (>= 1:3.5), libgomp1 (>= 4.2.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Suggests: r-cran-runit, r-bioc-biomart, r-bioc-genomicfeatures
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/ShortRead/
Description: GNU R classes and methods for high-throughput short-read sequencing data
This BioConductor module is a package for input, quality assessment,
manipulation and output of high-throughput sequencing data. ShortRead is
provided in the R and Bioconductor environments, allowing ready access
to additional facilities for advanced statistical analysis, data
transformation, visualization and integration with diverse genomic
resources.
drwxr-xr-x root/root 0 2017-10-22 17:30 ./
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/R/
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/
-rw-r--r-- root/root 1158 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/CITATION
-rw-r--r-- root/root 1321 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/DESCRIPTION
-rw-r--r-- root/root 5917 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/INDEX
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/Meta/
-rw-r--r-- root/root 5588 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/Meta/Rd.rds
-rw-r--r-- root/root 112 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/Meta/features.rds
-rw-r--r-- root/root 5744 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/Meta/hsearch.rds
-rw-r--r-- root/root 4151 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/Meta/links.rds
-rw-r--r-- root/root 848 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/Meta/nsInfo.rds
-rw-r--r-- root/root 1384 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/Meta/package.rds
-rw-r--r-- root/root 261 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/Meta/vignette.rds
-rw-r--r-- root/root 1147 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/NAMESPACE
-rw-r--r-- root/root 12176 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/NEWS
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/R/
-rw-r--r-- root/root 1056 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/R/ShortRead
-rw-r--r-- root/root 933709 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/R/ShortRead.rdb
-rw-r--r-- root/root 11864 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/R/ShortRead.rdx
drwxr-xr-x root/root 0 2017-10-22 17:30 ./usr/lib/R/site-library/ShortRead/doc/
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Purging /<<BUILDDIR>>
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| Summary |
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Build Architecture: armhf
Build-Space: 19736
Build-Time: 89
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 609
Job: r-bioc-shortread_1.34.2-1
Machine Architecture: armhf
Package: r-bioc-shortread
Package-Time: 715
Source-Version: 1.34.2-1
Space: 19736
Status: successful
Version: 1.34.2-1
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Finished at 2017-10-29T00:31:20Z
Build needed 00:11:55, 19736k disk space