r-bioc-rtracklayer →
1.40.2-1 →
armhf → 2018-05-25 11:07:51
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| r-bioc-rtracklayer 1.40.2-1 (armhf) Fri, 25 May 2018 10:40:25 +0000 |
+==============================================================================+
Package: r-bioc-rtracklayer
Version: 1.40.2-1
Source Version: 1.40.2-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/buster-staging-armhf-sbuild-d5f8a244-3c67-444e-9c85-b18fe0b60791' 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 [10.8 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.5 MB]
Fetched 23.3 MB in 26s (905 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'r-bioc-rtracklayer' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-rtracklayer.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-rtracklayer.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1409 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-rtracklayer 1.40.2-1 (dsc) [2422 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-rtracklayer 1.40.2-1 (tar) [1380 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-rtracklayer 1.40.2-1 (diff) [26.6 kB]
Fetched 1409 kB in 0s (6596 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-rtracklayer-mmMvyj/r-bioc-rtracklayer-1.40.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rtracklayer-mmMvyj' 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-8nZ5gW/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-8nZ5gW/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-8nZ5gW/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-8nZ5gW/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (3286 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-8nZ5gW/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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 e2fsprogs-l10n 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 63 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15506 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) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-genomicranges (>= 1.31.8), r-cran-xml, r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-biostrings (>= 2.47.6), r-cran-rcurl, r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6)
Filtered Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-genomicranges (>= 1.31.8), r-cran-xml, r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-biostrings (>= 2.47.6), r-cran-rcurl, r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6)
dpkg-deb: building package 'sbuild-build-depends-r-bioc-rtracklayer-dummy' in '/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive/sbuild-build-depends-r-bioc-rtracklayer-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-rtracklayer-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-8nZ5gW/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Sources [635 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Packages [721 B]
Fetched 2689 B in 1s (3771 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-8nZ5gW/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install r-bioc-rtracklayer 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:
e2fsprogs-l10n 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-python dh-r dh-strip-nondeterminism
dwz file fontconfig fontconfig-config fonts-dejavu-core g++-7 gcc-7
gcc-7-base gettext gettext-base gfortran gfortran-7 gir1.2-glib-2.0
gir1.2-harfbuzz-0.0 groff-base icu-devtools intltool-debian
libarchive-zip-perl libasan4 libblas-dev libblas3 libbsd0 libbz2-dev
libcairo2 libcilkrts5 libcroco3 libcurl3 libdatrie1 libelf1 libexpat1
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgcc-7-dev libgfortran-7-dev libgfortran4 libgirepository-1.0-1
libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev
libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgssapi-krb5-2
libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice6
libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu57 libicu60 libisl19
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev
libmagic-mgc libmagic1 libmpdec2 libncurses-dev libncurses5-dev libncurses6
libncursesw6 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
libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib libreadline-dev
libreadline7 librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.0.2
libstdc++-7-dev libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl
libtinfo6 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 mime-support pkg-config
po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
python3.6 python3.6-minimal 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-formatr r-cran-futile.logger r-cran-futile.options
r-cran-lambda.r r-cran-lattice r-cran-matrix r-cran-matrixstats r-cran-rcurl
r-cran-snow r-cran-xml ucf unzip x11-common xauth xdg-utils zip zlib1g
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
libglib2.0-doc libgraphite2-utils 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 apparmor less www-browser libmail-box-perl python3-doc python3-tk
python3-venv python3.6-venv python3.6-doc binfmt-support 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-runit r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate
r-cran-foreach r-cran-batchjobs r-cran-bbmisc r-cran-doparallel r-cran-rmpi
r-bioc-variantannotation r-bioc-shortread r-cran-codetools r-cran-knitr
r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-genefilter r-bioc-rtracklayer
r-bioc-edger r-bioc-gviz r-bioc-annotationhub r-cran-digest r-bioc-graph
r-cran-data.table r-cran-rmarkdown r-cran-jsonlite r-cran-shiny
r-cran-testit r-cran-testthat r-cran-base64enc r-cran-ggplot2 r-cran-rsprng
r-cran-rlecuyer
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl shared-mime-info
xdg-user-dirs krb5-locales libgpm2 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-python dh-r dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
gfortran-7 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools
intltool-debian libarchive-zip-perl libblas-dev libblas3 libbsd0 libbz2-dev
libcairo2 libcroco3 libcurl3 libdatrie1 libelf1 libexpat1
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgfortran-7-dev libgfortran4 libgirepository-1.0-1 libglib2.0-0
libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin
libgraphite2-3 libgraphite2-dev libgssapi-krb5-2 libharfbuzz-dev
libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice6 libicu-dev
libicu-le-hb-dev libicu-le-hb0 libicu57 libicu60 libisl19 libjbig0
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev libmagic-mgc
libmagic1 libmpdec2 libncurses-dev libncurses5-dev libncurses6 libncursesw6
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 libpython3-stdlib
libpython3.6-minimal libpython3.6-stdlib libreadline-dev librtmp1
libsigsegv2 libsm6 libssh2-1 libssl1.0.2 libtcl8.6 libthai-data libthai0
libtiff5 libtimedate-perl libtinfo6 libtk8.6 libtool libx11-6 libx11-data
libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2
libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4 man-db mime-support
pkg-config po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3.6 python3.6-minimal 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-formatr r-cran-futile.logger r-cran-futile.options
r-cran-lambda.r r-cran-lattice r-cran-matrix r-cran-matrixstats r-cran-rcurl
r-cran-snow r-cran-xml sbuild-build-depends-r-bioc-rtracklayer-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 libcilkrts5 libgcc-7-dev libreadline7
libstdc++-7-dev libubsan0 zlib1g
11 upgraded, 172 newly installed, 0 to remove and 52 not upgraded.
Need to get 166 MB/166 MB of archives.
After this operation, 366 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-8nZ5gW/apt_archive ./ sbuild-build-depends-r-bioc-rtracklayer-dummy 0.invalid.0 [1000 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.7-1 [96.8 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-1 [87.3 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
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Get:14 http://172.17.0.1/private buster-staging/main armhf x11-common all 1:7.7+19 [251 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.5~rc1-1 [565 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.5~rc1-1 [1234 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtinfo6 armhf 6.1+20180210-3 [307 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libreadline7 armhf 7.0-5 [130 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.5~rc1-1 [1585 kB]
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Get:23 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.5~rc1-1 [147 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.5~rc1-1 [229 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.4-1 [19.3 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf dh-python all 3.20180326 [93.2 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.4-1 [22.3 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libasan4 armhf 7.3.0-19 [301 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libisl19 armhf 0.19-1 [427 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf g++-7 armhf 7.3.0-19 [5593 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf gcc-7 armhf 7.3.0-19 [5488 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf cpp-7 armhf 7.3.0-19 [5139 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libubsan0 armhf 7.3.0-19 [106 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libcilkrts5 armhf 7.3.0-19 [35.2 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libstdc++-7-dev armhf 7.3.0-19 [1506 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libgcc-7-dev armhf 7.3.0-19 [671 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf gcc-7-base armhf 7.3.0-19 [187 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2o-1 [888 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-2 [234 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-2 [106 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-2 [64.7 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.2 [12.1 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf ucf all 3.0038 [67.8 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf cdbs all 0.4.156 [83.1 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-2 [94.4 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.4 [160 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-9 [7414 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-6.1 [602 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [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 11.3.2 [994 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 1.1.3-1 [73.3 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8.1-2 [402 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.0-5 [280 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.0-5 [325 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libpixman-1-0 armhf 0.34.0-2 [451 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libxcb-render0 armhf 1.13-1 [107 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libxcb-shm0 armhf 1.13-1 [98.3 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.15.10-3 [575 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.16-2 [59.0 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.16-2 [116 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.16-2 [265 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.16-2 [135 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.1-1 [51.4 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libcurl3 armhf 7.60.0-1 [282 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.13.0-5 [403 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libfribidi0 armhf 0.19.7-2 [44.1 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libthai-data all 0.1.27-2 [168 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.11-1 [34.6 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libthai0 armhf 0.1.27-2 [50.2 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.42.0-1 [158 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.11-2 [73.5 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.7.6-1 [799 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.42.0-1 [53.2 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.42.0-1 [43.3 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf libsm6 armhf 2:1.2.2-1+b3 [31.2 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.8+dfsg-4 [863 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.9-5 [224 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.8-4 [657 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.4.4-1 [23.0 MB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.3.0-19 [232 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.3.0-19 [5459 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.2.0-1d1 [1352 B]
Get:118 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1 [1577 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf libncurses6 armhf 6.1+20180210-3 [78.3 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf libncursesw6 armhf 6.1+20180210-3 [103 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180210-3 [278 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180210-3 [924 B]
Get:124 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-9 [234 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-9 [226 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-9 [150 kB]
Get:130 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-9 [561 kB]
Get:131 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:132 http://172.17.0.1/private buster-staging/main armhf libpng-dev armhf 1.6.34-1 [274 kB]
Get:133 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:134 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.2-1.3 [284 kB]
Get:135 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:136 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:137 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:138 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.7.6-1 [584 kB]
Get:139 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.7.6-1 [590 kB]
Get:140 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.56.1-1 [77.6 kB]
Get:141 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.56.1-1 [142 kB]
Get:142 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.7.6-1 [597 kB]
Get:143 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.56.1-2 [2671 kB]
Get:144 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.56.1-2 [1694 kB]
Get:145 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.56.1-2 [1733 kB]
Get:146 http://172.17.0.1/private buster-staging/main armhf pkg-config armhf 0.29-4 [59.2 kB]
Get:147 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.56.1-2 [2807 kB]
Get:148 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.11-2 [22.2 kB]
Get:149 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.7.6-1 [879 kB]
Get:150 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:151 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:152 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:153 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:154 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.4.4-1 [4488 B]
Get:155 http://172.17.0.1/private buster-staging/main armhf dh-r all 20180514 [20.2 kB]
Get:156 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.26.0-2 [582 kB]
Get:157 http://172.17.0.1/private buster-staging/main armhf r-bioc-biobase armhf 2.40.0-2 [2025 kB]
Get:158 http://172.17.0.1/private buster-staging/main armhf r-cran-formatr armhf 1.5-2 [126 kB]
Get:159 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2.3-1 [87.7 kB]
Get:160 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.1-1 [16.0 kB]
Get:161 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-2 [93.8 kB]
Get:162 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.2-1.1 [65.4 kB]
Get:163 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.14.1-1 [955 kB]
Get:164 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.18.2-1 [1353 kB]
Get:165 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.14.10-1 [1466 kB]
Get:166 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.20.0-2 [378 kB]
Get:167 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.48.0-2 [13.6 MB]
Get:168 http://172.17.0.1/private buster-staging/main armhf r-cran-matrixstats armhf 0.53.1-1 [560 kB]
Get:169 http://172.17.0.1/private buster-staging/main armhf r-bioc-delayedarray all 0.6.0-2 [900 kB]
Get:170 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-3 [22.5 kB]
Get:171 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.10-1 [618 kB]
Get:172 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.1.0-2 [8213 kB]
Get:173 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.16.0-2 [3529 kB]
Get:174 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.32.3-1 [1566 kB]
Get:175 http://172.17.0.1/private buster-staging/main armhf r-cran-lattice armhf 0.20-35-1+b1 [723 kB]
Get:176 http://172.17.0.1/private buster-staging/main armhf r-cran-matrix armhf 1.2-14-1 [2320 kB]
Get:177 http://172.17.0.1/private buster-staging/main armhf r-bioc-summarizedexperiment all 1.10.1-1 [1573 kB]
Get:178 http://172.17.0.1/private buster-staging/main armhf r-bioc-rsamtools armhf 1.32.0-2 [3281 kB]
Get:179 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicalignments armhf 1.16.0-2 [1690 kB]
Get:180 http://172.17.0.1/private buster-staging/main armhf r-cran-xml armhf 3.98-1.11-1 [1668 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up zlib1g:armhf (1:1.2.11.dfsg-1) ...
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Unpacking libxss1:armhf (1:1.2.2-1) ...
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Setting up libreadline7:armhf (7.0-5) ...
Selecting previously unselected package libpython3.6-stdlib:armhf.
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8-20180414-1+rpi1 linux-libc-dev_4.15.17-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 cdbs_0.4.156 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-19 dash_0.5.8-2.10 dctrl-tools_2.24-2 debconf_1.5.66 debhelper_11.3.2 debianutils_4.8.4 dh-autoreconf_19 dh-python_3.20180326 dh-r_20180514 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 e2fsprogs-l10n_1.44.1-2 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 findutils_4.6.0+git+20171230-2 fontconfig_2.13.0-5 fontconfig-config_2.13.0-5 fonts-dejavu-core_2.37-1 g++_4:7.2.0-1d1 g++-7_7.3.0-19 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_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-19 gcc-7-base_7.3.0-19 gcc-8-base_8-20180414-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gfortran_4:7.2.0-1d1 gfortran-7_7.3.0-19 gir1.2-glib-2.0_1.56.1-1 gir1.2-harfbuzz-0.0_1.7.6-1 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 icu-devtools_60.2-6 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-19 libassuan0_2.5.1-2 libatomic1_8-20180414-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-15+rpi1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.31.1-0.5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcairo2_1.15.10-3 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1+rpi1 libcilkrts5_7.3.0-19 libcom-err2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libcurl3_7.60.0-1 libdatrie1_0.2.11-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libelf1_0.170-0.4 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libfontconfig1_2.13.0-5 libfreetype6_2.8.1-2 libfribidi0_0.19.7-2 libgcc-7-dev_7.3.0-19 libgcc1_1:8-20180414-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran-7-dev_7.3.0-19 libgfortran4_7.3.0-19 libgirepository-1.0-1_1.56.1-1 libglib2.0-0_2.56.1-2 libglib2.0-bin_2.56.1-2 libglib2.0-data_2.56.1-2 libglib2.0-dev_2.56.1-2 libglib2.0-dev-bin_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180414-1+rpi1 libgpg-error0_1.29-4 libgraphite2-3_1.3.11-2 libgraphite2-dev_1.3.11-2 libgssapi-krb5-2_1.16-2 libharfbuzz-dev_1.7.6-1 libharfbuzz-gobject0_1.7.6-1 libharfbuzz-icu0_1.7.6-1 libharfbuzz0b_1.7.6-1 libhogweed4_3.4-1 libice6_2:1.0.9-2 libicu-dev_60.2-6 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu57_57.1-9 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libisl19_0.19-1 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 liblapack-dev_3.8.0-1 liblapack3_3.8.0-1 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_1.8.1.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180210-3 libncurses5_6.1-1 libncurses5-dev_6.1+20180210-3 libncurses6_6.1+20180210-3 libncursesw5_6.1-1 libncursesw6_6.1+20180210-3 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.5-3 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam0g_1.1.8-3.7 libpango-1.0-0_1.42.0-1 libpangocairo-1.0-0_1.42.0-1 libpangoft2-1.0-0_1.42.0-1 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre16-3_2:8.39-9 libpcre3_2:8.39-9 libpcre3-dev_2:8.39-9 libpcre32-3_2:8.39-9 libpcrecpp0v5_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-2 libpipeline1_1.5.0-1 libpixman-1-0_0.34.0-2 libplymouth4_0.9.3-2 libpng-dev_1.6.34-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.14-1 libpsl5_0.20.1-1 libpython3-stdlib_3.6.4-1 libpython3.6-minimal_3.6.5~rc1-1 libpython3.6-stdlib_3.6.5~rc1-1 libreadline-dev_7.0-5 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.23.1-1 libss2_1.44.1-2 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2o-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-19 libstdc++6_8-20180414-1+rpi1 libsystemd0_238-4 libtasn1-6_4.13-2 libtcl8.6_8.6.8+dfsg-4 libthai-data_0.1.27-2 libthai0_0.1.27-2 libtiff5_4.0.9-5 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtinfo6_6.1+20180210-3 libtk8.6_8.6.8-4 libtool_2.4.6-2.1 libubsan0_7.3.0-19 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libx11-6_2:1.6.5-1 libx11-data_2:1.6.5-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13-1 libxcb-shm0_1.13-1 libxcb1_1.13-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-6.1 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 libzstd1_1.3.3+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.15.17-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mime-support_3.60 mount_2.31.1-0.5 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-2 perl-base_5.26.2-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.14-1 python3_3.6.4-1 python3-distutils_3.6.5~rc1-1 python3-lib2to3_3.6.5~rc1-1 python3-minimal_3.6.4-1 python3.6_3.6.5~rc1-1 python3.6-minimal_3.6.5~rc1-1 r-base-core_3.4.4-1 r-base-dev_3.4.4-1 r-bioc-biobase_2.40.0-2 r-bioc-biocgenerics_0.26.0-2 r-bioc-biocparallel_1.14.1-1 r-bioc-biostrings_2.48.0-2 r-bioc-delayedarray_0.6.0-2 r-bioc-genomeinfodb_1.16.0-2 r-bioc-genomeinfodbdata_1.1.0-2 r-bioc-genomicalignments_1.16.0-2 r-bioc-genomicranges_1.32.3-1 r-bioc-iranges_2.14.10-1 r-bioc-rsamtools_1.32.0-2 r-bioc-s4vectors_0.18.2-1 r-bioc-summarizedexperiment_1.10.1-1 r-bioc-xvector_0.20.0-2 r-cran-bitops_1.0-6-3 r-cran-formatr_1.5-2 r-cran-futile.logger_1.4.3-2 r-cran-futile.options_1.0.1-1 r-cran-lambda.r_1.2.3-1 r-cran-lattice_0.20-35-1+b1 r-cran-matrix_1.2-14-1 r-cran-matrixstats_0.53.1-1 r-cran-rcurl_1.95-4.10-1 r-cran-snow_1:0.4.2-1.1 r-cran-xml_3.98-1.11-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rtracklayer-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 ucf_3.0038 udev_238-4 unzip_6.0-21 util-linux_2.31.1-0.5 x11-common_1:7.7+19 xauth_1:1.0.10-1 xdg-utils_1.1.3-1 xz-utils_5.2.2-1.3 zip_3.0-11 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat May 12 13:15:28 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-rtracklayer_1.40.2-1.dsc
dpkg-source: info: extracting r-bioc-rtracklayer in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-rtracklayer_1.40.2.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rtracklayer_1.40.2-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch
dpkg-source: info: applying delete_configure.patch
Check disc 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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-d5f8a244-3c67-444e-9c85-b18fe0b60791
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-rtracklayer
dpkg-buildpackage: info: source version 1.40.2-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build r-bioc-rtracklayer-1.40.2
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: rtracklayer Version: 1.40.2
I: Building using R version 3.4.4-1
I: R API version: r-api-3.4
I: Using built-time from d/changelog: Sat, 12 May 2018 15:10:46 +0200
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library --clean . "--built-timestamp='Sat, 12 May 2018 15:10:46 +0200'"
* installing *source* package 'rtracklayer' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... no
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 -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -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 -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -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 -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -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 -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readGFF.c -o readGFF.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bigWig.c -o bigWig.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chain_io.c -o chain_io.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c twoBit.c -o twoBit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c handlers.c -o handlers.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/common.c -o ucsc/common.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:331:5: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(STDERR_FILENO, errMsg, strlen(errMsg));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/dystring.c -o ucsc/dystring.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/obscure.c -o ucsc/obscure.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/dlist.c -o ucsc/dlist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/udc.c -o ucsc/udc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/net.c -o ucsc/net.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/internet.c -o ucsc/internet.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/https.c -o ucsc/https.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/verbose.c -o ucsc/verbose.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/os.c -o ucsc/os.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/_portimpl.c -o ucsc/_portimpl.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
installing to /<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
Creating a generic function from function 'uri' in package 'rtracklayer'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rtracklayer)
rm -f /<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer/LICENSE
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 290.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 291.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 294.
W: Ignoring specified R dependency: R (>= 3.3)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.31.8)
I: Using r-bioc-bsgenome for Suggests:BSgenome (>= 1.33.4)
W: Cannot find a debian package for Suggests:humanStemCell
W: Cannot find a debian package for Suggests:microRNA (>= 1.1.1)
I: Using r-bioc-genefilter for Suggests:genefilter
I: Using r-bioc-limma for Suggests:limma
W: Cannot find a debian package for Suggests:org.Hs.eg.db
W: Cannot find a debian package for Suggests:hgu133plus2.db
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19
W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg19.knownGene
I: Using r-cran-runit for Suggests:RUnit
I: Using r-cran-xml for Imports:XML (>= 1.98-0)
I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.25.1)
I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.17.25)
I: Using r-bioc-iranges for Imports:IRanges (>= 2.13.13)
I: Using r-bioc-xvector for Imports:XVector (>= 0.19.7)
I: Using r-bioc-genomeinfodb for Imports:GenomeInfoDb (>= 1.15.2)
I: Using r-bioc-biostrings for Imports:Biostrings (>= 2.47.6)
I: Using r-cran-rcurl for Imports:RCurl (>= 1.4-2)
I: Using r-bioc-rsamtools for Imports:Rsamtools (>= 1.31.2)
I: Using r-bioc-genomicalignments for Imports:GenomicAlignments (>= 1.15.6)
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_installinit -a -O--buildsystem=R
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dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer/libs/rtracklayer.so was not linked against libstdc++.so.6 (it uses none of the library's symbols)
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dpkg-deb: building package 'r-bioc-rtracklayer' in '../r-bioc-rtracklayer_1.40.2-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-rtracklayer-dbgsym' in '../r-bioc-rtracklayer-dbgsym_1.40.2-1_armhf.deb'.
dpkg-genbuildinfo --build=any
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dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
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dpkg-buildpackage: info: binary-only upload (no source included)
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Build finished at 2018-05-25T11:06:48Z
Finished
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I: Built successfully
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| Changes |
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r-bioc-rtracklayer_1.40.2-1_armhf.changes:
------------------------------------------
Format: 1.8
Date: Sat, 12 May 2018 15:10:46 +0200
Source: r-bioc-rtracklayer
Binary: r-bioc-rtracklayer
Architecture: armhf
Version: 1.40.2-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-rtracklayer - GNU R interface to genome browsers and their annotation tracks
Changes:
r-bioc-rtracklayer (1.40.2-1) unstable; urgency=medium
.
* New upstream version
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r-bioc-rtracklayer-dbgsym_1.40.2-1_armhf.deb
--------------------------------------------
new Debian package, version 2.0.
size 359524 bytes: control archive=544 bytes.
410 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-rtracklayer-dbgsym
Source: r-bioc-rtracklayer
Version: 1.40.2-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 424
Depends: r-bioc-rtracklayer (= 1.40.2-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-rtracklayer
Build-Ids: 77642a5e930844adbd7f57a13624a07793b78c4a
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lrwxrwxrwx root/root 0 2018-05-12 13:10 ./usr/share/doc/r-bioc-rtracklayer-dbgsym -> r-bioc-rtracklayer
r-bioc-rtracklayer_1.40.2-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 1855464 bytes: control archive=2980 bytes.
1270 bytes, 17 lines control
6550 bytes, 74 lines md5sums
Package: r-bioc-rtracklayer
Version: 1.40.2-1
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 2747
Depends: r-base-core (>= 3.4.4-1), r-api-3.4, r-bioc-genomicranges (>= 1.31.8), r-cran-xml (>= 1.98-0), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-biostrings (>= 2.47.6), r-cran-rcurl (>= 1.4-2), r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6), libc6 (>= 2.15), libgcc1 (>= 1:3.5), libstdc++6 (>= 4.1.1), zlib1g (>= 1:1.1.4)
Suggests: r-bioc-bsgenome (>= 1.33.4), r-bioc-genefilter, r-bioc-limma, r-bioc-genomicfeatures, r-cran-runit
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/rtracklayer/
Description: GNU R interface to genome browsers and their annotation tracks
Extensible framework for interacting with multiple genome browsers
(currently UCSC built-in) and manipulating annotation tracks in various
formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
built-in). The user may export/import tracks to/from the supported
browsers, as well as query and modify the browser state, such as the
current viewport.
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| Summary |
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Build Architecture: armhf
Build-Space: 9344
Build-Time: 320
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 1211
Job: r-bioc-rtracklayer_1.40.2-1
Machine Architecture: armhf
Package: r-bioc-rtracklayer
Package-Time: 1583
Source-Version: 1.40.2-1
Space: 9344
Status: successful
Version: 1.40.2-1
--------------------------------------------------------------------------------
Finished at 2018-05-25T11:06:48Z
Build needed 00:26:23, 9344k disc space