[Debian-med-packaging] Bug#735543: autopkgtest fails on missing runit, stderr, and test failures
Michael Lawrence
lawrence.michael at gene.com
Thu Jan 16 17:12:11 UTC 2014
Weird. Everything passes check on the Bioc build servers. Please send your
sessionInfo() output. Or, try updating the necessary packages according to
those installed on the Bioc build server. See:
http://bioconductor.org/checkResults/2.13/bioc-LATEST/.
On Thu, Jan 16, 2014 at 4:53 AM, Andreas Tille <andreas at an3as.eu> wrote:
> Hi Martin,
>
> thanks for your bug report. I have tested this with latest upstream
> (1.22.1) without any better result. So I put upstream Michael Lawrence
> in CC and hope he might be able to sort this out.
>
> Michael, are we doing something wrong when running the test suite script
>
> #!/bin/sh -e
>
> LC_ALL=C R --no-save <<EOT
> require("rtracklayer")
> rtracklayer:::.test()
> EOT
>
>
> ?
>
> Kind regards
>
> Andreas.
>
> On Thu, Jan 16, 2014 at 12:09:17PM +0100, Martin Pitt wrote:
> > Package: r-bioc-rtracklayer
> > Version: 1.22.0-1
> > Tags: patch
> > User: ubuntu-devel at lists.ubuntu.com
> > Usertags: origin-ubuntu ubuntu-patch trusty
> >
> > Hello,
> >
> > r-bioc-rtracklayer's autopkgtest currently fails [1]:
> >
> > Error in BiocGenerics:::testPackage("rtracklayer") :
> > RUnit package not found
> >
> > After adding it (r-cran-runit), it fails because the test produces a
> > lot of stderror. Attached debdiff fixes these two, but now the test
> > encounters some actual failures:
> >
> > Error in seqlevels(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlevels': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> > (it repeats that a few times). I attach the full test log for
> > reference. Do you have an idea what's wrong there?
> >
> > Thanks for considering,
> >
> > Martin
> >
> > [1]
> https://jenkins.qa.ubuntu.com/job/trusty-adt-r-bioc-rtracklayer/6/ARCH=i386,label=adt/console
> > --
> > Martin Pitt | http://www.piware.de
> > Ubuntu Developer (www.ubuntu.com) | Debian Developer (www.debian.org)
>
> > diff -Nru r-bioc-rtracklayer-1.22.0/debian/changelog
> r-bioc-rtracklayer-1.22.0/debian/changelog
> > --- r-bioc-rtracklayer-1.22.0/debian/changelog 2013-12-28
> 01:59:48.000000000 +0100
> > +++ r-bioc-rtracklayer-1.22.0/debian/changelog 2014-01-16
> 12:06:12.000000000 +0100
> > @@ -1,3 +1,10 @@
> > +r-bioc-rtracklayer (1.22.0-1ubuntu1) UNRELEASED; urgency=medium
> > +
> > + * debian/tests/control: Add missing r-cran-runit test dependency, and
> allow
> > + stderr output.
> > +
> > + -- Martin Pitt <martin.pitt at ubuntu.com> Thu, 16 Jan 2014 12:00:35
> +0100
> > +
> > r-bioc-rtracklayer (1.22.0-1) unstable; urgency=low
> >
> > * Initial release (closes: #733283).
> > diff -Nru r-bioc-rtracklayer-1.22.0/debian/tests/control
> r-bioc-rtracklayer-1.22.0/debian/tests/control
> > --- r-bioc-rtracklayer-1.22.0/debian/tests/control 2013-11-05
> 09:42:06.000000000 +0100
> > +++ r-bioc-rtracklayer-1.22.0/debian/tests/control 2014-01-16
> 12:00:33.000000000 +0100
> > @@ -1 +1,3 @@
> > Tests: run-unit-test
> > +Depends: @, r-cran-runit
> > +Restrictions: allow-stderr
>
> > adt-run1: options: {'set_lang': False, 'timeout_install': None,
> 'binaries_fortests': 'auto', 'actions': [<Action ubtree ubtree0 .>],
> 'VSERVER_DUMMY': None, 'unbuilt_tree': None, 'summary':
> '/home/ubuntu/adt-log/summary.log', 'timeout_test': None, 'binary': None,
> 'logfile': '/home/ubuntu/adt-log//log', 'timeout_short': None, 'vserver':
> ['adt-virt-null'], 'source': None, 'output_dir': '/home/ubuntu/adt-log/',
> 'debuglevel': 1, 'gainroot': None, 'timeout_build': None,
> 'built_binaries_filter': None, 'user': 'ubuntu', 'timeout_factor': 1.0,
> 'gnupghome': '~/.autopkgtest/gpg', 'quiet': False, 'timeout_copy': 1000,
> 'built_tree': None, 'binaries': 'auto', 'binaries_forbuilds': 'auto'};
> timeouts: {'test': 10000, 'copy': 1000, 'short': 100, 'build': 100000,
> 'install': 3000}
> > adt-run1: ** init
> > adt-run1: ** start
> > adt-run: $ vserver: adt-virt-null
> > adt-run1: ** open, scratch=None
> > adt-run1: ** cmdl = ['sh', '-c', 'exec "$@"', 'x']
> > adt-run1: * initialising
> > adt-run1: * preparing for key generation
> > adt-run: $ genkey: sh -ec <SCRIPT> x /home/ubuntu/.autopkgtest/gpg
> > adt-run1: $
> > adt-run1: $ exec >&2
> > adt-run1: $ cd "$1"
> > adt-run1: $ cat <<"END" >key-gen-params
> > adt-run1: $ Key-Type: DSA
> > adt-run1: $ Key-Length: 1024
> > adt-run1: $ Key-Usage: sign
> > adt-run1: $ Name-Real: autopkgtest per-run key
> > adt-run1: $ Name-Comment: do not trust this key
> > adt-run1: $ Name-Email: autopkgtest at example.com
> > adt-run1: $ END
> > adt-run1: $ set -x
> > adt-run1: $ gpg --homedir="$1" --batch --gen-key key-gen-params
> > + gpg --homedir=/home/ubuntu/.autopkgtest/gpg --batch --gen-key
> key-gen-params
> > gpg: keyring `/home/ubuntu/.autopkgtest/gpg/secring.gpg' created
> > gpg: keyring `/home/ubuntu/.autopkgtest/gpg/pubring.gpg' created
> >
> +++++..+++++++++++++++.++++++++++++++++++++++++++++++++++++++++.+++++...+++++++++++++++.+++++.+++++.++++++++++++++++++++.+++++++++++++++.+++++>.++++++++++..>+++++.........+++++
> > gpg: /home/ubuntu/.autopkgtest/gpg/trustdb.gpg: trustdb created
> > gpg: key 6B36EE88 marked as ultimately trusted
> > adt-run1: * reset
> > adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ builds ...
> > adt-run: @@@@@@@@@@@@@@@@@@@@ ubtree ubtree0
> > adt-run1: ** blame += arg:.
> > adt-run1: ** prepare1, modified=False, deps_processed=[], deps_new=[]
> > adt-run1: ** needs_reset, previously=False
> > adt-run: $ ubtree0-extract: sh -ec <SCRIPT> x
> /tmp/adt-run.sMCbhA/ubtree0-build/tmpdir
> /tmp/adt-run.sMCbhA/ubtree0-build/real-tree
> > adt-run1: $ exec 3>&1 >&2
> > adt-run1: $ set -x
> > adt-run1: $ spec="$2"
> > adt-run1: $ origpwd=/tmp/adt-run.sMCbhA/ubtree0-ubtree
> > adt-run1: $ mkdir -p /tmp/adt-run.sMCbhA/ubtree0-build
> > adt-run1: $ cd /tmp/adt-run.sMCbhA/ubtree0-build
> > adt-run1: $ chown ubuntu . ..
> > adt-run1: $ TMPDIR="$1"
> > adt-run1: $ rm -rf -- "$TMPDIR"
> > adt-run1: $ export TMPDIR
> > adt-run1: $ su -s /bin/sh ubuntu -c 'mkdir -m 1777 -- "$TMPDIR"'
> > adt-run1: $ spec="$spec" origpwd="$origpwd" su -s /bin/sh ubuntu -c '
> > adt-run1: $ rm -rf "$spec"
> > adt-run1: $ mkdir "$spec"
> > adt-run1: $ cp -rP --preserve=timestamps,links -- "$origpwd"/.
> "$spec"/.
> > adt-run1: $ '
> > adt-run1: $ cd [a-z0-9]*-*/.
> > adt-run1: $ pwd >&3
> > adt-run1: $ set +e; test -f debian/tests/control; echo $? >&3
> > + spec=/tmp/adt-run.sMCbhA/ubtree0-build/real-tree
> > + origpwd=/tmp/adt-run.sMCbhA/ubtree0-ubtree
> > + mkdir -p /tmp/adt-run.sMCbhA/ubtree0-build
> > + cd /tmp/adt-run.sMCbhA/ubtree0-build
> > + chown ubuntu . ..
> > + TMPDIR=/tmp/adt-run.sMCbhA/ubtree0-build/tmpdir
> > + rm -rf -- /tmp/adt-run.sMCbhA/ubtree0-build/tmpdir
> > + export TMPDIR
> > + su -s /bin/sh ubuntu -c mkdir -m 1777 -- "$TMPDIR"
> > + spec=/tmp/adt-run.sMCbhA/ubtree0-build/real-tree
> origpwd=/tmp/adt-run.sMCbhA/ubtree0-ubtree su -s /bin/sh ubuntu -c
> > rm -rf "$spec"
> > mkdir "$spec"
> > cp -rP --preserve=timestamps,links -- "$origpwd"/. "$spec"/.
> >
> > + cd real-tree/.
> > + pwd
> > + set +e
> > + test -f debian/tests/control
> > + echo 0
> > adt-run1: constructed; path=debian/tests/run-unit-test
> > adt-run1: .depends=[u'@', u'r-cran-runit']
> > adt-run: * <ubtree:ubtree0> build not needed
> > adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ builds done.
> > adt-run1: * reset
> > adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ tests ...
> > adt-run: @@@@@@@@@@@@@@@@@@@@ test ubtree ubtree0
> > adt-run1: ** needs_reset, previously=True
> > adt-run1: ** blame += arg:.
> > adt-run1: constructed; path=debian/tests/run-unit-test
> > adt-run1: .depends=[u'@', u'r-cran-runit']
> > adt-run: @@@@@@@@@@ run_tests ...
> > adt-run: & ubtree0t-run-unit-test: preparing
> > adt-run: & ubtree0t-run-unit-test: processing dependency @
> > adt-run: & ubtree0t-run-unit-test: synthesised dependency
> r-bioc-rtracklayer
> > adt-run: & ubtree0t-run-unit-test: processing dependency r-cran-runit
> > adt-run: & ubtree0t-run-unit-test: literal dependency r-cran-runit
> > adt-run1: ** prepare1, modified=True, deps_processed=[],
> deps_new=[u'r-bioc-rtracklayer', u'r-cran-runit']
> > adt-run1: ** prepare2, deps_new=[u'r-bioc-rtracklayer', u'r-cran-runit']
> > adt-run1: * publish
> > adt-run1: * no registered binaries, not publishing anything
> > adt-run1: ** installing dependencies [u'r-bioc-rtracklayer',
> u'r-cran-runit']
> > adt-run1: dependencies: install-deps: satisfying r-bioc-rtracklayer,
> r-cran-runit
> > adt-run: dependencies: install-deps: running
> ['/usr/lib/pbuilder/pbuilder-satisfydepends-classic', '--binary-all',
> '--internal-chrootexec', '/home/ubuntu/adt-log/satdep-auxverb', '-c',
> '/home/ubuntu/adt-log/deps.dsc']
> > -> Attempting to parse the build-deps
> > -> Considering build-dep r-bioc-rtracklayer
> > -> Trying r-bioc-rtracklayer
> > -> Considering build-dep r-cran-runit
> > -> Trying r-cran-runit
> > -> Installing r-bioc-rtracklayer r-cran-runit
> > Reading package lists...
> > Building dependency tree...
> > Reading state information...
> > The following extra packages will be installed:
> > fontconfig fontconfig-config fonts-dejavu-core libblas3 libcairo2
> > libcurl3-nss libdatrie1 libfontconfig1 libgfortran3 libgraphite2-3
> > libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3
> libnspr4
> > libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
> libpaper-utils
> > libpaper1 libpixman-1-0 libsm6 libtcl8.5 libthai-data libthai0 libtiff5
> > libtk8.5 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6
> > r-base-core r-bioc-biocgenerics r-bioc-biostrings r-bioc-bsgenome
> > r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-xvector
> > r-cran-bitops r-cran-rcurl r-cran-xml tcl8.5 tk8.5 x11-common
> xdg-utils zip
> > Suggested packages:
> > ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp
> > ttf-arphic-bkai00mp ess r-doc-info r-doc-pdf r-mathlib r-base-html
> > r-bioc-pasillabamsubset r-bioc-shortread tcl-tclreadline gvfs-bin
> > Recommended packages:
> > r-recommended r-base-dev r-doc-html xterm x-terminal-emulator
> > libfile-mimeinfo-perl x11-utils x11-xserver-utils
> > The following NEW packages will be installed:
> > fontconfig fontconfig-config fonts-dejavu-core libblas3 libcairo2
> > libcurl3-nss libdatrie1 libfontconfig1 libgfortran3 libgraphite2-3
> > libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3
> libnspr4
> > libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
> libpaper-utils
> > libpaper1 libpixman-1-0 libsm6 libtcl8.5 libthai-data libthai0 libtiff5
> > libtk8.5 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6
> > r-base-core r-bioc-biocgenerics r-bioc-biostrings r-bioc-bsgenome
> > r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-rtracklayer
> > r-bioc-xvector r-cran-bitops r-cran-rcurl r-cran-runit r-cran-xml
> tcl8.5
> > tk8.5 x11-common xdg-utils zip
> > 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded.
> > Need to get 46.0 MB of archives.
> > After this operation, 93.0 MB of additional disk space will be used.
> > Get:1 http://archive.ubuntu.com/ubuntu/ trusty/main fonts-dejavu-core
> all 2.34-1ubuntu1 [1,024 kB]
> > Get:2 http://archive.ubuntu.com/ubuntu/ trusty/main fontconfig-config
> all 2.11.0-0ubuntu3 [47.3 kB]
> > Get:3 http://archive.ubuntu.com/ubuntu/ trusty/main libfontconfig1
> amd64 2.11.0-0ubuntu3 [123 kB]
> > Get:4 http://archive.ubuntu.com/ubuntu/ trusty/main libpixman-1-0 amd64
> 0.30.2-2ubuntu1 [227 kB]
> > Get:5 http://archive.ubuntu.com/ubuntu/ trusty/main libxcb-render0
> amd64 1.10-2ubuntu1 [11.0 kB]
> > Get:6 http://archive.ubuntu.com/ubuntu/ trusty/main libxcb-shm0 amd64
> 1.10-2ubuntu1 [5,432 B]
> > Get:7 http://archive.ubuntu.com/ubuntu/ trusty/main libxrender1 amd64
> 1:0.9.8-1 [20.9 kB]
> > Get:8 http://archive.ubuntu.com/ubuntu/ trusty/main libcairo2 amd64
> 1.12.16-0ubuntu2 [625 kB]
> > Get:9 http://archive.ubuntu.com/ubuntu/ trusty/main libnspr4 amd64
> 2:4.10.2-1ubuntu1 [110 kB]
> > Get:10 http://archive.ubuntu.com/ubuntu/ trusty/main libnss3 amd64
> 2:3.15.3.1-1.1ubuntu1 [1,076 kB]
> > Get:11 http://archive.ubuntu.com/ubuntu/ trusty/main libcurl3-nss amd64
> 7.34.0-1ubuntu1 [174 kB]
> > Get:12 http://archive.ubuntu.com/ubuntu/ trusty/main libdatrie1 amd64
> 0.2.8-1 [16.7 kB]
> > Get:13 http://archive.ubuntu.com/ubuntu/ trusty-proposed/main
> libgfortran3 amd64 4.8.2-14ubuntu1 [249 kB]
> > Get:14 http://archive.ubuntu.com/ubuntu/ trusty/main libgraphite2-3
> amd64 1.2.4-1ubuntu1 [53.8 kB]
> > Get:15 http://archive.ubuntu.com/ubuntu/ trusty/main libharfbuzz0b
> amd64 0.9.24-2ubuntu3 [124 kB]
> > Get:16 http://archive.ubuntu.com/ubuntu/ trusty/main x11-common all
> 1:7.7+1ubuntu7 [55.4 kB]
> > Get:17 http://archive.ubuntu.com/ubuntu/ trusty/main libice6 amd64
> 2:1.0.8-2 [47.0 kB]
> > Get:18 http://archive.ubuntu.com/ubuntu/ trusty/main libjpeg-turbo8
> amd64 1.3.0-0ubuntu2 [104 kB]
> > Get:19 http://archive.ubuntu.com/ubuntu/ trusty/main libthai-data all
> 0.1.20-3 [130 kB]
> > Get:20 http://archive.ubuntu.com/ubuntu/ trusty/main libthai0 amd64
> 0.1.20-3 [16.9 kB]
> > Get:21 http://archive.ubuntu.com/ubuntu/ trusty/main fontconfig amd64
> 2.11.0-0ubuntu3 [176 kB]
> > Get:22 http://archive.ubuntu.com/ubuntu/ trusty/main libpango-1.0-0
> amd64 1.36.0-1ubuntu2 [149 kB]
> > Get:23 http://archive.ubuntu.com/ubuntu/ trusty/main libpangoft2-1.0-0
> amd64 1.36.0-1ubuntu2 [32.1 kB]
> > Get:24 http://archive.ubuntu.com/ubuntu/ trusty/main
> libpangocairo-1.0-0 amd64 1.36.0-1ubuntu2 [19.5 kB]
> > Get:25 http://archive.ubuntu.com/ubuntu/ trusty/main libpaper1 amd64
> 1.1.24+nmu2ubuntu3 [13.4 kB]
> > Get:26 http://archive.ubuntu.com/ubuntu/ trusty/main libsm6 amd64
> 2:1.2.1-2 [18.1 kB]
> > Get:27 http://archive.ubuntu.com/ubuntu/ trusty/main libtcl8.5 amd64
> 8.5.15-2ubuntu1 [684 kB]
> > Get:28 http://archive.ubuntu.com/ubuntu/ trusty/main libjbig0 amd64
> 2.0-2ubuntu4 [25.9 kB]
> > Get:29 http://archive.ubuntu.com/ubuntu/ trusty/main libjpeg8 amd64
> 8c-2ubuntu8 [2,194 B]
> > Get:30 http://archive.ubuntu.com/ubuntu/ trusty/main libtiff5 amd64
> 4.0.3-7 [142 kB]
> > Get:31 http://archive.ubuntu.com/ubuntu/ trusty/main libxft2 amd64
> 2.3.1-1ubuntu1 [36.3 kB]
> > Get:32 http://archive.ubuntu.com/ubuntu/ trusty/main libxss1 amd64
> 1:1.2.2-1 [8,582 B]
> > Get:33 http://archive.ubuntu.com/ubuntu/ trusty/main libtk8.5 amd64
> 8.5.15-2ubuntu2 [640 kB]
> > Get:34 http://archive.ubuntu.com/ubuntu/ trusty/main libxt6 amd64
> 1:1.1.4-1 [185 kB]
> > Get:35 http://archive.ubuntu.com/ubuntu/ trusty/main libblas3 amd64
> 1.2.20110419-7 [215 kB]
> > Get:36 http://archive.ubuntu.com/ubuntu/ trusty/main liblapack3 amd64
> 3.5.0-2 [1,729 kB]
> > Get:37 http://archive.ubuntu.com/ubuntu/ trusty/main libpaper-utils
> amd64 1.1.24+nmu2ubuntu3 [8,244 B]
> > Get:38 http://archive.ubuntu.com/ubuntu/ trusty/main zip amd64 3.0-8
> [262 kB]
> > Get:39 http://archive.ubuntu.com/ubuntu/ trusty/main xdg-utils all
> 1.1.0~rc1-2ubuntu7 [65.6 kB]
> > Get:40 http://archive.ubuntu.com/ubuntu/ trusty/main tcl8.5 amd64
> 8.5.15-2ubuntu1 [13.9 kB]
> > Get:41 http://archive.ubuntu.com/ubuntu/ trusty/main tk8.5 amd64
> 8.5.15-2ubuntu2 [12.0 kB]
> > Get:42 http://archive.ubuntu.com/ubuntu/ trusty/universe r-base-core
> amd64 3.0.2-1ubuntu1 [21.5 MB]
> > Get:43 http://archive.ubuntu.com/ubuntu/ trusty/universe
> r-bioc-biocgenerics all 0.8.0-1 [386 kB]
> > Get:44 http://archive.ubuntu.com/ubuntu/ trusty-proposed/universe
> r-bioc-iranges amd64 1.20.6-1 [1,854 kB]
> > Get:45 http://archive.ubuntu.com/ubuntu/ trusty-proposed/universe
> r-bioc-xvector amd64 0.2.0-1 [329 kB]
> > Get:46 http://archive.ubuntu.com/ubuntu/ trusty-proposed/universe
> r-bioc-biostrings amd64 2.30.1-1 [2,228 kB]
> > Get:47 http://archive.ubuntu.com/ubuntu/ trusty-proposed/universe
> r-bioc-genomicranges amd64 1.14.3-1 [2,840 kB]
> > Get:48 http://archive.ubuntu.com/ubuntu/ trusty/universe
> r-bioc-bsgenome amd64 1.30.0-1 [716 kB]
> > Get:49 http://archive.ubuntu.com/ubuntu/ trusty/universe r-cran-bitops
> amd64 1.0-6-1 [23.4 kB]
> > Get:50 http://archive.ubuntu.com/ubuntu/ trusty-proposed/universe
> r-bioc-rsamtools amd64 1.14.2-1 [3,214 kB]
> > Get:51 http://archive.ubuntu.com/ubuntu/ trusty/universe r-cran-xml
> amd64 3.98-1.1-1 [1,789 kB]
> > Get:52 http://archive.ubuntu.com/ubuntu/ trusty/universe r-cran-rcurl
> amd64 1.95-4.1-1 [523 kB]
> > Get:53 http://archive.ubuntu.com/ubuntu/ trusty-proposed/universe
> r-bioc-rtracklayer amd64 1.22.0-1 [1,753 kB]
> > Get:54 http://archive.ubuntu.com/ubuntu/ trusty/universe r-cran-runit
> all 0.4.26-2 [181 kB]
> >
> Extracting templates from packages: 55%
> Extracting templates from packages: 100%
> > Preconfiguring packages ...
> > Fetched 46.0 MB in 9s (5,009 kB/s)
> > Selecting previously unselected package fonts-dejavu-core.
> > (Reading database ... 66615 files and directories currently installed.)
> > Unpacking fonts-dejavu-core (from
> .../fonts-dejavu-core_2.34-1ubuntu1_all.deb) ...
> > Selecting previously unselected package fontconfig-config.
> > Unpacking fontconfig-config (from
> .../fontconfig-config_2.11.0-0ubuntu3_all.deb) ...
> > Selecting previously unselected package libfontconfig1:amd64.
> > Unpacking libfontconfig1:amd64 (from
> .../libfontconfig1_2.11.0-0ubuntu3_amd64.deb) ...
> > Selecting previously unselected package libpixman-1-0:amd64.
> > Unpacking libpixman-1-0:amd64 (from
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> > Selecting previously unselected package libxcb-render0:amd64.
> > Unpacking libxcb-render0:amd64 (from
> .../libxcb-render0_1.10-2ubuntu1_amd64.deb) ...
> > Selecting previously unselected package libxcb-shm0:amd64.
> > Unpacking libxcb-shm0:amd64 (from
> .../libxcb-shm0_1.10-2ubuntu1_amd64.deb) ...
> > Selecting previously unselected package libxrender1:amd64.
> > Unpacking libxrender1:amd64 (from .../libxrender1_1%3a0.9.8-1_amd64.deb)
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> > Selecting previously unselected package libcairo2:amd64.
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> .../libcairo2_1.12.16-0ubuntu2_amd64.deb) ...
> > Selecting previously unselected package libnspr4:amd64.
> > Unpacking libnspr4:amd64 (from
> .../libnspr4_2%3a4.10.2-1ubuntu1_amd64.deb) ...
> > Selecting previously unselected package libnss3:amd64.
> > Unpacking libnss3:amd64 (from
> .../libnss3_2%3a3.15.3.1-1.1ubuntu1_amd64.deb) ...
> > Selecting previously unselected package libcurl3-nss:amd64.
> > Unpacking libcurl3-nss:amd64 (from
> .../libcurl3-nss_7.34.0-1ubuntu1_amd64.deb) ...
> > Selecting previously unselected package libdatrie1:amd64.
> > Unpacking libdatrie1:amd64 (from .../libdatrie1_0.2.8-1_amd64.deb) ...
> > Selecting previously unselected package libgfortran3:amd64.
> > Unpacking libgfortran3:amd64 (from
> .../libgfortran3_4.8.2-14ubuntu1_amd64.deb) ...
> > Selecting previously unselected package libgraphite2-3:amd64.
> > Unpacking libgraphite2-3:amd64 (from
> .../libgraphite2-3_1.2.4-1ubuntu1_amd64.deb) ...
> > Selecting previously unselected package libharfbuzz0b:amd64.
> > Unpacking libharfbuzz0b:amd64 (from
> .../libharfbuzz0b_0.9.24-2ubuntu3_amd64.deb) ...
> > Selecting previously unselected package x11-common.
> > Unpacking x11-common (from .../x11-common_1%3a7.7+1ubuntu7_all.deb) ...
> > Selecting previously unselected package libice6:amd64.
> > Unpacking libice6:amd64 (from .../libice6_2%3a1.0.8-2_amd64.deb) ...
> > Selecting previously unselected package libjpeg-turbo8:amd64.
> > Unpacking libjpeg-turbo8:amd64 (from
> .../libjpeg-turbo8_1.3.0-0ubuntu2_amd64.deb) ...
> > Selecting previously unselected package libthai-data.
> > Unpacking libthai-data (from .../libthai-data_0.1.20-3_all.deb) ...
> > Selecting previously unselected package libthai0:amd64.
> > Unpacking libthai0:amd64 (from .../libthai0_0.1.20-3_amd64.deb) ...
> > Selecting previously unselected package fontconfig.
> > Unpacking fontconfig (from .../fontconfig_2.11.0-0ubuntu3_amd64.deb) ...
> > Selecting previously unselected package libpango-1.0-0:amd64.
> > Unpacking libpango-1.0-0:amd64 (from
> .../libpango-1.0-0_1.36.0-1ubuntu2_amd64.deb) ...
> > Selecting previously unselected package libpangoft2-1.0-0:amd64.
> > Unpacking libpangoft2-1.0-0:amd64 (from
> .../libpangoft2-1.0-0_1.36.0-1ubuntu2_amd64.deb) ...
> > Selecting previously unselected package libpangocairo-1.0-0:amd64.
> > Unpacking libpangocairo-1.0-0:amd64 (from
> .../libpangocairo-1.0-0_1.36.0-1ubuntu2_amd64.deb) ...
> > Selecting previously unselected package libpaper1:amd64.
> > Unpacking libpaper1:amd64 (from
> .../libpaper1_1.1.24+nmu2ubuntu3_amd64.deb) ...
> > Selecting previously unselected package libsm6:amd64.
> > Unpacking libsm6:amd64 (from .../libsm6_2%3a1.2.1-2_amd64.deb) ...
> > Selecting previously unselected package libtcl8.5:amd64.
> > Unpacking libtcl8.5:amd64 (from .../libtcl8.5_8.5.15-2ubuntu1_amd64.deb)
> ...
> > Selecting previously unselected package libjbig0:amd64.
> > Unpacking libjbig0:amd64 (from .../libjbig0_2.0-2ubuntu4_amd64.deb) ...
> > Selecting previously unselected package libjpeg8:amd64.
> > Unpacking libjpeg8:amd64 (from .../libjpeg8_8c-2ubuntu8_amd64.deb) ...
> > Selecting previously unselected package libtiff5:amd64.
> > Unpacking libtiff5:amd64 (from .../libtiff5_4.0.3-7_amd64.deb) ...
> > Selecting previously unselected package libxft2:amd64.
> > Unpacking libxft2:amd64 (from .../libxft2_2.3.1-1ubuntu1_amd64.deb) ...
> > Selecting previously unselected package libxss1:amd64.
> > Unpacking libxss1:amd64 (from .../libxss1_1%3a1.2.2-1_amd64.deb) ...
> > Selecting previously unselected package libtk8.5:amd64.
> > Unpacking libtk8.5:amd64 (from .../libtk8.5_8.5.15-2ubuntu2_amd64.deb)
> ...
> > Selecting previously unselected package libxt6:amd64.
> > Unpacking libxt6:amd64 (from .../libxt6_1%3a1.1.4-1_amd64.deb) ...
> > Selecting previously unselected package libblas3.
> > Unpacking libblas3 (from .../libblas3_1.2.20110419-7_amd64.deb) ...
> > Selecting previously unselected package liblapack3.
> > Unpacking liblapack3 (from .../liblapack3_3.5.0-2_amd64.deb) ...
> > Selecting previously unselected package libpaper-utils.
> > Unpacking libpaper-utils (from
> .../libpaper-utils_1.1.24+nmu2ubuntu3_amd64.deb) ...
> > Selecting previously unselected package zip.
> > Unpacking zip (from .../archives/zip_3.0-8_amd64.deb) ...
> > Selecting previously unselected package xdg-utils.
> > Unpacking xdg-utils (from .../xdg-utils_1.1.0~rc1-2ubuntu7_all.deb) ...
> > Selecting previously unselected package tcl8.5.
> > Unpacking tcl8.5 (from .../tcl8.5_8.5.15-2ubuntu1_amd64.deb) ...
> > Selecting previously unselected package tk8.5.
> > Unpacking tk8.5 (from .../tk8.5_8.5.15-2ubuntu2_amd64.deb) ...
> > Selecting previously unselected package r-base-core.
> > Unpacking r-base-core (from .../r-base-core_3.0.2-1ubuntu1_amd64.deb) ...
> > Selecting previously unselected package r-bioc-biocgenerics.
> > Unpacking r-bioc-biocgenerics (from
> .../r-bioc-biocgenerics_0.8.0-1_all.deb) ...
> > Selecting previously unselected package r-bioc-iranges.
> > Unpacking r-bioc-iranges (from .../r-bioc-iranges_1.20.6-1_amd64.deb) ...
> > Selecting previously unselected package r-bioc-xvector.
> > Unpacking r-bioc-xvector (from .../r-bioc-xvector_0.2.0-1_amd64.deb) ...
> > Selecting previously unselected package r-bioc-biostrings.
> > Unpacking r-bioc-biostrings (from
> .../r-bioc-biostrings_2.30.1-1_amd64.deb) ...
> > Selecting previously unselected package r-bioc-genomicranges.
> > Unpacking r-bioc-genomicranges (from
> .../r-bioc-genomicranges_1.14.3-1_amd64.deb) ...
> > Selecting previously unselected package r-bioc-bsgenome.
> > Unpacking r-bioc-bsgenome (from .../r-bioc-bsgenome_1.30.0-1_amd64.deb)
> ...
> > Selecting previously unselected package r-cran-bitops.
> > Unpacking r-cran-bitops (from .../r-cran-bitops_1.0-6-1_amd64.deb) ...
> > Selecting previously unselected package r-bioc-rsamtools.
> > Unpacking r-bioc-rsamtools (from
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> > Selecting previously unselected package r-cran-xml.
> > Unpacking r-cran-xml (from .../r-cran-xml_3.98-1.1-1_amd64.deb) ...
> > Selecting previously unselected package r-cran-rcurl.
> > Unpacking r-cran-rcurl (from .../r-cran-rcurl_1.95-4.1-1_amd64.deb) ...
> > Selecting previously unselected package r-bioc-rtracklayer.
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> > Selecting previously unselected package r-cran-runit.
> > Unpacking r-cran-runit (from .../r-cran-runit_0.4.26-2_all.deb) ...
> > Processing triggers for man-db ...
> > Processing triggers for ureadahead ...
> > Processing triggers for install-info ...
> > Processing triggers for mime-support ...
> > Setting up fonts-dejavu-core (2.34-1ubuntu1) ...
> > Setting up fontconfig-config (2.11.0-0ubuntu3) ...
> > Setting up libfontconfig1:amd64 (2.11.0-0ubuntu3) ...
> > Setting up libpixman-1-0:amd64 (0.30.2-2ubuntu1) ...
> > Setting up libxcb-render0:amd64 (1.10-2ubuntu1) ...
> > Setting up libxcb-shm0:amd64 (1.10-2ubuntu1) ...
> > Setting up libxrender1:amd64 (1:0.9.8-1) ...
> > Setting up libcairo2:amd64 (1.12.16-0ubuntu2) ...
> > Setting up libnspr4:amd64 (2:4.10.2-1ubuntu1) ...
> > Setting up libnss3:amd64 (2:3.15.3.1-1.1ubuntu1) ...
> > Setting up libcurl3-nss:amd64 (7.34.0-1ubuntu1) ...
> > Setting up libdatrie1:amd64 (0.2.8-1) ...
> > Setting up libgfortran3:amd64 (4.8.2-14ubuntu1) ...
> > Setting up libgraphite2-3:amd64 (1.2.4-1ubuntu1) ...
> > Setting up libharfbuzz0b:amd64 (0.9.24-2ubuntu3) ...
> > Setting up x11-common (1:7.7+1ubuntu7) ...
> > * Setting up X socket directories...
> > ...done.
> > Setting up libjpeg-turbo8:amd64 (1.3.0-0ubuntu2) ...
> > Setting up libthai-data (0.1.20-3) ...
> > Setting up libthai0:amd64 (0.1.20-3) ...
> > Setting up fontconfig (2.11.0-0ubuntu3) ...
> > Regenerating fonts cache... done.
> > Setting up libpango-1.0-0:amd64 (1.36.0-1ubuntu2) ...
> > Setting up libpangoft2-1.0-0:amd64 (1.36.0-1ubuntu2) ...
> > Setting up libpangocairo-1.0-0:amd64 (1.36.0-1ubuntu2) ...
> > Setting up libpaper1:amd64 (1.1.24+nmu2ubuntu3) ...
> >
> > Creating config file /etc/papersize with new version
> > Setting up libtcl8.5:amd64 (8.5.15-2ubuntu1) ...
> > Setting up libjbig0:amd64 (2.0-2ubuntu4) ...
> > Setting up libjpeg8:amd64 (8c-2ubuntu8) ...
> > Setting up libtiff5:amd64 (4.0.3-7) ...
> > Setting up libxft2:amd64 (2.3.1-1ubuntu1) ...
> > Setting up libblas3 (1.2.20110419-7) ...
> > update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide
> /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
> > Setting up liblapack3 (3.5.0-2) ...
> > update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide
> /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
> > Setting up libpaper-utils (1.1.24+nmu2ubuntu3) ...
> > Setting up zip (3.0-8) ...
> > Setting up xdg-utils (1.1.0~rc1-2ubuntu7) ...
> > Setting up tcl8.5 (8.5.15-2ubuntu1) ...
> > Processing triggers for ureadahead ...
> > Setting up libice6:amd64 (2:1.0.8-2) ...
> > Setting up libsm6:amd64 (2:1.2.1-2) ...
> > Setting up libxss1:amd64 (1:1.2.2-1) ...
> > Setting up libtk8.5:amd64 (8.5.15-2ubuntu2) ...
> > Setting up libxt6:amd64 (1:1.1.4-1) ...
> > Setting up tk8.5 (8.5.15-2ubuntu2) ...
> > Setting up r-base-core (3.0.2-1ubuntu1) ...
> >
> > Creating config file /etc/R/Renviron with new version
> > Setting up r-bioc-biocgenerics (0.8.0-1) ...
> > Setting up r-bioc-iranges (1.20.6-1) ...
> > Setting up r-bioc-xvector (0.2.0-1) ...
> > Setting up r-bioc-biostrings (2.30.1-1) ...
> > Setting up r-bioc-genomicranges (1.14.3-1) ...
> > Setting up r-bioc-bsgenome (1.30.0-1) ...
> > Setting up r-cran-bitops (1.0-6-1) ...
> > Setting up r-bioc-rsamtools (1.14.2-1) ...
> > Setting up r-cran-xml (3.98-1.1-1) ...
> > Setting up r-cran-rcurl (1.95-4.1-1) ...
> > Setting up r-bioc-rtracklayer (1.22.0-1) ...
> > Setting up r-cran-runit (0.4.26-2) ...
> > Processing triggers for libc-bin ...
> > adt-run: & ubtree0t-run-unit-test:
> [----------------------------------------
> > -> Finished parsing the build-deps
> >
> > R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
> > Copyright (C) 2013 The R Foundation for Statistical Computing
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > You are welcome to redistribute it under certain conditions.
> > Type 'license()' or 'licence()' for distribution details.
> >
> > R is a collaborative project with many contributors.
> > Type 'contributors()' for more information and
> > 'citation()' on how to cite R or R packages in publications.
> >
> > Type 'demo()' for some demos, 'help()' for on-line help, or
> > 'help.start()' for an HTML browser interface to help.
> > Type 'q()' to quit R.
> >
> > > require("rtracklayer")
> > Loading required package: rtracklayer
> > Loading required package: GenomicRanges
> > Loading required package: BiocGenerics
> > Loading required package: parallel
> >
> > Attaching package: 'BiocGenerics'
> >
> > The following objects are masked from 'package:parallel':
> >
> > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> > clusterExport, clusterMap, parApply, parCapply, parLapply,
> > parLapplyLB, parRapply, parSapply, parSapplyLB
> >
> > The following object is masked from 'package:stats':
> >
> > xtabs
> >
> > The following objects are masked from 'package:base':
> >
> > Filter, Find, Map, Position, Reduce, anyDuplicated, append,
> > as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq,
> > get, intersect, is.unsorted, lapply, mapply, match, mget, order,
> > paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rep.int,
> > rownames, sapply, setdiff, sort, table, tapply, union, unique,
> > unlist
> >
> > Loading required package: IRanges
> > Loading required package: XVector
> > > rtracklayer:::.test()
> > Warning message:
> > Starting with BioC 2.13, calling import() with 'asRangedData=TRUE' is
> > deprecated. If you wish import() to return a RangedData object,
> > then you can coerce the returned object with 'as(..., "RangedData")'.
> > However, we strongly recommend that you start migrating your code to
> > operate on GRanges objects instead of RangedData objects.
> > Starting with BioC 2.14, support for RangedData objects will be
> limited.
> > Please ask on the bioc-devel mailing list if you have questions
> > or concerns about this (http://bioconductor.org/help/mailing-list/)
> > Timing stopped at: 1.256 0.016 1.279
> > Error in seqlevels(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlevels': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> > Timing stopped at: 0.643 0.006 0.65
> > Error in seqlevels(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlevels': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> > Timing stopped at: 0.063 0 0.064
> > Error in seqlengths(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlengths': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> > Timing stopped at: 2.547 0.021 2.573
> > Error in seqlevels(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlevels': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> > Timing stopped at: 0.799 0.006 0.807
> > Error in seqlevels(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlevels': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> >
> >
> > RUNIT TEST PROTOCOL -- Thu Jan 16 12:03:51 2014
> > ***********************************************
> > Number of test functions: 7
> > Number of errors: 5
> > Number of failures: 0
> >
> >
> > 1 Test Suite :
> > rtracklayer RUnit Tests - 7 test functions, 5 errors, 0 failures
> > ERROR in test_bed: Error in seqlevels(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlevels': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> > ERROR in test_bedGraph: Error in seqlevels(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlevels': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> > ERROR in test_bw: Error in seqlengths(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlengths': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> > ERROR in test_gff: Error in seqlevels(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlevels': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> > ERROR in test_wig: Error in seqlevels(seqinfo(x)) :
> > error in evaluating the argument 'x' in selecting a method for
> function 'seqlevels': Error in (function (classes, fdef, mtable) :
> > unable to find an inherited method for function 'seqinfo' for
> signature '"NULL"'
> > Calls: seqinfo -> <Anonymous>
> >
> >
> > Test files with failing tests
> >
> > test_bed.R
> > test_bed
> >
> > test_bedGraph.R
> > test_bedGraph
> >
> > test_bw.R
> > test_bw
> >
> > test_gff.R
> > test_gff
> >
> > test_wig.R
> > test_wig
> >
> >
> > Error in BiocGenerics:::testPackage("rtracklayer") :
> > unit tests failed for package rtracklayer
> > Calls: <Anonymous> -> <Anonymous>
> > Execution halted
> > adt-run1: testbed executing test finished with exit status 1
> > adt-run: & ubtree0t-run-unit-test:
> ----------------------------------------]
> > adt-run: & ubtree0t-run-unit-test: - - - - - - - - - - results - - - -
> - - - - - -
> > ubtree0t-run-unit-test FAIL non-zero exit status 1
> > adt-run1: ** needs_reset, previously=False
> > adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ tests done.
> > adt-run1: ** stop
> > adt-run1: ** close, scratch=/tmp/adt-run.sMCbhA
>
>
>
>
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at lists.alioth.debian.org
> >
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
>
> --
> http://fam-tille.de
>
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