<div dir="ltr">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: <a href="http://bioconductor.org/checkResults/2.13/bioc-LATEST/">http://bioconductor.org/checkResults/2.13/bioc-LATEST/</a>.<br>
<br> <br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jan 16, 2014 at 4:53 AM, Andreas Tille <span dir="ltr"><<a href="mailto:andreas@an3as.eu" target="_blank">andreas@an3as.eu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Martin,<br>
<br>
thanks for your bug report. I have tested this with latest upstream<br>
(1.22.1) without any better result. So I put upstream Michael Lawrence<br>
in CC and hope he might be able to sort this out.<br>
<br>
Michael, are we doing something wrong when running the test suite script<br>
<br>
#!/bin/sh -e<br>
<br>
LC_ALL=C R --no-save <<EOT<br>
require("rtracklayer")<br>
rtracklayer:::.test()<br>
EOT<br>
<br>
<br>
?<br>
<br>
Kind regards<br>
<br>
Andreas.<br>
<br>
On Thu, Jan 16, 2014 at 12:09:17PM +0100, Martin Pitt wrote:<br>
> Package: r-bioc-rtracklayer<br>
> Version: 1.22.0-1<br>
> Tags: patch<br>
> User: <a href="mailto:ubuntu-devel@lists.ubuntu.com">ubuntu-devel@lists.ubuntu.com</a><br>
> Usertags: origin-ubuntu ubuntu-patch trusty<br>
><br>
> Hello,<br>
><br>
> r-bioc-rtracklayer's autopkgtest currently fails [1]:<br>
><br>
> Error in BiocGenerics:::testPackage("rtracklayer") :<br>
> RUnit package not found<br>
><br>
> After adding it (r-cran-runit), it fails because the test produces a<br>
> lot of stderror. Attached debdiff fixes these two, but now the test<br>
> encounters some actual failures:<br>
><br>
> Error in seqlevels(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
> (it repeats that a few times). I attach the full test log for<br>
> reference. Do you have an idea what's wrong there?<br>
><br>
> Thanks for considering,<br>
><br>
> Martin<br>
><br>
> [1] <a href="https://jenkins.qa.ubuntu.com/job/trusty-adt-r-bioc-rtracklayer/6/ARCH=i386,label=adt/console" target="_blank">https://jenkins.qa.ubuntu.com/job/trusty-adt-r-bioc-rtracklayer/6/ARCH=i386,label=adt/console</a><br>
> --<br>
> Martin Pitt | <a href="http://www.piware.de" target="_blank">http://www.piware.de</a><br>
> Ubuntu Developer (<a href="http://www.ubuntu.com" target="_blank">www.ubuntu.com</a>) | Debian Developer (<a href="http://www.debian.org" target="_blank">www.debian.org</a>)<br>
<br>
> diff -Nru r-bioc-rtracklayer-1.22.0/debian/changelog r-bioc-rtracklayer-1.22.0/debian/changelog<br>
> --- r-bioc-rtracklayer-1.22.0/debian/changelog 2013-12-28 01:59:48.000000000 +0100<br>
> +++ r-bioc-rtracklayer-1.22.0/debian/changelog 2014-01-16 12:06:12.000000000 +0100<br>
> @@ -1,3 +1,10 @@<br>
> +r-bioc-rtracklayer (1.22.0-1ubuntu1) UNRELEASED; urgency=medium<br>
> +<br>
> + * debian/tests/control: Add missing r-cran-runit test dependency, and allow<br>
> + stderr output.<br>
> +<br>
> + -- Martin Pitt <<a href="mailto:martin.pitt@ubuntu.com">martin.pitt@ubuntu.com</a>> Thu, 16 Jan 2014 12:00:35 +0100<br>
> +<br>
> r-bioc-rtracklayer (1.22.0-1) unstable; urgency=low<br>
><br>
> * Initial release (closes: #733283).<br>
> diff -Nru r-bioc-rtracklayer-1.22.0/debian/tests/control r-bioc-rtracklayer-1.22.0/debian/tests/control<br>
> --- r-bioc-rtracklayer-1.22.0/debian/tests/control 2013-11-05 09:42:06.000000000 +0100<br>
> +++ r-bioc-rtracklayer-1.22.0/debian/tests/control 2014-01-16 12:00:33.000000000 +0100<br>
> @@ -1 +1,3 @@<br>
> Tests: run-unit-test<br>
> +Depends: @, r-cran-runit<br>
> +Restrictions: allow-stderr<br>
<br>
> 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}<br>
> adt-run1: ** init<br>
> adt-run1: ** start<br>
> adt-run: $ vserver: adt-virt-null<br>
> adt-run1: ** open, scratch=None<br>
> adt-run1: ** cmdl = ['sh', '-c', 'exec "$@"', 'x']<br>
> adt-run1: * initialising<br>
> adt-run1: * preparing for key generation<br>
> adt-run: $ genkey: sh -ec <SCRIPT> x /home/ubuntu/.autopkgtest/gpg<br>
> adt-run1: $<br>
> adt-run1: $ exec >&2<br>
> adt-run1: $ cd "$1"<br>
> adt-run1: $ cat <<"END" >key-gen-params<br>
> adt-run1: $ Key-Type: DSA<br>
> adt-run1: $ Key-Length: 1024<br>
> adt-run1: $ Key-Usage: sign<br>
> adt-run1: $ Name-Real: autopkgtest per-run key<br>
> adt-run1: $ Name-Comment: do not trust this key<br>
> adt-run1: $ Name-Email: <a href="mailto:autopkgtest@example.com">autopkgtest@example.com</a><br>
> adt-run1: $ END<br>
> adt-run1: $ set -x<br>
> adt-run1: $ gpg --homedir="$1" --batch --gen-key key-gen-params<br>
> + gpg --homedir=/home/ubuntu/.autopkgtest/gpg --batch --gen-key key-gen-params<br>
> gpg: keyring `/home/ubuntu/.autopkgtest/gpg/secring.gpg' created<br>
> gpg: keyring `/home/ubuntu/.autopkgtest/gpg/pubring.gpg' created<br>
> +++++..+++++++++++++++.++++++++++++++++++++++++++++++++++++++++.+++++...+++++++++++++++.+++++.+++++.++++++++++++++++++++.+++++++++++++++.+++++>.++++++++++..>+++++.........+++++<br>
> gpg: /home/ubuntu/.autopkgtest/gpg/trustdb.gpg: trustdb created<br>
> gpg: key 6B36EE88 marked as ultimately trusted<br>
> adt-run1: * reset<br>
> adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ builds ...<br>
> adt-run: @@@@@@@@@@@@@@@@@@@@ ubtree ubtree0<br>
> adt-run1: ** blame += arg:.<br>
> adt-run1: ** prepare1, modified=False, deps_processed=[], deps_new=[]<br>
> adt-run1: ** needs_reset, previously=False<br>
> adt-run: $ ubtree0-extract: sh -ec <SCRIPT> x /tmp/adt-run.sMCbhA/ubtree0-build/tmpdir /tmp/adt-run.sMCbhA/ubtree0-build/real-tree<br>
> adt-run1: $ exec 3>&1 >&2<br>
> adt-run1: $ set -x<br>
> adt-run1: $ spec="$2"<br>
> adt-run1: $ origpwd=/tmp/adt-run.sMCbhA/ubtree0-ubtree<br>
> adt-run1: $ mkdir -p /tmp/adt-run.sMCbhA/ubtree0-build<br>
> adt-run1: $ cd /tmp/adt-run.sMCbhA/ubtree0-build<br>
> adt-run1: $ chown ubuntu . ..<br>
> adt-run1: $ TMPDIR="$1"<br>
> adt-run1: $ rm -rf -- "$TMPDIR"<br>
> adt-run1: $ export TMPDIR<br>
> adt-run1: $ su -s /bin/sh ubuntu -c 'mkdir -m 1777 -- "$TMPDIR"'<br>
> adt-run1: $ spec="$spec" origpwd="$origpwd" su -s /bin/sh ubuntu -c '<br>
> adt-run1: $ rm -rf "$spec"<br>
> adt-run1: $ mkdir "$spec"<br>
> adt-run1: $ cp -rP --preserve=timestamps,links -- "$origpwd"/. "$spec"/.<br>
> adt-run1: $ '<br>
> adt-run1: $ cd [a-z0-9]*-*/.<br>
> adt-run1: $ pwd >&3<br>
> adt-run1: $ set +e; test -f debian/tests/control; echo $? >&3<br>
> + spec=/tmp/adt-run.sMCbhA/ubtree0-build/real-tree<br>
> + origpwd=/tmp/adt-run.sMCbhA/ubtree0-ubtree<br>
> + mkdir -p /tmp/adt-run.sMCbhA/ubtree0-build<br>
> + cd /tmp/adt-run.sMCbhA/ubtree0-build<br>
> + chown ubuntu . ..<br>
> + TMPDIR=/tmp/adt-run.sMCbhA/ubtree0-build/tmpdir<br>
> + rm -rf -- /tmp/adt-run.sMCbhA/ubtree0-build/tmpdir<br>
> + export TMPDIR<br>
> + su -s /bin/sh ubuntu -c mkdir -m 1777 -- "$TMPDIR"<br>
> + spec=/tmp/adt-run.sMCbhA/ubtree0-build/real-tree origpwd=/tmp/adt-run.sMCbhA/ubtree0-ubtree su -s /bin/sh ubuntu -c<br>
> rm -rf "$spec"<br>
> mkdir "$spec"<br>
> cp -rP --preserve=timestamps,links -- "$origpwd"/. "$spec"/.<br>
><br>
> + cd real-tree/.<br>
> + pwd<br>
> + set +e<br>
> + test -f debian/tests/control<br>
> + echo 0<br>
> adt-run1: constructed; path=debian/tests/run-unit-test<br>
> adt-run1: .depends=[u'@', u'r-cran-runit']<br>
> adt-run: * <ubtree:ubtree0> build not needed<br>
> adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ builds done.<br>
> adt-run1: * reset<br>
> adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ tests ...<br>
> adt-run: @@@@@@@@@@@@@@@@@@@@ test ubtree ubtree0<br>
> adt-run1: ** needs_reset, previously=True<br>
> adt-run1: ** blame += arg:.<br>
> adt-run1: constructed; path=debian/tests/run-unit-test<br>
> adt-run1: .depends=[u'@', u'r-cran-runit']<br>
> adt-run: @@@@@@@@@@ run_tests ...<br>
> adt-run: & ubtree0t-run-unit-test: preparing<br>
> adt-run: & ubtree0t-run-unit-test: processing dependency @<br>
> adt-run: & ubtree0t-run-unit-test: synthesised dependency r-bioc-rtracklayer<br>
> adt-run: & ubtree0t-run-unit-test: processing dependency r-cran-runit<br>
> adt-run: & ubtree0t-run-unit-test: literal dependency r-cran-runit<br>
> adt-run1: ** prepare1, modified=True, deps_processed=[], deps_new=[u'r-bioc-rtracklayer', u'r-cran-runit']<br>
> adt-run1: ** prepare2, deps_new=[u'r-bioc-rtracklayer', u'r-cran-runit']<br>
> adt-run1: * publish<br>
> adt-run1: * no registered binaries, not publishing anything<br>
> adt-run1: ** installing dependencies [u'r-bioc-rtracklayer', u'r-cran-runit']<br>
> adt-run1: dependencies: install-deps: satisfying r-bioc-rtracklayer, r-cran-runit<br>
> 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']<br>
> -> Attempting to parse the build-deps<br>
> -> Considering build-dep r-bioc-rtracklayer<br>
> -> Trying r-bioc-rtracklayer<br>
> -> Considering build-dep r-cran-runit<br>
> -> Trying r-cran-runit<br>
> -> Installing r-bioc-rtracklayer r-cran-runit<br>
> Reading package lists...<br>
> Building dependency tree...<br>
> Reading state information...<br>
> The following extra packages will be installed:<br>
> fontconfig fontconfig-config fonts-dejavu-core libblas3 libcairo2<br>
> libcurl3-nss libdatrie1 libfontconfig1 libgfortran3 libgraphite2-3<br>
> libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 libnspr4<br>
> libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils<br>
> libpaper1 libpixman-1-0 libsm6 libtcl8.5 libthai-data libthai0 libtiff5<br>
> libtk8.5 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6<br>
> r-base-core r-bioc-biocgenerics r-bioc-biostrings r-bioc-bsgenome<br>
> r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-xvector<br>
> r-cran-bitops r-cran-rcurl r-cran-xml tcl8.5 tk8.5 x11-common xdg-utils zip<br>
> Suggested packages:<br>
> ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp<br>
> ttf-arphic-bkai00mp ess r-doc-info r-doc-pdf r-mathlib r-base-html<br>
> r-bioc-pasillabamsubset r-bioc-shortread tcl-tclreadline gvfs-bin<br>
> Recommended packages:<br>
> r-recommended r-base-dev r-doc-html xterm x-terminal-emulator<br>
> libfile-mimeinfo-perl x11-utils x11-xserver-utils<br>
> The following NEW packages will be installed:<br>
> fontconfig fontconfig-config fonts-dejavu-core libblas3 libcairo2<br>
> libcurl3-nss libdatrie1 libfontconfig1 libgfortran3 libgraphite2-3<br>
> libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 libnspr4<br>
> libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils<br>
> libpaper1 libpixman-1-0 libsm6 libtcl8.5 libthai-data libthai0 libtiff5<br>
> libtk8.5 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6<br>
> r-base-core r-bioc-biocgenerics r-bioc-biostrings r-bioc-bsgenome<br>
> r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-rtracklayer<br>
> r-bioc-xvector r-cran-bitops r-cran-rcurl r-cran-runit r-cran-xml tcl8.5<br>
> tk8.5 x11-common xdg-utils zip<br>
> 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded.<br>
> Need to get 46.0 MB of archives.<br>
> After this operation, 93.0 MB of additional disk space will be used.<br>
> Get:1 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main fonts-dejavu-core all 2.34-1ubuntu1 [1,024 kB]<br>
> Get:2 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main fontconfig-config all 2.11.0-0ubuntu3 [47.3 kB]<br>
> Get:3 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libfontconfig1 amd64 2.11.0-0ubuntu3 [123 kB]<br>
> Get:4 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libpixman-1-0 amd64 0.30.2-2ubuntu1 [227 kB]<br>
> Get:5 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libxcb-render0 amd64 1.10-2ubuntu1 [11.0 kB]<br>
> Get:6 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libxcb-shm0 amd64 1.10-2ubuntu1 [5,432 B]<br>
> Get:7 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libxrender1 amd64 1:0.9.8-1 [20.9 kB]<br>
> Get:8 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libcairo2 amd64 1.12.16-0ubuntu2 [625 kB]<br>
> Get:9 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libnspr4 amd64 2:4.10.2-1ubuntu1 [110 kB]<br>
> Get:10 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libnss3 amd64 2:3.15.3.1-1.1ubuntu1 [1,076 kB]<br>
> Get:11 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libcurl3-nss amd64 7.34.0-1ubuntu1 [174 kB]<br>
> Get:12 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libdatrie1 amd64 0.2.8-1 [16.7 kB]<br>
> Get:13 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty-proposed/main libgfortran3 amd64 4.8.2-14ubuntu1 [249 kB]<br>
> Get:14 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libgraphite2-3 amd64 1.2.4-1ubuntu1 [53.8 kB]<br>
> Get:15 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libharfbuzz0b amd64 0.9.24-2ubuntu3 [124 kB]<br>
> Get:16 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main x11-common all 1:7.7+1ubuntu7 [55.4 kB]<br>
> Get:17 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libice6 amd64 2:1.0.8-2 [47.0 kB]<br>
> Get:18 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libjpeg-turbo8 amd64 1.3.0-0ubuntu2 [104 kB]<br>
> Get:19 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libthai-data all 0.1.20-3 [130 kB]<br>
> Get:20 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libthai0 amd64 0.1.20-3 [16.9 kB]<br>
> Get:21 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main fontconfig amd64 2.11.0-0ubuntu3 [176 kB]<br>
> Get:22 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libpango-1.0-0 amd64 1.36.0-1ubuntu2 [149 kB]<br>
> Get:23 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libpangoft2-1.0-0 amd64 1.36.0-1ubuntu2 [32.1 kB]<br>
> Get:24 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libpangocairo-1.0-0 amd64 1.36.0-1ubuntu2 [19.5 kB]<br>
> Get:25 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libpaper1 amd64 1.1.24+nmu2ubuntu3 [13.4 kB]<br>
> Get:26 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libsm6 amd64 2:1.2.1-2 [18.1 kB]<br>
> Get:27 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libtcl8.5 amd64 8.5.15-2ubuntu1 [684 kB]<br>
> Get:28 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libjbig0 amd64 2.0-2ubuntu4 [25.9 kB]<br>
> Get:29 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libjpeg8 amd64 8c-2ubuntu8 [2,194 B]<br>
> Get:30 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libtiff5 amd64 4.0.3-7 [142 kB]<br>
> Get:31 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libxft2 amd64 2.3.1-1ubuntu1 [36.3 kB]<br>
> Get:32 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libxss1 amd64 1:1.2.2-1 [8,582 B]<br>
> Get:33 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libtk8.5 amd64 8.5.15-2ubuntu2 [640 kB]<br>
> Get:34 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libxt6 amd64 1:1.1.4-1 [185 kB]<br>
> Get:35 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libblas3 amd64 1.2.20110419-7 [215 kB]<br>
> Get:36 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main liblapack3 amd64 3.5.0-2 [1,729 kB]<br>
> Get:37 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main libpaper-utils amd64 1.1.24+nmu2ubuntu3 [8,244 B]<br>
> Get:38 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main zip amd64 3.0-8 [262 kB]<br>
> Get:39 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main xdg-utils all 1.1.0~rc1-2ubuntu7 [65.6 kB]<br>
> Get:40 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main tcl8.5 amd64 8.5.15-2ubuntu1 [13.9 kB]<br>
> Get:41 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/main tk8.5 amd64 8.5.15-2ubuntu2 [12.0 kB]<br>
> Get:42 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/universe r-base-core amd64 3.0.2-1ubuntu1 [21.5 MB]<br>
> Get:43 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/universe r-bioc-biocgenerics all 0.8.0-1 [386 kB]<br>
> Get:44 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty-proposed/universe r-bioc-iranges amd64 1.20.6-1 [1,854 kB]<br>
> Get:45 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty-proposed/universe r-bioc-xvector amd64 0.2.0-1 [329 kB]<br>
> Get:46 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty-proposed/universe r-bioc-biostrings amd64 2.30.1-1 [2,228 kB]<br>
> Get:47 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty-proposed/universe r-bioc-genomicranges amd64 1.14.3-1 [2,840 kB]<br>
> Get:48 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/universe r-bioc-bsgenome amd64 1.30.0-1 [716 kB]<br>
> Get:49 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/universe r-cran-bitops amd64 1.0-6-1 [23.4 kB]<br>
> Get:50 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty-proposed/universe r-bioc-rsamtools amd64 1.14.2-1 [3,214 kB]<br>
> Get:51 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/universe r-cran-xml amd64 3.98-1.1-1 [1,789 kB]<br>
> Get:52 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/universe r-cran-rcurl amd64 1.95-4.1-1 [523 kB]<br>
> Get:53 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty-proposed/universe r-bioc-rtracklayer amd64 1.22.0-1 [1,753 kB]<br>
> Get:54 <a href="http://archive.ubuntu.com/ubuntu/" target="_blank">http://archive.ubuntu.com/ubuntu/</a> trusty/universe r-cran-runit all 0.4.26-2 [181 kB]<br>
><br>
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><br>
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> adt-run: & ubtree0t-run-unit-test: [----------------------------------------<br>
> -> Finished parsing the build-deps<br>
><br>
> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"<br>
> Copyright (C) 2013 The R Foundation for Statistical Computing<br>
> Platform: x86_64-pc-linux-gnu (64-bit)<br>
><br>
> R is free software and comes with ABSOLUTELY NO WARRANTY.<br>
> You are welcome to redistribute it under certain conditions.<br>
> Type 'license()' or 'licence()' for distribution details.<br>
><br>
> R is a collaborative project with many contributors.<br>
> Type 'contributors()' for more information and<br>
> 'citation()' on how to cite R or R packages in publications.<br>
><br>
> Type 'demo()' for some demos, 'help()' for on-line help, or<br>
> 'help.start()' for an HTML browser interface to help.<br>
> Type 'q()' to quit R.<br>
><br>
> > require("rtracklayer")<br>
> Loading required package: rtracklayer<br>
> Loading required package: GenomicRanges<br>
> Loading required package: BiocGenerics<br>
> Loading required package: parallel<br>
><br>
> Attaching package: 'BiocGenerics'<br>
><br>
> The following objects are masked from 'package:parallel':<br>
><br>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,<br>
> clusterExport, clusterMap, parApply, parCapply, parLapply,<br>
> parLapplyLB, parRapply, parSapply, parSapplyLB<br>
><br>
> The following object is masked from 'package:stats':<br>
><br>
> xtabs<br>
><br>
> The following objects are masked from 'package:base':<br>
><br>
> Filter, Find, Map, Position, Reduce, anyDuplicated, append,<br>
> as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq,<br>
> get, intersect, is.unsorted, lapply, mapply, match, mget, order,<br>
> paste, pmax, <a href="http://pmax.int" target="_blank">pmax.int</a>, pmin, <a href="http://pmin.int" target="_blank">pmin.int</a>, rank, rbind, <a href="http://rep.int" target="_blank">rep.int</a>,<br>
> rownames, sapply, setdiff, sort, table, tapply, union, unique,<br>
> unlist<br>
><br>
> Loading required package: IRanges<br>
> Loading required package: XVector<br>
> > rtracklayer:::.test()<br>
> Warning message:<br>
> Starting with BioC 2.13, calling import() with 'asRangedData=TRUE' is<br>
> deprecated. If you wish import() to return a RangedData object,<br>
> then you can coerce the returned object with 'as(..., "RangedData")'.<br>
> However, we strongly recommend that you start migrating your code to<br>
> operate on GRanges objects instead of RangedData objects.<br>
> Starting with BioC 2.14, support for RangedData objects will be limited.<br>
> Please ask on the bioc-devel mailing list if you have questions<br>
> or concerns about this (<a href="http://bioconductor.org/help/mailing-list/" target="_blank">http://bioconductor.org/help/mailing-list/</a>)<br>
> Timing stopped at: 1.256 0.016 1.279<br>
> Error in seqlevels(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
> Timing stopped at: 0.643 0.006 0.65<br>
> Error in seqlevels(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
> Timing stopped at: 0.063 0 0.064<br>
> Error in seqlengths(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlengths': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
> Timing stopped at: 2.547 0.021 2.573<br>
> Error in seqlevels(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
> Timing stopped at: 0.799 0.006 0.807<br>
> Error in seqlevels(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
><br>
><br>
> RUNIT TEST PROTOCOL -- Thu Jan 16 12:03:51 2014<br>
> ***********************************************<br>
> Number of test functions: 7<br>
> Number of errors: 5<br>
> Number of failures: 0<br>
><br>
><br>
> 1 Test Suite :<br>
> rtracklayer RUnit Tests - 7 test functions, 5 errors, 0 failures<br>
> ERROR in test_bed: Error in seqlevels(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
> ERROR in test_bedGraph: Error in seqlevels(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
> ERROR in test_bw: Error in seqlengths(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlengths': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
> ERROR in test_gff: Error in seqlevels(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
> ERROR in test_wig: Error in seqlevels(seqinfo(x)) :<br>
> error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :<br>
> unable to find an inherited method for function 'seqinfo' for signature '"NULL"'<br>
> Calls: seqinfo -> <Anonymous><br>
><br>
><br>
> Test files with failing tests<br>
><br>
> test_bed.R<br>
> test_bed<br>
><br>
> test_bedGraph.R<br>
> test_bedGraph<br>
><br>
> test_bw.R<br>
> test_bw<br>
><br>
> test_gff.R<br>
> test_gff<br>
><br>
> test_wig.R<br>
> test_wig<br>
><br>
><br>
> Error in BiocGenerics:::testPackage("rtracklayer") :<br>
> unit tests failed for package rtracklayer<br>
> Calls: <Anonymous> -> <Anonymous><br>
> Execution halted<br>
> adt-run1: testbed executing test finished with exit status 1<br>
> adt-run: & ubtree0t-run-unit-test: ----------------------------------------]<br>
> adt-run: & ubtree0t-run-unit-test: - - - - - - - - - - results - - - - - - - - - -<br>
> ubtree0t-run-unit-test FAIL non-zero exit status 1<br>
> adt-run1: ** needs_reset, previously=False<br>
> adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ tests done.<br>
> adt-run1: ** stop<br>
> adt-run1: ** close, scratch=/tmp/adt-run.sMCbhA<br>
<br>
<br>
<br>
<br>
> _______________________________________________<br>
> Debian-med-packaging mailing list<br>
> <a href="mailto:Debian-med-packaging@lists.alioth.debian.org">Debian-med-packaging@lists.alioth.debian.org</a><br>
> <a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging" target="_blank">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging</a><br>
<span class="HOEnZb"><font color="#888888"><br>
<br>
--<br>
<a href="http://fam-tille.de" target="_blank">http://fam-tille.de</a><br>
</font></span></blockquote></div><br></div>