[Debian-med-packaging] Bug#735543: autopkgtest fails on missing runit, stderr, and test failures
Andreas Tille
andreas at an3as.eu
Thu Jan 16 12:53:25 UTC 2014
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.
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> 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]
>
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> * Setting up X socket directories...
> ...done.
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> Regenerating fonts cache... done.
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> Setting up liblapack3 (3.5.0-2) ...
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>
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> 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
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