[Debian-med-packaging] Bug#735548: autopkgtest fails on missing runit and stderr, missing TxDb.Hsapiens.UCSC.hg19.knownGene
Martin Pitt
martin.pitt at ubuntu.com
Thu Jan 16 11:42:29 UTC 2014
Package: r-bioc-genomicfeatures
Version: 1.14.2-1
Hello,
r-bioc-genomicfeatures' autopkgtest currently fails [1]:
Error in BiocGenerics:::testPackage("GenomicFeatures") :
RUnit package not found
After adding it (r-cran-runit), it fails because the test produces a
lot of stderror.
Attached debdiff fixes both, but the autopkgtest now fails on missing
packages:
GenomicFeatures RUnit Tests - 29 test functions, 5 errors, 0 failures
ERROR in /usr/lib/R/site-library/GenomicFeatures/unitTests/test_TranscriptDb_seqinfo.R: Error while sourcing /usr/lib/R/site-library/GenomicFeatures/unitTests/test_TranscriptDb_seqinfo.R : Error in library(TxDb.Hsapiens.UCSC.hg19.knownGene) :
there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
(this repeats a number of times). It seems this isn't packaged? The
closest match seems to be r-bioc-bsgenome [2] but it doesn't have
exactly this. I tried adding it as a test dependency, but it didn't
help much. I attach the full test log with this additional dependency
(which isn't in the debdiff, though).
Thanks for considering,
Martin
[1] https://jenkins.qa.ubuntu.com/job/trusty-adt-r-bioc-genomicfeatures/1/ARCH=i386,label=adt/console
[2] http://packages.debian.org/sid/i386/r-bioc-bsgenome/filelist
--
Martin Pitt | http://www.piware.de
Ubuntu Developer (www.ubuntu.com) | Debian Developer (www.debian.org)
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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 3318799D 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.zUMSTM/ubtree0-build/tmpdir /tmp/adt-run.zUMSTM/ubtree0-build/real-tree
adt-run1: $ exec 3>&1 >&2
adt-run1: $ set -x
adt-run1: $ spec="$2"
adt-run1: $ origpwd=/tmp/adt-run.zUMSTM/ubtree0-ubtree
adt-run1: $ mkdir -p /tmp/adt-run.zUMSTM/ubtree0-build
adt-run1: $ cd /tmp/adt-run.zUMSTM/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 $? >&3
+ spec=/tmp/adt-run.zUMSTM/ubtree0-build/real-tree
+ origpwd=/tmp/adt-run.zUMSTM/ubtree0-ubtree
+ mkdir -p /tmp/adt-run.zUMSTM/ubtree0-build
+ cd /tmp/adt-run.zUMSTM/ubtree0-build
+ chown ubuntu . ..
+ TMPDIR=/tmp/adt-run.zUMSTM/ubtree0-build/tmpdir
+ rm -rf -- /tmp/adt-run.zUMSTM/ubtree0-build/tmpdir
+ export TMPDIR
+ su -s /bin/sh ubuntu -c mkdir -m 1777 -- "$TMPDIR"
+ spec=/tmp/adt-run.zUMSTM/ubtree0-build/real-tree origpwd=/tmp/adt-run.zUMSTM/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', u'r-bioc-bsgenome']
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', u'r-bioc-bsgenome']
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-genomicfeatures
adt-run: & ubtree0t-run-unit-test: processing dependency r-cran-runit
adt-run: & ubtree0t-run-unit-test: literal dependency r-cran-runit
adt-run: & ubtree0t-run-unit-test: processing dependency r-bioc-bsgenome
adt-run: & ubtree0t-run-unit-test: literal dependency r-bioc-bsgenome
adt-run1: ** prepare1, modified=True, deps_processed=[], deps_new=[u'r-bioc-genomicfeatures', u'r-cran-runit', u'r-bioc-bsgenome']
adt-run1: ** prepare2, deps_new=[u'r-bioc-genomicfeatures', u'r-cran-runit', u'r-bioc-bsgenome']
adt-run1: * publish
adt-run1: * no registered binaries, not publishing anything
adt-run1: ** installing dependencies [u'r-bioc-genomicfeatures', u'r-cran-runit', u'r-bioc-bsgenome']
adt-run1: dependencies: install-deps: satisfying r-bioc-genomicfeatures, r-cran-runit, r-bioc-bsgenome
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-genomicfeatures
-> Trying r-bioc-genomicfeatures
-> Considering build-dep r-cran-runit
-> Trying r-cran-runit
-> Considering build-dep r-bioc-bsgenome
-> Trying r-bioc-bsgenome
-> Installing r-bioc-genomicfeatures r-cran-runit r-bioc-bsgenome
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-annotationdbi r-bioc-biobase r-bioc-biocgenerics
r-bioc-biomart r-bioc-biostrings r-bioc-genomicranges r-bioc-iranges
r-bioc-rsamtools r-bioc-rtracklayer r-bioc-xvector r-cran-bitops r-cran-dbi
r-cran-rcurl r-cran-rsqlite 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 r-cran-rmysql 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-annotationdbi r-bioc-biobase r-bioc-biocgenerics
r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-genomicfeatures
r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-rtracklayer
r-bioc-xvector r-cran-bitops r-cran-dbi r-cran-rcurl r-cran-rsqlite
r-cran-runit r-cran-xml tcl8.5 tk8.5 x11-common xdg-utils zip
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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("GenomicFeatures")
Loading required package: GenomicFeatures
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: GenomicRanges
Loading required package: XVector
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following objects are masked from 'package:BiocGenerics':
conditions, conditions<-, counts, counts<-, design, design<-,
dispTable, dispTable<-, estimateDispersions, estimateSizeFactors,
sizeFactors, sizeFactors<-
> GenomicFeatures:::.test()
There were 12 warnings (use warnings() to see them)
Error in library(TxDb.Hsapiens.UCSC.hg19.knownGene) :
there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Error in library(BSgenome.Hsapiens.UCSC.hg19) :
there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
Deducing exon rank from relative coordinates provided
Estimating transcript ranges.
extracting transcript information
Extracting gene IDs
extracting transcript information
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Now generating chrominfo from available sequence names. No chromosome length information is available.
extracting transcript information
Estimating transcript ranges.
Extracting gene IDs
Processing splicing information for gtf file.
Prepare the 'metadata' data frame ... metadata: OK
extracting transcript information
Extracting gene IDs
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Now generating chrominfo from available sequence names. No chromosome length information is available.
extracting transcript information
Extracting gene IDs
extracting transcript information
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Deducing exon rank from relative coordinates provided
extracting transcript information
Extracting gene IDs
extracting transcript information
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
extracting transcript information
Estimating transcript ranges.
Extracting gene IDs
Processing splicing information for gtf file.
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Error in eval(expr, envir, enclos) :
object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found
In addition: There were 24 warnings (use warnings() to see them)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: seqnames.db
Timing stopped at: 0.078 0.002 0.081
Error in seqnameStyle(seqinfo(x)) :
It is not possibe to match the seqnameStyle of this object to the seqnames.db database
In addition: There were 14 warnings (use warnings() to see them)
Loading required package: seqnames.db
Timing stopped at: 0.104 0.001 0.106
Error in seqnameStyle(seqinfo(x)) :
It is not possibe to match the seqnameStyle of this object to the seqnames.db database
In addition: There were 14 warnings (use warnings() to see them)
Warning messages:
1: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.2 and runtime version 3.8.2)
2: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.2 and runtime version 3.8.2)
Warning messages:
1: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.2 and runtime version 3.8.2)
2: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.2 and runtime version 3.8.2)
Warning messages:
1: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.2 and runtime version 3.8.2)
2: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.2 and runtime version 3.8.2)
RUNIT TEST PROTOCOL -- Thu Jan 16 12:38:36 2014
***********************************************
Number of test functions: 29
Number of errors: 5
Number of failures: 0
1 Test Suite :
GenomicFeatures RUnit Tests - 29 test functions, 5 errors, 0 failures
ERROR in /usr/lib/R/site-library/GenomicFeatures/unitTests/test_TranscriptDb_seqinfo.R: Error while sourcing /usr/lib/R/site-library/GenomicFeatures/unitTests/test_TranscriptDb_seqinfo.R : Error in library(TxDb.Hsapiens.UCSC.hg19.knownGene) :
there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
ERROR in /usr/lib/R/site-library/GenomicFeatures/unitTests/test_getPromoterSeq-methods.R: Error while sourcing /usr/lib/R/site-library/GenomicFeatures/unitTests/test_getPromoterSeq-methods.R : Error in library(BSgenome.Hsapiens.UCSC.hg19) :
there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
ERROR in /usr/lib/R/site-library/GenomicFeatures/unitTests/test_select-methods.R: Error while sourcing /usr/lib/R/site-library/GenomicFeatures/unitTests/test_select-methods.R : Error in eval(expr, envir, enclos) :
object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found
ERROR in test_transcripts_seqnameStyleSwap: Error in seqnameStyle(seqinfo(x)) :
It is not possibe to match the seqnameStyle of this object to the seqnames.db database
ERROR in test_transcriptsBy_seqnameStyleSwap: Error in seqnameStyle(seqinfo(x)) :
It is not possibe to match the seqnameStyle of this object to the seqnames.db database
Test files with failing tests
test_TranscriptDb_seqinfo.R
/usr/lib/R/site-library/GenomicFeatures/unitTests/test_TranscriptDb_seqinfo.R
test_getPromoterSeq-methods.R
/usr/lib/R/site-library/GenomicFeatures/unitTests/test_getPromoterSeq-methods.R
test_select-methods.R
/usr/lib/R/site-library/GenomicFeatures/unitTests/test_select-methods.R
test_transcripts.R
test_transcripts_seqnameStyleSwap
test_transcriptsBy.R
test_transcriptsBy_seqnameStyleSwap
Error in BiocGenerics:::testPackage("GenomicFeatures") :
unit tests failed for package GenomicFeatures
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.zUMSTM
-------------- next part --------------
diff -Nru r-bioc-genomicfeatures-1.14.2/debian/changelog r-bioc-genomicfeatures-1.14.2/debian/changelog
--- r-bioc-genomicfeatures-1.14.2/debian/changelog 2013-12-29 00:43:38.000000000 +0100
+++ r-bioc-genomicfeatures-1.14.2/debian/changelog 2014-01-16 12:31:20.000000000 +0100
@@ -1,3 +1,10 @@
+r-bioc-genomicfeatures (1.14.2-1ubuntu1) 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 12:31:07 +0100
+
r-bioc-genomicfeatures (1.14.2-1) unstable; urgency=low
* Initial release (closes: #733329)
diff -Nru r-bioc-genomicfeatures-1.14.2/debian/tests/control r-bioc-genomicfeatures-1.14.2/debian/tests/control
--- r-bioc-genomicfeatures-1.14.2/debian/tests/control 2013-11-05 09:42:06.000000000 +0100
+++ r-bioc-genomicfeatures-1.14.2/debian/tests/control 2014-01-16 12:36:22.000000000 +0100
@@ -1 +1,3 @@
Tests: run-unit-test
+Depends: @, r-cran-runit
+Restrictions: allow-stderr
-------------- next part --------------
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