[Debian-med-packaging] Bug#735543: autopkgtest fails on missing runit, stderr, and test failures

Martin Pitt martin.pitt at ubuntu.com
Thu Jan 16 11:09:17 UTC 2014 

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)
-------------- next part --------------
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
-------------- next part --------------
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: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]
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Get:51 http://archive.ubuntu.com/ubuntu/ trusty/universe r-cran-xml amd64 3.98-1.1-1 [1,789 kB]
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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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adt-run: & ubtree0t-run-unit-test: [----------------------------------------
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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)

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> 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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