[Debian-med-packaging] Bug#720776: bioperl: FTBFS with perl 5.18: test failures

[Dominic Hargreaves]

Source: bioperl
Version: 1.6.901-3
Severity: serious
Justification: transition imminent
User: debian-perl at lists.debian.org
Usertags: perl-5.18-transition
Tags: sid jessie

This package FTBFS with perl 5.18:

#   Failed test at t/Assembly/ContigSpectrum.t line 311.
#          got: '88.8076923076923'
#     expected: '88.7692307692308'

#   Failed test at Bio/Root/Test.pm line 435.
#          got: '74.727'
#     expected: '74.7486'

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not find sequence species1635|5973 in contig contig00001_6
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Assembly::Contig::get_seq_by_name Bio/Assembly/Contig.pm:1063
STACK: t/Assembly/ContigSpectrum.t:336
-----------------------------------------------------------
# Looks like you planned 236 tests but ran 215.
# Looks like you failed 2 tests of 215 run.
# Looks like your test exited with 255 just after 215.
t/Assembly/ContigSpectrum.t .................. 
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 23/236 subtests 

...

#   Failed test at t/Map/Map.t line 322.
#          got: 'Bio::Map::Position=HASH(0xa6595ec)'
#     expected: 'Bio::Map::Position=HASH(0xa6592b8)'

#   Failed test at t/Map/Map.t line 323.
#          got: 'Bio::Map::Position=HASH(0xa6592b8)'
#     expected: 'Bio::Map::Position=HASH(0xa6595ec)'

#   Failed test at t/Map/Map.t line 324.
#          got: undef
#     expected: 'Bio::Map::Position=HASH(0xa65a048)'
Can't call method "toString" on an undefined value at t/Map/Map.t line 325.
# Looks like you planned 267 tests but ran 134.
# Looks like you failed 3 tests of 134 run.
# Looks like your test exited with 255 just after 134.
t/Map/Map.t .................................. 
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 136/267 subtests 

...

#   Failed test at t/Ontology/IO/obo.t line 47.
#          got: '2'
#     expected: '5'

#   Failed test at t/Ontology/IO/obo.t line 49.

#   Failed test at t/Ontology/IO/obo.t line 51.

#   Failed test at t/Ontology/IO/obo.t line 53.

#   Failed test at t/Ontology/IO/obo.t line 55.

#   Failed test at t/Ontology/IO/obo.t line 57.

#   Failed test at t/Ontology/IO/obo.t line 61.
#          got: '10'
#     expected: '2'

#   Failed test 'Got positively regulates predicate'
#   at t/Ontology/IO/obo.t line 182.
#          got: 'REGULATES'
#     expected: 'POSITIVELY_REGULATES'
# Looks like you failed 8 tests of 92.
t/Ontology/IO/obo.t .......................... 
Dubious, test returned 8 (wstat 2048, 0x800)
Failed 8/92 subtests 

..

#   Failed test 'POD test for Bio/Tools/GuessSeqFormat.pm'
#   at /usr/share/perl5/Test/Pod.pm line 186.
# Bio/Tools/GuessSeqFormat.pm (233): Non-ASCII character seen before =encoding i
n 'K<E4>h<E4>ri,'. Assuming ISO8859-1

#   Failed test 'POD test for Bio/Tools/Geneid.pm'
#   at /usr/share/perl5/Test/Pod.pm line 186.
# Bio/Tools/Geneid.pm (37): Non-ASCII character seen before =encoding in 'Guig
<F3>'. Assuming ISO8859-1

#   Failed test 'POD test for Bio/Tools/Run/WrapperBase.pm'
#   at /usr/share/perl5/Test/Pod.pm line 186.
# Bio/Tools/Run/WrapperBase.pm (181): Non-ASCII character seen before =encoding in 'NB:<CA>This'. Assuming ISO8859-1

#   Failed test 'POD test for Bio/Tree/Statistics.pm'
#   at /usr/share/perl5/Test/Pod.pm line 186.
Wide character in print at /usr/share/perl/5.18/Test/Builder.pm line 1759.
# Bio/Tree/Statistics.pm (214): Non-ASCII character seen before =encoding in 'defining'. Assuming UTF-8

#   Failed test 'POD test for examples/biblio/biblio-eutils-example.pl'
#   at /usr/share/perl5/Test/Pod.pm line 186.
# examples/biblio/biblio-eutils-example.pl (108): Non-ASCII character seen before =encoding in '<LastName>Kub<ED>ckov<E1></LastName>'. Assuming ISO8859-1
# Looks like you failed 5 tests of 1011.
t/PodSyntax.t ................................ 
Dubious, test returned 5 (wstat 1280, 0x500)
Failed 5/1011 subtests 

..


Test Summary Report
-------------------
t/Assembly/ContigSpectrum.t                (Wstat: 65280 Tests: 215 Failed: 2)
  Failed tests:  203, 205
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 236 tests but ran 215.
t/Map/Map.t                                (Wstat: 65280 Tests: 134 Failed: 3)
  Failed tests:  132-134
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 267 tests but ran 134.
t/Ontology/IO/obo.t                        (Wstat: 2048 Tests: 92 Failed: 8)
  Failed tests:  14-20, 65
  Non-zero exit status: 8
t/PodSyntax.t                              (Wstat: 1280 Tests: 1011 Failed: 5)
  Failed tests:  197, 239, 307, 345, 964
  Non-zero exit status: 5
Files=349, Tests=22424, 291 wallclock secs ( 3.27 usr  2.58 sys + 141.92 cusr 15.12 csys = 162.89 CPU)
Result: FAIL

Please ask debian-perl at lists.debian.org if you need help with preparing
or testing a change; if you have a suitable test i386 system you can
install perl 5.18 by adding experimental to your sources as well as the
repository at <http://people.debian.org/~dom/perl/test/perl-5.18.0/>

You can also find more about the perl 5.18 transition, which we hope
to start this week[1], at <http://bugs.debian.org/712615>.

Thanks for your work!

Cheers,
Dominic.

[1] apologies for the late appearance of this bug report; earlier
test coverage did not cover this package