| From: | gregoa [...] cpan.org |
| Subject: | bioperl: FTBFS with perl 5.18: test failures |
This bug has been forwarded from http://bugs.debian.org/720776
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Source: bioperl
Version: 1.6.901-3
Severity: serious
Justification: transition imminent
User: debian-perl@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 'deļ¬ning'. 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@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
<--<--<--<--<--<--<--<--<--<--<--<--<--<--<--<--<--<--<--<--
Thanks in advance,
gregor herrmann, Debian Perl Group