[Help] Fwd: Bug#720776: bioperl: FTBFS with perl 5.18: test failures
Hi Perl team,
the Perl addicted team members in Debian Med team are currently a bit
occupied by real life work. I'd be happy about a patch. I could also
imagine that Debian Perl team might like to take over this package if
you consider this a good idea (the Ruby team recently has asked us for
handing them over BioRuby which we were happy to hand over to competent
team).
What do you think?
Kind regards
Andreas.
----- Forwarded message from Dominic Hargreaves <dom@earth.li> -----
Date: Sun, 25 Aug 2013 13:41:38 +0100
From: Dominic Hargreaves <dom@earth.li>
To: submit@bugs.debian.org
Subject: Bug#720776: bioperl: FTBFS with perl 5.18: test failures
X-Debian-PR-Message: report 720776
X-Debian-PR-Package: src:bioperl
X-Debian-PR-Keywords: jessie sid
X-Debian-PR-Source: bioperl
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 '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@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
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