Re: [Help] Fwd: Bug#720776: bioperl: FTBFS with perl 5.18: test failures
On 08/26/2013 10:10 AM, Andreas Tille wrote:
> 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
Hi,
I am have a look at this, failing tests look a bit weird....
I need however to install new perl release from experimental, I think I
will create a new virtualbox image for this.
However, any help will be welcome...
Olivier
>
> 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
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
> ----- End forwarded message -----
>
>
> --
> gpg key id: 4096R/326D8438 (keyring.debian.org)
> Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Reply to: