[Bioperl-l] test failures in main trunk

[Bruno Vecchi]

The second test ("Can't locate ok.pm in @INC...") can be fixed by
using use_ok('My::Module') instead of use ok 'My::Module' in the test
files.

I've had a few of those in the past, and that fix did the trick.

Cheers,

Bruno.


2009/9/18 Mark A. Jensen <maj at fortinbras.us>:
>
>> Will have to see why List::MoreUtils is being used, but if it's  necessary
>> it's an additional dep.
>
> I didn't do it, officer....
>
>>
>> chris
>>
>> On Sep 18, 2009, at 9:11 AM, Scott Cain wrote:
>>
>>> With Chris trying to get a release out, I wanted to report these  test
>>> failures from a fairly virgin system Ubuntu server 8.04.
>>>
>>> Scott
>>>
>>>
>>>
>>> t/SeqIO/raw.t ................................ 1/24 Can't locate
>>>  Algorithm/Diff.pm in @INC (@INC contains: t/lib . /home/gmod/bioperl-
>>> live/blib/lib /home/gmod/bioperl-live/blib/arch /home/gmod/bioperl- live
>>> /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/ 5.8.8
>>> /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/ perl/5.8
>>> /usr/local/lib/site_perl) at t/SeqIO/raw.t line 72.
>>> BEGIN failed--compilation aborted at t/SeqIO/raw.t line 72.
>>> # Looks like you planned 24 tests but ran 1.
>>> # Looks like your test exited with 2 just after 1.
>>> t/SeqIO/raw.t ................................ Dubious, test  returned 2
>>> (wstat 512, 0x200)
>>>
>>> t/SeqTools/Backtranslate.t ................... Can't locate ok.pm in
>>>  @INC (@INC contains: t/lib /home/gmod/bioperl-live/blib/lib /home/
>>> gmod/bioperl-live/blib/arch /home/gmod/bioperl-live /etc/perl /usr/
>>> local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/
>>> share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/ site_perl
>>> .) at t/SeqTools/Backtranslate.t line 9.
>>> BEGIN failed--compilation aborted at t/SeqTools/Backtranslate.t line  9.
>>> # Looks like your test exited with 2 before it could output anything.
>>> t/SeqTools/Backtranslate.t ................... Dubious, test  returned 2
>>> (wstat 512, 0x200)
>>> Failed 8/8 subtests
>>>
>>> t/SeqTools/SeqPattern.t ...................... 1/28
>>> #   Failed test 'use Bio::Tools::SeqPattern;'
>>> #   at t/SeqTools/SeqPattern.t line 12.
>>> #     Tried to use 'Bio::Tools::SeqPattern'.
>>> #     Error:  Can't locate List/MoreUtils.pm in @INC (@INC contains:
>>>  t/lib . /home/gmod/bioperl-live/blib/lib /home/gmod/bioperl-live/ blib/arch
>>> /home/gmod/bioperl-live /etc/perl /usr/local/lib/perl/ 5.8.8
>>> /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5 /
>>> usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl) at
>>>  Bio/Tools/SeqPattern/Backtranslate.pm line 22.
>>> # BEGIN failed--compilation aborted at Bio/Tools/SeqPattern/
>>> Backtranslate.pm line 22.
>>> # Compilation failed in require at Bio/Tools/SeqPattern.pm line 212.
>>> # Compilation failed in require at (eval 17) line 2.
>>> # BEGIN failed--compilation aborted at (eval 17) line 2.
>>> Use of uninitialized value in concatenation (.) or string at Bio/
>>> Tools/SeqPattern.pm line 431.
>>> Use of uninitialized value in concatenation (.) or string at Bio/
>>> Tools/SeqPattern.pm line 432.
>>>
>>> #   Failed test at t/SeqTools/SeqPattern.t line 25.
>>> #          got: '(CT).{1,80}(C[[]]CT).(AGGGG){1,200}'
>>> #     expected: '(CT).{1,80}(C[GA][GA]CT).(AGGGG){1,200}'
>>> Use of uninitialized value in concatenation (.) or string at Bio/
>>> Tools/SeqPattern.pm line 431.
>>> Use of uninitialized value in concatenation (.) or string at Bio/
>>> Tools/SeqPattern.pm line 432.
>>>
>>> #   Failed test at t/SeqTools/SeqPattern.t line 31.
>>> #          got: '(CT).(C[][]CT){1,80}.(AGGGG){1,200}'
>>> #     expected: '(CT).(C[AG][AG]CT){1,80}.(AGGGG){1,200}'
>>> Use of uninitialized value in concatenation (.) or string at Bio/
>>> Tools/SeqPattern.pm line 371.
>>> Use of uninitialized value in concatenation (.) or string at Bio/
>>> Tools/SeqPattern.pm line 372.
>>>
>>> #   Failed test at t/SeqTools/SeqPattern.t line 38.
>>> #          got: 'A[][]H'
>>> #     expected: 'A[EQ][DN]H'
>>> "_reverse_translate_motif" is not exported by the
>>>  Bio::Tools::SeqPattern::Backtranslate module
>>> Can't continue after import errors at Bio/Tools/SeqPattern.pm line 539
>>> # Looks like you planned 28 tests but ran 9.
>>> # Looks like you failed 4 tests of 9 run.
>>> # Looks like your test exited with 255 just after 9.
>>> t/SeqTools/SeqPattern.t ...................... Dubious, test  returned
>>> 255 (wstat 65280, 0xff00)
>>> Failed 23/28 subtests
>>>
>>>
>>> -----------------------------------------------------------------------
>>> Scott Cain, Ph. D. scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>>
>>>
>>>
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>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
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