[Bioperl-l] test failures in main trunk

[Mark A. Jensen]

> 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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> 
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