[Bioperl-l] OMIM tests failing

[Hilmar Lapp]

Juguang is modifying the parser, yes. I've noticed it failing too.

Juguang, if you can, try to avoid committing intermediate versions that  
aren't completed or tested and cause test failures. If for some reason  
or another you can't avoid that, *first* send an email to the list  
saying that what you need to commit is going to temporarily break tests  
blah and foo.

	-hilmar

On Friday, October 31, 2003, at 05:29  PM, Allen Day wrote:

> any idea what's going on here?  i see some recent commits (yesterday,
> first in 7 months) by juguang.  it worked two days ago...
>
> -allen
>
> [5:27pm]allenday at sumo:/raid5a/allenday/cvsroot/bioperl-live> make
> test_OMIMentry
> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib
> -I/usr/lib/perl5/5.8.0/i386-linux-thread-multi -I/usr/lib/perl5/5.8.0  
> -e
> 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;'
> t/OMIMentry.t
> t/OMIMentry....ok 5/145
> ------------- EXCEPTION  -------------
> MSG: a hash referenced needed
> STACK Bio::Phenotype::OMIM::OMIMentry::clinical_symptoms
> blib/lib/Bio/Phenotype/OMIM/OMIMentry.pm:537
> STACK toplevel t/OMIMentry.t:60
>
> --------------------------------------
> t/OMIMentry....dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 17-145
>         Failed 129/145 tests, 11.03% okay
> Failed Test   Stat Wstat Total Fail  Failed  List of Failed
> ----------------------------------------------------------------------- 
> --------
> t/OMIMentry.t  255 65280   145  129  88.97%  17-145
> Failed 1/1 test scripts, 0.00% okay. 129/145 subtests failed, 11.03%  
> okay.
> make: *** [test_OMIMentry] Error 2
> [5:27pm]allenday at sumo:/raid5a/allenday/cvsroot/bioperl-live> make
> test_OMIMentryAllelicVariant
> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib
> -I/usr/lib/perl5/5.8.0/i386-linux-thread-multi -I/usr/lib/perl5/5.8.0  
> -e
> 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;'
> t/OMIMentryAllelicVariant.t
> t/OMIMentryAllelicVariant....ok
> All tests successful.
> Files=1, Tests=26,  0 wallclock secs ( 0.14 cusr +  0.01 csys =  0.15  
> CPU)
> [5:28pm]allenday at sumo:/raid5a/allenday/cvsroot/bioperl-live> make
> test_OMIMparser
> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib
> -I/usr/lib/perl5/5.8.0/i386-linux-thread-multi -I/usr/lib/perl5/5.8.0  
> -e
> 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;'
> t/OMIMparser.t
> t/OMIMparser....ok 1/173
> ------------- EXCEPTION  -------------
> MSG: a part/organism must be assigned
> STACK Bio::Phenotype::OMIM::OMIMentry::add_clinical_symptoms
> blib/lib/Bio/Phenotype/OMIM/OMIMentry.pm:567
> STACK Bio::Phenotype::OMIM::OMIMparser::_finer_parse_symptoms
> blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm:550
> STACK Bio::Phenotype::OMIM::OMIMparser::_createOMIMentry
> blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm:531
> STACK Bio::Phenotype::OMIM::OMIMparser::next_phenotype
> blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm:272
> STACK toplevel t/OMIMparser.t:31
>
> --------------------------------------
> t/OMIMparser....dubious
>         Test returned status 25 (wstat 6400, 0x1900)
> DIED. FAILED tests 2-173
>         Failed 172/173 tests, 0.58% okay
> Failed Test    Stat Wstat Total Fail  Failed  List of Failed
> ----------------------------------------------------------------------- 
> --------
> t/OMIMparser.t   25  6400   173  172  99.42%  2-173
> Failed 1/1 test scripts, 0.00% okay. 172/173 subtests failed, 0.58%  
> okay.
> make: *** [test_OMIMparser] Error 2
> [5:28pm]allenday at sumo:/raid5a/allenday/cvsroot/bioperl-live>
>
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>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------