[Bioperl-l] Re: bioperl-live make test failure

[Jason Stajich]

fixed.
On Oct 11, 2005, at 12:39 PM, Scott Cain wrote:

> Hi Jason,
>
> You are still working on the 1.5.1 release from HEAD, right?  I  
> just did
> a cvs update -d, and make test fails thusly:
>
> t/tigrxml....................ok 1/48Bio::SeqIO: tigrxml cannot be  
> found
> Exception
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Failed to load module Bio::SeqIO::tigrxml. Can't locate XML/ 
> SAX/Writer.pm in @INC (@INC contains: t /Users/cain/cvs_stuff/ 
> bioperl-live/blib/lib /Users/cain/cvs_stuff/bioperl-live/blib/arch / 
> sw/lib/perl5 /sw/lib/perl5/darwin /usr/local/lib/perl5/5.8.4/ 
> darwin-2level /usr/local/lib/perl5/5.8.4 /usr/local/lib/perl5/ 
> site_perl/5.8.4/darwin-2level /usr/local/lib/perl5/site_perl/5.8.4 / 
> usr/local/lib/perl5/site_perl .) at /Users/cain/cvs_stuff/bioperl- 
> live/blib/lib/Bio/SeqIO/tigrxml.pm line 71.
> BEGIN failed--compilation aborted at /Users/cain/cvs_stuff/bioperl- 
> live/blib/lib/Bio/SeqIO/tigrxml.pm line 71.
> Compilation failed in require at /Users/cain/cvs_stuff/bioperl-live/ 
> blib/lib/Bio/Root/Root.pm line 396.
>
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Users/cain/cvs_stuff/bioperl-live/ 
> blib/lib/Bio/Root/Root.pm:328
> STACK: Bio::Root::Root::_load_module /Users/cain/cvs_stuff/bioperl- 
> live/blib/lib/Bio/Root/Root.pm:398
> STACK: Bio::SeqIO::_load_format_module /Users/cain/cvs_stuff/ 
> bioperl-live/blib/lib/Bio/SeqIO.pm:552
> STACK: Bio::SeqIO::new /Users/cain/cvs_stuff/bioperl-live/blib/lib/ 
> Bio/SeqIO.pm:379
> STACK: t/tigrxml.t:22
> -----------------------------------------------------------
>
> For more information about the SeqIO system please see the SeqIO docs.
> This includes ways of checking for formats at compile time, not run  
> time
> Can't call method "verbose" on an undefined value at t/tigrxml.t  
> line 26.
> t/tigrxml....................dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 2-48
>         Failed 47/48 tests, 2.08% okay
>
>
> This is on Mac OSX 10.3, perl 5.8.4 built from source.
>
> Thanks,
> Scott
>
> -- 
> ---------------------------------------------------------------------- 
> --
> Scott Cain, Ph. D.                                          
> cain at cshl.edu
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
>
>