[Bioperl-l] AlignIO

[Chris Fields]

Daniel,

It's hard to determine what's going on in this case w/o seeing the verbose output from one of those test reports.  I would say it is probably a missing dependency (maybe Data::Stag), but I haven't seen anything like this before.

chris

On Apr 19, 2011, at 8:02 PM, Daniel Campo wrote:

> Hi, 
> I am trying to install BioPerl in my MacOSX using CPAN.
> After running the tests I got the following:
> 
> 
> 
> Failed Test                         Stat Wstat Total Fail  List of Failed
> -------------------------------------------------------------------------------
> t/AlignIO/AlignIO.t                  255 65280    28   42  8-28
> t/AlignIO/arp.t                      255 65280    48   92  3-48
> t/Annotation/Annotation.t            255 65280   158   83  9 116 118-158
> t/ClusterIO/SequenceFamily.t         255 65280    19   34  3-19
> t/LocalDB/Flat.t                     255 65280    24   20  15-24
> t/LocalDB/Index.t                    255 65280    64   66  32-64
> t/SeqIO/Handler.t                    255 65280   561 1120  2-561
> t/SeqIO/chaos.t                        1   256     8    1  1
> t/SeqIO/swiss.t                      255 65280   240  479  1-240
> t/SeqTools/GuessSeqFormat.t            1   256    49    2  25 50
> t/Tools/Analysis/Protein/Scansite.t  255 65280    14   20  5-14
> 63 tests and 305 subtests skipped.
> Failed 11/329 test scripts. 981/17708 subtests failed.
> Files=329, Tests=17708, 97 wallclock secs (81.97 cusr + 10.56 csys = 92.53 CPU)
> Failed 11/329 test programs. 981/17708 subtests failed.
>  CJFIELDS/BioPerl-1.6.1.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports CJFIELDS/BioPerl-1.6.1.tar.gz
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
> CMUNGALL/Data-Stag-0.11.tar.gz               : make NO
> RKOBES/ExtUtils-Manifest-1.58.tar.gz         : install NO
> CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO
> 
> 
> 
> And my concern is that I need to run a script that needs the module AlignIO. But that module seems to not have passed the test.
> Could you please help me on this?
> Thank you very much in advance.
> 
> Daniel.
> 
> 
> ---
> Daniel Campo Falgueras
> Postdoctoral Research Associate
> Molecular and Computational Biology
> University of Southern California
> 1050 Childs Way, RRI. 324C
> Los Angeles, CA, 90089-2910
> (+1) 213-821-3976
> dcampo at usc.edu
> http://college.usc.edu/cf/faculty-and-staff/staff.cfm?pid=1027679
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
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