[Bioperl-l] Make test fails

[Jason Stajich]

I don't know that this is miserable, how many passed? ;)

I think you might want to get a fresh copy of spidey.pm and re-try  
that test, it works fine on my machine, maybe you have local changes  
that got merged during the CVS update - if there are ">>>" lines in  
your spidey.pm code it could be causing problems.

I see the protgraph failure too depending on which version of  
Graph::Directed I have installed.

The t/embl.t warning is intended, although we may want to silence it  
unless BIOPERLDEBUG environment variable is set.

The rest of the failures are wrt remote websites which we don't have  
control over, so things seem to drift.  I see the t/ELM.t failure  
too, need to see if Richard or someone can take a looksie. The DB.t  
tests are all failing, I don't know what is the problem with the  
website, but I think we'll definitely disable them without  
BIOPERLDEBUG set.

-jason

On Aug 31, 2005, at 12:32 AM, Ryan Golhar wrote:

> I just updated my copy of bioperl live from cvs and when I do a 'make
> test', it fails miserably.  Here's the relevant output:
>
> t/DB.........................FAILED test 24
>         Failed 1/84 tests, 98.81% okay
> t/DBCUTG.....................ok
>         22/24 skipped: tests which require remote servers - set env
> variable BIO
> PERLDEBUG to test
> t/DBFasta....................ok
> t/DNAMutation................ok
> t/Domcut.....................ok
>         22/25 skipped: tests which require remote servers - set env
> variable BIO
> PERLDEBUG to test
> t/ECnumber...................ok
> t/ELM........................
> -------------------- WARNING ---------------------
> MSG: Bio::Tools::Analysis::Protein::ELM Request Error:
> 400 (Bad Request) URL must be absolute
> Client-Date: Wed, 31 Aug 2005 04:23:10 GMT
>
>
>
> ---------------------------------------------------
> ok
> t/embl.......................
> -------------------- WARNING ---------------------
> MSG: Bio::PrimarySeq=HASH(0x9f74ff8) is not a SeqI compliant sequence
> object!
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: test is not a SeqI compliant sequence object!
> ---------------------------------------------------
> ok
> t/EMBL_DB....................ok
> t/ESEfinder..................error is 0
> ok
>         10/12 skipped: tests which require remote servers - set env
> variable BIO
> PERLDEBUG to test
> t/FeatureIO..................
> -------------------- WARNING ---------------------
> MSG: '##feature-ontology' directive handling not yet implemented
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: '##attribute-ontology' directive handling not yet implemented
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: '##source-ontology' directive handling not yet implemented
> ---------------------------------------------------
> ok
> t/Index......................
> -------------------- WARNING ---------------------
> MSG: overwriting a current value stored for AJ288898
>
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: overwriting a current value stored for AI129902
>
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: overwriting a current value stored for BAB68554
>
> ---------------------------------------------------
> ok
> t/protgraph..................doing subgraphs
> |||||||in subgraph - size30
> in subgraph - size33
> in subgraph - size3
> in subgraph - size3
> in subgraph - size5
> Can't call method "object_id" on unblessed reference at t/protgraph.t
> line 81, <
> GEN1> line 82.
> dubious
>         Test returned status 25 (wstat 6400, 0x1900)
>         after all the subtests completed successfully
> t/Spidey.....................Global symbol "$exon_num" requires  
> explicit
> package
>  name at /tmp/bioperl-live/blib/lib/Bio/Tools/Spidey/Results.pm line
> 309.
> Global symbol "$gen_start" requires explicit package name at
> /tmp/bioperl-live/b
> lib/lib/Bio/Tools/Spidey/Results.pm line 309.
> Global symbol "$gen_stop" requires explicit package name at
> /tmp/bioperl-live/bl
> ib/lib/Bio/Tools/Spidey/Results.pm line 309.
> Global symbol "$cdna_start" requires explicit package name at
> /tmp/bioperl-live/
> blib/lib/Bio/Tools/Spidey/Results.pm line 309.
> Global symbol "$cdna_stop" requires explicit package name at
> /tmp/bioperl-live/b
> lib/lib/Bio/Tools/Spidey/Results.pm line 309.
>
>
> Any idea why I'm getting these errors?  Should I blow away my
> bioperl-live directory and checkout a whole new version?
>
> My spidey modules shouldn't be failing...my last update to it was
> working fine...
>
> Ryan
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/