[Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db

Hilmar Lapp hlapp at gmx.net
Fri Jan 30 12:13:54 EST 2009


I think this has something to do with the database connection  
configuration file (t/DBHarness.conf). I suspect in your version it  
sets 'port' to an empty string, rather than not setting it at all, or  
setting it explicitly to undef.

The test that's failing is one of a series of tests that verify that  
the connection attributes can be round-tripped through a DSN string.  
Specifying 'port' in the DSN string as an empty value is illegal  
though, so it gets left out whether it's undef or an empty string.  
When parsed back, the port isn't found in the string and hence left  
undef (meaning, use whatever your DBD driver thinks is the right  
default).

	-hilmar

On Jan 29, 2009, at 7:28 AM, Johann PELLET wrote:

> Dear Chris,
>
> I have the following error on my Mac machine: (BioPerl 1.6, BioPerl- 
> run
> 1.6) when I try to install Bioperl-db ( biosql-1.0.1):
>
> t/01dbadaptor.....1/23
> #   Failed test in t/01dbadaptor.t at line 44.
> #          got: undef
> #     expected: ''
> # Looks like you failed 1 test of 23.
> t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100)
> Failed 1/23 subtests
> t/02species.......ok
> t/03simpleseq.....ok
> t/04swiss.........ok
> t/05seqfeature....ok
> t/06comment.......ok
> t/07dblink........ok
> t/08genbank.......ok
> t/09fuzzy2........5/23
> #   Failed (TODO) test in t/09fuzzy2.t at line 64.
> #          got: undef
> #     expected: 'Q9QYG8'
> t/09fuzzy2........ok
> t/10ensembl.......ok
> t/11locuslink.....ok
> t/12ontology......ok
> t/13remove........ok
> t/14query.........ok
> t/15cluster.......ok
> t/16obda..........ok
>
> Test Summary Report
> -------------------
> t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1)
>  Failed test:  16
>  Non-zero exit status: 1
> Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr  0.10 sys + 11.15  
> cusr  1.11 csys = 12.63 CPU)
> Result: FAIL
> Failed 1/16 test programs. 1/1479 subtests failed.
>
> -- --
>
> Johann Pellet
> IE Bioinformatique
> INSERM U851, I-MAP CERVI
> 21, Avenue Tony Garnier
> 69365 Lyon cedex 07 France
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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