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

[Chris Fields]

So, for this particular test, should it pass with either an empty  
string or undef?  It apparently works for all other tests.

chris

On Jan 30, 2009, at 11:13 AM, Hilmar Lapp wrote:

> 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
>>
>>
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
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