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

Chris Fields cjfields at illinois.edu
Mon Feb 2 11:40:43 EST 2009


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
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> 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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