[Bioperl-l] Clean handling of SQLite choice when running ./Build test

[Chris Fields]

That warning is due to an error check in the test suite, where Bio::DB::Fasta bails if the FASTA file is not indexed correctly (bad data):

$test_dbdir = setup_temp_dir('bad_dbfa');
throws_ok {$db = Bio::DB::Fasta->new($test_dbdir, -reindex => 1)} qr/FASTA header doesn't match/;

I'm guessing when Bio::DB::Fasta bails with an error it gets rid of the index file in DESTROY, hence the warning.  It's harmless, but we can probably catch that warning and squelch it; let me see what I can come up with.

chris

On Apr 12, 2011, at 10:43 AM, Scott Cain wrote:

> Hi Chris,
> 
> I was about to do this myself when I saw your email; thanks!  It
> passes all tests now.  The only tests that fail for me right now are
> the Align::Graphics tests.  Also, there is a strange warning for
> Bio::DB::Fasta, but the tests still pass.  The message is this:
> 
> ok 16
> indexing was interrupted, so unlinking
> /var/folders/b2/b2QPieqCF08SwC33tp0hmU+++TI/-Tmp-/CXuyf4rpl7/bad_dbfa/directory.index
> at Bio/DB/Fasta.pm line 1061.
> ok 17 - threw Regexp ((?-xism:FASTA header doesn't match))
> 
> 
> Scott
> 
> 
> On Tue, Apr 12, 2011 at 11:13 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> I added some simple code to the tests to catch this (on the master branch).  Seems to work; Scott, can you confirm that?
>> 
>> chris
>> 
>> On Apr 12, 2011, at 8:38 AM, Scott Cain wrote:
>> 
>>> Hi Lincoln and Chris,
>>> 
>>> I'm wondering what we should do about the SQLite option for testing
>>> when running ./Build test.  Currently (for me at least :-) when I
>>> select SQLite as the testing database when running perl Build.PL, the
>>> Bio::DB::GFF tests get "dubious" (which is fairly amazing, since there
>>> isn't a SQLite adaptor for Bio::DB::GFF), but it runs a different
>>> number of tests that planned, thus the dubious.  My inclination would
>>> be to not include SQLite as a testing option to avoid this problem,
>>> otherwise I suppose the Bio::DB::GFF test could be modified to use the
>>> memory adaptor when SQLite is the chosen testing database.
>>> 
>>> Scott
>>> 
>>> 
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
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>> 
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research