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

[Chris Fields]

Warnings for DB::Fasta now fixed (just caught the sig locally and noop'd it).

What are the failures for Align::Graphics?

chris


On Apr 12, 2011, at 10:59 AM, Chris Fields wrote:

> 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
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>> 
>> 
>> 
>> -- 
>> ------------------------------------------------------------------------
>> 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
> http://lists.open-bio.org/mailman/listinfo/bioperl-l