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

[Scott Cain]

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
>>
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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