[Bioperl-l] GD version required/Align::Graphics (was: Re: Clean handling of SQLite choice when running ./Build test

[Scott Cain]

Hi Chris,

I hadn't looked at the Align::Graphics failures until you asked (I
didn't think of it as my problem :-)  It turned out the failures were
happening because I didn't have GD::Group.  So I used cpan to install
GD::Group and it turns out it is distributed with GD now, but
presumably not with the version I had (and now, of course, I don't
know what version I had).  So, I guess the question is, what version
started including GD::Group and do we need to add it as a recommends
and make it skip when it's not present?

Scott


On Tue, Apr 12, 2011 at 12:11 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 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
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research