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

[Scott Cain]

Hi Chris,

Bio::Graphics only requires 2.30 at the moment.  Perhaps putting in
GD::Group separately would make the most sense.

Scott


On Tue, Apr 12, 2011 at 1:35 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Looks like GD v2.41.  We can either require a specific version of GD or list GD::Group separately (this should probably tie in with what Bio::Graphics requires).
>
> chris
>
> On Apr 12, 2011, at 11:45 AM, Scott Cain wrote:
>
>> 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
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>>>> 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