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

[Chris Fields]

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
>>> 
>>> 
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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
> 
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