[Bioperl-l] GD version required/Align::Graphics (was: Re: Clean handling of SQLite choice when running ./Build test
Lincoln Stein
lincoln.stein at gmail.com
Tue Apr 12 14:56:39 EDT 2011
Bio::Graphics tests whether GD supports startGroup() and endGroup() before
making either call.
Lincoln
On Tue, Apr 12, 2011 at 1:39 PM, Scott Cain <scott at scottcain.net> wrote:
> 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
> >>>> 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
>
--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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