Bug #28881 for Bio-Grep: missing dependencies

Fri Aug 17 14:42:18 2007 basu [...] pharm.stonybrook.edu - Ticket created

CC:	Siddhartha Basu <basu [...] pharm.stonybrook.edu>
Subject:	missing dependencies
Date:	Fri, 17 Aug 2007 14:38:25 -0400
To:	bug-Bio-Grep [...] rt.cpan.org
From:	Siddhartha Basu <basu [...] pharm.stonybrook.edu>

Hi, Just saw Bio-Grep released in cpan, and the good feature is that it can return bioperl objects after the database search. However, i don't see any bioperl dependencies mentioned in Build.PL file. * Why it presumes that bioperl is already being installed in user's machine ? * Isn't that a prerequisite for the installation and if so it should also mention the least version it requires ? * Or is it an alpha software still not ready for any king of testing of deployable use. I will stay away in that case. Thanks. -siddhartha

Sat Aug 18 11:04:29 2007 LIMAONE [...] cpan.org - Correspondence added

From:

LIMAONE [...] cpan.org

Hi, currently, only the tests check for bioperl. I am not sure what the best way here is. bioperl-run and frieds use Bio::Root::Version => '1.5.2' as dependency so this is probably the way to go. But I am not sure what happens when it is not installed. Does it break cpantesters? (http://cpantesters.perl.org/show/Bio-Grep.html#Bio-Grep-v0.9.2) or does it magically install bioperl? To your other questions: I am developing Bio::Grep with bioperl v1.5.2, but at least a few months ago, everything worked fine with v1.4. We are using the vmatch parser now for about 2 years without having found any serious bugs, so it *should* be quite stable.

Sat Aug 18 11:04:36 2007 The RT System itself - Status changed from 'new' to 'open'

Mon Aug 20 11:40:14 2007 basu [...] pharm.stonybrook.edu - Correspondence added

Subject:	Re: [rt.cpan.org #28881] missing dependencies
Date:	Mon, 20 Aug 2007 11:37:32 -0400
To:	bug-Bio-Grep [...] rt.cpan.org
From:	Siddhartha Basu <basu [...] pharm.stonybrook.edu>

via RT wrote: Show quoted text

> <URL: http://rt.cpan.org/Ticket/Display.html?id=28881 > > > Hi, > > currently, only the tests check for bioperl. > > I am not sure what the best way here is. > bioperl-run and frieds use Bio::Root::Version => '1.5.2' as dependency > so this is probably the way to go. But I am not sure what happens when > it is not installed. Does it break cpantesters? > (http://cpantesters.perl.org/show/Bio-Grep.html#Bio-Grep-v0.9.2) > or does it magically install bioperl?

* Since bioperl is not mentioned is 'Build.PL', it is not automatically installed and the test suite skipped the tests. I believe putting that 'Bio::Root::Version => 1.5.2' in 'Build.PL' should prompt for automatic installation. * When i sent the message there were no cpan tester results, now i see them and they are all passed. Show quoted text

> > To your other questions: > > I am developing Bio::Grep with bioperl v1.5.2, but at least a few months > ago, everything worked fine with v1.4. > > We are using the vmatch parser now for about 2 years without having > found any serious bugs, so it *should* be quite stable. > >

Thanks for the info. However, for this module which significantly depends on bioperl to function, what are the reasons/motivations to create a separate namespace/api instead of submitting under bioperl umbrella (for example under Bio::Tools::Run namespace). -siddhartha

Mon Aug 20 12:25:27 2007 LIMAONE [...] cpan.org - Correspondence added

From:

LIMAONE [...] cpan.org

On Mon Aug 20 11:40:14 2007, basu@pharm.stonybrook.edu wrote: Show quoted text

> installed and the test suite skipped the tests. I believe putting that > 'Bio::Root::Version => 1.5.2' in 'Build.PL' should prompt for > automatic installation.

ok, I'll try that... Show quoted text

> Thanks for the info. However, for this module which significantly > depends on bioperl to function, what are the reasons/motivations to > create a separate namespace/api instead of submitting under bioperl > umbrella (for example under Bio::Tools::Run namespace).

The motivation was to have one simple API for several tools. If a feature is not available in one back-end, I'll try to add this feature in Bio::Grep. For example upstream and downstream in GUUGle. One could (should?) generalize the parsers and make them follow the Bio::Tools::Run guidelines. Bio::Grep could then function as a simple wrapper, for example: push @params, '-q ' . $self->settings->query; ... my $factory = Bio::Tools::Run::Vmatch->new(@params); Maybe I'll do this in the not so near future. Show quoted text

> > -siddhartha

Tue Aug 21 14:56:34 2007 basu [...] pharm.stonybrook.edu - Correspondence added

Subject:	Re: [rt.cpan.org #28881] missing dependencies
Date:	Tue, 21 Aug 2007 14:39:59 -0400
To:	bug-Bio-Grep [...] rt.cpan.org
From:	Siddhartha Basu <basu [...] pharm.stonybrook.edu>

via RT wrote: Show quoted text

> <URL: http://rt.cpan.org/Ticket/Display.html?id=28881 > > > On Mon Aug 20 11:40:14 2007, basu@pharm.stonybrook.edu wrote:

>> installed and the test suite skipped the tests. I believe putting that >> 'Bio::Root::Version => 1.5.2' in 'Build.PL' should prompt for >> automatic installation.

> ok, I'll try that... >

>> Thanks for the info. However, for this module which significantly >> depends on bioperl to function, what are the reasons/motivations to >> create a separate namespace/api instead of submitting under bioperl >> umbrella (for example under Bio::Tools::Run namespace).

> > The motivation was to have one simple API for several tools. If a > feature is not available in one back-end, I'll try to add this feature > in Bio::Grep. For example upstream and downstream in GUUGle. > > One could (should?) generalize the parsers and make them follow the > Bio::Tools::Run guidelines. Bio::Grep could then function as a simple > wrapper, for example: > > push @params, '-q ' . $self->settings->query; > ... > my $factory = Bio::Tools::Run::Vmatch->new(@params); > > Maybe I'll do this in the not so near future.

That should be great. I believe with the new release this ticket should be closed. -siddhartha Show quoted text

> >

>> -siddhartha

> > >

Wed Aug 22 09:48:15 2007 LIMAONE [...] cpan.org - Status changed from 'open' to 'resolved'