[Bioperl-l] dependencies in Makefile.PL

Chris Fields cjfields at uiuc.edu
Mon Sep 25 17:07:41 EDT 2006


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: Monday, September 25, 2006 3:34 PM
> To: Sendu Bala
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] dependencies in Makefile.PL
> 
> Everything that contains compiled code, or depends on stuff that
> contains compiled code.
> 
> E.g., GD and friends, all expat-depending XML readers/writers
> 
> 	-hilmar
> 

There are binary versions of libgd and expat available for ActivePerl and
Win32 (which tends to be the most troublesome platform).  If you install
GD.pm and XML::SAX::Expat using PPM, precompiled binary versions of both are
installed along with the perl modules.  It's not as easy to update to the
most current versions, but I have GD, expat, libxml2, and a few others, all
of which work wonderfully.

The really tough ones are the bioperl-ext XS modules.  I never managed to
get that working on Windows (and I don't plan on killing myself over trying
to get it running anytime soon).  It does work under Cygwin, though, or at
least the install docs indicate so.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign


> On Sep 25, 2006, at 2:17 PM, Sendu Bala wrote:
> 
> > Sendu Bala wrote:
> >> Nathan Haigh wrote:
> >>> File::Spec is mentioned in the PREREQ_PM section of Makefile.PL
> >>> but is
> >>> not mentioned in %packages - which is correct? Is File::Spec no
> >>> longer
> >>> needed?
> >>> IO::Scalar is now commented out of %packages, but is still
> >>> included in
> >>> PREREQ_PM - again, which is correct?
> >>
> >> I'm not sure how Makefile.PL is supposed to work, but I can say that
> >> File::Spec and IO::Scaler are certainly required for Bioperl. Of
> >> course,
> >> they're in Bundle::BioPerl which presumably is (must be!) itself a
> >> requirement, so maybe that's why there's confusion in the
> >> Makefile.PL.
> >
> > Oh, woops, Bundle::BioPerl is supposed to be optional. So its more
> > correct to say that certain things in Bioperl require Bundle::BioPerl
> > (because they require the modules it contains), but those certain
> > things
> > can themselves be considered optional.
> >
> > Even Bundle::BioPerl doesn't install some modules which it considers
> > even 'more' optional...
> >
> > Yes, it gets kind of muddy and needs to be fully clarified/
> > simplified I
> > think. Is there a real burden to installing a couple of extra modules?
> > If not, I'd say that we just stop considering things as optional.
> > If its
> > in Bioperl, it should work after you complete an installation process
> > (eg. make, make install for linux, whatever the equivalent is under
> > Windows). If there is something in Bioperl core that seems like a
> > burden
> > for most users to have to install, move it out to a different package.
> >
> > So what are the burdensome things that don't easily work out of the
> > box?
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 
> 
> 
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