[Bioperl-l] dependencies in Makefile.PL

Chris Fields cjfields at uiuc.edu
Mon Sep 25 17:44:02 EDT 2006


I have run into the same issues on Mac OS X.  This especially involved
anything that used expat or DBD::mysql.  Reinstalling the binaries always
seemed to fix the problem (well, at least it passed tests).

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

> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: Monday, September 25, 2006 4:30 PM
> To: Chris Fields
> Cc: 'Sendu Bala'; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] dependencies in Makefile.PL
> 
> I didn't say that there are no binary versions available. My
> experience (on Linux and Mac OSX) is only that oftentimes these will
> clash with something pre-installed (but not having the right version).
> 
> I believe though that these version troubles have gotten better.
> 
> 	-hilmar
> 
> On Sep 25, 2006, at 5:07 PM, Chris Fields wrote:
> 
> >
> >> -----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?
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> 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 :
> >> ===========================================================
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> 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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