[Bioperl-l] dependencies in Makefile.PL

Hilmar Lapp hlapp at gmx.net
Mon Sep 25 17:29:48 EDT 2006


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 :
>> ===========================================================
>>
>>
>>
>>
>>
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>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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