[Bioperl-l] bp 1.2.3 ppm install fails

[Lincoln Stein]

More fundamentally, however, the BioPerl PPM should have no more and no less 
dependencies than the BioPerl CPAN.  We need to do it this way so that we 
have a common platform on which to evaluate bug reports, &c.

Lincoln

On Tuesday 07 October 2003 10:49 am, Chris Fields wrote:
> Scott,
>
> Randy Kobes has a number of PPM's for Windows that ActiveState doesn't
> provide, for both Perl 5.6 and 5.8.  I believe ActiveState has an automated
> build engine that will not post PPM's to the PPM depositories unless they
> successfully build (no failed tests).  The only other way to get them to
> post is to specifically ask for it on ASPN, and that may take them a
> while.  I think I picked up most of the required external modules from
> there, including GD (v 2.07).
>
> If using ppm3:
>
> rep add Kobes http://theoryx5.uwinnipeg.ca/cgi-bin/ppmserver?urn:/PPMServer
>
> I think ppm2 is similar, but I haven't used it in a while.
>
> Chris Fields
>
> At 08:32 AM 10/7/2003, you wrote:
> >Brian,
> >
> >As far as I can tell, the '-force' option in ppm (for perl 5.8) is only
> >useful for reinstalling modules that it thinks are already installed
> >(and even then, it doesn't always do that).  I'm not sure what a good
> >solution is, since I don't think the ActiveState framework allows
> >"optional" modules.   :-/
> >
> >As a side note, I did find a libxml that I could install via ppm
> >elsewhere with google, but this mess means that I have to give
> >directions to users who want to install GBrowse via ppm how to get
> >libxml even though they don't need it for GBrowse.
> >
> >Thanks,
> >Scott
> >
> >On Tue, 2003-10-07 at 07:57, Brian Osborne wrote:
> > > Scott,
> > >
> > > > As a side note, it seems like a bad idea to force the installation of
> > >
> > > every prereq module for bioperl
> > >
> > > Definitely a bad idea, that's why Bioperl doesn't do this. In the CPAN
> > > shell, for example, you can do "force install". There is also a "force
> > > install" option in ActiveState, something like setting force-install to
> > > 1? Please check the ActiveState documentation and tell me if I'm wrong.
> > >
> > > A few months ago I took a look at the "required modules" list in
> >
> > Bioperl and
> >
> > > found that many of them were not supplied by ActiveState, just as
> > > you're finding.
> > >
> > > Brian O.
> > >
> > > -----Original Message-----
> > > From: bioperl-l-bounces at portal.open-bio.org
> > > [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Scott Cain
> > > Sent: Monday, October 06, 2003 4:07 PM
> > > To: bioperl-l at bioperl.org
> > > Cc: cain at cshl.org
> > > Subject: [Bioperl-l] bp 1.2.3 ppm install fails
> > >
> > > Hello all,
> > >
> > > First, thanks to the kind soul who provided the 1.2.3 version of
> > > bioperl as a ppm.  Unfortunately, I can't seem to get it installed due
> > > to a failed dependency.  While using AS Perl 5.8, it seems that none of
> > > the repositories know what 'libxml-perl' is, and since it is listed as
> > > a prerequisite in the ppd file, installation cannot continue.  Is there
> > > somewhere special to get that from?  At the moment, I am only searching
> > > the ActiveState and bioperl repositories.
> > >
> > > As a side note, it seems like a bad idea to force the installation of
> > > every prereq module for bioperl.  In my case, I have no need of
> > > libxml-perl, but can't install bioperl for a lack of it.
> > >
> > > Thanks,
> > > Scott
> > >
> > > ----------------------------------------------------------------------
> > > Scott Cain, Ph. D.                                       cain at cshl.org
> > > GMOD Coordinator, http://www.gmod.org/                   (216)392-3087
> > > ----------------------------------------------------------------------
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >--
> >------------------------------------------------------------------------
> >Scott Cain, Ph. D.                                         cain at cshl.org
> >GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> >Cold Spring Harbor Laboratory
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at portal.open-bio.org
> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> __________________________________
>
> Chris Fields - Postdoctoral Researcher
> Lab of Dr. Robert Switzer
>
> Address:
>
> University of Illinois at Urbana-Champaign
> Dept. of Biochemistry - 323 RAL
> 600 S. Mathews Ave.
> Urbana, IL 61801
>
> Phone : (217) 333-7098
> Fax : (217) 244-5858
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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