[Bioperl-l] BioPerl Bundle::BioPerl

[Allen Day]

Bio::SeqIO::interpro uses it too.

On Wed, 25 Aug 2004, Jason Stajich wrote:

> Well I would just force it through  - unless you are using
> Bio::SeqIO::bsml it really isn't that important of a dependancy.
> 
> cpan> force install XML::DOM
> 
> I use FC1 and RHL9 with no problem as well as OSX.
> 
> -jason
> On Wed, 25 Aug 2004, John Legato wrote:
> 
> >
> > I am having trouble installing Bundle::BioPerl on a Red Hat 9 machine,
> >
> > One of my problems seems to be related to XML::DOM, it fails make test:
> >
> > Failed Test       Stat Wstat Total Fail  Failed  List of Failed
> > -------------------------------------------------------------------------------
> > t/dom_jp_attr.t                 23    6  26.09%  3 9 12 14 19 22
> > t/dom_jp_cdata.t                 3    1  33.33%  3
> > t/dom_jp_minus.t                 2    1  50.00%  2
> > t/dom_jp_modify.t               16    1   6.25%  16
> > t/dom_jp_print.t                 3    2  66.67%  2-3
> >
> > I have built Perl 5.8.5 and  libxml2-2.6.12 from
> > source as well as expat 1.95.8. I've tried setting LANG to en_US as
> > suggested in some news group postings. Is Red Hat 9 a lost cause?
> > I am encountering one problem after another in my attempts to
> > install BioPerl via CPAN, I'd like to install the complete distribution.
> > Building Perl from source seemed to fix some of the issues but there seems
> > to be quite a few incompatibilities related to older library versions
> > in Red Hat 9 .
> > What distribution are most BioPerl developers/users using?
> > I am considering moving to Debian or Fedora but I've been sticking to
> > Red Hat 9 because of a need to run Oracle 10g.
> >
> > John
> >
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> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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