[Bioperl-l] BioPerl Bundle::BioPerl

John Legato jlegato at helix.nih.gov
Wed Aug 25 07:43:29 EDT 2004

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.


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