[Bioperl-l] Have problem to install bioperl, need help

[Fengkai Zhang (Tony)]

Thanks Jason.

I tried to force install by "force install Bundle::BioPerl".  After
installation, I tried to verify it and got errors:
*************************************************************
cpan> ! use IO::String
cpan> ! use Bio::Perl
Can't locate Bio/Perl.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3
/usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2
/usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0
/usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2
/usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0
/usr/lib/perl5/vendor_perl) at (eval 33) line 2.
BEGIN failed--compilation aborted at (eval 33) line 2.
*************************************************************

Any idea how to fix it?

-------------------
> Just force it.  The tests are more for the developers' benefit than
for
> those installing Bioperl.
> 
> I believe most of these failed tests are fixed in CVS.  The
Variation_IO
> has to do with how the older XML::Writer worked as compared to the
current
> version.  DB.t test was due to a bug in the released module.  Don't
> remember what the TreeIO problem was.
> 
> -jason
> On Fri, 11 Jun 2004, Fengkai Zhang (Tony) wrote:
> 
> > When I try to use "install Bundle::BioPerl", some tests are
failed.
> > Here is the summary:
> >
> > Failed Test      Stat Wstat Total Fail  Failed  List of Failed
> >
----------------------------------------------------------------------
> > ---------
> > t/DB.t                         78    9  11.54%  79-87
> > t/TreeIO.t                     41    1   2.44%  42
> > t/Variation_IO.t               25    3  12.00%  15 20 25
> > 121 subtests skipped.
> > Failed 3/179 test scripts, 98.32% okay. -7/8268 subtests failed,
> > 100.08% okay.
> > make: *** [test_dynamic] Error 255
> >   /usr/bin/make test -- NOT OK
> >
> > I am using Fedora Core 2 on Dell Optiplex GX270 and perl program
is
> > installed from FC2 CD with version 5.8.3. May I use force to
install
> > anyway? How should I fix the problem? Thanks ahead for your help.
> >
> > Tony
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
> 

------------------------------------------------------
Fengkai Zhang (Tony) MD, MMath(Bioinformatics), BS(CS)
Postdoc Research Associate
Virginia Institute for Psychiatric and 
Behavioral Genetics
Virginia Commonwealth University
800 E. Leigh St.
PO.Box 980126
Richmond, VA 23298-0126
Tel: 804-828-9710
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