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

[Chris Dagdigian]

Bundle::BioPerl does not install bioperl, it only installs the various 
modules that bioperl depends on. This is quite clear I think in the 
documentation :)


-Chris



On Fri, 11 Jun 2004, Fengkai Zhang (Tony) wrote:

> 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
> ------------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 
Chris Dagdigian, <dag at sonsorol.org>
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