[Bioperl-l] Bio::Pedigree modules

Jason Stajich jason at cgt.mc.duke.edu
Thu Feb 20 20:24:28 EST 2003

This modules are entirely a work in progress so I wouldn't expect them to
work for you - if you want to be part of the development process please
contact me.


On Thu, 20 Feb 2003, Man-Suen Chan wrote:

> Hi
> I am trying to use the bio-pedigree modules but am having problems getting  them to work. I tried to run a script provided with the module and got the following message:
>  /tmp/bioperl-pedigree/scripts/pedplot.pl -p example1.pped -d example1.pdat
> Bio/Pedigree/PedIO/linkage.pm: linkage cannot be found
> Exception Global symbol "$name" requires explicit package name at /usr/lib/perl5/site_perl/5.6.0/Bio/Pedigree/Pedigree.pm line 151.
> Global symbol "$name" requires explicit package name at /usr/lib/perl5/site_perl/5.6.0/Bio/Pedigree/Pedigree.pm line 151.
> Compilation failed in require at /usr/lib/perl5/site_perl/5.6.0/Bio/Pedigree/PedIO/linkage.pm line 65.
> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.6.0/Bio/Pedigree/PedIO/linkage.pm line 65.
> Compilation failed in require at /usr/lib/perl5/site_perl/5.6.0/Bio/Pedigree/PedIO.pm line 437.
> For more information about the PedIO system please see the PedIO docs.
> This includes ways of checking for formats at compile time, not run time
> Can't call method "read_pedigree" on an undefined value at /tmp/bioperl-pedigree/scripts/pedplot.pl line 35.
> When I did "make test" I had a lot of tests failed. I think the line that causes the problem is
> require Bio::Pedigree::Pedigree;
> I would also be interested in general on anyone's experience with these modules.
> Thanks
> Man-Suen Chan
> Dr Man-Suen Chan
> Bioinformatician
> Department of Paediatrics
> Institute of Molecular Medicine
> University of Oxford
> John Radcliffe Hospital
> Oxford OX3 9DS, UK
> tel 01865 222310
> tel 01865 287715 (Wellcome Trust Centre for Human Genetics)
> fax 01865 222626
> email: man-suen.chan at paediatrics.ox.ac.uk
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

More information about the Bioperl-l mailing list