[Bioperl-l] bioperl-run and Bio::Root::AccessorMaker

Alex Lancaster alexl at users.sourceforge.net
Wed Apr 18 04:50:51 EDT 2007


In packaging bioperl-run for Fedora, I think I stumbled across a bug
in the bioperl-run package.  It appears from this edit:

http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/Bio/Root/Attic/AccessorMaker.pm?hideattic=0&cvsroot=bioperl

that Bio::Root::AccessorMaker was removed in bioperl 1.5.x, but
bioperl-run 1.5.2_100 still contains modules that use this module:

$ cd bioperl-run-1.5.2_100
$ grep -r AccessorMaker  *
Bio/Tools/Run/Phylo/Forester/SDI.pm:use Bio::Root::AccessorMaker (
Bio/Tools/Run/JavaRunner.pm:use Bio::Root::AccessorMaker ('$'=>[qw(jar
class min_version)]);
Bio/Tools/Run/AbstractRunner.pm:use Bio::Root::AccessorMaker
('$'=>[qw(input_file output_file)]);

This causes the automatic Perl dependency generator for RPM to add
Bio::Root::AccessorMake as a requires which means RPM will refuse to
install perl-bioperl-run because it's looking for the now-removed-
from-Core-bioperl module

$ sudo rpm -Uvh --test
/home/alex/rpmbuild/RPMS/noarch/perl-bioperl-run-1.5.2_100-1.noarch.rpm 
error: Failed dependencies:
        perl(Bio::Root::AccessorMaker) is needed by
        perl-bioperl-run-1.5.2_100-1.noarch

Are the SDI and JavaRunner modules being actively developed?  What's
the best course of action for these modules, should I just exclude
them from the package for now? since they won't work, even if if you
tell RPM to ignore the dependency warning.

Alex


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