[Bioperl-l] Immediate-effect deprecations

Alex Lancaster alexl at users.sourceforge.net
Wed Apr 18 21:17:34 EDT 2007

>>>>> "SB" == Sendu Bala  writes:


SB> I can remove the modules from cvs and create
SB> bioperl-run-1.5.2_101, resolving the packaging issue. I plan on
SB> doing precisely this within the next seven days unless someone
SB> puts a hand up to stop me.

In the meantime, until bioperl-run-1.5.2_101 is available, is it safe
just to remove these four .pm files during the packaging so they
don't get installed?  It looks like these four files are
self-contained and are only required/used by each other:

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

$ grep -r AbstractRunner *
Tools/Run/JavaRunner.pm:use Bio::Tools::Run::AbstractRunner;
Tools/Run/JavaRunner.pm:our @ISA=qw(Bio::Tools::Run::AbstractRunner);
Tools/Run/AbstractRunner.pm:package Bio::Tools::Run::AbstractRunner;

$ grep -r JavaRunner *
Tools/Run/Phylo/Forester/SDI.pm:use Bio::Tools::Run::JavaRunner;
Tools/Run/Phylo/Forester/SDI.pm:our @ISA=qw(Bio::Tools::Run::JavaRunner);
Tools/Run/JavaRunner.pm:package Bio::Tools::Run::JavaRunner;
Tools/Run/JavaRunner.pm: Usage   : $runner = Bio::Tools::Run::JavaRunner->new(-jar => $jar)
Tools/Run/JavaRunner.pm: Function: Builds a new Bio::Tools::Run::JavaRunner object
Tools/Run/JavaRunner.pm: Returns : Bio::Tools::Run::JavaRunner
Tools/Run/JavaRunner.pm:Bio::Tools::Run::JavaRunner - run java programs
Tools/Run/JavaRunner.pm:   my $runner = Bio::Tools::Run::JavaRunner->new(-jar => $jar);

$ grep -r Forester *
Tools/Run/Phylo/Forester/SDI.pm:package Bio::Tools::Run::Phylo::Forester::SDI;
Tools/Run/Phylo/Forester/SDI.pm:    my $runner = Bio::Tools::Run::Phylo::Forester::SDI->new();
Tools/Run/Phylo/Forester/SDI.pm:This wrapper is for SDI in Forester package. 
Tools/Run/Phylo/Forester/SDI.pm:For more details on Forester, please see 


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