[Bioperl-pipeline] Make test failures for local install

[Wiepert, Mathieu]

Hi,

When doing an install that is not for the system (i.e. using a perl Makefile.pl PREFIX=/my/local/dir), make test always gives me lots of errors.  Many of these errors have to do with modules not being found in include paths.  I didn't get why some modules work, and some don't.  I then noticed that all the modules that cause this have themselves in the use list.  I then noticed that they had the wrong directory.

Like 
Genscan.pm has:  use Bio::Tools::Genscan

I am guessing that there was some refactoring and the modules were moved from Bio::Tools to Bio::Tools::Run.  Also, I am not sure, why a module need to use itself?  This is unusual behavior, most modules don't do this, from what I can see.  Unless there is some funky functionality you get with this "recursive use?"

Anyway, I commented out all these "use" lines, and at least those problems went away.  Is this something that can be fixed?

I was also curious why this didn't fail on a machine I can install as root.  I found that I had all these old modules lying around.  I guess the build process doesn't clean them up, is there a clean way to do that, or is it a manual rm job.

I emailed here since it looked like most of the owners of the modules were pipeline folks?

The test that seem to have this problem are
t/Eponine...........Can't locate Bio/Tools/Eponine.pm in @INC (@INC contains ...
t/Genewise..........Can't locate Bio/Tools/Genewise.pm in @INC (@INC contain ...
t/Molphy............(Can't locate Bio/Tools/Phylo/Molphy.pm in @INC (@INC co ...
Can't locate Bio/Tools/Phylo/Molphy.pm in @INC (@INC contains: t blib/arch b ...
BEGIN failed--compilation aborted at t/Molphy.t line 53.                     ...
t/PAML..............Can't locate Bio/Tools/Phylo/PAML.pm in @INC (@INC conta ...
t/Pise..............Can't locate Bio/Factory/Pise.pm in @INC (@INC contains: ...
BEGIN failed--compilation aborted at t/Pise.t line 34.                       ...
t/Prints............Can't locate Bio/Tools/Prints.pm in @INC (@INC contains: ...
t/RepeatMasker......Can't locate Bio/Tools/RepeatMasker.pm in @INC (@INC con ...
t/Seg...............Can't locate Bio/Tools/Seg.pm in @INC (@INC contains: t  ...
t/Tmhmm.............Can't locate Bio/Tools/Tmhmm.pm in @INC (@INC contains:  ...

Thanks,

-Mat