[Bioperl-pipeline] Make test failures for local install

[Wiepert, Mathieu]

Scratch that, I see that they are all in bioperl-live. Can I pass an include or prefix to make test to find these things?  They are all in my ./bioperl-live/blib/.

Oh well...

-Mat

> -----Original Message-----
> From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu]
> Sent: Wednesday, September 25, 2002 9:29 AM
> To: 'bioperl-pipeline@bioperl.org'
> Subject: [Bioperl-pipeline] Make test failures for local install
> 
> 
> 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
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