[Bioperl-l] some tests fail on Mac OS X

[Jason Stajich]

On Sun, 14 Dec 2003, Koen van der Drift wrote:

>
> On Dec 13, 2003, at 5:04 PM, Jason Stajich wrote:
>
> >> Weird, I have it installed too, but these two tests still fail.
> >>
> >>
> > you sure it is the right version for your perl?  perldoc HTML::Entities
> > definitely works?
>
> Yes - it's version 3.27 on 10.3.1, also installed with fink.
>
>
> >> I'd like to help, but am not sure how. Is there a way to run an
> >> individual test without using 'make test' ?
> >>
> >
> > % make test_ESEfinder
> >
> > OR
> >
> > % perl -I. -w t/ESEfinder.t
>
> thanks, I'll try that.
>
>
> BTW, I am the maintainer of bioperl for fink. I am using the 1.303
> release to test for the next package version.
>
> One thing that I noticed is that the scripts are directly installed
> into /sw/bin instead of in the directory that is actually used to build
> the package (/sw/src/root-bioperl-pm/sw/bin/). I have looked at
> Makefile.PL, but my knowledge of perl is not that good that I could
> figure out why this happens. Is there a way that I can patch
> Makefile.PL so that the scripts get installed in the place required for
> fink?

I think when you run perl Makefile.PL you want to give it
perl Makefile.PL PREFIX=/sw/src/root-bioperl-pm/sw

See how LWP or other pkgs which have associated scripts in them install I
guess.



> thanks,
>
>
> - Koen.
>

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