[Bioperl-l] dependencies in Makefile.PL

Chris Fields cjfields at uiuc.edu
Mon Sep 25 18:28:07 UTC 2006

Sorry, stupid Outlook.  What I meant to say is, when I run the
BioDBSeqfeature.t tests, they all pass, but I get this at the end:

ok 1
ok 2
ok 3
ok 4
ok 41
ok 42
ok 43
Can't remove file C:\Temp\07KmXQ4Fv6/sequence.4076.fasta (Permission denied)
at C:/Perl/lib/File/Temp.pm line 898
Can't remove directory C:\Temp\07KmXQ4Fv6 (Directory not empty) at
C:/Perl/lib/File/Temp.pm line 898

Seems like something to do with permissions, yes?

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> Sent: Monday, September 25, 2006 1:08 PM
> To: n.haigh at sheffield.ac.uk; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] dependencies in Makefile.PL
> Nathan Haigh wrote:
> > File::Spec is mentioned in the PREREQ_PM section of Makefile.PL but is
> > not mentioned in %packages - which is correct? Is File::Spec no longer
> > needed?
> > IO::Scalar is now commented out of %packages, but is still included in
> > PREREQ_PM - again, which is correct?
> I'm not sure how Makefile.PL is supposed to work, but I can say that
> File::Spec and IO::Scaler are certainly required for Bioperl. Of course,
> they're in Bundle::BioPerl which presumably is (must be!) itself a
> requirement, so maybe that's why there's confusion in the Makefile.PL.
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