[Bioperl-l] Problems with Bioperl-ext package on WinVista?

[Yee Man Chan]

I noticed that Bio/Tools/HMM.pm was removed from the trunk. So I added it back in. I think you shouldn't get the warnings with this version.

Yee Man

--- On Mon, 8/17/09, Chris Fields <cjfields at illinois.edu> wrote:

> From: Chris Fields <cjfields at illinois.edu>
> Subject: Re: [Bioperl-l] Problems with Bioperl-ext package on WinVista?
> To: "Chris Fields" <cjfields at illinois.edu>
> Cc: "Robert Buels" <rmb32 at cornell.edu>, "BioPerl List" <bioperl-l at lists.open-bio.org>, "Yee Man Chan" <ymc at yahoo.com>
> Date: Monday, August 17, 2009, 2:28 PM
> Take that back.  Yes the 'FL'
> warning is still there, but no tests are run b/c (simply
> put) there are no regression tests (no use of Test or
> Test::More).  If you run './Build test --verbose' you
> can see the run, but no test output.  That should be
> easy to fix, though.
> 
> chris
> 
> On Aug 17, 2009, at 4:22 PM, Chris Fields wrote:
> 
> > Still seeing that odd warning popping up:
> > 
> > cjfields4:Bio-Tools-HMM cjfields$ ./Build test
> --verbose
> > t/001_basics.t .. Argument "FL" isn't numeric in
> numeric lt (<) at
> /Users/cjfields/bioperl/Bio-Tools-HMM/blib/lib/Bio/Tools/HMM.pm
> line 185.
> > 
> > Have you tried using Yee Man's original Makefile.PL to
> see if it works better?  There appear to be some
> differences in the compilation, including a linking warning
> popping up.
> > 
> > chris
> > 
> > On Aug 17, 2009, at 3:32 PM, Robert Buels wrote:
> > 
> >> OK, I split Bio::Tools::HMM and Bio::Ext::HMM off
> into a new distro at Bio-Tools-HMM in the repo.  The
> tests are not passing, I think that some bugs need to be
> fixed in the logic of things.
> >> 
> >> Yee Man, could you have a look?  To download
> the newly repackaged code:
> >> 
> >> svn co svn+ssh://your_login@dev.open-bio.org/home/svn-repositories/bioperl/Bio-Tools-HMM/trunk
> Bio-Tools-HMM
> >> 
> >> perl Build.PL; ./Build test
> >> 
> >> Please check that things are compiling OK, check
> the test logic, upgrade the tests to use Test::More, and get
> the tests to the point where they are passing.
> >> 
> >> At that point, it should be ready for CPAN, but we
> need to decide how we want to coordinate that with releases
> of bioperl-live and bioperl-ext.
> >> 
> >> Rob
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
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