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

[Chris Fields]

Yee Man,

Will look into that.  I do recall that disappearing last night, so  
I'll go look at the commit log.

I have committed some regression tests using Bio::Root::Test.  This'll  
need to be extensively tested b/c we're comparing floating point  
numbers, though I do use our custom float_is() test to run these (so  
we only compare first six signif).  These are passing for me on 64bit  
perl 5.10.0; I may try these on a local 64bit linux (I need to set up  
bioperl on it first).

chris

On Aug 17, 2009, at 5:19 PM, Yee Man Chan wrote:

> I believe this warnings should have been fixed with the latest Bio/ 
> Tools/HMM.pm. Are you sure you are using the lastest Bio/Tools/ 
> HMM.pm? I noticed that there are two pairs of "use strict" and "use  
> warnings" in this version. :P
>
> 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: "Robert Buels" <rmb32 at cornell.edu>
>> Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>, "Yee Man Chan" <ymc at yahoo.com 
>> >
>> Date: Monday, August 17, 2009, 2:22 PM
>> 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
>>
>>
>
>
>