[Bioperl-l] Packaging Bio::Ext::HMM for CPAN, was Re: Problems with Bioperl-ext package on WinVista?

[Chris Fields]

Yee Man, Robert,

All tests are passing; there was a small change in the expected  
floating point, but no warning now.

Re: passing this on to CPAN, I think it needs a distinct version from  
BioPerl (something that should probably happen with any spinoffs).  I  
foresee two options (and a possible conflict):

1) Use the same versioning scheme, starting with 1.6.1.
2) Use a simpler scheme a'la Bio::Graphics, which I suggest.   
Tripartite versions are a PITA, we'll only need to keep that in core.

Conflict: Bio::Tools::HMM is currently part of the 1.6 branch (in  
1.6.0).  If this stays in 1.6.1 then we have two versions of the  
module floating out there.

I think we should go ahead and remove Bio::Tools::HMM from 1.6.1, and  
I could attempt to push the initial Bio-Ext-HMM release after core  
1.6.1 is out.  After that, I could then add Yee Man as PAUSE co- 
maintainer for those modules (which means Yee Man needs to sign up for  
a PAUSE account).  Any objections to that?

chris

On Aug 17, 2009, at 7:24 PM, Yee Man Chan wrote:

> I get it now. So it is now spinned off. Anyway, I updated the HMM.pm  
> in Bio-Tools-HMM with the latest version. I think it should work.
>
> Yee Man
>
> --- On Mon, 8/17/09, Robert Buels <rmb32 at cornell.edu> wrote:
>
>> From: Robert Buels <rmb32 at cornell.edu>
>> Subject: Re: [Bioperl-l] Problems with Bioperl-ext package on  
>> WinVista?
>> To: "Yee Man Chan" <ymc at yahoo.com>
>> Cc: "Chris Fields" <cjfields at illinois.edu>, "BioPerl List" <bioperl-l at lists.open-bio.org 
>> >
>> Date: Monday, August 17, 2009, 4:00 PM
>> Yee Man Chan wrote:
>>> 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.
>>
>> Please read my email above with instructions for checkout
>> out the new Bio-Tools-HMM component, where Bio::Tools::HMM
>> has been moved.  Please do not add the Bio::Tools::HMM
>> module back into bioperl-live.
>>
>> I think you might be confused about the functions of 'svn
>> add', 'svn commit', etc, because I don't see any actual
>> addition of the module in the commit logs.  Please read
>> through the SVN manual at http://svnbook.red-bean.com/ if you need
>> clarification.
>>
>> Rob
>>
>>
>
>
>