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

[Chris Fields]

(just to point out to everyone, Yee Man's contact information was in  
the POD)

Yee Man,

I have the output in the below link:

http://gist.github.com/167542

There are similar problems popping up on 32- and 64-bit perl 5.10.0,  
Mac OS X 10.5.  Haven't had time to debug it unfortunately.

I think we should seriously consider spinning this code off into it's  
own distribution for CPAN.  It's unfortunately bit-rotting away in  
bioperl-ext.  If you want to continue supporting it I can help set  
that up.

chris

On Aug 13, 2009, at 6:58 PM, Yee Man Chan wrote:

> Hi
>
>    So is this an HMM only problem? Or does it apply to other bioperl- 
> ext modules?
>
>    What exactly are the compilation errors for HMM? I believe my  
> implementation is just a simple one based on Rabiner's paper.
>
> http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.ubc.ca%2F 
> ~murphyk%2FBayes 
> %2Frabiner.pdf&ei=QqiESvClHNCfkQXbh8mWBw&rct=j&q=rabiner 
> +hmm&usg=AFQjCNHeXLhTHmuKUXKKCHYSs58TxVGfZg
>
>    I don't think I did anything fancy that makes it machine  
> dependent or non-ANSI C.
>
> Yee Man
>
> --- On Thu, 8/13/09, 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: "Jonny Dalzell" <jdalzell03 at qub.ac.uk>, "BioPerl List" <Bioperl-l at lists.open-bio.org 
>> >, "Yee Man Chan" <ymc at yahoo.com>
>> Date: Thursday, August 13, 2009, 3:18 PM
>>
>> On Aug 13, 2009, at 4:37 PM, Robert Buels wrote:
>>
>>> Jonny Dalzell wrote:
>>>> Is it ridiculous of me to expect ubuntu to take
>> care of this for me?  How do
>>>> I go about compiling the HMM?
>>> Yes.  This is a very specialized thing that
>> you're doing, and Ubuntu does not have the resources to
>> package every single thing.
>>>
>>> Unfortunately, it looks like bioperl-ext package is
>> not installable under Ubuntu 9.04 anyway, which is what I'm
>> running.  For others on this list, if somebody is
>> interested in doing maintaining it, I'd be happy to help out
>> by testing on Debian-based Linux platforms.  We need to
>> clarify this package's maintenance status: if there is
>> nobody interested in maintaining it, I would recommend that
>> bioperl-ext be removed from distribution.  It's not in
>> anybody's interest to have unmaintained software out there
>> causing confusion.
>>
>> I have cc'd Yee Man Chan for this.  If there isn't a
>> response or the message bounces, we do one of two things:
>>
>> 1) consider it deprecated (probably safest).
>> 2) spin it out into a separate module.
>>
>> Just tried to comile it myself and am getting errors (using
>> 64bit perl 5.10), so I think, unless someone wants to take
>> this on, option #1 is best.
>>
>>> So Jonny, in short, I would say "do not use
>> bioperl-ext".
>>
>> In general, that's a safe bet.  We're moving most of
>> our C/C++ bindings to BioLib.
>>
>>> Step back.  What are you trying to
>> accomplish?  Chris already recommended some alternative
>> methods in his email of 8/11 on this subject.  Perhaps
>> we can guide you to some software that is actively
>> maintained and will meet your needs.
>>>
>>> Rob
>>
>> Exactly.  Lots of other (better supported!) options
>> out there.  HMMER, SeqAn, and others.
>>
>> chris
>>
>
>
>