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

[Chris Fields]

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