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

[Yee Man Chan]

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
>