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

[Yee Man Chan]

Ah.. I find that the typemap can become as simple as this
=====================
TYPEMAP
HMM *    T_PTROBJ
=====================

Then the generated HMM.c will have a function called INT2PTR to do the pointer conversion. I believe this should solve the warnings. 

Attached are the updated HMM.xs and typemap. Can someone with a 64-bit machine give it a try?

Thank you
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: "Yee Man Chan" <ymc at yahoo.com>
> Cc: "Robert Buels" <rmb32 at cornell.edu>, "Jonny Dalzell" <jdalzell03 at qub.ac.uk>, "BioPerl List" <Bioperl-l at lists.open-bio.org>
> Date: Thursday, August 13, 2009, 5:31 PM
> (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
> >> 
> > 
> > 
> > 
> 
>

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