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

[Yee Man Chan]

Hi all

Based on my understanding of the warning messages, the problem seems to come from the "typemap" file when I cast the return from SvIV from an integer to a pointer. I suppose this might cause problems in 64-bit machines.

But when I look at perlguts and perlxs, it does seem to me that the way I did in typemap is the suggested way to do it because the IV type is "guaranteed to be big enough to hold a pointer". Nevertheless, I modified my typemap file to look exactly like what's in perlxs. (See PS)

Does anyone know how to deal with this problem? Or can anyone of you give me access to a 64-bit machine to sort this out?

Thank you!
Yee Man

PS This is a typemap file using exactly the same lines suggested by perlxs. It works in my 32-bit machine. Can someone try it on a 64-bit machine? Thanks 
================================================
TYPEMAP
HMM *    T_HMM

INPUT
T_HMM
        if (sv_isobject($arg) && (SvTYPE(SvRV($arg)) == SVt_PVMG))
           $var = ($type)SvIV((SV*)SvRV( $arg ));
        else{
           warn( \"${Package}::$func_name() -- $var is not a blessed SV referenc
e\" );
           XSRETURN_UNDEF;
        }

OUTPUT
T_HMM
        sv_setref_pv($arg, "Bio::Ext::HMM::HMM", (void*) $var);
========================================================

--- 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
> >> 
> > 
> > 
> > 
> 
>