[Bioperl-l] Problems with Bioperl-ext package on WinVista?
Yee Man Chan
ymc at yahoo.com
Sat Aug 15 02:57:15 UTC 2009
Hi Chris
I find that there is a memory access bug in my code. Attached is the fixed HMM.xs. This file together with the simpler typemap should fix all problems. (I hope..)
Please let me know if it works for you.
Sorry for the bug...
Yee Man
--- On Fri, 8/14/09, 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: Friday, August 14, 2009, 8:31 AM
> Yee Man,
>
> I tested this out locally (perl 5.8.8 32-bit, perl 5.10.0
> 64-bit) and on dev.open-bio.org (which is perl 5.8.8,
> appears to be 32-bit). The patch results in cleaning
> up warnings for 5.10.0 but results in similar warnings for
> 5.8.8 (linux or OS X).
>
> On OS X perl 5.8.8, this sometimes passes (note the first
> attempt fails, the second succeeds), so it's not entirely a
> 32-bit issue:
>
> http://gist.github.com/167860
>
> OS X and perl 5.10.0, this always fails as the previous
> gist shows, but demonstrates similar behavior (multiple
> attempts to test get different responses):
>
> http://gist.github.com/167542
>
> On linux, everything passes with or w/o the patched files
> (patched files have warnings as indicated above):
>
> Specs for all three perl executables (they vary a bit):
>
> http://gist.github.com/167883
>
> chris
>
> On Aug 14, 2009, at 3:27 AM, Yee Man Chan wrote:
>
> > 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
> >>>>
> >>>
> >>>
> >>>
> >>
> >>
> >
> > __________________________________________________
> > Do You Yahoo!?
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> protection around
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> <HMM.xs><typemap>_______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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