[Bioperl-l] Problems with Bioperl-ext package on WinVista?
Yee Man Chan
ymc at yahoo.com
Sun Aug 16 01:23:28 UTC 2009
I just committed HMM.xs and typemap to SVN. Can you test it to confirm it works in 64-bit machines?
Thanks
Yee Man
--- On Sat, 8/15/09, 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: "Yee Man Chan" <ymc at yahoo.com>, "BioPerl List" <bioperl-l at lists.open-bio.org>
> Date: Saturday, August 15, 2009, 12:11 PM
> I'm not sure, but it makes more sense
> to commit these changes directly. Yee, need us to set
> you up with a commit bit? If so, fill out the
> information on this page:
>
> http://www.bioperl.org/wiki/SVN_Account_Request
>
> and forward it to support at open-bio.org.
> I'll sponsor you.
>
> chris
>
> On Aug 15, 2009, at 11:44 AM, Robert Buels wrote:
>
> > The usual procedure for developing code is to exchange
> code via commits to a version control system. Yee, do
> you know how to use Subversion? Does Yee need a commit bit?
> >
> > Rob
> >
> > Yee Man Chan wrote:
> >> 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!?
> >>>> Tired of spam? Yahoo! Mail has the
> best spam
> >>> protection around
> >>>> http://mail.yahoo.com
> >>>
> <HMM.xs><typemap>_______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>
> >
> >
> > --Robert Buels
> > Bioinformatics Analyst, Sol Genomics Network
> > Boyce Thompson Institute for Plant Research
> > Tower Rd
> > Ithaca, NY 14853
> > Tel: 503-889-8539
> > rmb32 at cornell.edu
> > http://www.sgn.cornell.edu
>
>
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