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

Sat Aug 15 16:44:03 UTC 2009

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
>>>>>>
>>>>>
>>>>>
>>>>
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>> <HMM.xs><typemap>_______________________________________________
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>>
> 
> 
>       

-- 
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