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

Sat Aug 15 19:11:48 UTC 2009

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
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>> __________________________________________________
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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