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

Sun Aug 16 02:05:41 UTC 2009

I'm still seeing the same errors on Mac OS X for 64-bit perl 5.10.0.   
Mac OS X, native perl (v5.8.8) passes fine now (as well as perl 5.8.8  
on dev.open-bio.org).

I'm wondering if this is a problem with my local perl build.  I'm very  
tempted to push the HMM-related code into a separate distribution  
(bioperl-hmm) and make a CPAN release out of it so it gets wider  
testing via CPAN testers; it would just require a minimum bioperl 1.6  
installation for Bio::Tools::HMM and any related modules.  Yee, would  
that be okay with you?

chris

On Aug 15, 2009, at 8:23 PM, Yee Man Chan wrote:

>
> 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
>>
>>
>
>
>