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

Fri Aug 14 15:31:49 UTC 2009

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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