[Bioperl-l] The Power of R

[Mark A. Jensen]

What solution did you responders wind up using? Do people generally get RSPerl 
to work and wash their hands of it afterwards? Or do you finally hand-code a 
good deal? thx
----- Original Message ----- 
From: "Dr. T. I. Simpson" <ian.simpson at ed.ac.uk>
To: "Chris Fields" <cjfields at illinois.edu>; "Boris Umylny" <umylny at apbri.org>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, January 07, 2009 9:55 AM
Subject: Re: [Bioperl-l] The Power of R


>I agree with Chris on this.
>
> Used RSPerl about a year ago to integrate some clustering experiments in R 
> with a Perl script that fed data to R and picked up output, but it was  mighty 
> painful and accessing R objects through RSPerl was indeed a PITA.
>
> Ian.
>
>
> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields <cjfields at illinois.edu> 
> wrote:
>
>> Not to bash this, as it is a decent piece of software, but...  : >
>>
>> 1) Painful to install, and doesn't support a local perl installation  (keeps 
>> attempting to go back and use my 5.8.8 instead of my local 5.10).
>> 2) Not on CPAN.
>> 3) Though this is supposed to be bidirectional, R from Perl is not well 
>> supported and apparently does not work for Windows.
>> 4) Doesn't appear to be well-supported in general.
>>
>> I do not intend on writing a full perl suite for R/BioC analyses if I  end up 
>> having to work around problems with the critical module.
>>
>> -c
>>
>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote:
>>
>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)?
>>>
>>>
>>> Boris
>>>
>>>
>>> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu
>>> >
>>> To: "Mark A. Jensen" <maj at fortinbras.us>
>>> Cc: <bioperl-l at lists.open-bio.org>
>>> Sent: Wednesday, January 07, 2009 2:04 PM
>>> Subject: Re: [Bioperl-l] The Power of R
>>>
>>>
>>>> Now if we can only get a decent Perl-R interface which isn't a PITA to 
>>>> install...
>>>>
>>>> chris
>>>>
>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote:
>>>>
>>>>> So says the New York Times:
>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html
>>>>>
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>
>
>
> -- 
> Dr T. I. Simpson
> School of Biomedical Sciences
> University of Edinburgh
> Hugh Robson Building
> George Square
> Edinburgh
> EH8 9XD
>
> ian.simpson at ed.ac.uk
>
>
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