R help - May 2009 - RSPerl and Statistics::R

Greetings!
 
Being a Perl hacker for some time, and wanting to leverage what R provides,
I've been trying to work with Statistics::R and RSPerl.
 
The former has a race condition that breeds some unreliability and the latter
seems to have issues all around, and neither has been updated in some time.
 
Are these projects are abandoned, or is there some effort currently being
undertaken to either refresh or reinvent the glue binding Perl and R together?
 
If not, then I'm probably going to give it a go myself, but I'm sort of
hoping that there's a jewel of a library out there that doesn't come up
as quickly in Google as the aforementioned libraries.
 
 
Thanks,
 
Daniel M. Klein
 


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RSPerl is not abandonded, but I haven't had much time to work on it.

If you can send me an example to reproduce the race condition, we can 
probably think about a solution.

  D.

Daniel Klein wrote:
> Greetings!
>  
> Being a Perl hacker for some time, and wanting to leverage what R provides,
I've been trying to work with Statistics::R and RSPerl.
>  
> The former has a race condition that breeds some unreliability and the
latter seems to have issues all around, and neither has been updated in some
time.
>  
> Are these projects are abandoned, or is there some effort currently being
undertaken to either refresh or reinvent the glue binding Perl and R together?
>  
> If not, then I'm probably going to give it a go myself, but I'm
sort of hoping that there's a jewel of a library out there that doesn't
come up as quickly in Google as the aforementioned libraries.
>  
>  
> Thanks,
>  
> Daniel M. Klein
>  
> 
> 
> This email (including attachments and files, if any) is confidential, may
be privileged and is intended for the above-named recipient(s) only. If you have
received this message in error, please notify me by return email and delete this
message from your system. Any unauthorized use or disclosure of this message is
strictly prohibited. Copyright in this email and any document created by Genesis
Genomics will be and remain vested in us and will not be transferred to you.
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

> Being a Perl hacker for some time, and wanting to leverage what R  
> provides, I've been trying to work with Statistics::R and RSPerl.
>
> The former has a race condition that breeds some unreliability and  
> the latter seems to have issues all around, and neither has been  
> updated in some time.
I have been using RSPerl for quite a long time, and for the same  
purpose as you (i.e. I'm only interested in running R from Perl, not  
vice versa).  I've had to hack practically every release of RSPerl to  
get it to build and install on my computers, especially on Mac OS X  
(where the R build process is completely at odds with universal  
binaries and the default Perl configuration).  Once installed, it's  
been very fast and reliable, though, at least for simple operations  
(basically, I want to pass numeric vectors between R and Perl and  
apply R functions to them).

When I became aware of Statistics::R, I was surprised about its  
extremely simple approach, because I expected this design to run afoul  
of all sorts of race conditions, buffers not being flushed, etc.;  
which your posting appears to confirm.  In my own software, I use  
Perl's Expect module as a fallback, but this is _extremely_ inefficient.
> Are these projects are abandoned, or is there some effort currently  
> being undertaken to either refresh or reinvent the glue binding Perl  
> and R together?
>
> If not, then I'm probably going to give it a go myself, but I'm
sort
> of hoping that there's a jewel of a library out there that doesn't
> come up as quickly in Google as the aforementioned libraries.
With all the problems that RSPerl has -- and they're mostly related to  
using R from Perl AFAIK -- I'm wondering if it wouldn't make for  
people like us to develop a Perl client for the Rserve protocol (see
http://www.rforge.net/Rserve/)
.


Best,
Stefan Evert

[ stefan.evert at uos.de | http://purl.org/stefan.evert ]

Taking a quick gander at RServe ? interesting. 

I think that some of the magic RSPerl is doing in munging R data types
into Perl constructs is the tricky part of the exercise. While I like
the close binding to R itself that RSPerl uses, going through an
intermediary like RServe might prove easier in that regard. At least,
given the java examples, the casts of the data values are more
explicit.

It's worth considering; the protocol doesn't look terribly onerous.

Thinking about it... just for giggles... RServe could probably
facilitate a user-space filesystem representation of an R environment
via the FUSE (or MacFUSE) projects. Not that it would useful, but I'm
sure there's a student project in it somewhere :)


Cheers,

DMK 


>>> Stefan Evert <stefan.evert at uos.de> 07/05/2009 7:27 pm
>>>
With all the problems that RSPerl has -- and they're mostly related to 

using R from Perl AFAIK -- I'm wondering if it wouldn't make for  
people like us to develop a Perl client for the Rserve protocol (see
http://www.rforge.net/Rserve/) 
.


Best,
Stefan Evert

[ stefan.evert at uos.de | http://purl.org/stefan.evert ]





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may be privileged and is intended for the above-named recipient(s) only.
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email and any document created by Genesis Genomics will be and remain
vested in us and will not be transferred to you.