[R] R and samr under Linux

[markaoki]

hi,
I have determined some of my own answers, so will share here.

There are binary associations within the R libraries specific to the 
environment
that created them, be it Windows or Linux, 32 or 64 bit. I found these 
associations in the
Meta directory of the libraries. So, R libraries cannot be shared across 
different
platforms as I had hoped as R libraries have a binary component.

As for samr, and some of the other Linux packages available, these packages 
must first be
compiled by R, which in so doing produces the 'missing' Meta directory, 
among other
critical output.

The procedure I used for Linux was to download a package, for example samr.
I then extracted its contents, which produced a 'samr' directory.

I changed to that directory and, from a command line, issued the following:

#R CMD INSTALL -l samr samr

This compiles the directory (last argument) into the library samr (first 
argument),
the best that I can determine anyway.

The result was yet another samr directory containing all of the expected 
contents, including the
Meta directory, under this one.

I copied this samr directory to:
/usr/lib64/R/library

...and repeated these steps for the 'impute' library, apparently needed by 
samr, and
then tried again to run the developer's software (I didn't write it) and it 
worked.

So, Im up and running on 64-bit Linux and R / samr.
Maybe these steps are not the best, but they worked for me.

Hope this helps any other newbies out there : )!

-mark aoki


----- Original Message ----- 
From: "markaoki" <markaoki at navisan.com>
To: <r-help at r-project.org>
Sent: Sunday, January 20, 2008 2:39 PM
Subject: [R] R and samr under Linux


> hi,
>
> This is my first day with R, pls pardon my newbie gaffs.
>
>
>
> Im running under Linux, samr V1.25 and R (V2.4.1 and 2.6.1), 32 and 64 
> bit.
>
>
>
> Either way, when I run using samr library I get the error:
>
> "samr is not a valid package - installed < 2.0.0?"
>
>
>
> I see in R source code a conditional leading to this message:
>
> pfile <-system.file ("Meta", "package.rds", package=package, libloc =
> which.lib.loc);
>
>
>
> The samr does not have a "Meta" directory, or underlying package.rds, as 
> the
> other
>
> packages have. So, it seems to fail this check.
>
>
>
> 1. It seems to me that the offered Linux samr package V1.25 is not
> compatible with
>
> these versions (2.4 / 2.6) of R. Is this a correct conclusion?
>
>
>
> 2. R seems to be an interpreted language, and its 'libraries' seem to be
> just text files. Thus, it seems I could find a Windows implementation of
> samr and copy it to my Linux. Any ideas about this theory?
>
>
>
> 3. Does R language have a way for me to define which processor in a 
> cluster
> I would
>
> like to execute a section of code upon, like in MPI?
>
>
>
> Please let me know some of these things, if you can help.
>
> Thanks for helping me,
>
> -m.aoki
>
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