[R] R and samr under Linux

[James W. MacDonald]

Hi Mark,

markaoki wrote:
> 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 : )!

I think your intentions are good, but your advice is actually horrible!

All you needed was (from within R):

install.packages("samr", dependencies=TRUE)

which will install the package correctly, along with any required 
dependencies.

Best,

Jim


> 
> -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
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623