[R] Problem with .libPaths & Rterm.exe (under Vista)

[Wolfgang Raffelsberger]

Dear list,

I’m using R embedded in another program (coded in tcl/tk) under Windows 
Vista. In this context I don’t launch Rgui.exe but rather Rtem.exe.


Now I have a problem finding libraries not specifically installed as 
administrator (and which are not in the path ‘program files’ but in 
Contacts\Documents of the current user). To be precise, the user 
launching my tcl/tk program can’t find the libraries he previously 
installed locally (as Vista does by default when not launched 
specifically with administrator rights).

However, when (manually) launching Rterm.exe directly (or R.exe) the 
command .libPaths() returns correctly 2 locations (the personal local 
library and the ‘common’ one in ‘program files’) as it does with RGui.exe .

Does anyone have an idea how or why I can’t see the location of the 
additional libraries ?

Could it be a problem with the attributes of : Rterm.exe --vanilla -q < 
myRcode.r

(Note that I had no difficulties with these attributes calling R under 
Win XP or Linux, but never faced the problem of multiple locations for 
libraries.)


please find below the code form *(a)* launching : Rterm.exe –vanilla –q 
< myRcode.r (where ‘local’ libs are *NOT found*) :**

>  .libPaths()

"C://PROGRA~1/R/R-26~1.0/library"

>  require(affy)

Le chargement a nécessité le package : affy

Warning messages:

1: In library(package, lib.loc = lib.loc, character.only = TRUE, 
logical.return = TRUE, :

aucun package nommé 'affy' n'est trouvé

 > # this translates into "no package called "affy" was found"

>  sessionInfo()

R version 2.6.0 (2007-10-03)

i386-pc-mingw32

locale:

LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERattached 
base packages:

[1] stats graphics grDevices utils datasets methods base




and the code from (b) manually launching : Rterm.exe (where ‘local’ libs 
are found OK) :

>  .libPaths()

[1] "C:\\Users\\wr\\Contacts\\Documents/R/win-library/2.6"

[2] "C:/PROGRA~1/R/R-26~1.0/library"

>

>require(affy) # was NOT installed in : program files/...

Le chargement a nécessité le package : affy

Le chargement a nécessité le package : Biobase

Le chargement a nécessité le package : tools

Welcome to Bioconductor

Vignettes contain introductory material. To view, type

'openVignette()'. To cite Bioconductor, see

'citation("Biobase")' and for packages 'citation(pkgname)'.

Le chargement a nécessité le package : affyio

Le chargement a nécessité le package : preprocessCore

>

>  sessionInfo()

R version 2.6.0 (2007-10-03)

i386-pc-mingw32

locale:

LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252

attached base packages:

[1] stats graphics grDevices utils datasets methods base

As you can see only a single path is found, which is the default 
collection of libraries in the path of the R installation itself.

Does anyone have an idea how I could identify the libPath for a given 
user and by which argument added to R.exe I could allow accessing these 
libraries, too ?

Thanks’ in advance,
Wolfgang Raffelsberger


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. . .

Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
IGBMC
1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
Tel (+33) 388 65 3300 Fax (+33) 388 65 3276
wolfgang.raffelsberger at igbmc.u-strasbg.fr