On Thu, 4 Oct 2007, Wolfgang Raffelsberger wrote:
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 ?
You mean the additional library what contains packages? It really does
help to get your terminology straight here.
What libraries are on .libPaths() is controlled by environment variables,
so debugging those will be the key. This is all explained on the help
page for .libPaths.
Could it be a problem with the attributes of : Rterm.exe --vanilla -q <
myRcode.r
Yes, it could. Look up what --vanilla does in ?Startup: it skips places
where the environment variables are usually set.
(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
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . .
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
[EMAIL PROTECTED]
______________________________________________
R-help@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.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
______________________________________________
R-help@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.
