See ?.libPaths : as so often, all that is needed is attentive reading
of the documentation:
The library search path is initialized at startup from the
environment variable ‘R_LIBS’ (which should be a colon-separated
list of directories at which R library trees are rooted) followed
by those in environment variable ‘R_LIBS_USER’. Only directories
which exist at the time will be included.
By default ‘R_LIBS’ is unset, and ‘R_LIBS_USER’ is set to
directory ‘R/R.version$platform-library/x.y’ of the home directory
(or ‘Library/R/x.y/library’ for Mac OS X AQUA builds), for R
x.y.z.
Answer: set R_LIBS_USER or delete
/root/R/x86_64-pc-linux-gnu-library/2.12
On Thu, 10 Feb 2011, Juergen Rose wrote:
High,
on all of my computers the first entry in libPaths for root
was /usr/lib64/R/library or /usr/lib/R/library. Now it change at one
(lynx) anyway to
root@lynx:/root(2)# R
R version 2.12.1 (2010-12-16)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
.libPaths()
[1] /root/R/x86_64-pc-linux-gnu-library/2.12
[2] /usr/lib64/R/library
If I try to install packages with:
install.packages(something)
it goes to /root/R/x86_64-pc-linux-gnu-library/2.12/ and not as
expected to /usr/lib64/R/library.
If I do .libPaths(/usr/lib64/R/library) I can temporarily reset
libPaths to expected value, but after the next start of R I have
again /root/R/x86_64-pc-linux-gnu-library/2.12 as first entry in
libPaths:
.libPaths(/usr/lib64/R/library)
.libPaths()
[1] /usr/lib64/R/library
Save workspace image? [y/n/c]: y
[1]+ Donecompare_conf_files 2 /dev/null
root@lynx:/root(3)# R
R version 2.12.1 (2010-12-16)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
.libPaths()
[1] /root/R/x86_64-pc-linux-gnu-library/2.12
[2] /usr/lib64/R/library
How can I reset libPaths permanently for root to /usr/lib64/R/library?
I have:
root@lynx:/root(4)# R --version
R version 2.12.1 (2010-12-16)
..
Regards.
--
Juergen Rose r...@rz.uni-potsdam.de
Uni-Potsdam
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
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