R help - Oct 2003 - /usr/lib/R/library vs /usr/local/lib/R/site-library

I would appreciate getting a clarification of /usr/lib/R/library vs
/usr/local/lib/R/site-library.  I am running R 1.8 on Debian Linux.  On one
occasion doing update.packages() resulted in versions of one or more libraries
being placed in one of these directories without removing the old version, and
the old version took precedence over the new.  I'm sorry I did not save the
steps I used.  I would appreciate reading how best to manage libraries. 
Currently I have the following in /usr/local/lib/R/site-library: Design, Hmisc,
Rcmdr, acepack, car.  /usr/lib/R/library contains the following:

KernSmooth  boot     eda      lqs      modreg  nnet     stepfun   ts
MASS        class    foreign  methods  mva     rpart    survival
R.css       cluster  grid     mgcv     nlme    spatial  tcltk
base        ctest    lattice  mle      nls     splines  tools

Thanks -Frank
---
Frank E Harrell Jr    Professor and Chair            School of Medicine
                      Department of Biostatistics    Vanderbilt University
---
Frank E Harrell Jr    Professor and Chair            School of Medicine
                      Department of Biostatistics    Vanderbilt University

Frank E Harrell Jr wrote:
>I would appreciate getting a clarification of /usr/lib/R/library vs
/usr/local/lib/R/site-library.  I am running R 1.8 on Debian Linux.  On one
occasion doing update.packages() resulted in versions of one or more libraries
being placed in one of these directories without removing the old version, and
the old version took precedence over the new.  I'm sorry I did not save the
steps I used.  I would appreciate reading how best to manage libraries. 
Currently I have the following in /usr/local/lib/R/site-library: Design, Hmisc,
Rcmdr, acepack, car.  /usr/lib/R/library contains the following:
>
>KernSmooth  boot     eda      lqs      modreg  nnet     stepfun   ts
>MASS        class    foreign  methods  mva     rpart    survival
>R.css       cluster  grid     mgcv     nlme    spatial  tcltk
>base        ctest    lattice  mle      nls     splines  tools
>
>Thanks -Frank
>---
>Frank E Harrell Jr    Professor and Chair            School of Medicine
>                      Department of Biostatistics    Vanderbilt University
>---
>Frank E Harrell Jr    Professor and Chair            School of Medicine
>                      Department of Biostatistics    Vanderbilt University
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>  
>
I had the same problem on my workstation -  stable version of debian. 
probably depending on a site-installation based on
the R- source files.

I removed usr/local/lib/R,  changed the line  R_LIBS to 
R_LIBS=${R_LIBS-'/usr/lib/R/library'} in /etc/R/Renviron
and installed the missing packages again, they were installed in 
/usr/lib/R/library and
seem to work well - at least so long.

mahmood arai

Frank E Harrell Jr <f.harrell at vanderbilt.edu> writes:

1> I would appreciate getting a clarification of /usr/lib/R/library vs
1> /usr/local/lib/R/site-library.  I am running R 1.8 on Debian Linux.
1> On one occasion doing update.packages() resulted in versions of one
1> or more libraries being placed in one of these directories without
1> removing the old version, and the old version took precedence over
1> the new.  I'm sorry I did not save the steps I used.  I would
1> appreciate reading how best to manage libraries.  Currently I have
1> the following in /usr/local/lib/R/site-library: Design, Hmisc,
1> Rcmdr, acepack, car.  /usr/lib/R/library contains the
following:
>
> KernSmooth  boot     eda      lqs      modreg  nnet     stepfun   ts
> MASS        class    foreign  methods  mva     rpart    survival
> R.css       cluster  grid     mgcv     nlme    spatial  tcltk
> base        ctest    lattice  mle      nls     splines  tools
>
On Debian (and I'm sure Dirk will pipe in), /usr/lib/R/library is for
apt-installed by the core R packages, /usr/lib/R/site-library is for
apt-installed R packages (from CRAN, or Jim Lindsey's works), and
/usr/local/lib/R/site-library where you want to put locally installed
stuff (i.e. "install.packages()" should put there).  

best,
-tony

-- 
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Biomedical and Health Informatics   University of Washington
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