R devel - Jul 2015 - Installing/updating packages on a lab network

I'm the faculty member in my department who advises our IT staff on the 
details of installing R for
students and faculty on our Windows 7 lab network.  We are about to 
upgrade from R 3.1.1 to
R 3.2.1, and once that is done, this version of R and all installed 
packages will be frozen in the
image that appears in C:/Program Files/R/R-3.2.1/ on every lab computer, 
and this image is
refreshed on each computer at each new login.

Every user has a persistent home directory across all university lab 
computers, typically their
F:/ drive (students) and/or X:/ drive (faculty).  I need to give 
instructions to our IT staff for how to
arrange for a personal library, say
F:/~R/library
to be be set automatically, and included in .libPaths() so that 
install.packages() and update.packages()
will work using that path.

At present, there is no file R_HOME/etc/Renviron.site and 
R_HOME/etc/Rprofile.site is the vanilla
version with everything commented out, including
# set a site library
# .Library.site <- file.path(chartr("\\", "/", R.home()),
"site-library")

Environmental variables set for users include
HOMEDRIVE=F:
HOMEPATH=\
HOMESHARE=\\vfadmin.yorku.yorku.ca\HH\HOME\friendly
with the latter mapped to the X: drive

What is the code to be added to Rprofile.site to make this work?

thanks,
-Michael



-- 
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, Quantitative Methods
York University      Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele Street    Web:http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA

Just add the line

R_LIBS_SITE=F:/R/library

to the file R_HOME/etc/x64/Renviron.site

Best,
Uwe Ligges





On 28.07.2015 15:53, Michael Friendly wrote:
> I'm the faculty member in my department who advises our IT staff on the
> details of installing R for
> students and faculty on our Windows 7 lab network.  We are about to
> upgrade from R 3.1.1 to
> R 3.2.1, and once that is done, this version of R and all installed
> packages will be frozen in the
> image that appears in C:/Program Files/R/R-3.2.1/ on every lab computer,
> and this image is
> refreshed on each computer at each new login.
>
> Every user has a persistent home directory across all university lab
> computers, typically their
> F:/ drive (students) and/or X:/ drive (faculty).  I need to give
> instructions to our IT staff for how to
> arrange for a personal library, say
> F:/~R/library
> to be be set automatically, and included in .libPaths() so that
> install.packages() and update.packages()
> will work using that path.
>
> At present, there is no file R_HOME/etc/Renviron.site and
> R_HOME/etc/Rprofile.site is the vanilla
> version with everything commented out, including
> # set a site library
> # .Library.site <- file.path(chartr("\\", "/",
R.home()), "site-library")
>
> Environmental variables set for users include
> HOMEDRIVE=F:
> HOMEPATH=\
> HOMESHARE=\\vfadmin.yorku.yorku.ca\HH\HOME\friendly
> with the latter mapped to the X: drive
>
> What is the code to be added to Rprofile.site to make this work?
>
> thanks,
> -Michael
>
>
>

On 7/28/2015 1:32 PM, Uwe Ligges wrote:
> Just add the line
>
> R_LIBS_SITE=F:/R/library
>
> to the file R_HOME/etc/x64/Renviron.site
Thanks, Uwe

I have no way to test this and our IT people who do the installation 
know nothing of R, so follow-up questions:

*  There is no R_HOME/etc/x64/Renviron.site file, but there is a 
R_HOME/etc/Rprofile.site I can modify and
ask them to install.  Would the equivalent in Rprofile.site be
Sys.setenv(R_LIBS_SITE="F:/R/library")

* Does this require that the R_LIBS_SITE folder exist and be writable by 
the user?

  Here is what I see in the current version:

   .libPaths(), the library trees where R looks for packages gives:
   [1] "G:/uitapps/HEBB_R_LIB2/library"
   [2] "C:/Program Files/R/R/R-3.1.1/library"

   If I try to install a new package, e.g.,
   install.packages("rockchalk")

   I get "G:/uitapps/HEBB_R_LIB2/library is not writeable.  Use a 
personal library instead?", followed by a popup window,
   "Create ~R/library? (y/n)"

   This then installs the package, but to 
"C:/Users/friendly/Desktop/~R/library".  In the current login session,
.libPaths() will
   then have this path, so in a new R session, load(rockchalk) will work.

   However, once I logout, all that disappears, so I have to start over 
again to install or update a package.

-- 
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, Quantitative Methods
York University      Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele Street    Web:http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA