Hi,
On Jul 21, 2009, at 3:56 PM, ravi wrote:
Hi,
I am interested in customizing the installation of R. I have
gone through the “R Installation and Administration” manual. But some
of the stuff is not clear to me and I would like to get clarifications
on the following points (for a Windows installation with
R_HOME=C:\\R\\R-2.9.1 ) :
1. I understand that I need to create a
file, .Renviron with the following path : R_HOME\\etc\\.Renviron where
a number of environmental variables can be set. I would first like to
know if the file to be created is Renviron or .Renviron.
If the files in the R install on my mac would provide a hint, I'm
guessing it should be Renviron (no period).
Both versions
are mentioned in the manual. By the way, many functions in R start
with
a period.
Really? Which functions have you found that you want to use start with
a period?
Anyway, I'm guessing these are functions are ones that probably
shouldn't be used by "an end user."
Is there any special significance to a name (file, function
etc) if it starts with a period?
Files that start with a period are typically reserved for "hidden
files", at least on unix/linux machines ... not sure about windows
machines.
2. I want to have two different
libraries – one for the packages that follow with the R installation
and a second one for any additional packages that I add afterwards. By
doing this, I hope to avoid repeating the installation of these
packages
once again after an update of R.
I wouldn't recommend doing this in this in this scenario. "Minor"
upgrades in R (ie. 2.9.0 to 2.9.1) don't really require you to
reinstall your packages, but an upgrade from 2.8 to 2.9 should also
involve upgrading all packages you have installed.
In either event, you can install a package in a particular directory
by setting the target directory path in the "lib" argument to the
"install.packages" function.
I understand that I can set the paths
to these libraries with the environmental variables R_LIBS or
R_LIBS_USER in the .Renviron file. But I am not entirely sure about
the
difference between these two environmental variables. It is mentioned
in the manual that multiple paths (for different libraries) can be
specified. Does this mean that I can set the paths with any of these
environmental variables? Or, should I set R_LIBS=R_HOME\\library and
R_LIBS_USER to my private library? Does this also mean that any
package that
I add with the install.packages() function will then end up in the
private library?
3. If I want to start R with a certain set of
packages loaded on startup, I understand that I need to create a file
.Rprofile with the path R_HOME\\etc\\.Rprofile. Again, should it be
.Rprofile or Rprofile (or, is it Rprofile.site which I see is already
present in my R installation)?
It should be .Rprofile -- probably you want to put this file in your
home directory.
Is the following syntax OK for
specifying the environmental variable
R_DEFAULT_PACKAGES = {“base”, “datasets”,”utils”,”ggplot2”,“lattice”}
How can I add, for example, ggplot2 and lattice to the list of
default packages that R normally starts with?
A simple way is to just add the appropriate "library" calls at the
start of your ~/.Rprofile file
4.
If I add a .Renviron file to my working directory, will it override
that in R_HOME? Or, is it the other way around? Can I add a .Rprofile
file as well to the working directory where I can specify the
R_DEFAULT_PACKAGES a little differently?
Have a look at ?Startup and I don't think R loads an .Rprofile file in
your current working directory (at least, it's not doing it for me).
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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