[R] Installing packages from command line on Linux RHEL4
Kermit Short
k_short at lanl.gov
Mon May 21 20:05:02 CEST 2007
Dirk-
Many thanks for your reply. As I mentioned, I know very little
about programming in 'R' and what I've got is a BASH script. If needs be,
I'll look up how to read in a text file through R and add that into your
script in lieu of the (argv) stuff, but you wouldn't happen to know how to
accomplish the same thing using the
R CMD INSTALL
Shell command?
Thanks!
-Kermit
-----Original Message-----
From: Dirk Eddelbuettel [mailto:edd at debian.org]
Sent: Monday, May 21, 2007 12:00 PM
To: k_short at lanl.gov
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Installing packages from command line on Linux RHEL4
Hi Kernit,
On 21 May 2007 at 11:37, Kermit Short wrote:
| Greetings.
|
| I am a System Administrator, and thus have very little knowledge of R
| itself. I have been asked to install a list of some 200 packages (from
| CRAM) to R. Rather than installing each package manually, I was hoping I
| could script this. I've written a BASH script that hopefully will do
this,
| but I'm wondering about the Mirror Selection portion of the installation
| process. I've looked and can't find anywhere a parameter to supply that
| specifies a mirror to use so that I don't have to manually select it for
| each package I want to install. In this case, with nearly 200 packages to
| install, this could become quite tedious. Does anyone have any
| suggestions?
The narrow answer is try adding
repos="http://cran.us.r-project.org"
Also, and if I may, the littler front-end (essentially "#!" shebang support
for R)
helps there:
basebud:~> cat bin/installPackages.r
#!/usr/bin/env r
#
# a simple example to install all the listed arguments as packages
if (is.null(argv)) {
cat("Usage: installPackages.r pkg1 [pkg2 [pkg3 [...]]]\n")
q()
}
for (pkg in argv) {
install.packages(pkg, lib="/usr/local/lib/R/site-library", depend=TRUE)
}
You would still need to add repos="..." there. I tend to do that in my
~/.Rprofile.
Hth, Dirk
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
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