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Installing packages from command line on Linux RHEL4

5 messages · Dirk Eddelbuettel, Kermit Short, Adaikalavan Ramasamy

Original
Dirk Eddelbuettel
# 
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
Kermit Short
# 
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
Dirk Eddelbuettel
# 
Kermit,
On 21 May 2007 at 12:05, Kermit Short wrote:
| 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?

I'm confused. Your 1st email asked about the mirror selection. Now you want
to install from local files. Those are two different problems.

Please consult the 'R Admin' manual, or go back to the list with preferably
concrete questions, or reproducible examples.

Hth, Dirk
Adaikalavan Ramasamy
# 
Assuming the R packages have been downloaded locally and end with 
tar.gz, then how about simply changing to where the files are located 
and typing the following command?

  ls *.tar.gz | while read x; do echo "R CMD INSTALL $x"; done | bash


Alternatively, you can use the install.packages() function in R.

Regards, Adai
Kermit Short wrote: