Re: [R] Installing packages from command line on Linux RHEL4
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:
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:[EMAIL PROTECTED]
Sent: Monday, May 21, 2007 12:00 PM
To: [EMAIL PROTECTED]
Cc: r-help@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
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Installing packages from command line on Linux RHEL4
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? Thanks! -Kermit Short [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing packages from command line on Linux RHEL4
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:[EMAIL PROTECTED]
Sent: Monday, May 21, 2007 12:00 PM
To: [EMAIL PROTECTED]
Cc: r-help@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
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing packages from command line on Linux RHEL4
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 -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
