Kermit Short
2007-May-21 17:37 UTC
[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 K_short@lanl.gov [[alternative HTML version deleted]]
Dirk Eddelbuettel
2007-May-21 17:59 UTC
[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="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