Howdy Niek, We have a non-Easybuild module tree. The attachment from before lives in /software/tamusc/modulefiles/R. It loads the EB R and then sets the needed env vars for building extensions.
Note that I don't maintain the R extensions so don't have details. Here are the scripts written by my colleague Maikel Pennings for such things. You'd have to ask him to explain them. Jack Perdue Lead Systems Administrator High Performance Research Computing TAMU Division of Research [email protected] http://sc.tamu.edu SC Helpdesk: [email protected] On 06/18/2015 09:27 AM, Niek de Klein wrote:
Hi Jack, Thank you for your answer. I don't understand the attached file. How do you use that to install extensions, and how do you keep it so that if you want to migrate to another cluster you can install R with the exact same R libraries installed? Do you keep a separate file with all the R packages you installed extra? Thanks, Niek On Thu, Jun 18, 2015 at 4:20 PM, Jack Perdue <[email protected]> wrote:Howdy Niek, FWIW, here is our latest build of R (with lots of dependencies added): http://www.siliconslick.com/easybuild/ebfiles_repo_cleaned/ada/R/R-3.2.0-intel-2015B-default-mt.eb For extensions, we have another (non-EB) module (attached) for installing extensions to the above by hand. Between the two, we've: a) tried to make sure we aren't using system libs (e.g. TCL) b) are able to satisfy user requests for misc. R extensions (automagically) Jack Perdue Lead Systems Administrator High Performance Research Computing TAMU Division of Research [email protected] http://sc.tamu.edu SC Helpdesk: [email protected] On 06/18/2015 08:57 AM, Niek de Klein wrote:Hi mailinglist, I'm probably missing something here and unnecessarily complicating things. I am trying to get R installed with just a few packages we use. One of the packages, ggplot2, has a lot of dependencies. So when I try to install R with one of the existing EasyBuild files and have ggplot2 as the dependency it will throw an error due to the dependencies of ggplot2 not being installed, and I have to add the dependencies to the .eb file. And then add the dependencies of the dependencies to the .eb file, etc etc. When installing libraries from within R you can simply give the option "dependency=True" and it will automagically install all dependencies for you. Is there an option like that when installing R and some R libraries? Thanks, Niek
install-R-packages.sh
Description: Bourne shell script
# first get the neccessary env variables
rpackageroot=Sys.getenv("RPACKAGEROOT",unset="")
rmpidir=Sys.getenv("RMPIDIR",unset="")
# get the list of installed packages
installed <- installed.packages()[,1]
# define a function to check if a package has been installed
is.installed <- function(mypkg) is.element(mypkg, installed)
#the full path to the package file
packages_file <- paste(rpackageroot,"/packages/packages",sep="")
print(packages_file)
# read the file of packages that need to be installed
input <- read.delim(packages_file)
# the vector of package can be reached by extracting the column named PACKAGE
packages <- input$PACKAGE
# first thing to do is to install Rmpi package, since this requires special configuration flags
# and other packages depend on this one
if (! is.installed("Rmpi")) {
mpiargs <- paste("--with-mpi=",rmpidir," --with-Rmpi-type=INTELMPI",sep="")
# use the local Rmpi install
rmpi_package <- paste(rpackageroot,"/packages/Rmpi.tar.gz",sep="")
print("===============RMPI_PACKAGE===============")
print(rmpi_package)
install.packages(rmpi_package,configure.args=mpiargs)
# install.packages("Rmpi",configure.args=mpiargs,repo="http://cran.us.r-project.org";)
}
# iterate over all the packages and install them only if they were not installed yet
for (pkg in packages) {
if (! is.installed(pkg)) {
install.packages(pkg,repo="http://cran.us.r-project.org";)
}
}
print("... all packages are installed, exiting now")
quit()
