On 12/16/2016 10:22 AM, Siddiqui, Shahzeb wrote:
Hello,
I would like to create a easyconfig for each R package, I find that to
be best suitable for our environment at Pfizer. I know we can pass
along the R packages in the R easybuild using exts_list . The only
issue is we have our own set of R packages that we need to install,
and I am not sure in which order they need to be installed.
It’s important to separate the R installation from the R packages
because in the case of a build error in R package it would fail to
build R if they are both together.
I would like to build R packages as modules which will be particularly
important for some special R packages that require a special
dependency. For instance we need R2Jags and that has a dependency for
JAGS. I have JAGS in a module environment so I would like R2Jags
module file to load Jags before a user can use R2Jags.
When loading base R module it will allow user to have access to base R
packages that is quite small. The special R packages that are build
with Easybuild will have their R module only visible when loading R.
This can be done via MODULEPATH variable.
Similar to how you have Python package like numpy, I would like this
framework for R packages.
If you want to look over my experiment for automatically building
easyconfigs based on CRAN data, see:
http://www.siliconslick.com/easybuild/R_madness/
There are the scripts (which will need work), the easyconfigs created,
and the modules built from those.
I thought it was a great idea. Others on our staff, not so much
(they are content to use R and Python's built in tools for installing to
a directory out of the EasyBuild tree).
Personally, as someone who likes to keep track of what versions he's using
(and not have some "pip" update something under my feet), I'd spend time
doing the same for Python... but I got plenty other stuff to keep me busy
[I'm having a good old time with --minimal-toolchains and my new 2016D
toolchains based on GCCcore/6.2.0]
jack
Shahzeb Siddiqui
HPC Linux Engineer
B2220-447.2
Groton, CT
