On 12/16/2016 10:54 AM, Siddiqui, Shahzeb wrote:
Hi Jack,
I checked out your work, this is great work. Did you consider sending your
easyconfig files to EB. I think your collection of easyconfig files is a good
starting point for building out the R collection. I think it is imperative to
have R collection by version because these R packages change along with the
version of R.
I would like if we can make a R collection for R 3.3.1 which is the latest one.
If anything, I would send the script(s) to EB... I wouldn't want to
swamp them
with any more easyconfigs than I haven't already swamped them with (got lots
that I need to send in).
But I would want to do Python and Perl too. And I'd want support for things
like Bioconducter and whoever.
It wasn't real popular here but we tend to make things easy for users
(to not confuse them).
Making it easy for ourselves seems to be another argument (hard to
disagree with the ease of "pip install").
But if I was doing performance analysis like I've done in the past I'd
want to nail
down every version I'm using and make sure that some random update
didn't warp my data.
jack
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Jack Perdue
Sent: Friday, December 16, 2016 11:39 AM
To: [email protected]
Subject: Re: [easybuild] R extra packages
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
