It comes down to whether we want simplicity in R, Python, or Perl installation by having packages installed inside the easyconfig file. It works well for most packages assuming there is no issue during build. There are cases when some package don't build properly and having to troubleshoot them with an entire list of packages become difficult.
I would like to decouple the R packages into individual easyconfig file, because I can resolve any dependencies and work on installing the particular package. Even if the process might be repetitive for most builds, at least the R collection will be built correctly. Another benefit is that I would like to package into RPMs, and it would be beneficial to create a RPM for each R package rather than just the main R. Just like how RHEL provides Python RPMs for its base and Python related packages, I think we can achieve this with Easybuild. I also need packages from Bioconductor and would like this in Easybuild. -----Original Message----- From: easybuild-requ...@lists.ugent.be [mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Jack Perdue Sent: Friday, December 16, 2016 1:38 PM To: easybuild@lists.ugent.be Subject: Re: [easybuild] R extra packages 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: easybuild-requ...@lists.ugent.be > [mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Jack Perdue > Sent: Friday, December 16, 2016 11:39 AM > To: easybuild@lists.ugent.be > 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 >> >>
