Hi Niek, I think many people in this list has suffer the R dependencies nightmare.
I wrote an small scirpt which if you already have a R easyconfig will try to give you which are the latest versions available in R repos. It's not perfect but it helps a little bit at least. Here you have it in case it's helpfful for you https://github.com/pescobar/random-scripts/blob/master/easybuild-update-R-libs.py regards Pablo. 2015-06-18 16:38 GMT+02:00 Jack Perdue <[email protected]>: > 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 > >> > > -- Pablo Escobar López HPC systems engineer Biozentrum, University of Basel Swiss Institute of Bioinformatics SIB Email: [email protected] Phone: +41 61 267 21 80 http://www.biozentrum.unibas.ch
