Thanks all!
On Thu, Jun 18, 2015 at 5:16 PM, Pablo Escobar Lopez <[email protected]> wrote: > 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
