Oh one more detail I try to keep the version of R, Rlib and Rprofile in sync so that there's always a set of say "3.2.0", "3.2.1". I'll see how that works out.
/Martin On Thu, Jul 30, 2015 at 10:47 AM Martin <[email protected]> wrote: > On Thu, Jul 30, 2015 at 1:23 AM Fotis Georgatos <[email protected]> > wrote: > >> I would lobby for a R/3.2.2 build (release to come out mid August), >> incorporating as much collective wisdom as possible, perhaps tuned for >> bio needs. >> What would you think? A PR upon 3.2.1 could be a first approximation of >> it. > > > I settled with the following approach (which to me is agnostic to the > field of research): > > These are the default things of an R stack: > > Rstack.eb: > > # this is just drafted but I hope you get the idea > version = "3.2.0" # right now creating 3.2.1 > depends = ( > "R" # no packages at all not even recommended > "Rprofile" # just sets R_PROFILE, R_ENVIRON > "Rlib" # site-wide libraries that should be available also holds > dependencies for stuff like GLPK, MySQL, Postgres..... > ) > > Rprofile and Rlib are separated because I found that there are more often > than not settings to be changed for users and this keeps reinstallation > times way down since I don't have to rebuild the whole library. > > Rlib is basically an empty easybuild with a bunch of dependencies and a > directory "site-library" -- I guess it could be external but the dependency > resolution mechanism of EB is just nice to have and e.g. have stuff like > protocol buffers in "the right place". This keeps R itself rather clean but > still enable the use of a "batteries included" R install. > > I'm still thinking about how to do the same with Python. I'd like to have > a bare python and one (or maybe a few) libraries that can then be loaded. > As opposed to "full fledged python install" or "one module per package". > > /Martin > > -- > -- > http://www.xing.com/profile/Martin_Marcher > http://www.linkedin.com/in/martinmarcher > Mobil: +43 / 660 / 62 45 103 > UID: ATU68801424 > -- -- http://www.xing.com/profile/Martin_Marcher http://www.linkedin.com/in/martinmarcher Mobil: +43 / 660 / 62 45 103 UID: ATU68801424
