Hi, Yes I know about -k it just seems so cumbersome to do that :(
The combination of a broken corporate proxy and files that go missing really makes this a mess (for me, EB itself is great, I just have to suffer the slow Enterprise Death). I'll look into the script, thanks. Martin On Tue, Mar 31, 2015 at 5:58 PM Pablo Escobar Lopez < [email protected]> wrote: > Hi Martin, > > R extensions change quite often and the url also changes so the normal > approach is "manual fix". In case it's useful for you I wrote this script > some days ago to deal with this, it's not perfect and still requires some > manual work but it works for ~90% of the R libraries so it saves you some > time > > https://github.com/pescobar/random-scripts/blob/master/easybuild-update-R-libs.py > > To install extra R libraries you can just add the new library to the > exts_list and then rerun the easyconfig with "eb R-3.1.2.eb -k -f" This > way only libraries not already installed will be compiled. This is commonly > used to add extra libraries for R/Perl/Python. This is the easybuild help: > > -k, --skip Skip existing software (useful for installing > additional packages) (def False) > > > regards, > pablo. > > 2015-03-31 17:41 GMT+02:00 Martin <[email protected]>: > >> Hi, >> >> I'm trying to install R-3.1.2-goolf-1.5.14.eb. >> >> I'm running a simple: >> >> eb R-3.1.2-goolf-1.5.14.eb --robot -s fetch >> >> but it fails on most of the packages in exts_list. How are people >> dealing with this? >> >> Are you just going thru the list and manually fix the versions, I keep >> thinking there has to be a better way. >> >> Also how do you (later) install an additional package? Extend the list >> in exts_list and "reinstall" or provide another module? Are there >> established best practices for this? >> >> thanks, >> Martin >> >> >> > > > -- > 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 >
