How about getting rid of of versions (at least for Bioconductor) and just let R itself deal with it. I find that "BiocInstaller::biocLite(....)" does work quite nicely. Be it an upstream mirror or a site local mirror, with a site local mirror the set of packages is under the local of the the site and there's no need to remove them during a mirror sync so one would at least have some kind of archive...
Of course that may then introduce other things like: "Is there a smart way to set an Rprofile.site from within an easyconfig?" (Yes I'm being greedy, EB in general works well enough for me to worry about these Luxury problems) /Martin On Tue, Mar 31, 2015 at 6:15 PM Martin <[email protected]> wrote: > 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 >> >
