Hi all,
It took a little longer, but I think I now have a fully functional
generateEasyConfig.R script that is ready for distribution; "It works on our
clusters" :)... I've requested access to
https://github.com/fgeorgatos/easybuild.experimental
by creating an "issue" as per instructions in the README.md, but it looks like
Fotis Georgatos is on holiday... For now I forked the repo and published the
generator here:
https://github.com/pneerincx/easybuild.experimental/blob/master/users/pneerincx/generateEasyConfig.R
DISCLAIMER 1: The generated easyconfig will contain any packages you had
installed and which are available from CRAN or BioConductor repo's.
If you have R packages from elsewhere you may have to tweak the
generator.
DISCLAIMER 2: The generator assumes you will want an R with graphics
capabilities for plotting. Therefore it includes dependencies on easyconfigs
for various libs.
For libpng-1.6.17 and freetype-2.6 I had to create new
easyconfigs and patches as these libs contain bugs and some R packages fail to
compile with the plain vanilla libs.
I'll create a pull request for these new easyconfigs, but it will
take some time before these are available from the latest and greatest
EasyBuild release...
Cheers,
Pi
On Jun 29, 2015, at 6:00 PM, Pablo Escobar Lopez <pablo.escobarlo...@unibas.ch>
wrote:
> ok, thanks for your effort Pieter
>
> 2015-06-29 16:25 GMT+02:00 Pieter Neerincx <pieter.neeri...@gmail.com>:
>
> On Jun 29, 2015, at 3:37 PM, Pablo Escobar Lopez
> <pablo.escobarlo...@unibas.ch> wrote:
>
> >
> >
> > 2015-06-24 10:58 GMT+02:00 Pieter Neerincx <pieter.neeri...@gmail.com>:
> >
> > Yesterday I started working on an R-script that generates an *.eb from an
> > existing R installation. This is based on Stefano's code (Many thanks for
> > sharing that!) and adds some commandline switches, help and code to figure
> > out whether a package came from a CRAN repo or from BioConductor. Hence
> > this is slightly different compared to the above as it generates a complete
> > *.eb from pure R, but I can easily add an option to only generate a pkglist
> > file, which may then be used by an existing *.eb.
> >
> > Is it Ok if I add this with a README to the ..../r/R/ dir in the
> > EasyConfigs repo and create a pull request or would you prefer this kind of
> > supplementary code to go elsewhere?
> >
> >
> >
> > is this code published somewhere?
>
> As soon as I solved the last bugs I'll publish and report back to this list...
>
> Cheers,
>
> Pi
>
> > thanks
> > Pablo.
> >
> >
> >
> > --
> > Pablo Escobar López
> > HPC systems engineer
> > Biozentrum, University of Basel
> > Swiss Institute of Bioinformatics SIB
> > Email: pablo.escobarlo...@unibas.ch
> > Phone: +41 61 267 21 80
> > http://www.biozentrum.unibas.ch
>
> -------------------------------------------------------------
> phone: +31 6 143 66 783
> e-mail: pieter.neeri...@gmail.com
> skype: pieter.online
> -------------------------------------------------------------
>
>
>
>
> --
> Pablo Escobar López
> HPC systems engineer
> Biozentrum, University of Basel
> Swiss Institute of Bioinformatics SIB
> Email: pablo.escobarlo...@unibas.ch
> Phone: +41 61 267 21 80
> http://www.biozentrum.unibas.ch
-------------------------------------------------------------
phone: +31 6 143 66 783
e-mail: pieter.neeri...@gmail.com
skype: pieter.online
-------------------------------------------------------------
