Configure R on raijin

 module load R/3.5.1
mdsumner/geometry, hypertidy/quadmesh, hypertidy/angstroms

General notes

We do not install R packages centrally. You will need to install what you want locally. Our R web page shows what you need to do:

https://opus.nci.org.au/display/Help/R

For v3.5.1 you need to load

module load intel-fc/2018.3.222 module load intel-cc/2018.3.222

do not load any gcc modules unless you really have to. Especially stay away from gcc later than 4.9.0.

For some of the packages you need, you may have to load another modules, for example RnetCDF will likely need netcdf module. Always choose the latest available.

processx - fix for devtools

https://github.com/r-lib/processx/issues/165

• git clone https://github.com/r-lib/processx.git
• apply ~/.R/Makevars as above
• R CMD build processx
• R CMD INSTALL processx_3.2.1.tar.gz

https://github.com/mdsumner/nectar/wiki/Configure-R-on-raijin

module load R/3.5.1                ## uhuh
module load netcdf/4.6.1p          ## ncdf4, RNetCDF, sf, rgdal, vapour, tidync
module unload intel-cc/12.1.9.293  ## old
module unload intel-fc/12.1.9.293

module load intel-cc/17.0.1.132    ## modern
#<del>module load udunits/2.1.24         ## RNetCDF </del>
module load mesa/8.0.5             ## rgl (quadmesh)
module load  gdal/2.2.2            ## rgdal, sf, vapour
module load  proj/4.9.3            ## proj4, quadmesh


module load gcc/6.2.0
module load intel-fc/17.0.1.132
module load intel-mkl/17.0.1.132

module load  geos/3.5.0            ## rgeos, angstroms

• readr
• dplyr
• rgeos
• RcppEigen https://github.com/traitecoevo/plant/issues/186

install.packages: ncdf4, devtools, raster, dplyr, RcppEigen

remotes::install_github:

mdsumner/geometry, hypertidy/quadmesh, hypertidy/angstroms

library(quadmesh)
library(angstroms)