R
Link to section 'Setting Up R Preferences with .Rprofile' of 'R' Setting Up R Preferences with .Rprofile
Different clusters have different hardware and softwares. So, if you have access to multiple clusters, you must install your R packages separately for each cluster. Each cluster has multiple versions of R and packages installed with one version of R may not work with another version of R. So, libraries for each R version must be installed in a separate directory. You can define the directory where your R packages will be installed using the environment variable R_LIBS_USER.
For your convenience, a sample .Rprofile example file is provided that can be downloaded to your cluster account and renamed into /.Rprofile (or appended to one) to customize your installation preferences. Detailed instructions:
curl -#LO https://www.rcac.purdue.edu/files/knowledge/run/examples/apps/r/Rprofile_example
mv -ib Rprofile_example ~/.Rprofile
The above installation step needs to be done only once on each of the clusters you have access to. Now load the R module and run R to confirm the unique libPaths:
module load r/4.2.2
R
R> .libPaths()
[1] "/home/zhan4429/R/bell/4.2.2-gcc-9.3.0-xxbnk6s"
[2] "/apps/spack/bell/apps/r/4.2.2-gcc-9.3.0-xxbnk6s/rlib/R/library"
Link to section 'Challenging packages' of 'R' Challenging packages
Below are packages users may have difficulty in installation.
Link to section 'nloptr' of 'R' nloptr
In Bell, the installation may fail due to the default cmake version is too old. The solution is easy, users just need to load the newer versions of cmake:
module load cmake/3.20.6
module load r
Rscript -e 'install.packages("nloptr")'
In Brown or other older clusters, because our system's cmake and gcc compilers are old, we may not be able to install the latest version of nloptr. The walkaround is that users can install the older versions of nloptr:
module load r
R
> myrepos = c("https://cran.case.edu")
> install.packages("devtools", repos = myrepos)
> library(devtools)
> install_version("nloptr", version = "> 1.2.2, < 2.0.0", repos = myrepos)
Link to section 'Error: C++17 standard requested but CXX17 is not defined' of 'R' Error: C++17 standard requested but CXX17 is not defined
When users want to install some packages, such as colourvalues, the installation may fail due to Error: C++17 standard requested but CXX17 is not defined. Please follow the below command to fix it:
module load r
module spider gcc
module load gcc/xxx ## the lateste gcc is recommended
mkdir -p ~/.R
echo 'CXX17 = g++ -std=gnu++17 -fPIC' > ~/.R/Makevars
R
> install.packages("xxxx")
Link to section 'RCurl' of 'R' RCurl
Some R packages rely on curl. When you install these packages such as RCurl, you may see such error: checking for curl-config... no Cannot find curl-config To install such packages, you need to load the curl module:
module load curl
module load r
R
> install.packages("RCurl")
Link to section 'raster, stars and sf' of 'R' raster, stars and sf
These R packages have some dependencies. To install them, users will need to load several modules. Note that these modules have multiple versions, and the latest version is recommended. However, the default version may not be the latest version. To check the latest version, please run module spider XX.
module spider gdal
module spider geos
module spider proj
module spider sqlite
module load gdal/XXX geos/XXX proj/XXX sqlite/XXX ## XXX is the version to use. The latest version is recommended.
module load r/XXX
R
> install.packages("raster")
install.packages("stars")
install.packages("sf")