Installing Other R packages on O2

Please make sure to setup an R Personal Library on O2 to install packages locally.

Here you can find valuable information on how to install R packages requiring some external dependencies.

R package - rtracklayer

# Load modules module purge module load gcc/9.2.0 R/4.4.0 # Install cURL locally mkdir $HOME/CURL_LOCAL && cd $HOME/CURL_LOCAL wget tar xvzf curl-8.7.1.tar.gz && cd curl-8.7.1 ./configure --with-openssl --prefix $HOME/CURL_LOCAL make make install # Create a Makevars file with the following output mkdir ~/.R echo "CFLAGS=-I/home/$USER/CURL_LOCAL/include" >> ~/.R/Makevars echo "CXXFLAGS=-I/home/$USER/CURL_LOCAL/include" >> ~/.R/Makevars echo "LDFLAGS=-L/home/$USER/CURL_LOCAL/lib" >> ~/.R/Makevars # Launch R and install rtracklayer R BiocManager::install("rtracklayer")

R package - igraph

# Load Modules module purge module load gcc/9.2.0 R/4.3.1 glpk/5.0 # Create ~/.R/Makevars mkdir ~/.R echo "CFLAGS+=-I/n/app/glpk/5.0-gcc-9.2.0/include" >> ~/.R/Makevars echo "CPPFLAGS+=-I/n/app/glpk/5.0-gcc-9.2.0/include" >> ~/.R/Makevars echo "LDFLAGS+=-L/n/app/glpk/5.0-gcc-9.2.0/lib" >> ~/.R/Makevars echo "CPATH+=/n/app/glpk/5.0-gcc-9.2.0/include" >> ~/.R/Makevars # Start R R # Install package install.packages('igraph')

R package - nloptr

You must use an R version compiled against GCC v9.2.0 and load the CMake module. For example:

# Load modules module purge module load gcc/9.2.0 R/4.2.1 cmake/3.22.2 # Start R R # Install package install.package('nloptr')

R package - Devtools

Load the git2 module if using an older R version (e.g., 4.0.1):

If using the R>=4.2.1 module, then it is not required to load the git2 module.

R package - Seurat

R packages - SF and Monocle3

R package - ACTIONet

The R package has not been maintained for the last few years; currently it is only possible to use through a singularity container.

R package - InferCNV

R package - Rmpi

The package must be installed using an sbatch job. For example:

1. Create an sbatch script with the following content

2. Submit script via the sbatch command