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.

1 R package - beachmat and glmGamPoi
2 R package - curl
3 R package - igraph
4 R package - nloptr
5 R package - Devtools
6 R package - Seurat
7 R packages - SF and Monocle3
8 R package - ACTIONet
9 R package - InferCNV
10 R package - Rmpi

R package - beachmat and glmGamPoi

# Load modules
module purge
module load gcc/9.2.0 R/4.3.3

# Launch R
R

# Install packages
install.packages('BiocManager')
BiocManager::install('beachmat')
BiocManager::install("glmGamPoi")

The beachmat and glmGamPoi packages do not work with recent R versions. To install them on O2, you can load the R/4.3.3 module, which is an older R version compatible with both packages.

R package - curl

# Load modules
module purge
module load gcc/9.2.0 curl/8.12.1 R/4.4.0

R
install.packages('curl')

The curl package is needed to install popular R packages such as devtools, rtracklayer and Seurat (v5). To install the curl R package, you will need to load the curl/8.12.1 module.

Important: The curl/8.12.1 module is a temporary workaround and only needed until the OS for O2 is updated from CentOS to Red Hat 9.

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:

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

HMS IT RC O2