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 - igraph
3 R package - nloptr
4 R package - Devtools
5 R package - Seurat
6 R packages - SF
7 R package - InferCNV

R package - beachmat and glmGamPoi

# Load modules
module purge
module load gcc/14.2.0 R/4.4.2

# Launch R
R

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

R package - igraph

# Load Modules
module purge
module load gcc/14.2.0 R/4.4.2

# Start R
R

# Install package
install.packages('igraph')

R package - nloptr

# Load modules
module purge
module load gcc/14.2.0 R/4.4.2

# Start R
R

# Install package
install.packages('nloptr')

R package - Devtools

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

# Load modules
module purge
module load gcc/14.2.0 R/4.4.2

# Start R
R

# Install pkg
install.packages('devtools')

R package - Seurat

# Load Modules
module purge
module load gcc/14.2.0 R/4.4.2

# Start R
R

# Install pkg
install.packages('Seurat')

R packages - SF

# Load Modules
module purge
module load gcc/14.2.0 R/4.4.2

# Start R
R

# Install Pkg
install.packages('sf')

R package - InferCNV

## Install JAGS
# Setup Working Directory
cd $HOME
mkdir build_jags && cd build_jags

# Download & Decompress JAGS
wget -O JAGS-4.3.2.tgz https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.2.tar.gz/download
tar xzvf JAGS-4.3.2.tgz && cd JAGS-4.3.2

# Load modules 
module load gcc/14.2.0 R/4.4.2

# Export Variables
export PKG_CONFIG_PATH=/n/app/openblas/0.3.28-gcc-14.2.0/lib/pkgconfig/:$PKG_CONFIG_PATH
export LDFLAGS="-L/n/app/openblas/0.3.28-gcc-14.2.0/lib/"

# Install JAGS
mkdir $HOME/JAGS
./configure --prefix=$HOME/JAGS
make -j 4
make install

# Clean up; build_jags directory is no longer needed
rm -r $HOME/build_jags

# Add JAGS path to variables 
export LD_LIBRARY_PATH=$HOME/JAGS/lib:$LD_LIBRARY_PATH
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/JAGS/lib/pkgconfig

# Launch R
R

# Install R package
install.packages("BiocManager")
BiocManager::install("infercnv")