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 - 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 - sf
module purge
module load gcc/14.2.0
module load R/4.4.2
module load udunits/2.2.28
R
install.packages('sf')R package - sf + gdal
Steps to install sf with GDAL support. This is sometimes needed when installing other R packages that require the GDAL system library.
module purge
module load gcc/14.2.0
module load R/4.4.2
module load udunits/2.2.28
module load geos/3.13.1
module load proj/9.6.2
module load cmake/3.31.2
module load gdal/3.11.3
R
install.packages('sf',configure.args='--with-gdal-config=/n/app/gdal/3.11.3-gcc-14.2.0/bin/gdal-config --with-proj-include=/n/app/proj/9.6.2-gcc-14.2.0/include --with-proj-lib=/n/app/proj/9.6.2-gcc-14.2.0/lib64 --with-proj-share=/n/app/proj/9.6.2-gcc-14.2.0/share/proj')
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 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")