The fbseqOpenMP package is an internal backend of the fbseq package that runs the Markov chain Monte Carlo (MCMC) procedure behind the scenes. It should install on most machines that have OpenMP, but it is slow for large datasets. For a faster backend, which uses parallel computing via CUDA-capable general-purpose graphics processing units (GPUs), use the fbseqCUDA package.
The required R version and R packages listed in the "Depends", "Imports", and "Suggests" fields of the "package's DESCRIPTION file.
Navigate to a list of stable releases on the project's GitHub page. Download the desired tar.gz bundle, then install it either with install.packages(..., repos = NULL, type="source") from within R R CMD INSTALL from the Unix/Linux command line.
For this option, you need the devtools package, available from CRAN or GitHub. Open R and run
library(devtools)
install_github("wlandau/fbseqOpenMP")
Open a command line program such as Terminal in Mac/Linux and enter the following commands.
git clone git@github.com:wlandau/fbseqOpenMP.git
R CMD build fbseqOpenMP
R CMD INSTALL ...
where ... is replaced by the name of the tarball produced by R CMD build.
To check if OpenMP is correctly enabled for the package, run fbseqOpenMP::check_OpenMP().