2. Installation

Dependencies

The longhaul package requires several dependencies from both CRAN and Bioconductor to function properly. It is important to note that longhaul is compatible with R version 4.4 or higher, as some dependencies, such as UCSC.utils, may not run on older versions of R. Additionally, please ensure compatibility with the current Bioconductor version.

Installing Dependencies

Before installing longhaul, ensure your R installation is version 4.4 or later. You can check your R version by running R.version.string in your R console.

# Check R version
R.Version()$version.string  # Ensure R version 4.4 or higher

To install the required dependencies, follow these steps:

Install Core Dependencies from CRAN

These packages are available directly from CRAN and can be installed using the standard install.packages method.

# Install core dependencies from CRAN
install.packages(c("dplyr", "tidyr"))

Install Bioconductor Dependencies

Packages from Bioconductor require the BiocManager for installation.

# Install BiocManager if not already installed
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# Install packages from Bioconductor
BiocManager::install(c("GenomicRanges", "UCSC.utils", "rtracklayer"))

Bioconductor Version

# Check Bioconductor version
BiocManager::version()

# Install the latest version of Bioconductor if needed
BiocManager::install(version = "3.21")

Installation

You can install the longhaul package from GitHub using the devtools package:

# Install devtools if you haven't already
install.packages("devtools")

# Install longhaul from GitHub
devtools::install_github("DavidsonGroup/longhaul")