Installation
In WebGestaltR: Gene Set Analysis Toolkit WebGestaltR

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(WebGestaltR)

Requirements

Rust 1.66.0 or later (GNU version if on Windows)
R 4.0.0 or later (Windows requires 4.2+)

System dependencies on Linux

Installing from source on Linux additionally requires development headers for the system libraries used by WebGestaltR's dependencies. On Debian or Ubuntu:

sudo apt-get install libssl-dev libxml2-dev libcurl4-openssl-dev \
    libfontconfig1-dev libfreetype6-dev libharfbuzz-dev libfribidi-dev \
    libpng-dev libtiff5-dev libjpeg-dev

libharfbuzz-dev and libfribidi-dev are needed by systemfonts and textshaping, which the required svglite package depends on. Without them, svglite fails to install and WebGestaltR reports it as a missing dependency. On Fedora or RHEL the equivalents are openssl-devel, libxml2-devel, libcurl-devel, fontconfig-devel, freetype-devel, harfbuzz-devel, fribidi-devel, libpng-devel, libtiff-devel and libjpeg-turbo-devel.

Windows and macOS users installing a binary from CRAN do not need any of this.

Since WebGestaltR v1.0.0, Rust is used for core computations in the R package. Therefore, to install WebGestaltR, please download and install Rust from https://rust-lang.org/tools/install/. For Mac, Linux, or Unix users, Rust can be installed from the command line, and Windows users can download a GUI installer. If using Windows: please make sure to install the GNU version of Rust. This will be an option when you run the installer.

For Windows Users: Install the gnu version of Rust, not the MSVC version. The Rust installer will ask for the version you want to download.

Restart your terminal after installing Rust to ensure the Rust compiler is available in your path. You can check that Rust is installed correctly by running rustc --version in your terminal.

After installing Rust, you can install WebGestaltR by running the following command in an R session:

# install.packages("devtools") # run if devtools not already installed
devtools::install_github("bzhanglab/WebGestaltR")

During installation, the Rust compiler will be called to build the computation library used by WebGestaltR. If you run into problems with installation of the new version, please open a new issue.