Install leo.gwas with the most robust path first, then
use fallback commands when specific dependencies fail.
options(timeout = 1000000)
# 1) Install pak
install.packages("pak", repos = "https://cloud.r-project.org")
# 2) Install leo.basic
pak::pkg_install("laleoarrow/leo.basic")
# 3) Use leo.basic helper to install leo.gwas dependencies with multiple CPU cores
leo.basic::install_deps("leo.gwas", ncpus = 8)
# 4) Install leo.gwas
pak::pkg_install("laleoarrow/leo.gwas")If dependency resolution is still unlucky, run the following manually
and retry leo.gwas installation.
# MR-related dependencies
remotes::install_github("MRCIEU/TwoSampleMR")
# PLINK helper (optional; needed for local clumping workflows)
# This package may occasionally fail on CI/source unpack in some environments.
devtools::install_github("explodecomputer/plinkbinr")
# Bioconductor dependency example
BiocManager::install("minfi")
# CatBoost (official binary-installation page)
# https://catboost.ai/docs/en/installation/r-installation-binary-installation
# Recommended binary install command as of 2026-02 (macOS universal2)
pak::pak("url::https://github.com/catboost/catboost/releases/download/v1.2.8/catboost-R-darwin-universal2-1.2.8.tgz")
# Equivalent remotes command example
remotes::install_url(
"https://github.com/catboost/catboost/releases/download/v1.2.8/catboost-R-darwin-universal2-1.2.8.tgz",
INSTALL_opts = c("--no-multiarch", "--no-test-load", "--no-staged-install")
)
# ggrastr fallback
devtools::install_github("VPetukhov/ggrastr", build_vignettes = FALSE)If library(leo.gwas) and
packageVersion("leo.gwas") run successfully, installation
is complete.
catboost, caret, plinkbinr,
and some genomics packages are optional for specific functions.