update_install_R.R

## Create the install.R file dynamically from the project's dependencies
## =====================================================================

## Milan Malfait
## 2022/01/28


## Find all project dependencies
deps <- renv::dependencies()
deps <- unique(deps$Package)
deps <- deps[!(deps %in% c("BiocManager", "renv"))] # don't include these

## Get source repositories from renv.lock file
lock <- jsonlite::read_json("renv.lock")
bioc_ver <- lock$Bioconductor$Version
lock_pkgs <- lock$Packages
pkgs <- lock_pkgs[names(lock_pkgs) %in% deps]
is_gh <- vapply(pkgs, function(x) x$Source == "GitHub", logical(1))

gh_pkgs <- pkgs[is_gh]
gh_pkg_remotes <- vapply(gh_pkgs, function(x) {
    sprintf("%s/%s@%s", x$RemoteUsername, x$RemoteRepo, x$RemoteRef)
}, character(1))

to_install <- names(pkgs)
to_install[which(is_gh)] <- gh_pkg_remotes[names(which(is_gh))]

## Write the install.R file
out_file <- file("install.R")
writeLines(
    paste(
        "## This file is generated by `update_install_R.R`, DO NOT EDIT BY HAND!!!",
        '\ninstall.packages(c("remotes", "BiocManager"))',
        paste0('BiocManager::install(version = "', bioc_ver, '")'),
        "\nBiocManager::install(c(",
        paste("  ", sub("(.*)", '"\\1"', to_install), collapse = ",\n"),
        "))",
        sep = "\n"
    ),
    con = out_file
)
close(out_file)