EVOLUTION-MANAGER

Edit File: installRub.r

#!/usr/bin/r # # A installer for r-universe binaries (on Ubuntu 'jammy' only) # # Copyright (C) 2023 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) library(utils) # for osVersion rver <- gsub("^([\\d].[\\d]).*$", "\\1", as.character(getRversion()), perl=TRUE) uburel <- "jammy" ## configuration for docopt doc <- paste0("Usage: installRub.r [-h] [-x] [-k] [-r REL] [-v VER] [-u UNIV] PACKAGES -u --universe UNIV required argument specifying universe [default: ] -v --version VER R 'major.minor' version release pair to install for [default: ", rver, "] -r --release REL Ubuntu LTS release to install to install for [default: ", uburel, "] -k --keepoption so not set option 'bspm.version.check' to 'TRUE' as is default -h --help show this help text -x --usage show help and short example usage. PACKAGES can also be a shorthand 'package@universe'. See '-x | --usage' for more.") opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("In general, PACKAGES... can be one or more R package names available in then selected r-universe repository; its CRAN (as well as some core BioConductor) dependencies will be provided automatically by r2u. It can also be a shorthand 'package@universe'. Note that while CRAN works extremely hard to always provide an installable set of working packages, r-universe works under a different model and its packages cannot offer any such guarantees. Also note that while we use 'r2u' for the CRAN (and, to some extend, BioConductor) parts full-filling *all* dependencies completely, the binaries from r-universe do not carry any (system-)dependency info so you may end up with missing libries you may need to add. Where an r-universe package exists on CRAN you can cover your ground by first installing the CRAN version and then the r-universe version. Examples: installRub.r -u rcppcore Rcpp RcppArmadillo # installs (never than CRAN / r2u) Rcpp(Armadillo) installRub.r -u eddelbuettel RcppKalman # installs non-CRAN package RcppKalman installRub.r rcpp@rcppcore # alternate to install Rcpp from RcppCore universe installRub.r polars@rpolars # alternate to install polars from rpolars universe installRub.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (getRversion() < "4.2.0") stop("R version 4.2.0 or later is required.", call. = FALSE) if (!exists("osVersion")) stop("Cannot find 'osVersion'. Weird.", call. = FALSE) if (!startsWith(utils::osVersion, "Ubuntu")) stop("Ubuntu is required as host system.", call. = FALSE) if (!requireNamespace("bspm", quietly=TRUE)) stop("The 'bspm' package is required.", call. = FALSE) if (is.null(opt$universe) && length(opt$PACKAGES) == 1) { tokens <- strsplit(opt$PACKAGES, "@")[[1]] opt$PACKAGES <- tokens[1] opt$universe <- tokens[2] } univ <- paste0("https://", opt$universe, ".r-universe.dev/bin/linux/", opt$release, "/", opt$version) if (!opt$keepoption) options(bspm.version.check=TRUE) install.packages(pkgs = opt$PACKAGES, repos = c(univ, "https://cloud.r-project.org"))