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[ci] consolidate R package installs into a CI script (#6808)
* [ci] consolidate R package installs into a CI script * use CRAN_MIRROR and R_LIB_PATH consistently * shorter lines and fix reference * fix type option * add extension * fix invocations on Windows * more fixes * binary * use package_type binary on Windows * Update .ci/test-r-package-windows.ps1 * more fixes * Apply suggestions from code review Co-authored-by: Nikita Titov <[email protected]> * make install-r-deps more flexible * Apply suggestions from code review Co-authored-by: Nikita Titov <[email protected]> --------- Co-authored-by: Nikita Titov <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,125 @@ | ||
| # Install R dependencies, using only base R. | ||
| # | ||
| # Supported arguments: | ||
| # | ||
| # --all Install all the 'Depends', 'Imports', 'LinkingTo', and 'Suggests' dependencies | ||
| # (automatically implies --build --test). | ||
| # | ||
| # --build Install the packages needed to build. | ||
| # | ||
| # --exclude=<pkg1,pkg2,...> Comma-delimited list of packages to NOT install. | ||
| # | ||
| # --include=<pkg1,pkg2,...> Comma-delimited list of additional packages to install. | ||
| # These will always be installed, unless also used in "--exclude". | ||
| # | ||
| # --test Install packages needed to run tests. | ||
| # | ||
|
|
||
|
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| # [description] Parse command line arguments into an R list. | ||
| # Returns a list where keys are arguments and values | ||
| # are either TRUE (for flags) or a vector of values passed via a | ||
| # comma-delimited list. | ||
| .parse_args <- function(args) { | ||
| out <- list( | ||
| "--all" = FALSE | ||
| , "--build" = FALSE | ||
| , "--exclude" = character(0L) | ||
| , "--include" = character(0L) | ||
| , "--test" = FALSE | ||
| ) | ||
| for (arg in args) { | ||
| parsed_arg <- unlist(strsplit(arg, "=", fixed = TRUE)) | ||
| arg_name <- parsed_arg[[1L]] | ||
| if (!(arg_name %in% names(out))) { | ||
| stop(sprintf("Unrecognized argument: '%s'", arg_name)) | ||
| } | ||
| if (length(parsed_arg) == 2L) { | ||
| # lists, like "--include=roxygen2,testthat" | ||
| values <- unlist(strsplit(parsed_arg[[2L]], ",", fixed = TRUE)) | ||
| out[[arg_name]] <- values | ||
| } else { | ||
| # flags, like "--build" | ||
| out[[arg]] <- TRUE | ||
| } | ||
| } | ||
| return(out) | ||
| } | ||
|
|
||
| args <- .parse_args( | ||
| commandArgs(trailingOnly = TRUE) | ||
| ) | ||
|
|
||
| # which dependencies to install | ||
| ALL_DEPS <- isTRUE(args[["--all"]]) | ||
| BUILD_DEPS <- ALL_DEPS || isTRUE(args[["--build"]]) | ||
| TEST_DEPS <- ALL_DEPS || isTRUE(args[["--test"]]) | ||
|
|
||
| # force downloading of binary packages on macOS | ||
| COMPILE_FROM_SOURCE <- "both" | ||
| PACKAGE_TYPE <- getOption("pkgType") | ||
|
|
||
| # CRAN has precompiled binaries for macOS and Windows... prefer those, | ||
| # for faster installation. | ||
| if (Sys.info()[["sysname"]] == "Darwin" || .Platform$OS.type == "windows") { | ||
| COMPILE_FROM_SOURCE <- "never" | ||
| PACKAGE_TYPE <- "binary" | ||
| } | ||
| options( | ||
| install.packages.check.source = "no" | ||
| , install.packages.compile.from.source = COMPILE_FROM_SOURCE | ||
| ) | ||
|
|
||
| # always use the same CRAN mirror | ||
| CRAN_MIRROR <- Sys.getenv("CRAN_MIRROR", unset = "https://cran.r-project.org") | ||
|
|
||
| # we always want these | ||
| deps_to_install <- c( | ||
| "data.table" | ||
| , "jsonlite" | ||
| , "Matrix" | ||
| , "R6" | ||
| ) | ||
|
|
||
| if (isTRUE(BUILD_DEPS)) { | ||
| deps_to_install <- c( | ||
| deps_to_install | ||
| , "knitr" | ||
| , "markdown" | ||
| ) | ||
| } | ||
|
|
||
| if (isTRUE(TEST_DEPS)) { | ||
| deps_to_install <- c( | ||
| deps_to_install | ||
| , "RhpcBLASctl" | ||
| , "testthat" | ||
| ) | ||
| } | ||
|
|
||
| # add packages passed through '--include' | ||
| deps_to_install <- unique(c( | ||
| deps_to_install | ||
| , args[["--include"]] | ||
| )) | ||
|
|
||
| # remove packages passed through '--exclude' | ||
| deps_to_install <- setdiff( | ||
| x = deps_to_install | ||
| , args[["--exclude"]] | ||
| ) | ||
|
|
||
| msg <- sprintf( | ||
| "[install-r-deps] installing R packages: %s\n" | ||
| , toString(sort(deps_to_install)) | ||
| ) | ||
| cat(msg) | ||
|
|
||
| install.packages( # nolint[undesirable_function] | ||
| pkgs = deps_to_install | ||
| , dependencies = c("Depends", "Imports", "LinkingTo") | ||
| , lib = Sys.getenv("R_LIB_PATH", unset = .libPaths()[[1L]]) | ||
| , repos = CRAN_MIRROR | ||
| , type = PACKAGE_TYPE | ||
| , Ncpus = parallel::detectCores() | ||
| ) |
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