tutorial-jana2/bin/dependencies.R

0001 install_required_packages <- function(lib = NULL, repos = getOption("repos", default = c(CRAN = "https://cran.rstudio.com/"))) {
0002
0003   if (is.null(lib)) {
0004     lib <- .libPaths()[[1]]
0005   }
0006
0007   message("lib paths: ", paste(lib, collapse = ", "))
0008   # Note: RMarkdown is needed for renv to detect packages in Rmd documents.
0009   required_pkgs <- c("rprojroot", "desc", "remotes", "renv", "BiocManager", "rmarkdown")
0010   installed_pkgs <- rownames(installed.packages(lib.loc = lib))
0011   missing_pkgs <- setdiff(required_pkgs, installed_pkgs)
0012
0013   # The default installation of R will have "@CRAN@" as the default repository,
0014   # which directs contrib.url() to either force the user to choose a mirror if
0015   # interactive or fail if not. Since we are not interactve, we need to force
0016   # the mirror here.
0017   if ("@CRAN@" %in% repos) {
0018     repos <- c(CRAN = "https://cran.rstudio.com/")
0019   }
0020
0021   if (length(missing_pkgs) != 0) {
0022     install.packages(missing_pkgs, lib = lib, repos = repos)
0023   }
0024 }
0025
0026 find_root <- function() {
0027
0028   cfg  <- rprojroot::has_file_pattern("^_config.y*ml$")
0029   root <- rprojroot::find_root(cfg)
0030
0031   root
0032 }
0033
0034 # set the BiocManager repositories and return a function that resets the default
0035 # repositories.
0036 #
0037 # @example
0038 # bioc_repos_example <- function() {
0039 #   message("User repos")
0040 #   as.data.frame(getOption("repos"))
0041 #   reset_repos <- use_bioc_repos()
0042 #   on.exit(reset_repos())
0043 #   message("Bioc repos")
0044 #   as.data.frame(getOption("repos"))
0045 # }
0046 # bioc_repos_example()
0047 # as.data.frame(getOption("repos")
0048 use_bioc_repos <- function() {
0049   repos <- getOption("repos")
0050   suppressMessages(options(repos = BiocManager::repositories()))
0051   function() {
0052     options(repos = repos)
0053   }
0054 }
0055
0056 identify_dependencies <- function() {
0057
0058   root <- find_root()
0059
0060   reset_repos <- use_bioc_repos()
0061   on.exit(reset_repos(), add = TRUE)
0062   eps <- file.path(root, "_episodes_rmd")
0063   bin <- file.path(root, "bin")
0064
0065   required_pkgs <- unique(c(
0066     ## Packages for episodes
0067     renv::dependencies(eps, progress = FALSE, error = "ignored")$Package,
0068     ## Packages for tools
0069     renv::dependencies(bin, progress = FALSE, error = "ignored")$Package
0070   ))
0071
0072   required_pkgs
0073 }
0074
0075 create_description <- function(required_pkgs) {
0076   d <- desc::description$new("!new")
0077   d$set_deps(data.frame(type = "Imports", package = required_pkgs, version = "*"))
0078   d$write("DESCRIPTION")
0079   # We have to write the description twice to get the hidden dependencies
0080   # because renv only considers explicit dependencies.
0081   #
0082   # This is needed because some of the hidden dependencis will require system
0083   # libraries to be configured.
0084   suppressMessages(repo <- BiocManager::repositories())
0085   deps <- remotes::dev_package_deps(dependencies = TRUE, repos = repo)
0086   deps <- deps$package[deps$diff < 0]
0087   if (length(deps)) {
0088     # only create new DESCRIPTION file if there are dependencies to install
0089     d$set_deps(data.frame(type = "Imports", package = deps, version = "*"))
0090     d$write("DESCRIPTION")
0091   }
0092 }
0093
0094 install_dependencies <- function(required_pkgs, ...) {
0095
0096   reset_repos <- use_bioc_repos()
0097   on.exit(reset_repos(), add = TRUE)
0098
0099   create_description(required_pkgs)
0100   on.exit(file.remove("DESCRIPTION"), add = TRUE)
0101   remotes::install_deps(dependencies = TRUE, ...)
0102
0103   if (require("knitr") && packageVersion("knitr") < '1.9.19') {
0104     stop("knitr must be version 1.9.20 or higher")
0105   }
0106
0107 }