[r/ci] Set options(pkgType = "binary") for MacOS (#2257)

* [r/ci] Set `options(pkgType = "binary")` for macOS

Force binary-only installation for macOS. By setting as an option in
`~/.Rprofile`; this should affect both package installation and updating
through `utils::install.packages()`, `utils::update.packages()`, and
`remotes::install_deps()`

resolves #2254

.github/workflows/r-ci.yml

@@ -16,7 +16,7 @@ env:
   COVERAGE_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   _R_CHECK_TESTS_NLINES_: 0
   CATCHSEGV: "TRUE"
-  
+
 jobs:
   ci:
     strategy:
@@ -52,6 +52,11 @@ jobs:
       - name: Bootstrap
         run: cd apis/r && tools/r-ci.sh bootstrap
 
+      - name: Set pkgType to binary (macOS)
+        if: ${{ matrix.os == 'macOS-latest' }}
+        run: cat("\noptions(pkgType = 'binary')\n", file = "~/.Rprofile", append = TRUE)
+        shell: Rscript {0}
+
       - name: Install BioConductor package SingleCellExperiment
         run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment
 
@@ -77,6 +82,10 @@ jobs:
       - name: Dependencies
         run: cd apis/r && tools/r-ci.sh install_all
 
+      - name: Install dataset packages from source (macOS)
+        if: ${{ matrix.os == 'macOS-latest' }}
+        run: cd apis/r && _CI_PKG_TYPE_=both _CI_USE_BIOC_=true Rscript tools/install_missing_deps.R
+
       - name: CMake
         uses: lukka/get-cmake@latest
 
@@ -116,4 +125,3 @@ jobs:
       - name: View Logs
         run: apis/r/tools/r-ci.sh dump_logs
         if: failure()
-

apis/r/tools/install_missing_deps.R

@@ -0,0 +1,111 @@
+#!/usr/bin/env Rscript
+
+wd <- Sys.getenv("_CI_WORKING_DIRECTORY_", unset = getwd())
+pkgtype <- Sys.getenv("_CI_PKG_TYPE_", unset = getOption("pkgType"))
+
+if (isTRUE(as.logical(Sys.getenv("_CI_USE_BIOC_")))) {
+  message("Setting up Bioconductor repos")
+  setRepositories(ind = 1:3)
+}
+
+desc <- as.list(x = as.data.frame(x = read.dcf(
+  file = file.path(wd, "DESCRIPTION"),
+  fields = c(
+    "Depends",
+    "Imports",
+    "LinkingTo",
+    "Suggests",
+    "Enhances",
+    "Additional_repositories"
+  )
+)))
+
+desc <- Filter(f = Negate(f = is.na), x = desc)
+
+if (!is.null(desc$Additional_repositories)) {
+  desc$Additional_repositories <- trimws(x = unlist(x = strsplit(
+    x = desc$Additional_repositories,
+    split = ','
+  )))
+}
+
+repos <- c(desc$Additional_repositories, getOption("repos"))
+desc$Additional_repositories <- NULL
+
+message("Identifying dependencies to install")
+desc <- lapply(
+  X = desc,
+  FUN = function(x) {
+    x <- trimws(x = unlist(x = strsplit(x = x, split = ",")))
+    x <- strsplit(x = x, split = " \\(>= ")
+    for (i in seq_along(along.with = x)) {
+      x[[i]][2L] <- x[[i]][2L]
+    }
+    x <- as.data.frame(x = t(x = data.frame(x)))
+    row.names(x = x) <- NULL
+    names(x = x) <- c("Package", "Version")
+    x$Version <- sub(pattern = "\\)$", replacement = "", x = x$Version)
+    if (length(idx <- which(x = x$Package == "R"))) {
+      x <- x[-idx, , drop = FALSE]
+    }
+    if (!nrow(x = x)) {
+      return(x)
+    }
+    x$Version[is.na(x = x$Version)] <- "0.0.0"
+    x$Installed <- logical(length = nrow(x = x))
+    pb <- txtProgressBar(max = nrow(x), style = 3L, file = stderr())
+    on.exit(expr = close(con = pb), add = TRUE)
+    for (i in seq_len(length.out = nrow(x = x))) {
+      x$Installed[i] <- requireNamespace(x$Package[i], quietly = TRUE) &&
+        utils::packageVersion(x$Package[i]) >= x$Version[i]
+      setTxtProgressBar(pb = pb, value = i)
+    }
+    return(x)
+  }
+)
+
+desc <- do.call(what = "rbind", args = desc)
+row.names(x = desc) <- NULL
+
+desc <- desc[!desc$Installed, , drop = FALSE]
+
+if (nrow(x = desc)) {
+  message(
+    "Found ",
+    nrow(x = desc),
+    " missing ",
+    ngettext(n = nrow(x = desc), msg1 = "dependency", msg2 = "dependencies")
+  )
+  message("Finding additional downstream dependencies")
+  db <- utils::available.packages(repos = repos, type = pkgtype)
+  deps <- unique(x = unlist(
+    x = tools::package_dependencies(
+      packages = desc$Package,
+      db = db,
+      recursive = TRUE
+    ),
+    use.names = FALSE
+  ))
+  deps <- setdiff(x = deps, y = c(utils::sessionInfo()$basePkgs, desc$Package))
+  deps <- Filter(
+    f = Negate(f = \(x) isTRUE(requireNamespace(x, quietly = TRUE))),
+    x = deps
+  )
+  if (length(x = deps)) {
+    message(
+      "Found ",
+      length(x = deps),
+      " additional ",
+      ngettext(n = length(x = deps), msg1 = "pacakge", msg2 = "packages")
+    )
+  }
+  pkgs <- union(x = deps, y = desc$Package)
+  message(
+    "Installing ",
+    length(x = pkgs),
+    ngettext(n = length(x = pkgs), msg1 = " package", msg2 = " packages"),
+    ":\n",
+    paste(" -", pkgs, collapse = "\n")
+  )
+  install.packages(pkgs, type = pkgtype, repos = repos)
+}