new spadesOptions -- spades.reqdPkgsDontLoad - to explicitly prevent loading

DESCRIPTION

@@ -14,8 +14,8 @@ Description: Provides the core framework for a discrete event system to
 URL:
     https://spades-core.predictiveecology.org/,
     https://github.com/PredictiveEcology/SpaDES.core
-Date: 2024-10-13
-Version: 2.1.5.9002
+Date: 2024-11-13
+Version: 2.1.5.9003
 Authors@R: c(
     person("Alex M", "Chubaty", , "achubaty@for-cast.ca", role = c("aut"),
            comment = c(ORCID = "0000-0001-7146-8135")),

NEWS.md

@@ -2,6 +2,11 @@
 
 * fix issue with `Plots()` where plots were discarded if no filename was specified;
 * minor documentation improvements;
+* new option: `spades.reqdPkgsDontLoad`, a character vector. If anything is specified, 
+then it will not be loaded with `require` or `library`, but it will be installed, if needed,
+and if `spades.useRequire = TRUE`, which is the default. Default for this new option is
+"box", which is one of potentially many in the R universe that throws an error if it is 
+loaded.
 
 # SpaDES.core 2.1.5
 

R/options.R

@@ -136,6 +136,11 @@
 #'   and the differences can be seen in a hidden object in the stashed `simList`.
 #'   There is a message which describes how to find that. \cr
 #'
+#'   `spades.reqdPkgsDontLoad` \tab `"box"` \tab Specify any packages that should not
+#'   be \emph{loaded} i.e., no `library` or `require`, but they should be installed if
+#'   listed. The default (`"box"`) is a package that returns a warning if it is
+#'   loaded, and so it is excluded from loading.\cr
+#'
 #'   `spades.saveFileExtensions` \tab `NULL` \tab
 #'   a `data.frame` with 3 columns, `exts`, `fun`, and `package` indicating which
 #'   file extension, and which function from which package will be used when
@@ -217,6 +222,7 @@ spadesOptions <- function() {
     spades.plots = NULL,
     spades.qsThreads = 1L,
     spades.recoveryMode = 1,
+    spades.reqdPkgsDontLoad = "box",
     spades.restartRInterval = 0,
     spades.restartR.clearFiles = TRUE,
     spades.restartR.RDataFilename = "sim_restartR.RData",

R/simulation-parseModule.R

@@ -643,3 +643,15 @@ newEnvsByModule <- function(sim, modu) {
   sim@.xData$.mods[[modu]]$.objects <- new.env(parent = emptyenv())
   sim
 }
+
+
+reqdPkgsDontLoad <- function(allPkgs, pkgsDontLoad = getOption("spades.reqdPkgsDontLoad", NULL)) {
+  if (spadesReqdPkgsDontLoad(pkgsDontLoad)) {
+    allPkgs <- allPkgs[!Require::extractPkgName(allPkgs) %in% pkgsDontLoad]
+  }
+  allPkgs
+}
+
+spadesReqdPkgsDontLoad <- function(pkgsDontLoad) {
+  is.character(pkgsDontLoad)
+}

R/simulation-simInit.R

@@ -1547,9 +1547,18 @@ loadPkgs <- function(reqdPkgs) {
     # Check for SpaDES.core minimum version
     checkSpaDES.coreMinVersion(allPkgs)
     allPkgs <- grep("^SpaDES.core\\>", allPkgs, value = TRUE, invert = TRUE)
+
+    pkgsDontLoad <- getOption("spades.reqdPkgsDontLoad", NULL)
+    allPkgs <- reqdPkgsDontLoad(allPkgs, pkgsDontLoad)
+
     if (getOption("spades.useRequire")) {
       getCRANrepos(ind = 1) # running this first is neutral if it is set
-      Require(allPkgs, standAlone = FALSE, upgrade = FALSE)
+      Require(allPkgs, require = require, standAlone = FALSE, upgrade = FALSE)
+      if (!is.null(pkgsDontLoad)) {
+        verbose <- getOption("reproducible.verbose")
+        Require::Require(pkgsDontLoad, require = FALSE, standAlone = FALSE,
+                         upgrade = FALSE, verbose = verbose - 1)
+      }
       # RequireWithHandling(allPkgs, standAlone = FALSE, upgrade = FALSE)
     } else {
       allPkgs <- unique(Require::extractPkgName(allPkgs))

tests/testthat/test-simulation.R

@@ -1037,3 +1037,63 @@ test_that("debug using logging", {
   })
   expect_true(length(mess1) == 0)
 })
+
+test_that("options('reproducible.reqdPkgsDontLoad", {
+  dontLoad <- "ggplot2" # can't be sp, raster because already loaded
+
+  skip_if_not_installed(dontLoad)
+  unloadNamespace(dontLoad)
+  withr::local_options(spades.reqdPkgsDontLoad = dontLoad)
+
+  testInit()
+
+  newModule("test", tmpdir, open = FALSE)
+
+  # Sept 18 2018 -- Changed to use "seconds" -- better comparison with simple loop
+  cat(file = file.path(tmpdir, "test", "test.R"), '
+    defineModule(sim, list(
+    name = "test",
+    description = "insert module description here",
+    keywords = c("insert key words here"),
+    authors = person(c("Eliot", "J", "B"), "McIntire", email = "eliot.mcintire@nrcan-rncan.gc.ca", role = c("aut", "cre")),
+    childModules = character(0),
+    version = list(SpaDES.core = "0.1.0", test = "0.0.1"),
+    spatialExtent = terra::ext(rep(0, 4)),
+    timeframe = as.POSIXlt(c(NA, NA)),
+    timeunit = "year",
+    citation = list("citation.bib"),
+    documentation = list("README.md", "test.Rmd"),',
+paste0("    reqdPkgs = list(\'", dontLoad, "\'),"),'
+    parameters = rbind(
+    ),
+    inputObjects = bindrows(
+    ),
+    outputObjects = bindrows(
+    )
+    ))
+
+    doEvent.test = function(sim, eventTime, eventType, debug = FALSE) {
+    switch(
+    eventType,
+    init = {
+    })
+    return(invisible(sim))
+    }
+
+', fill = TRUE)
+  expect_false(isNamespaceLoaded(dontLoad))
+  warn <- capture_warnings(
+  sim <- simInit(modules = "test", paths = list(modulePath = tmpdir),
+                   times = list(start = 0, end = 1, timeunit = "year"))
+  )
+  expect_false(isNamespaceLoaded(dontLoad))
+
+  options(spades.reqdPkgsDontLoad = NULL)
+  warn <- capture_warnings(
+    sim <- simInit(modules = "test", paths = list(modulePath = tmpdir),
+                   times = list(start = 0, end = 1, timeunit = "year"))
+  )
+  expect_true(isNamespaceLoaded(dontLoad))
+  unloadNamespace(dontLoad)
+
+})