Use box for package isolation in modules

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: 2025-01-17
+Version: 2.1.5.9008
 Authors@R: c(
     person("Alex M", "Chubaty", , "[email protected]", role = c("aut"),
            comment = c(ORCID = "0000-0001-7146-8135")),
@@ -31,8 +31,9 @@ Authors@R: c(
 Depends:
     R (>= 4.2),
     quickPlot (>= 1.0.2),
-    reproducible (>= 2.1.1)
+    reproducible (>= 2.1.2.9006)
 Imports:
+    box,
     cli,
     data.table (>= 1.11.0),
     fs,
@@ -51,11 +52,13 @@ Suggests:
     CircStats,
     codetools,
     covr,
+    DBI,
     DiagrammeR (>= 0.8.2),
     future,
     future.callr,
     ggplot2,
     ggplotify,
+    gitcreds,
     httr,
     knitr,
     lattice,
@@ -102,6 +105,7 @@ Collate:
     'code-checking.R'
     'convertToPackage.R'
     'copy.R'
+    'createDESCRIPTIONandDocs.R'
     'debugging.R'
     'downloadData.R'
     'simulation-parseModule.R'

NAMESPACE

@@ -84,6 +84,7 @@ export(conditionalEvents)
 export(convertTimeunit)
 export(convertToPackage)
 export(copyModule)
+export(createDESCRIPTIONandDocs)
 export(createsOutput)
 export(current)
 export(currentModule)
@@ -187,6 +188,7 @@ export(restartSpades)
 export(rndstr)
 export(saveFiles)
 export(saveSimList)
+export(saveState)
 export(savedSimEnv)
 export(scheduleConditionalEvent)
 export(scheduleEvent)
@@ -397,6 +399,7 @@ importFrom(reproducible,.cacheMessageObjectToRetrieve)
 importFrom(reproducible,.checkCacheRepo)
 importFrom(reproducible,.file.move)
 importFrom(reproducible,.grepSysCalls)
+importFrom(reproducible,.objSizeWithTry)
 importFrom(reproducible,.orderDotsUnderscoreFirst)
 importFrom(reproducible,.preDigestByClass)
 importFrom(reproducible,.prepareOutput)

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/Plots.R

@@ -147,6 +147,7 @@ ggplotClassesCanHandle <- c("eps", "ps", "tex", "pdf", "jpeg", "tiff", "png", "b
 #'             .plotInitialTime = 1)
 #'     }
 #'   } # end ggplot
+#'   unlink("figures") # clean up
 #' } # end of dontrun
 Plots <- function(data, fn, filename,
                   types = quote(params(sim)[[currentModule(sim)]]$.plots),
@@ -333,7 +334,7 @@ Plots <- function(data, fn, filename,
   }
 
   if (needSaveRaw) {
-    if (is(data, "Raster")) {
+    if (is(data, "Raster") || is(data, "SpatRaster")) {
       rasterFilename <- file.path(path, paste0(filename, "_data.tif"))
       writeRaster(data, filename = rasterFilename, overwrite = TRUE)
       if (exists("sim", inherits = FALSE))
@@ -355,7 +356,6 @@ Plots <- function(data, fn, filename,
         )
     }
   }
-
   if (needSave) {
     if (is.null(simIsIn)) {
       if (is.call(path))

R/cache.R

@@ -424,6 +424,7 @@ setMethod(
   definition = function(object, preDigest, origArguments, ...) {
     dots <- list(...)
     whSimList <- which(unlist(lapply(origArguments, is, "simList")))[1]
+    whSimList <- names(whSimList)
 
     # remove the "newCache" attribute, which is irrelevant for digest
     if (!is.null(attr(object, ".Cache")$newCache)) {
@@ -684,8 +685,10 @@ setMethod(
           }
           # Now changed objects
           if (length(unlist(changedModEnvObjs))) {
+            # if (identical(currentModule(object), "canClimateData")) browser()
             Map(nam = names(changedModEnvObjs), objs = changedModEnvObjs, function(nam, objs) {
-              objNames <- names(objs$.objects)
+              objNames <- names(objs$.objects) # used to be "names(...)" -- but don't want `._` objs
+              objNames <- grep("^._.+", objNames, value = TRUE, invert = TRUE)
               if (!is.null(objNames))
                 list2env(mget(objNames, envir = [email protected]$.mods[[nam]][[".objects"]]),
                          envir = [email protected]$.mods[[nam]][[".objects"]])
@@ -914,7 +917,7 @@ if (!exists("objSize")) {
 #' and the other slots in the `simList` (e.g., events, completed, modules, etc.).
 #' The returned object also has an attribute, "total", which shows the total size.
 #'
-#' @importFrom reproducible objSize
+#' @importFrom reproducible objSize .objSizeWithTry
 #' @importFrom lobstr obj_size
 #' @inheritParams reproducible::objSize
 #'
@@ -925,18 +928,27 @@ if (!exists("objSize")) {
 #' a <- simInit(objects = list(d = 1:10, b = 2:20))
 #' objSize(a)
 #' utils::object.size(a)
-objSize.simList <- function(x, quick = TRUE, ...) {
+objSize.simList <- function(x, quick = FALSE, recursive = FALSE, ...) {
 
-  total <- obj_size(x, quick = TRUE)
-  aa <- objSize([email protected], quick = quick, ...)
+  total <- .objSizeWithTry(x)
+  # total <- try(obj_size(x, quick = TRUE), silent = TRUE) # failing due to lobstr issue #72
+  if (!is(total, "try-error") && isTRUE(recursive)) {
+    aa <- objSize([email protected], quick = quick, recursive = recursive, ...)
 
-  simSlots <- grep("^\\.envir$|^\\.xData$", slotNames(x), value = TRUE, invert = TRUE)
-  names(simSlots) <- simSlots
-  otherParts <- objSize(lapply(simSlots, function(slotNam) slot(x, slotNam)), quick = quick, ...)
+    simSlots <- grep("^\\.envir$|^\\.xData$", slotNames(x), value = TRUE, invert = TRUE)
+    names(simSlots) <- simSlots
+    otherParts <- objSize(lapply(simSlots, function(slotNam) slot(x, slotNam)), quick = quick, ...)
 
-  if (!quick)
-    attr(total, "objSizes") <- list(sim = attr(aa, "objSize"),
-                                    other = attr(otherParts, "objSize"))
+    # if (!quick)
+    attr(total, "objSize") <- list(sim = attr(aa, "objSize"),
+                                   other = attr(otherParts, "objSize"))
+      # browser()
+      # attr(total, "objSize") <- sum(unlist(attr(aa, "objSize")), unlist(attr(otherParts, "objSize")))
+      # class(attr(total, "objSize")) <- "lobstr_bytes"
+
+  } # else {
+  #   total <- NA
+  # }
 
   return(total)
 }
@@ -961,7 +973,7 @@ objSize.simList <- function(x, quick = TRUE, ...) {
 .wrap.simList <- function(obj, cachePath, preDigest, drv = getOption("reproducible.drv", NULL),
                           conn = getOption("reproducible.conn", NULL),
                           verbose = getOption("reproducible.verbose"),
-                          outputObjects = NULL,
+                          outputObjects = NULL, cacheId,
                           ...) {
 
   # Copy everything (including . and ._) that is NOT a main object -- objects are the potentially very large things
@@ -987,7 +999,7 @@ objSize.simList <- function(x, quick = TRUE, ...) {
   # Deal with the potentially large things -- convert to list -- not a copy
   obj2 <- as.list(obj, all.names = FALSE) # don't copy the . or ._ objects, already done
   # Now the individual objects
-  out <- .wrap(obj2, cachePath = cachePath, outputObjects = outputObjects,
+  out <- .wrap(obj2, cachePath = cachePath, outputObjects = outputObjects, cacheId = cacheId,
                drv = drv, conn = conn, verbose = verbose, ...)
 
   # for (objName in names(out)) obj[[objName]] <- NULL