Verbose mod output

.github/workflows/draft-pdf.yml

@@ -33,3 +33,4 @@ jobs:
     #     message: '(auto) Paper PDF Draft'
     #     # This should be the path to the paper within your repo.
     #     add: 'paper/paper.pdf'
+

.github/workflows/main.yml

@@ -14,6 +14,7 @@ jobs:
 
   check:
     runs-on: ${{ matrix.config.os }}
+    timeout-minutes: 30 # Set timeout for this job to 30 minutes
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     strategy:
       fail-fast: false

.gitignore

@@ -8,6 +8,7 @@ MCSimMod.Rproj
 *.dll
 *.so
 *.html
+*.DS_Store
 
 mcsimmod_*.model
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MCSimMod
 Title: Working with 'MCSim' Models
-Version: 1.0
+Version: 1.0.9000
 Authors@R: c(
   person("Dustin F.", "Kapraun", role=c("aut", "cre"), email = "kapraun.dustin@epa.gov", comment = c(ORCID = "0000-0001-5570-6383")),
   person("Todd J.", "Zurlinden", role="aut", comment = c(ORCID = "0000-0003-1372-3913")),
@@ -26,7 +26,7 @@ Suggests:
   testthat (>= 3.0.0)
 Config/Needs/dev:
   devtools,
-  styler (== 1.10.3),
+  styler (== 1.11.0),
   testthat,
   covr
 Config/Needs/website:

R/MCSim_model.R

@@ -31,10 +31,11 @@ Model <- setRefClass("Model",
     #' @field parms Named vector of parameter values for the associated MCSim model.
     #' @field Y0 Named vector of initial conditions for the state variables of the associated MCSim model.
     #' @field paths List of character strings that are names of files associated with the model.
-    #' @field writeTemp Boolean specifying whether to write model files to a temporary directory. If value is TRUE, model files will be Written to a temporary directory; if value is FALSE, model files will be Written to the same directory that contains the model specification file.
+    #' @field writeTemp Boolean specifying whether to write model files to a temporary directory. If value is TRUE, model files will be written to a temporary directory; if value is FALSE, model files will be written to the same directory that contains the model specification file.
+    #' @field verboseOutput Boolean specifying whether to write translator messages to standard output. If value is TRUE, messages will be written to standard output; if value is FALSE, messages will be written to files in a temporary directory.
     mName = "character", mString = "character", initParms = "function",
     initStates = "function", Outputs = "ANY", parms = "numeric", Y0 = "numeric",
-    paths = "list", writeTemp = "logical"
+    paths = "list", writeTemp = "logical", verboseOutput = "logical"
   ),
   methods = list(
     initialize = function(...) {
@@ -97,7 +98,7 @@ Model <- setRefClass("Model",
       #    specification file has been changed since the last translation and
       #    compiling.
       if (!file.exists(paths$dll_file) | (force) | (!hash_exists) | (hash_exists & hash_has_changed)) {
-        compileModel(paths$model_file, paths$c_file, paths$dll_name, paths$dll_file, hash_file = paths$hash_file)
+        compileModel(paths$model_file, paths$c_file, paths$dll_name, paths$dll_file, hash_file = paths$hash_file, verbose_output = verboseOutput)
       }
 
       # Load the compiled model (DLL).

R/compileModel.R

@@ -9,11 +9,12 @@
 #' @param dll_name Name of a DLL or SO file without the extension (".dll" or ".so").
 #' @param dll_file Name of the same DLL or SO file with the appropriate extension (".dll" or ".so").
 #' @param hash_file Name of a file containing a hash key for determining if `model_file` has changed since the previous translation and compilation.
+#' @param verbose_output Boolean specifying whether to write translator messages to standard output. If value is TRUE, messages will be written to standard output; if value is FALSE, messages will be written to files in a temporary directory.
 #' @returns No return value. Creates files and saves them in locations specified by function arguments.
 #' @import tools
 #' @useDynLib MCSimMod, .registration=TRUE
 #' @export
-compileModel <- function(model_file, c_file, dll_name, dll_file, hash_file = NULL) {
+compileModel <- function(model_file, c_file, dll_name, dll_file, hash_file = NULL, verbose_output = FALSE) {
   # Unload DLL if it has been loaded.
   if (is.loaded("derivs", PACKAGE = dll_name)) {
     dyn.unload(dll_file)
@@ -34,38 +35,61 @@ compileModel <- function(model_file, c_file, dll_name, dll_file, hash_file = NUL
   mod_output <- paste(mod_output, collapse = "\n")
 
   # Save the translator output to a file.
-  temp_directory <- tempdir()
-  out_file <- file.path(temp_directory, "mod_output.txt")
-  write(mod_output, file = out_file)
+  if (!verbose_output) {
+    temp_directory <- tempdir()
+    out_file <- file.path(temp_directory, "mod_output.txt")
+    write(mod_output, file = out_file)
+  }
 
   # Check to see if there was an error during translation. If so, print a
-  # message about the location of the translation log file and stop execution.
+  # message about where to find full details and stop execution.
   if (grepl("*** Error:", mod_output, fixed = TRUE)) {
-    stop(
-      "An error was identified when translating the MCSim model specification ",
-      "text to C. Full details are available in the file ",
-      normalizePath(out_file), "."
-    )
+    if (verbose_output) {
+      stop(
+        "An error was identified when translating the MCSim model ",
+        "specification text to C. Full details follow.\n", mod_output
+      )
+    } else {
+      stop(
+        "An error was identified when translating the MCSim model ",
+        "specification text to C. Full details are available in the file ",
+        normalizePath(out_file), "."
+      )
+    }
   }
 
   # Check to see if there was a warning during translation. If so, print a
   # message about the location of the translation log file and raise a warning.
   else if (grepl("*** Warning:", mod_output, fixed = TRUE)) {
-    warning(
-      "A warning was identified when translating the MCSim model ",
-      "specification text to C. Full details are available in the file ",
-      normalizePath(out_file), ".\n"
-    )
+    if (verbose_output) {
+      warning(
+        "A warning was generated when translating the MCSim model ",
+        "specification text to C. Full details follow.\n", mod_output
+      )
+    } else {
+      warning(
+        "A warning was generated when translating the MCSim model ",
+        "specification text to C. Full details are available in the file ",
+        normalizePath(out_file), ".\n"
+      )
+    }
   }
 
   # If there was no error or warning during translation, just print a message
   # about the location of the translation log file.
   else {
-    message(
-      "Translation of model specification text complete. Full details are ",
-      "available in the file ",
-      normalizePath(out_file), ".\n"
-    )
+    if (verbose_output) {
+      message(
+        "Translation of model specification text complete. Full details ",
+        "follow.\n", mod_output
+      )
+    } else {
+      message(
+        "Translation of model specification text complete. Full details are ",
+        "available in the file ",
+        normalizePath(out_file), ".\n"
+      )
+    }
   }
 
   # Compile the C model to obtain an object file (ending with ".o") and a

R/createModel.R

@@ -24,8 +24,9 @@
 #' @param mName Name of an MCSim model specification file, excluding the file name extension `.model`.
 #' @param mString A character string containing MCSim model specification text.
 #' @param writeTemp Boolean specifying whether to write model files to a temporary directory. If value is TRUE (the default), model files will be Written to a temporary directory; if value is FALSE, model files will be Written to the same directory that contains the model specification file.
+#' @param verboseOutput Boolean specifying whether to write translator messages to standard output. If value is TRUE, messages will be written to standard output; if value is FALSE, messages will be written to files in a temporary directory.
 #' @returns Model object.
 #' @export
-createModel <- function(mName = character(0), mString = character(0), writeTemp = TRUE) {
-  return(Model(mName = mName, mString = mString, writeTemp = writeTemp))
+createModel <- function(mName = character(0), mString = character(0), writeTemp = TRUE, verboseOutput = FALSE) {
+  return(Model(mName = mName, mString = mString, writeTemp = writeTemp, verboseOutput = verboseOutput))
 }

README.md

@@ -72,8 +72,8 @@ R -e "covr::report(file = 'coverage_html/index.html')"
 ## Code Formatting
 To maintain a consistent format for all `MCSimMod` source code, we use the [styler](https://styler.r-lib.org/) package to format R code. Note that we use a specific version of the package.
 ```R
-# Install version 1.10.3 of the styler package.
-install.packages("styler", version = "1.10.3")
+# Install version 1.11.0 of the styler package.
+install.packages("styler", version = "1.11.0")
 
 # Apply styler format conventions to all files in the package.
 styler::style_pkg(".")

tests/testthat/test-compileModel.R

@@ -33,6 +33,6 @@ testthat::test_that("compileModel::warning", {
   model <- createModel(mString = modelString)
   testthat::expect_warning(
     model$loadModel(),
-    "A warning was identified when translating the MCSim model specification"
+    "A warning was generated when translating the MCSim model specification"
   )
 })