Use rSharp instead of rClr

.gitignore

@@ -44,3 +44,6 @@ vignettes/*.pdf
 rsconnect/
 doc
 Meta
+
+# test artifacts
+tests/testthat/*.pdf

DESCRIPTION

@@ -3,7 +3,7 @@ Package: ospsuite
 Title: R package to manipulate OSPSuite Models
 Version: 12.0.0
 Authors@R: 
-    c(person("Open-Systems-Pharmacology Community", role = "cph"),
+    c(person("Open-Systems-Pharmacology Community", role = c("cph", "fnd")),
       person("Michael", "Sevestre", role = c("aut", "cre"), email = "michael@design2code.ca"),
       person("Pavel", "Balazki", role = "aut"),
       person("Juri", "Solodenko", role = "aut", comment = c(ORCID = "0000-0001-6922-588X")),
@@ -20,7 +20,7 @@ BugReports:
     https://github.com/open-systems-pharmacology/ospsuite-r/issues
 Depends: 
     R (>= 3.6),
-    rClr (>= 0.9.1)
+    rSharp
 Imports: 
     dplyr (>= 1.0.0),
     ospsuite.utils (>= 1.4.0),

NAMESPACE

@@ -152,7 +152,7 @@ export(validateDimension)
 export(validateUnit)
 import(data.table)
 import(ospsuite.utils)
-import(rClr)
+import(rSharp)
 import(tidyr)
 import(tlf)
 import(xml2)

NEWS.md

@@ -28,6 +28,7 @@
     `quantityOrDimension` (was `dimension` previously). It can now use objects
     of class `Quantity` as inputs, to be consistent with the `toBaseUnit()`
     function.
+  - The package gains a new dependency `{rSharp}`
 
 ## Major Changes
 
@@ -44,6 +45,7 @@
   - `plotPopulationTimeProfile()` has a new `aggregation` argument that allow
     the user to choose between quantiles, arithmetic and geometric aggregations
     of y.
+  - The package loses dependency `{rClr}`
 
 
 ## Minor improvements and bug fixes

R/aging-data.R

@@ -9,35 +9,35 @@ AgingData <- R6::R6Class("AgingData",
   active = list(
     #' @field individualIds Array of individual ids (corresponding to the individualId column of the aging table)
     individualIds = function(value) {
-      private$wrapIntegerProperty("IndividualIds", value)
+      private$.wrapProperty("IndividualIds", value, asInteger = TRUE)
     },
     #' @field parameterPaths Array of parameter paths (corresponding to the ParameterPath column of the aging table)
     parameterPaths = function(value) {
-      private$wrapProperty("ParameterPaths", value)
+      private$.wrapProperty("ParameterPaths", value)
     },
     #' @field times Array of time values (corresponding to the Time column of the aging table)
     times = function(value) {
-      private$wrapProperty("Times", value)
+      private$.wrapProperty("Times", value)
     },
     #' @field values Array of parameter values (corresponding to the Value column of the aging table)
     values = function(value) {
-      private$wrapProperty("Values", value)
+      private$.wrapProperty("Values", value)
     }
   ),
   public = list(
     #' @description
     #' Initialize a new instance of the class
     #' @return A new `OSPSuite.R.Domain.AgingData` object.
     initialize = function() {
-      ref <- rClr::clrNew("OSPSuite.R.Domain.AgingData")
-      super$initialize(ref)
+      netObj <- rSharp::newObjectFromName("OSPSuite.R.Domain.AgingData")
+      super$initialize(netObj)
     },
 
     #' @description
     #' Print the object to the console
     #' @param ... Rest arguments.
     print = function(...) {
-      private$printClass()
+      private$.printClass()
       invisible(self)
     }
   )

R/api-config.R

@@ -9,20 +9,11 @@ ApiConfig <- R6::R6Class(
   active = list(
     #' @field pkParametersFilePath Full path of the pkParameter file
     pkParametersFilePath = function(value) {
-      private$wrapProperty("PKParametersFilePath", value)
+      private$.wrapProperty("PKParametersFilePath", value)
     },
     #' @field dimensionFilePath Full path of the dimension file
     dimensionFilePath = function(value) {
-      private$wrapProperty("DimensionFilePath", value)
-    }
-  ),
-  public = list(
-    #' @description
-    #' Initialize a new instance of the class
-    #' @return A new `ApiConfig` object.
-    initialize = function() {
-      ref <- rClr::clrNew("OSPSuite.R.ApiConfig")
-      super$initialize(ref)
+      private$.wrapProperty("DimensionFilePath", value)
     }
   )
 )

R/application.R

@@ -11,19 +11,19 @@ Application <- R6::R6Class(
     #' @field startTime Start time of application instance (Read-Only)
     startTime = function(value) {
       if (missing(value)) {
-        .toObjectType(private$wrapReadOnlyProperty("StartTime", value), Parameter)
+        .toObjectType(private$.wrapReadOnlyProperty("StartTime", value), Parameter)
       }
     },
     #' @field infusionTime Infusion time of application instance or null if undefined (Read-Only)
     infusionTime = function(value) {
       if (missing(value)) {
-        .toObjectType(private$wrapReadOnlyProperty("InfusionTime", value), Parameter)
+        .toObjectType(private$.wrapReadOnlyProperty("InfusionTime", value), Parameter)
       }
     },
     #' @field drugMass Applied drugmass of the application instance of null if undefined (Read-Only)
     drugMass = function(value) {
       if (missing(value)) {
-        .toObjectType(private$wrapReadOnlyProperty("DrugMass", value), Parameter)
+        .toObjectType(private$.wrapReadOnlyProperty("DrugMass", value), Parameter)
       }
     }
   ),
@@ -32,7 +32,7 @@ Application <- R6::R6Class(
     #' Print the object to the console
     #' @param ... Rest arguments.
     print = function(...) {
-      private$printClass()
+      private$.printClass()
       self$startTime$printValue()
 
       if (!is.null(self$infusionTime)) {

R/container.R

@@ -10,17 +10,17 @@ Container <- R6::R6Class(
   active = list(
     #' @field containerType Type of container
     containerType = function(value) {
-      private$wrapReadOnlyProperty("ContainerTypeAsString", value)
+      private$.wrapReadOnlyProperty("ContainerTypeAsString", value)
     }
   ),
   public = list(
     #' @description
     #' Print the object to the console
     #' @param ... Rest arguments.
     print = function(...) {
-      private$printClass()
-      private$printLine("Container type", self$containerType)
-      private$printLine("Path", self$path)
+      private$.printClass()
+      private$.printLine("Container type", self$containerType)
+      private$.printLine("Path", self$path)
       invisible(self)
     }
   )

R/data-column.R

@@ -12,69 +12,64 @@ DataColumn <- R6::R6Class(
   active = list(
     #' @field values Returns the values defined in the column
     values = function(value) {
-      private$wrapVectorProperty("Value", "ValuesAsArray", value, "ValuesAsArray")
+      private$.wrapVectorProperty("Value", "ValuesAsArray", value, "ValuesAsArray")
     },
     #' @field name Returns the name of the column  (Read-Only)
     name = function(value) {
-      private$wrapReadOnlyProperty("Name", value)
+      private$.wrapReadOnlyProperty("Name", value)
     },
     #' @field unit The base unit in which the values are defined (Read-Only)
     unit = function(value) {
-      if (!missing(value)) {
-        value <- enc2utf8(value)
-      }
-      private$.unit <- private$wrapExtensionMethodCached(WITH_DIMENSION_EXTENSION, "BaseUnitName", "unit", private$.unit, value)
+      private$.unit <- private$.wrapExtensionMethodCached(WITH_DIMENSION_EXTENSION, "BaseUnitName", "unit", private$.unit, value)
       return(private$.unit)
     },
     #' @field displayUnit The unit in which the values should be displayed
     displayUnit = function(value) {
       if (missing(value)) {
-        return(private$wrapExtensionMethod(WITH_DISPLAY_UNIT_EXTENSION, "DisplayUnitName", "displayUnit", value))
+        return(private$.wrapExtensionMethod(WITH_DISPLAY_UNIT_EXTENSION, "DisplayUnitName", "displayUnit", value))
       }
-      value <- enc2utf8(value)
       dimension <- getDimensionByName(self$dimension)
       # we use the ignore case parameter set  to true so that we do not have to worry about casing when set via scripts
-      unit <- rClr::clrCall(dimension, "FindUnit", value, TRUE)
+      unit <- dimension$call("FindUnit", value, TRUE)
       if (is.null(unit)) {
         stop(messages$errorUnitNotSupported(unit = value, dimension = self$dimension))
       }
-      rClr::clrSet(self$ref, "DisplayUnit", unit)
+      self$set("DisplayUnit", unit)
     },
     #' @field dimension The dimension of the values
     dimension = function(value) {
       if (missing(value)) {
         if (is.null(private$.dimension)) {
-          private$.dimension <- private$wrapExtensionMethodCached(WITH_DIMENSION_EXTENSION, "DimensionName", "dimension", private$.dimension, value)
+          private$.dimension <- private$.wrapExtensionMethodCached(WITH_DIMENSION_EXTENSION, "DimensionName", "dimension", private$.dimension, value)
         }
         return(private$.dimension)
       }
-      value <- enc2utf8(value)
       # updating the dimension
-      rClr::clrSet(self$ref, "Dimension", getDimensionByName(value))
+      self$set("Dimension", getDimensionByName(value))
       private$.dimension <- NULL
       private$.unit <- NULL
     },
     #' @field molWeight Molecular weight of associated observed data in internal unit
     #' In no molecular weight is defined, the value is `NULL`
     molWeight = function(value) {
-      dataInfo <- rClr::clrGet(self$ref, "DataInfo")
+      dataInfo <- self$get("DataInfo")
       if (missing(value)) {
-        return(rClr::clrGet(dataInfo, "MolWeight"))
+        return(dataInfo$get("MolWeight"))
       }
 
       validateIsNumeric(value)
-      rClr::clrSet(dataInfo, "MolWeight", value)
+      dataInfo$set("MolWeight", value)
     },
     #' @field LLOQ Lower Limit Of Quantification.
     #' In no LLOQ is defined, the value is `NULL`
     LLOQ = function(value) {
-      dataInfo <- rClr::clrGet(self$ref, "DataInfo")
+      dataInfo <- self$get("DataInfo")
       if (missing(value)) {
-        return(rClr::clrGet(dataInfo, "LLOQAsDouble"))
+        return(dataInfo$get("LLOQAsDouble"))
       }
 
       validateIsNumeric(value)
-      rClr::clrSet(dataInfo, "LLOQAsDouble", value)
+      dataInfo$set("LLOQAsDouble", value)
     }
   ),
   public = list(
@@ -83,9 +78,9 @@ DataColumn <- R6::R6Class(
     #' @param ... Rest arguments.
     print = function(...) {
       if (self$unit == "") {
-        private$printLine(self$name)
+        private$.printLine(self$name)
       } else {
-        private$printLine(self$name, paste0("base unit: [", self$unit, "]"))
+        private$.printLine(self$name, paste0("base unit: [", self$unit, "]"))
       }
       invisible(self)
     }