Change unit tests to use datasets from packages installed by default …

…with R.

R.NET/Factor.cs

@@ -25,17 +25,18 @@ protected internal Factor(REngine engine, IntPtr coerced)
         { }
 
         /// <summary>
-        /// Gets the levels of the factor.
+        /// Gets the levels of this factor.
         /// </summary>
+        /// <returns>Levels of this factor</returns>
         public string[] GetLevels()
         {
             return GetAttribute(Engine.GetPredefinedSymbol("R_LevelsSymbol")).AsCharacter().ToArray();
         }
 
         /// <summary>
-        /// Gets the levels of the factor.
+        /// Gets the values in this factor.
         /// </summary>
-        /// <returns>Factors.</returns>
+        /// <returns>Values of this factor</returns>
         public string[] GetFactors()
         {
             var levels = GetLevels();

R.NET/Function.cs

@@ -72,7 +72,7 @@ protected SymbolicExpression InvokeViaPairlist(string[] argNames, SymbolicExpres
         {
             var names = new CharacterVector(Engine, argNames);
             var arguments = new GenericVector(Engine, args);
-            arguments.SetAttribute(Engine.GetPredefinedSymbol("R_NamesSymbol"), names);
+            arguments.SetNames(names);
             var argPairList = arguments.ToPairlist();
 
             //IntPtr newEnvironment = Engine.GetFunction<Rf_allocSExp>()(SymbolicExpressionType.Environment);

R.NET/GenericVector.cs

@@ -133,13 +133,20 @@ public override DynamicMetaObject GetMetaObject(System.Linq.Expressions.Expressi
             return new ListDynamicMeta(parameter, this);
         }
 
-        public void SetNames(string[] names) {
-            if (names.Length != this.Length) {
-                throw new ArgumentException ("Names vector must be same length as list");
+        public void SetNames(params string[] names)
+        {
+            CharacterVector cv = new CharacterVector(this.Engine, names);
+            SetNames(cv);
+        }
+
+        public void SetNames(CharacterVector names)
+        {
+            if (names.Length != this.Length)
+            {
+                throw new ArgumentException("Names vector must be same length as list");
             }
-            CharacterVector cv = new CharacterVector (this.Engine, names);
             SymbolicExpression namesSymbol = Engine.GetPredefinedSymbol("R_NamesSymbol");
-            SetAttribute (namesSymbol, cv);
+            SetAttribute(namesSymbol, names);
         }
     }
 }

R.NET/Properties/VersionInfo.cs

@@ -10,5 +10,5 @@
 // You can specify all the values or you can default the Build and Revision Numbers
 // by using the '*' as shown below:
 // [assembly: AssemblyVersion("1.0.*")]
-[assembly: AssemblyVersion("1.5.22.0")]
-[assembly: AssemblyInformationalVersion("1.5.22.0")]
+[assembly: AssemblyVersion("1.6.1.0")]
+[assembly: AssemblyInformationalVersion("1.6.1.0")]

R.NET/REngine.cs

@@ -845,8 +845,8 @@ public void ClearGlobalEnvironment(bool garbageCollectR = true, bool garbageColl
             this.Evaluate(rmStatement);
             if (garbageCollectDotNet)
             {
-                dotNetCollectAndWait();
-                dotNetCollectAndWait();
+                DoDotNetGarbageCollection();
+                DoDotNetGarbageCollection();
             }
             if (garbageCollectR)
                 ForceGarbageCollection();
@@ -864,7 +864,10 @@ private void doDetachPackages(string[] toDetach)
             }
         }
 
-        private static void dotNetCollectAndWait()
+        /// <summary>
+        /// Triggers a .NET garbage collection. May be useful in some testing circumstance, but users should avoid using this.
+        /// </summary>
+        public static void DoDotNetGarbageCollection()
         {
             GC.Collect();
             GC.WaitForPendingFinalizers();

RDotNet.TestBase/RDotNetTestFixture.cs

@@ -63,9 +63,10 @@ protected static double GetRMemorySize(REngine engine)
 
         protected static void GarbageCollectRandClr(REngine engine)
         {
-            GC.Collect();
-            // it seems important to call gc() twice to get a proper baseline.
+            // it seems needed to call gc() twice to get a proper baseline.
+            REngine.DoDotNetGarbageCollection();
             engine.ForceGarbageCollection();
+            REngine.DoDotNetGarbageCollection();
             engine.ForceGarbageCollection();
         }
 

RDotNet.Tests/DataFrameTest.cs

@@ -25,19 +25,41 @@ public void TestIsDataFrameFalse()
         public void TestDataFrameFactorColumns()
         {
             var engine = this.Engine;
-            // TODO: move to use a package installed by default with R
-            var mpg = getMpgDataFrame(engine);
-            var manufacturer = mpg[0].AsFactor().GetFactors();
-            Assert.AreEqual("audi", manufacturer[0]);
-            manufacturer = mpg[0].AsCharacter().ToArray();
-            Assert.AreEqual("audi", manufacturer[0]);
+            var biopsy = getBiopsyDataFrame(engine);
+            //$ class: Factor w/ 2 levels "benign","malignant": 1 1 1 1 1 2 1 1 1 1 ...
+            var factor = biopsy[10].AsFactor();
+            var classFact = factor.GetFactors();
+            Assert.AreEqual(699, classFact.Length);
+            Assert.AreEqual("benign", classFact[0]);
+            Assert.AreEqual("malignant", classFact[5]);
+            var levels = factor.GetLevels();
+            Assert.AreEqual(2, levels.Length);
+            Assert.AreEqual("benign", levels[0]);
+            Assert.AreEqual("malignant", levels[1]);
+
+            // Check that we get the following:
+//> head(as.character(biopsy$class))
+            //[1] "benign"    "benign"    "benign"    "benign"    "benign"    "malignant"
+            //   NOT:
+            //[1] "1"    "1"    "1"    "1"    "1"    "2" 
+            checkClassString(factor.AsCharacter().ToArray());
+            checkClassString(biopsy[10].AsCharacter().ToArray());
+
         }
 
-        private static DataFrame getMpgDataFrame(REngine engine)
+        private static void checkClassString(string[] values)
         {
-            engine.Evaluate("data(mpg, package='ggplot2')");
-            var mpg = engine.Evaluate("mpg").AsDataFrame();
-            return mpg;
+            Assert.AreEqual(699, values.Length);
+            for (int i = 0; i < 5; i++)
+                Assert.AreEqual("benign", values[i]);
+            Assert.AreEqual("malignant", values[5]);
+        }
+
+        private static DataFrame getBiopsyDataFrame(REngine engine)
+        {
+            engine.Evaluate("data(biopsy, package='MASS')");
+            var biopsy = engine.Evaluate("biopsy").AsDataFrame();
+            return biopsy;
         }
 
         //[Test]
@@ -101,46 +123,47 @@ private static IEnumerable[] createTestDfColumns()
         public void TestDataElementTwoDimIndex()
         {
             var engine = this.Engine;
-            var mpg = getMpgDataFrame(engine);
+            var biopsy = getBiopsyDataFrame(engine);
 
             /*
-              manufacturer model displ year cyl      trans drv cty hwy fl   class
-   1         audi    a4   1.8 1999   4   auto(l5)   f  18  29  p compact
-   2         audi    a4   1.8 1999   4 manual(m5)   f  21  29  p compact
-   3         audi    a4   2.0 2008   4 manual(m6)   f  20  31  p compact
-   4         audi    a4   2.0 2008   4   auto(av)   f  21  30  p compact
-   5         audi    a4   2.8 1999   6   auto(l5)   f  16  26  p compact
-   6         audi    a4   2.8 1999   6 manual(m5)   f  18  26  p compact
-             * > str(mpg)
-   'data.frame':   234 obs. of  11 variables:
-    $ manufacturer: Factor w/ 15 levels "audi","chevrolet",..: 1 1 1 1 1 1 1 1 1 1 ...
-    $ model       : Factor w/ 38 levels "4runner 4wd",..: 2 2 2 2 2 2 2 3 3 3 ...
-    $ displ       : num  1.8 1.8 2 2 2.8 2.8 3.1 1.8 1.8 2 ...
-    $ year        : int  1999 1999 2008 2008 1999 1999 2008 1999 1999 2008 ...
-    $ cyl         : int  4 4 4 4 6 6 6 4 4 4 ...
-    $ trans       : Factor w/ 10 levels "auto(av)","auto(l3)",..: 4 9 10 1 4 9 1 9 4 10 ...
-    $ drv         : Factor w/ 3 levels "4","f","r": 2 2 2 2 2 2 2 1 1 1 ...
-    $ cty         : int  18 21 20 21 16 18 18 18 16 20 ...
-    $ hwy         : int  29 29 31 30 26 26 27 26 25 28 ...
-    $ fl          : Factor w/ 5 levels "c","d","e","p",..: 4 4 4 4 4 4 4 4 4 4 ...
-    $ class       : Factor w/ 7 levels "2seater","compact",..: 2 2 2 2 2 2 2 2 2 2 ...
+
+             * > head(biopsy)
+       ID V1 V2 V3 V4 V5 V6 V7 V8 V9     class
+1 1000025  5  1  1  1  2  1  3  1  1    benign
+2 1002945  5  4  4  5  7 10  3  2  1    benign
+3 1015425  3  1  1  1  2  2  3  1  1    benign
+4 1016277  6  8  8  1  3  4  3  7  1    benign
+5 1017023  4  1  1  3  2  1  3  1  1    benign
+6 1017122  8 10 10  8  7 10  9  7  1 malignant
+
+             * > str((biopsy))
+'data.frame':   699 obs. of  11 variables:
+ $ ID   : chr  "1000025" "1002945" "1015425" "1016277" ...
+ $ V1   : int  5 5 3 6 4 8 1 2 2 4 ...
+ $ V2   : int  1 4 1 8 1 10 1 1 1 2 ...
+ $ V3   : int  1 4 1 8 1 10 1 2 1 1 ...
+ $ V4   : int  1 5 1 1 3 8 1 1 1 1 ...
+ $ V5   : int  2 7 2 3 2 7 2 2 2 2 ...
+ $ V6   : int  1 10 2 4 1 10 10 1 1 1 ...
+ $ V7   : int  3 3 3 3 3 9 3 3 1 2 ...
+ $ V8   : int  1 2 1 7 1 7 1 1 1 1 ...
+ $ V9   : int  1 1 1 1 1 1 1 1 5 1 ...
+ $ class: Factor w/ 2 levels "benign","malignant": 1 1 1 1 1 2 1 1 1 1 ...
 
             */
 
-            var obj = mpg[0, 0];
+            var obj = biopsy[0, 10];
             Assert.AreEqual(typeof(string), obj.GetType());
             var s = (string)obj;
-            Assert.AreEqual("audi", s);
-            Assert.AreEqual("audi", mpg[0, "manufacturer"]);
+            Assert.AreEqual("benign", s);
+            Assert.AreEqual("benign", biopsy[0, "class"]);
             // While R does 'something' where there is no names defined, the behavior seems inconsistent between rownames in data frames
             // and named vectors. Better not support this for the time being.
             //         Assert.AreEqual("audi", mpg["1", "manufacturer"]);
-            Assert.AreEqual("auto(av)", mpg[3, 5]);
-            Assert.AreEqual("auto(av)", mpg[3, "trans"]);
-            //         Assert.AreEqual("auto(av)", mpg["4", "trans"]);
-            Assert.AreEqual(2008, mpg[2, 3]);
-            Assert.AreEqual(2008, mpg[2, "year"]);
-            //         Assert.AreEqual(2008, mpg["3", "year"]);
+            Assert.AreEqual("malignant", biopsy[5, 10]);
+            Assert.AreEqual("malignant", biopsy[5, "class"]);
+            Assert.AreEqual(4, biopsy[1, 3]);
+            Assert.AreEqual(4, biopsy[1, "V3"]);
 
             IEnumerable[] columns;
             string[] columnNames;

RDotNet.Tests/REngineCleanupTest.cs

@@ -21,26 +21,30 @@ public void TestDetachPackagesDefault()
 
             var s = engine.Evaluate("search()").AsCharacter().ToArray();
             Assert.IsFalse(s.Contains("package:lattice"));
-            Assert.IsFalse(s.Contains("package:knitr"));
-            Assert.IsFalse(s.Contains("mpg"));
+            Assert.IsFalse(s.Contains("package:Matrix"));
+            Assert.IsFalse(s.Contains("package:MASS"));
+            Assert.IsFalse(s.Contains("biopsy"));
 
             engine.ClearGlobalEnvironment();
             engine.Evaluate("library(lattice)");
-            engine.Evaluate("library(knitr)");
-            engine.Evaluate("data(mpg, package='ggplot2')");
-            engine.Evaluate("attach(mpg)");
+            engine.Evaluate("library(Matrix)");
+            engine.Evaluate("library(MASS)");
+            engine.Evaluate("data(biopsy, package='MASS')");
+            engine.Evaluate("attach(biopsy)");
             s = engine.Evaluate("search()").AsCharacter().ToArray();
 
             Assert.IsTrue(s.Contains("package:lattice"));
-            Assert.IsTrue(s.Contains("package:knitr"));
-            Assert.IsTrue(s.Contains("mpg"));
+            Assert.IsTrue(s.Contains("package:Matrix"));
+            Assert.IsTrue(s.Contains("package:MASS"));
+            Assert.IsTrue(s.Contains("biopsy"));
 
             engine.ClearGlobalEnvironment(detachPackages: true);
 
             s = engine.Evaluate("search()").AsCharacter().ToArray();
             Assert.IsFalse(s.Contains("package:lattice"));
-            Assert.IsFalse(s.Contains("package:knitr"));
-            Assert.IsFalse(s.Contains("mpg"));
+            Assert.IsFalse(s.Contains("package:Matrix"));
+            Assert.IsFalse(s.Contains("package:MASS"));
+            Assert.IsFalse(s.Contains("biopsy"));
         }
     }
 }

RDotNet.Tests/REngineTest.cs

@@ -124,6 +124,9 @@ private void CheckProperMemoryReclaimR<T>(string statementCreateX, double expect
             var memoryAfterAlloc = GetBaselineRengineMemory(engine);
             Assert.That(memoryAfterAlloc - memoryInitial, Is.GreaterThan(expectedMinMegaBytesDifference));
             engine.Evaluate("rm(x)");
+            // We still have a reference from .NET, the variable sexp. Should not have been collected yet.
+            var memoryAfterRemoveRvar = GetBaselineRengineMemory(engine);
+            Assert.That(memoryAfterRemoveRvar - memoryInitial, Is.GreaterThan(expectedMinMegaBytesDifference));
             sexp = null;
             Thread.Sleep(100);
             var memoryAfterGC = GetBaselineRengineMemory(engine);