Merge commit '4a4a87fe64ece14e9594a3c42a372f3bd60bda20' into release/graal-vm/1.0

Author: ansalond

CHANGELOG.md

@@ -1,3 +1,37 @@
+# 1.0 RC 7
+
+New features
+
+* AWT based graphics devices (jpg, png, X11, ...) supported in native image
+
+Added missing R builtins and C API
+
+Bugfixes
+
+# 1.0 RC 6
+
+New features
+
+* Support for reading/writing graphical parameters via par
+  * in preparation for full graphics package support
+
+Added missing R builtins and C API
+
+* 'get' builtin supports the 'envir' argument
+* 'inspect' internal
+* SETLEVELS
+* Rf_isObject
+* SET_ENCLOS
+* R_nchar
+* R_forceAndCall
+
+Bugfixes
+
+* support for formulas that include '...'
+* updating attributes of NULL produces empty list with given attributes
+* treat CR/LF in readLine like GNU-R
+* fix in La_chol (incorrect pivot attribute in return)
+* various fixes in vector coercion code to produce GNU-R compatible warnings and errors
 
 # 1.0 RC 5
 
@@ -7,7 +41,7 @@ New features
   * allows to pass additional arguments for the underlying configure script
   * by default uses the following arguments: --with-x=no --with-aqua=no --enable-memory-profiling FFLAGS=-O2
 
-Updates in interop:
+Updates in interop
 
 * R code evaluated via interop never returns a Java primitive type, but always a vector
 * Vectors of size 1 that do not contain NA can be unboxed
@@ -16,7 +50,7 @@ Updates in interop:
   * if the value is `NA`, a special value that responds to `IS_NULL` with `true`. If this value is passed back to R it behaves as `NA` again
 * Note that sending the READ message to a list, environment, or other heterogenous data structure never gives atomic Java type but a primitive R vector
 
-Bug fixes:
+Bug fixes
 
 * Various smaller issues discovered during testing of CRAN packages.
 

ci.hocon

@@ -11,7 +11,9 @@ include "ci_common/common.hocon"
 # overlay = "1823c758582f31386f8ba4d89157265a23cebd04"
 builds = [
   ${gateTestLinux}            {capabilities : [linux, amd64, fast],  targets : [gate], name: "gate-test-linux-amd64"}
+  ${gateTestNoDSLCacheLinux}  {capabilities : [linux, amd64, fast],  targets : [gate], name: "gate-test-linux-amd64-no-dsl-cache"}
   ${gateTestNoSpecialsLinux}  {capabilities : [linux, amd64, fast],  targets : [gate], name: "gate-test-linux-amd64-nospecials"}
+  ${gateTestNoDSLCacheNoSpecialsLinux}  {capabilities : [linux, amd64, fast],  targets : [gate], name: "gate-test-linux-amd64-nospecials-no-dsl-cache"}
   ${gateTestDarwin}           {capabilities : [darwin_sierra, amd64], targets : [gate], name: "gate-test-darwin-amd64"}
   ${gateStyle}                {capabilities : [linux, amd64],  targets : [gate], name: "gate-style-linux-amd64"}
   ${gateBuildWithEcj}         {capabilities : [linux, amd64],  targets : [gate], name: "gate-ecj-linux-amd64"}

ci_common/common.hocon

@@ -106,12 +106,36 @@ gateTestCommon : ${common} {
 gateTestLinux : ${gateTestCommon}  {
 }
 
+gateTestNoDSLCacheLinux : ${common} {
+  environment : ${common.environment} {
+    FASTR_RELEASE: "true", # release build so that we also tests recommended pkgs installation
+    FASTR_OPTION_DSLCacheSizeFactor: "0"
+  }
+  run : [
+    ${gateCmd} ["Versions,JDKReleaseInfo,BuildJavaWithJavac,UnitTests: with specials,Rembedded"]
+    # to verify that we run with the desired configuration
+    ["mx", "r", "-e", "print(list(.fastr.option(as.character(quote(DSLCacheSizeFactor))),.fastr.option(as.character(quote(UseSpecials)))))"]
+  ]
+}
+
 gateTestNoSpecialsLinux : ${common}  {
   run : [
     ${gateCmd} ["Versions,JDKReleaseInfo,BuildJavaWithJavac,UnitTests: no specials"]
   ]
 }
 
+gateTestNoDSLCacheNoSpecialsLinux : ${common} {
+  environment : ${common.environment} {
+    FASTR_RELEASE: "true", # release build so that we also tests recommended pkgs installation
+    FASTR_OPTION_DSLCacheSizeFactor: "0"
+  }
+  run : [
+    ${gateCmd} ["Versions,JDKReleaseInfo,BuildJavaWithJavac,UnitTests: no specials"]
+    # to verify that we run with the desired configuration
+    ["mx", "r", "-e", "print(list(.fastr.option(as.character(quote(DSLCacheSizeFactor))),.fastr.option(as.character(quote(UseSpecials)))))"]
+  ]
+}
+
 darwinEnvironment : {
   environment :  {
     PATH : "/usr/local/bin:$JAVA_HOME/bin:$PATH"

com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/SyntaxErrorNode.java

@@ -26,15 +26,15 @@
 import com.oracle.truffle.api.source.SourceSection;
 import com.oracle.truffle.r.runtime.RInternalError;
 import com.oracle.truffle.r.runtime.context.Engine.ParseException;
+import com.oracle.truffle.r.runtime.nodes.RAttributableNode;
 import com.oracle.truffle.r.runtime.nodes.RInstrumentableNode;
-import com.oracle.truffle.r.runtime.nodes.RNode;
 import com.oracle.truffle.r.runtime.nodes.RSyntaxNode;
 
 /**
- * Node that represents piece of AST that would throw syntax error when parser. Used to delay
+ * Node that represents piece of AST that would throw syntax err or when parser. Used to delay
  * parsing error to the point when they should be reported.
  */
-final class SyntaxErrorNode extends RNode implements RSyntaxNode, RInstrumentableNode {
+final class SyntaxErrorNode extends RAttributableNode implements RSyntaxNode, RInstrumentableNode {
     private final ParseException exception;
     private final SourceSection sourceSection;
 

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/nodes/AsCharNode.java

@@ -34,11 +34,14 @@
 import com.oracle.truffle.r.runtime.data.RSymbol;
 import com.oracle.truffle.r.runtime.data.RTypes;
 import com.oracle.truffle.r.runtime.data.model.RAbstractAtomicVector;
+import com.oracle.truffle.r.runtime.data.model.RAbstractComplexVector;
+import com.oracle.truffle.r.runtime.data.model.RAbstractDoubleVector;
 import com.oracle.truffle.r.runtime.data.model.RAbstractStringVector;
 
 @TypeSystemReference(RTypes.class)
 public abstract class AsCharNode extends FFIUpCallNode.Arg1 {
     private static final CharSXPWrapper CharSXPWrapper_NA = CharSXPWrapper.create(RRuntime.STRING_NA);
+    private static final CharSXPWrapper CharSXPWrapper_NAString = CharSXPWrapper.create("NA");
 
     public abstract CharSXPWrapper execute(Object obj);
 
@@ -53,7 +56,8 @@ protected CharSXPWrapper asChar(RStringVector obj) {
             return CharSXPWrapper_NA;
         } else {
             obj.wrapStrings();
-            return obj.getWrappedDataAt(0);
+            CharSXPWrapper result = obj.getWrappedDataAt(0);
+            return RRuntime.isNA(result.getContents()) ? CharSXPWrapper_NA : result;
         }
     }
 
@@ -63,18 +67,29 @@ protected CharSXPWrapper asChar(RSymbol obj) {
     }
 
     @Specialization(guards = {"obj.getLength() > 0", "isNotStringVec(obj)"})
-    protected CharSXPWrapper asChar(RAbstractAtomicVector obj, //
+    protected CharSXPWrapper asChar(RAbstractAtomicVector obj,
                     @Cached("createNonPreserving()") CastStringNode castStringNode) {
         // for other than character vector, symbol or CHARSXP, the cast and creation of new vector
         // is inevitable and the user should know to take appropriate measures (i.e. PROTECT).
         Object castObj = castStringNode.executeString(obj);
+        CharSXPWrapper result;
         if (castObj instanceof String) {
-            return CharSXPWrapper.create((String) castObj);
+            result = CharSXPWrapper.create((String) castObj);
         } else if (castObj instanceof RAbstractStringVector) {
-            return CharSXPWrapper.create(((RAbstractStringVector) castObj).getDataAt(0));
+            result = CharSXPWrapper.create(((RAbstractStringVector) castObj).getDataAt(0));
         } else {
             throw RInternalError.shouldNotReachHere();
         }
+
+        if (RRuntime.isNA(result.getContents())) {
+            if (obj instanceof RAbstractComplexVector || obj instanceof RAbstractDoubleVector) {
+                return CharSXPWrapper_NAString;
+            } else {
+                return CharSXPWrapper_NA;
+            }
+        } else {
+            return result;
+        }
     }
 
     @Fallback

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/nodes/AsIntegerNode.java

@@ -27,6 +27,7 @@
 import com.oracle.truffle.api.dsl.Specialization;
 import com.oracle.truffle.api.dsl.TypeSystemReference;
 import com.oracle.truffle.r.nodes.unary.CastIntegerNode;
+import com.oracle.truffle.r.runtime.RError;
 import com.oracle.truffle.r.runtime.RInternalError;
 import com.oracle.truffle.r.runtime.RRuntime;
 import com.oracle.truffle.r.runtime.data.RTypes;
@@ -49,29 +50,38 @@ protected int asInteger(int obj) {
     }
 
     @Specialization
-    protected int asInteger(double obj) {
-        return (int) obj;
+    protected int asInteger(double obj,
+                    @Cached("createCastIntegerNode()") CastIntegerNode castIntegerNode) {
+        return (int) castIntegerNode.executeInt(obj);
     }
 
     @Specialization
-    protected int asReal(RAbstractDoubleVector obj) {
+    protected int asInteger(RAbstractDoubleVector obj,
+                    @Cached("createCastIntegerNode()") CastIntegerNode castIntegerNode) {
         if (obj.getLength() == 0) {
             return RRuntime.INT_NA;
         }
-        return (int) obj.getDataAt(0);
+        Object castObj = castIntegerNode.executeInt(obj);
+        if (castObj instanceof Integer) {
+            return (Integer) castObj;
+        } else if (castObj instanceof RAbstractIntVector) {
+            return ((RAbstractIntVector) castObj).getDataAt(0);
+        } else {
+            throw RInternalError.shouldNotReachHere();
+        }
     }
 
     @Specialization
-    protected int asReal(RAbstractIntVector obj) {
+    protected int asInteger(RAbstractIntVector obj) {
         if (obj.getLength() == 0) {
             return RRuntime.INT_NA;
         }
         return obj.getDataAt(0);
     }
 
     @Specialization(guards = "obj.getLength() > 0")
-    protected int asReal(RAbstractAtomicVector obj,
-                    @Cached("createNonPreserving()") CastIntegerNode castIntegerNode) {
+    protected int asInteger(RAbstractAtomicVector obj,
+                    @Cached("createCastIntegerNode()") CastIntegerNode castIntegerNode) {
         Object castObj = castIntegerNode.executeInt(obj);
         if (castObj instanceof Integer) {
             return (Integer) castObj;
@@ -83,11 +93,15 @@ protected int asReal(RAbstractAtomicVector obj,
     }
 
     @Fallback
-    protected int asRealFallback(@SuppressWarnings("unused") Object obj) {
+    protected int asIntegerFallback(@SuppressWarnings("unused") Object obj) {
         return RRuntime.INT_NA;
     }
 
     public static AsIntegerNode create() {
         return AsIntegerNodeGen.create();
     }
+
+    protected CastIntegerNode createCastIntegerNode() {
+        return CastIntegerNode.createNonPreserving(RError.SHOW_CALLER);
+    }
 }

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/nodes/AsLogicalNode.java

@@ -40,28 +40,31 @@ public abstract class AsLogicalNode extends FFIUpCallNode.Arg1 {
 
     @Specialization
     protected int asLogical(byte b) {
-        return b;
+        return RRuntime.isNA(b) ? RRuntime.INT_NA : b;
     }
 
     @Specialization
     protected int asLogical(RAbstractLogicalVector obj) {
         if (obj.getLength() == 0) {
             return RRuntime.INT_NA;
         }
-        return obj.getDataAt(0);
+        byte result = obj.getDataAt(0);
+        return RRuntime.isNA(result) ? RRuntime.INT_NA : result;
     }
 
     @Specialization(guards = "obj.getLength() > 0")
     protected int asLogical(RAbstractAtomicVector obj,
                     @Cached("createNonPreserving()") CastLogicalNode castLogicalNode) {
         Object castObj = castLogicalNode.doCast(obj);
+        byte result;
         if (castObj instanceof Byte) {
-            return (byte) castObj;
+            result = (byte) castObj;
         } else if (castObj instanceof RAbstractLogicalVector) {
-            return ((RAbstractLogicalVector) castObj).getDataAt(0);
+            result = ((RAbstractLogicalVector) castObj).getDataAt(0);
         } else {
             throw RInternalError.shouldNotReachHere();
         }
+        return RRuntime.isNA(result) ? RRuntime.INT_NA : result;
     }
 
     @Fallback

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/nodes/AsRealNode.java

@@ -49,7 +49,7 @@ protected double asReal(double obj) {
 
     @Specialization
     protected double asReal(int obj) {
-        return obj;
+        return RRuntime.isNA(obj) ? RRuntime.DOUBLE_NA : obj;
     }
 
     @Specialization
@@ -65,7 +65,8 @@ protected double asReal(RAbstractIntVector obj) {
         if (obj.getLength() == 0) {
             return RRuntime.DOUBLE_NA;
         }
-        return obj.getDataAt(0);
+        int result = obj.getDataAt(0);
+        return RRuntime.isNA(result) ? RRuntime.DOUBLE_NA : result;
     }
 
     @Specialization(guards = "obj.getLength() > 0")

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/nodes/AttributesAccessNodes.java

@@ -40,6 +40,7 @@
 import com.oracle.truffle.r.nodes.attributes.GetAttributeNode;
 import com.oracle.truffle.r.nodes.attributes.GetAttributesNode;
 import com.oracle.truffle.r.nodes.attributes.SetAttributeNode;
+import com.oracle.truffle.r.nodes.attributes.SpecialAttributesFunctions.GetRowNamesAttributeNode;
 import com.oracle.truffle.r.nodes.function.opt.UpdateShareableChildValueNode;
 import com.oracle.truffle.r.nodes.unary.CastNode;
 import com.oracle.truffle.r.runtime.ArgumentsSignature;
@@ -106,7 +107,11 @@ public Object doAttributable(RAttributable obj,
             assert names.getLength() == list.getLength();
             for (int i = list.getLength() - 1; i >= 0; i--) {
                 Object item = list.getDataAt(i);
-                RSymbol symbol = RDataFactory.createSymbol(names.getDataAt(i));
+                String name = names.getDataAt(i);
+                if (name.equals(RRuntime.ROWNAMES_ATTR_KEY)) {
+                    item = GetRowNamesAttributeNode.ensureRowNamesCompactFormat(item);
+                }
+                RSymbol symbol = RDataFactory.createSymbol(name);
                 result = RDataFactory.createPairList(item, result, symbol);
             }
             return result;
@@ -186,6 +191,9 @@ public Void doRAttributeStorage(RAttributeStorage x, RAttributeStorage y) {
                 copyRegAttributes = insert(CopyOfRegAttributesNode.create());
             }
             copyRegAttributes.execute(x, y);
+            if (x.isS4()) {
+                y.setS4();
+            }
             return null;
         }
 

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/nodes/MathFunctionsNodes.java

@@ -38,7 +38,7 @@
 import com.oracle.truffle.r.runtime.data.model.RAbstractDoubleVector;
 import com.oracle.truffle.r.runtime.data.nodes.GetReadonlyData;
 import com.oracle.truffle.r.runtime.ffi.interop.UnsafeAdapter;
-import com.oracle.truffle.r.runtime.interop.ForeignArray2R;
+import com.oracle.truffle.r.runtime.interop.ConvertForeignObjectNode;
 import com.oracle.truffle.r.runtime.nmath.BesselFunctions;
 import com.oracle.truffle.r.runtime.nmath.Beta;
 import com.oracle.truffle.r.runtime.nmath.Choose;
@@ -695,7 +695,7 @@ abstract static class BesselExNode extends Node {
 
         @Child private Node bIsPointerNode = Message.IS_POINTER.createNode();
         @Child private Node bAsPointerNode;
-        @Child private ForeignArray2R bForeignArray2R;
+        @Child private ConvertForeignObjectNode bConvertForeign;
 
         public abstract double execute(BesselExCaller caller, Object b);
 
@@ -717,11 +717,11 @@ protected double besselEx(BesselExCaller caller, Object b,
                     throw RInternalError.shouldNotReachHere("IS_POINTER message returned true, AS_POINTER should not fail");
                 }
             } else {
-                if (bForeignArray2R == null) {
+                if (bConvertForeign == null) {
                     CompilerDirectives.transferToInterpreterAndInvalidate();
-                    bForeignArray2R = insert(ForeignArray2R.create());
+                    bConvertForeign = insert(ConvertForeignObjectNode.create());
                 }
-                bVec = (RAbstractDoubleVector) bForeignArray2R.convert(bTO);
+                bVec = (RAbstractDoubleVector) bConvertForeign.convert(bTO);
             }
 
             return caller.call(bReadonlyData.execute(bVec.materialize()));