Merge commit 'fad3548f2d036fc81b9bccb3d0b557448e56a4d3' into release/graal-vm/1.0

Author: ansalond

CHANGELOG.md

@@ -1,3 +1,33 @@
+# 1.0 RC 12
+
+New Features:
+
+* the implementation of the `TruffleLanguage#toString` method uses R function `print`
+  * for example: the console in Chrome DevTools will print data.frames formatted like R would
+
+Added missing R builtins and C API
+
+* FastR provides GNU-R compatible `parseData` for expressions parsed via `parse(...,keep.source=T)`
+* `format.POSIXlt` supports following formats: %z, %Z, %x, %X.
+* dummy implementation of the ALTREP framework to avoid linking problems. Most of the functions fail at runtime. #48
+
+Bug fixes:
+
+* `sys.calls` gives wrong result when `eval` with `envir` argument is on the call stack
+* `is.na` was not correctly handling lists, for example: `is.na(list(function() 42))`
+* transfer `srcref` attribute to the result of `.subset` and `[`
+* `matrix(1,nrow=NULL,ncol=NULL)` caused internal FastR error instead of R user level error
+* option `--polyglot` works with the native image of FastR
+* added native functions optim() and optimness()
+* fixed various race conditions in parallel package
+* `strsplit(...,perl=T)` does not end up in an infinite loop if the pattern is not found by `pcre_exec`
+* `as.character.factor` error for levels containing NAs
+* `env2list` error for environments containing pairlists
+* `body<-` error for non-scalar values
+* `unlink` error for paths containing wildcard(s) but no path separator
+*  dims attribute errorneously set to RDoubleVector; exception when retrieving the dims #49
+* issues with the dplyr's `mutate` and `transmute`: #50 and #51
+
 # 1.0 RC 11
 
 * upgraded the R version to R-3.5.1

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

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2013, 2018, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2013, 2019, Oracle and/or its affiliates. All rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * This code is free software; you can redistribute it and/or modify it
@@ -275,17 +275,19 @@ public Object parseAndEval(Source source, MaterializedFrame frame, boolean print
 
     private List<RSyntaxNode> parseSource(Source source) throws ParseException {
         RParserFactory.Parser<RSyntaxNode> parser = RParserFactory.getParser();
-        return parser.script(source, new RASTBuilder(), context.getLanguage());
+        return parser.script(source, new RASTBuilder(true), context.getLanguage());
     }
 
     @Override
-    public RExpression parse(Source source) throws ParseException {
-        List<RSyntaxNode> list = parseSource(source);
-        Object[] data = new Object[list.size()];
-        for (int i = 0; i < data.length; i++) {
-            data[i] = RASTUtils.createLanguageElement(list.get(i));
+    public ParsedExpression parse(Source source, boolean keepSource) throws ParseException {
+        RParserFactory.Parser<RSyntaxNode> parser = RParserFactory.getParser();
+        RASTBuilder builder = new RASTBuilder(true);
+        List<RSyntaxNode> script = parser.script(source, builder, context.getLanguage());
+        Object[] data = new Object[script.size()];
+        for (int i = 0; i < script.size(); i++) {
+            data[i] = RASTUtils.createLanguageElement(script.get(i));
         }
-        return RDataFactory.createExpression(data);
+        return new ParsedExpression(RDataFactory.createExpression(data), builder.getParseData());
     }
 
     @Override
@@ -387,7 +389,7 @@ private EngineRootNode createRScriptRoot(Source fullSource, MaterializedFrame fr
                     List<RSyntaxNode> currentStmts = null;
                     try {
                         RParserFactory.Parser<RSyntaxNode> parser = RParserFactory.getParser();
-                        currentStmts = parser.statements(src, fullSource, startLine, new RASTBuilder(), context.getLanguage());
+                        currentStmts = parser.statements(src, fullSource, startLine, new RASTBuilder(true), context.getLanguage());
                     } catch (IncompleteSourceException e) {
                         lastParseException = e;
                         if (nextLineInput != null) {

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

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2015, 2018, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2015, 2019, Oracle and/or its affiliates. All rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * This code is free software; you can redistribute it and/or modify it
@@ -29,31 +29,41 @@
 import com.oracle.truffle.api.Scope;
 import com.oracle.truffle.api.TruffleLanguage;
 import com.oracle.truffle.api.frame.Frame;
+import com.oracle.truffle.api.frame.MaterializedFrame;
 import com.oracle.truffle.api.instrumentation.Instrumenter;
 import com.oracle.truffle.api.instrumentation.ProvidedTags;
 import com.oracle.truffle.api.instrumentation.StandardTags;
+import com.oracle.truffle.api.interop.TruffleObject;
 import com.oracle.truffle.api.nodes.ExecutableNode;
 import com.oracle.truffle.api.nodes.Node;
 import com.oracle.truffle.api.source.Source;
 import com.oracle.truffle.api.source.SourceSection;
 import com.oracle.truffle.r.engine.interop.RForeignAccessFactoryImpl;
 import com.oracle.truffle.r.nodes.RASTBuilder;
 import com.oracle.truffle.r.nodes.builtin.RBuiltinPackages;
+import com.oracle.truffle.r.nodes.function.PromiseHelperNode;
+import com.oracle.truffle.r.nodes.function.RMissingHelper;
 import com.oracle.truffle.r.nodes.instrumentation.RSyntaxTags;
 import com.oracle.truffle.r.nodes.instrumentation.RSyntaxTags.FunctionBodyBlockTag;
+import com.oracle.truffle.r.runtime.ArgumentsSignature;
 import com.oracle.truffle.r.runtime.ExitException;
 import com.oracle.truffle.r.runtime.FastROptions;
 import com.oracle.truffle.r.runtime.RAccuracyInfo;
+import com.oracle.truffle.r.runtime.RCaller;
 import com.oracle.truffle.r.runtime.RDeparse;
+import com.oracle.truffle.r.runtime.RError;
+import com.oracle.truffle.r.runtime.RError.Message;
 import com.oracle.truffle.r.runtime.RRuntime;
 import com.oracle.truffle.r.runtime.RSuicide;
+import com.oracle.truffle.r.runtime.conn.StdConnections.ContextStateImpl;
 import com.oracle.truffle.r.runtime.context.Engine.IncompleteSourceException;
 import com.oracle.truffle.r.runtime.context.Engine.ParseException;
 import com.oracle.truffle.r.runtime.context.RContext;
 import com.oracle.truffle.r.runtime.context.TruffleRLanguage;
 import com.oracle.truffle.r.runtime.data.RFunction;
 import com.oracle.truffle.r.runtime.data.RPromise;
 import com.oracle.truffle.r.runtime.data.RTypedValue;
+import com.oracle.truffle.r.runtime.env.REnvironment;
 import com.oracle.truffle.r.runtime.env.RScope;
 import com.oracle.truffle.r.runtime.ffi.RFFIFactory;
 import com.oracle.truffle.r.runtime.nodes.RBaseNode;
@@ -113,10 +123,9 @@ protected void initializeContext(RContext context) throws Exception {
     protected RContext createContext(Env env) {
         boolean initialContext = !systemInitialized;
         if (initialContext) {
-            RContext.initializeGlobalState(new RASTBuilder(), new RRuntimeASTAccessImpl(), RBuiltinPackages.getInstance(), new RForeignAccessFactoryImpl());
+            RContext.initializeGlobalState(new RASTBuilder(false), new RRuntimeASTAccessImpl(), RBuiltinPackages.getInstance(), new RForeignAccessFactoryImpl());
         }
-        RContext result = RContext.create(this, env, env.lookup(Instrumenter.class), initialContext);
-        return result;
+        return RContext.create(this, env, env.lookup(Instrumenter.class), initialContext);
     }
 
     @Override
@@ -128,19 +137,44 @@ protected void disposeContext(RContext context) {
     protected String toString(RContext context, Object value) {
         // the debugger also passes result of TruffleRLanguage.findMetaObject() to this method
         Object unwrapped = value;
+        // print promises by other means than the "print" function to avoid evaluating them
         if (unwrapped instanceof RPromise) {
             RPromise promise = (RPromise) unwrapped;
-            if (promise.isEvaluated()) {
-                unwrapped = RRuntime.asAbstractVector(promise.getValue());
+            if (promise.isEvaluated() || promise.isOptimized()) {
+                unwrapped = promise.getValue();
+            } else {
+                return RDeparse.deparse(unwrapped, RDeparse.MAX_CUTOFF, true, RDeparse.KEEPINTEGER, -1, 1024 * 1024);
             }
         }
-        if (unwrapped instanceof String) {
-            return (String) unwrapped;
+        // print missing explicitly, because "print" would report missing argument
+        if (RMissingHelper.isMissing(unwrapped)) {
+            return "missing";
+        }
+        Object asVector = RRuntime.asAbstractVector(unwrapped);
+        if (!(asVector instanceof TruffleObject)) {
+            throw RError.error(RError.NO_CALLER, Message.GENERIC, String.format("Printing value of type '%s' is not supported by the R language.", unwrapped.getClass().getSimpleName()));
+        }
+        Object printObj = REnvironment.baseEnv(context).get("print");
+        if (printObj instanceof RPromise) {
+            printObj = PromiseHelperNode.evaluateSlowPath((RPromise) printObj);
         }
-        if (unwrapped instanceof RTypedValue) {
-            return RDeparse.deparse(unwrapped, RDeparse.MAX_CUTOFF, true, RDeparse.KEEPINTEGER, -1, 1024 * 1024);
+        if (!(printObj instanceof RFunction)) {
+            throw RError.error(RError.NO_CALLER, Message.GENERIC, "Cannot retrieve the 'print' function from the base package.");
+        }
+        MaterializedFrame callingFrame = REnvironment.globalEnv(context).getFrame();
+        ContextStateImpl stateStdConnections = context.stateStdConnections;
+        try {
+            StringBuilder buffer = new StringBuilder();
+            stateStdConnections.setBuffer(buffer);
+            RContext.getEngine().evalFunction((RFunction) printObj, callingFrame, RCaller.topLevel, false, ArgumentsSignature.empty(1), asVector);
+            // remove the last "\n", which is useful for REPL, but not here
+            if (buffer.charAt(buffer.length() - 1) == '\n') {
+                buffer.setLength(buffer.length() - 1);
+            }
+            return buffer.toString();
+        } finally {
+            stateStdConnections.resetBuffer();
         }
-        return RRuntime.toString(unwrapped);
     }
 
     @Override

com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/interop/RAbstractVectorAccessFactory.java

@@ -484,14 +484,18 @@ public RootNode get() {
 
     private static final class Check extends RootNode {
 
+        private final ConditionProfile profile = ConditionProfile.createBinaryProfile();
+
         Check() {
             super(null);
         }
 
         @Override
         public Object execute(VirtualFrame frame) {
             final Object receiver = ForeignAccess.getReceiver(frame);
-            return receiver instanceof RAbstractAtomicVector && !(receiver instanceof RScalar);
+            return profile.profile(receiver instanceof RAbstractAtomicVector && !(receiver instanceof RScalar));
         }
+
     }
+
 }

com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/interop/RInteropNAMR.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2019, Oracle and/or its affiliates. All rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * This code is free software; you can redistribute it and/or modify it
@@ -44,4 +44,5 @@ protected static boolean test(TruffleObject receiver) {
             return receiver instanceof RInteropNA;
         }
     }
+
 }

com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/shell/REmbedded.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2016, 2018, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2016, 2019, Oracle and/or its affiliates. All rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * This code is free software; you can redistribute it and/or modify it
@@ -72,7 +72,7 @@ public class REmbedded {
     private static void initializeR(String[] args, boolean initMainLoop) {
         assert context == null;
         RContext.setEmbedded();
-        RCmdOptions options = RCmdOptions.parseArguments(RCmdOptions.Client.R, args, false);
+        RCmdOptions options = RCmdOptions.parseArguments(args, false);
 
         EmbeddedConsoleHandler embeddedConsoleHandler = new EmbeddedConsoleHandler();
 

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/common/JavaUpCallsRFFIImpl.java

@@ -98,7 +98,6 @@
 import com.oracle.truffle.r.runtime.data.RUnboundValue;
 import com.oracle.truffle.r.runtime.data.RVector;
 import com.oracle.truffle.r.runtime.data.model.RAbstractAtomicVector;
-import com.oracle.truffle.r.runtime.data.model.RAbstractListVector;
 import com.oracle.truffle.r.runtime.data.model.RAbstractStringVector;
 import com.oracle.truffle.r.runtime.data.model.RAbstractVector;
 import com.oracle.truffle.r.runtime.data.nodes.VectorAccess;
@@ -552,12 +551,7 @@ public void SETLENGTH(Object x, int l) {
 
     @Override
     public void SET_TRUELENGTH(Object x, int l) {
-        if (x instanceof CharSXPWrapper) {
-            ((CharSXPWrapper) x).setTruelength(l);
-            return;
-        }
-        RAbstractVector vec = (RAbstractVector) RRuntime.asAbstractVector(x);
-        vec.setTrueLength(l);
+        throw implementedAsNode();
     }
 
     @Override
@@ -619,18 +613,7 @@ public Object STRING_ELT(Object x, long i) {
 
     @Override
     public Object VECTOR_ELT(Object x, long i) {
-        Object vec = x;
-        if (vec instanceof RExpression) {
-            return ((RExpression) vec).getDataAt((int) i);
-        }
-        RAbstractListVector list = guaranteeInstanceOf(RRuntime.asAbstractVector(vec), RAbstractListVector.class);
-        if (list.getLength() == i) {
-            // Some packages abuse that there seems to be no bounds checking and the
-            // one-after-the-last element returns NULL, which they use to find out if they reached
-            // the end of the list...
-            return RNull.instance;
-        }
-        return list.getDataAt((int) i);
+        throw implementedAsNode();
     }
 
     @Override
@@ -1116,7 +1099,7 @@ public Object R_ParseVector(Object text, int n, Object srcFile) {
         Object[] resultData = new Object[2];
         try {
             Source source = RSource.fromTextInternal(textString, RSource.Internal.R_PARSEVECTOR);
-            RExpression exprs = RContext.getEngine().parse(source);
+            RExpression exprs = RContext.getEngine().parse(source, false).getExpression();
             resultData[0] = RDataFactory.createIntVectorFromScalar(ParseStatus.PARSE_OK.ordinal());
             resultData[1] = exprs;
         } catch (IncompleteSourceException ex) {
@@ -1404,9 +1387,8 @@ public Object R_ExternalPtrProtected(Object x) {
     }
 
     @Override
-    public void R_SetExternalPtrAddr(Object x, long addr) {
-        RExternalPtr p = guaranteeInstanceOf(x, RExternalPtr.class);
-        p.setAddr(new SymbolHandle(addr));
+    public void R_SetExternalPtrAddr(Object x, Object addr) {
+        throw implementedAsNode();
     }
 
     @Override
@@ -1558,7 +1540,7 @@ public Object R_MethodsNamespace() {
     @TruffleBoundary
     public void R_PreserveObject(Object obj) {
         guaranteeInstanceOf(obj, RObject.class);
-        IdentityHashMap<RObject, AtomicInteger> preserveList = getContext().preserveList;
+        IdentityHashMap<RObject, AtomicInteger> preserveList = getContext().rffiContextState.preserveList;
         AtomicInteger prevCnt = preserveList.putIfAbsent((RObject) obj, new AtomicInteger(1));
         if (prevCnt != null) {
             prevCnt.incrementAndGet();
@@ -1570,7 +1552,7 @@ public void R_PreserveObject(Object obj) {
     public void R_ReleaseObject(Object obj) {
         guaranteeInstanceOf(obj, RObject.class);
         RFFIContext context = getContext();
-        IdentityHashMap<RObject, AtomicInteger> preserveList = context.preserveList;
+        IdentityHashMap<RObject, AtomicInteger> preserveList = context.rffiContextState.preserveList;
         AtomicInteger atomicInteger = preserveList.get(obj);
         if (atomicInteger != null) {
             int decrementAndGet = atomicInteger.decrementAndGet();
@@ -1587,15 +1569,15 @@ public void R_ReleaseObject(Object obj) {
     @Override
     @TruffleBoundary
     public Object Rf_protect(Object x) {
-        getContext().protectStack.add(guaranteeInstanceOf(x, RObject.class));
+        getContext().rffiContextState.protectStack.add(guaranteeInstanceOf(x, RObject.class));
         return x;
     }
 
     @Override
     @TruffleBoundary
     public void Rf_unprotect(int x) {
         RFFIContext context = getContext();
-        ArrayList<RObject> stack = context.protectStack;
+        ArrayList<RObject> stack = context.rffiContextState.protectStack;
         for (int i = 0; i < x; i++) {
             context.registerReferenceUsedInNative(stack.remove(stack.size() - 1));
         }
@@ -1604,23 +1586,23 @@ public void Rf_unprotect(int x) {
     @Override
     @TruffleBoundary
     public int R_ProtectWithIndex(Object x) {
-        ArrayList<RObject> stack = getContext().protectStack;
+        ArrayList<RObject> stack = getContext().rffiContextState.protectStack;
         stack.add(guaranteeInstanceOf(x, RObject.class));
         return stack.size() - 1;
     }
 
     @Override
     @TruffleBoundary
     public void R_Reprotect(Object x, int y) {
-        ArrayList<RObject> stack = getContext().protectStack;
+        ArrayList<RObject> stack = getContext().rffiContextState.protectStack;
         stack.set(y, guaranteeInstanceOf(x, RObject.class));
     }
 
     @Override
     @TruffleBoundary
     public void Rf_unprotect_ptr(Object x) {
         RFFIContext context = getContext();
-        ArrayList<RObject> stack = context.protectStack;
+        ArrayList<RObject> stack = context.rffiContextState.protectStack;
         for (int i = stack.size() - 1; i >= 0; i--) {
             if (stack.get(i) == x) {
                 context.registerReferenceUsedInNative(stack.remove(i));

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/llvm/HandleLLVMUpCallExceptionNode.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2017, 2018, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2017, 2019, Oracle and/or its affiliates. All rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * This code is free software; you can redistribute it and/or modify it
@@ -24,9 +24,9 @@
 
 import com.oracle.truffle.api.CompilerDirectives.TruffleBoundary;
 import com.oracle.truffle.api.nodes.Node;
-import com.oracle.truffle.r.runtime.ffi.CallRFFI.HandleUpCallExceptionNode;
+import com.oracle.truffle.r.ffi.impl.upcalls.UpCallsRFFI;
 
-public class HandleLLVMUpCallExceptionNode extends Node implements HandleUpCallExceptionNode {
+public class HandleLLVMUpCallExceptionNode extends Node implements UpCallsRFFI.HandleUpCallExceptionNode {
     @Override
     @TruffleBoundary
     public void execute(Throwable ex) {