Merge commit 'c01c32f85d9' into release/graal-vm/1.0

Author: ansalond

.gitignore

@@ -70,7 +70,6 @@
 .metadata/
 .gdb_history
 *.swo
-*.csv
 *.iml
 *.swp
 *.class
@@ -103,7 +102,7 @@ scratch/
 bin/
 share/
 etc/
-doc/
+/doc/
 src_gen/
 /local/
 /.hgtip

3rd_party_licenses.txt

@@ -1,3 +1,35 @@
+# 1.0 RC 11
+
+* upgraded the R version to R-3.5.1
+  * base packages and other sources used directly from GNU-R upgraded to their R-3.5.1 versions
+  * fixed differences between R-3.4.0 and R-3.5.1
+
+* FastR does not print or log any details for internal errors unless it is run with `--jvm.DR:+PrintErrorStacktracesToFile`
+
+Added missing R builtins and C API
+
+* `Rf_duplicated`
+* `Rf_setVar`
+* `norm_rand`
+* `exp_rand`
+
+Bug fixes:
+
+* internal error in `mapply` with empty arguments list
+* `comment` and `comment<-` work with S4 objects
+* `iconvlist()` was failing on argument error #43
+* `range` works properly with lists
+* the reference count of `dimnames` of the result of `==` was not handled properly leading to incorrect results #40
+* `exists` did not work properly in all cases when used with the `mode` argument #44
+* 'charIndex out of range' when parsing an incomplete source #39
+* `no_proxy` environment variable was not parsed correctly
+* `read.csv` treats empty value as `NA` of the same type as the rest of the values in the column #42
+* `SET_NAMED` allows to decrease the reference count to support a pattern from `data.table`
+* exception when writing into the result returned from `split`
+* `switch` falls through only if the actual argument is empty constant: `switch('x',x=,y=42)` vs. `switch('x',x=quote(f(1,))[[3]],y=42)`
+* `oldClass<-` works with external pointers and other less common R types
+* C API function `Rf_setAttrib` coerces double vector to integer when setting "dim" attribute #46
+
 # 1.0 RC 10
 
 New features:

CHANGELOG.md

@@ -1,7 +1,7 @@
 # java 7 is needed by Truffle (for now)
 java7 : {name : oraclejdk, version : "7",    platformspecific: true}
 # java 8 must be a jvmci enabled variant
-java8 : {name : labsjdk, version : "8u172-jvmci-0.47", platformspecific: true}
+java8 : {name : labsjdk, version : "8u192-jvmci-0.52", platformspecific: true}
 java9 : {name : oraclejdk, version : "9.0.4+11", platformspecific: true}
 
 java8Downloads : {
@@ -64,6 +64,7 @@ packagesLinux : ${pkgEnvironment} {
     mercurial : ">=2.2"
     "pip:astroid" : "==1.1.0"
     "pip:pylint" : "==1.1.0"
+    "pip:ninja_syntax" : "==1.7.2"
     make : ">=3.83"
     gcc-build-essentials : "==4.9.1" # GCC 4.9.0 fails on cluster
     readline : "==6.3"
@@ -76,6 +77,7 @@ packagesLinux : ${pkgEnvironment} {
 packagesDarwin : {
   "pip:astroid" : "==1.1.0"
   "pip:pylint" : "==1.1.0"
+  "pip:ninja_syntax" : "==1.7.2"
   "pcre" : "==8.38"
 }
 
@@ -88,6 +90,7 @@ common : ${java8Downloads} ${packagesLinux}  {
   environment : {
 	PKG_TEST_ENV_miniUI : "LC_ALL=C"
 	PKG_TEST_ENV_compare : "LC_ALL=C"
+	FASTR_OPTION_PrintErrorStacktracesToFile: "true"
   }
 }
 

ci_common/common.hocon

@@ -22,14 +22,6 @@
  */
 package com.oracle.truffle.r.engine;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.stream.Collectors;
-
 import com.oracle.truffle.api.CallTarget;
 import com.oracle.truffle.api.CompilerAsserts;
 import com.oracle.truffle.api.CompilerDirectives;
@@ -63,6 +55,7 @@
 import com.oracle.truffle.r.nodes.function.RCallerHelper;
 import com.oracle.truffle.r.nodes.function.call.CallRFunctionNode;
 import com.oracle.truffle.r.nodes.function.opt.ShareObjectNode;
+import com.oracle.truffle.r.nodes.function.opt.UnShareObjectNode;
 import com.oracle.truffle.r.nodes.function.visibility.GetVisibilityNode;
 import com.oracle.truffle.r.nodes.function.visibility.SetVisibilityNode;
 import com.oracle.truffle.r.nodes.instrumentation.RInstrumentation;
@@ -80,8 +73,8 @@
 import com.oracle.truffle.r.runtime.RRuntime;
 import com.oracle.truffle.r.runtime.RSource;
 import com.oracle.truffle.r.runtime.ReturnException;
-import com.oracle.truffle.r.runtime.RootWithBody;
 import com.oracle.truffle.r.runtime.RootBodyNode;
+import com.oracle.truffle.r.runtime.RootWithBody;
 import com.oracle.truffle.r.runtime.ThreadTimings;
 import com.oracle.truffle.r.runtime.Utils;
 import com.oracle.truffle.r.runtime.Utils.DebugExitException;
@@ -103,6 +96,14 @@
 import com.oracle.truffle.r.runtime.nodes.RNode;
 import com.oracle.truffle.r.runtime.nodes.RSyntaxNode;
 
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
 /**
  * The engine for the FastR implementation. Handles parsing and evaluation. There is one instance of
  * this class per {@link RContext}.
@@ -171,7 +172,7 @@ private void initializeNonShared() {
             } catch (ParseException e) {
                 throw new RInternalError(e, "error while parsing system profile from %s", RProfile.systemProfile().getName());
             }
-            checkAndRunStartupShutdownFunction(".OptRequireMethods");
+            checkAndRunStartupShutdownFunction(".OptRequireMethods", ".OptRequireMethods()");
 
             suppressWarnings = false;
             Source siteProfile = context.stateRProfile.siteProfile();
@@ -192,37 +193,25 @@ private void initializeNonShared() {
             }
             if (context.getStartParams().restore()) {
                 // call sys.load.image(".RData", RCmdOption.QUIET
-                checkAndRunStartupShutdownFunction("sys.load.image", new String[]{"\".RData\"", context.getStartParams().isQuiet() ? "TRUE" : "FALSE"});
+                checkAndRunStartupShutdownFunction("sys.load.image", "sys.load.image('.RData'," + (context.getStartParams().isQuiet() ? "TRUE" : "FALSE") + ')');
             }
-            checkAndRunStartupShutdownFunction(".First");
-            checkAndRunStartupShutdownFunction(".First.sys");
+            checkAndRunStartupShutdownFunction(".First", ".First()");
+            checkAndRunStartupShutdownFunction(".First.sys", ".First.sys()");
 
             StartupTiming.timestamp("After Profiles Loaded");
         }
     }
 
     @Override
-    public void checkAndRunStartupShutdownFunction(String name, String... args) {
+    public void checkAndRunStartupShutdownFunction(String name, String code) {
+        // sanity check: code should be invocation of the function, so it should contain
+        // "{name}(some-args)"
+        assert code.contains("(") && code.contains(name);
         Object func = REnvironment.globalEnv().findFunction(name);
         if (func != null) {
-            String call = name;
-            if (args.length == 0) {
-                call += "()";
-            } else {
-                call += "(";
-                if (args.length > 0) {
-                    for (int i = 0; i < args.length; i++) {
-                        call += args[i];
-                        if (i != args.length - 1) {
-                            call += ", ";
-                        }
-                    }
-                }
-                call += ")";
-            }
             // Should this print the result?
             try {
-                parseAndEval(RSource.fromTextInternal(call, RSource.Internal.STARTUP_SHUTDOWN), globalFrame, false);
+                parseAndEval(RSource.fromTextInternal(code, RSource.Internal.STARTUP_SHUTDOWN), globalFrame, false);
             } catch (ParseException e) {
                 throw new RInternalError(e, "error while parsing startup function");
             }
@@ -292,7 +281,10 @@ private List<RSyntaxNode> parseSource(Source source) throws ParseException {
     @Override
     public RExpression parse(Source source) throws ParseException {
         List<RSyntaxNode> list = parseSource(source);
-        Object[] data = list.stream().map(node -> RASTUtils.createLanguageElement(node)).toArray();
+        Object[] data = new Object[list.size()];
+        for (int i = 0; i < data.length; i++) {
+            data[i] = RASTUtils.createLanguageElement(list.get(i));
+        }
         return RDataFactory.createExpression(data);
     }
 
@@ -377,15 +369,18 @@ private EngineRootNode createRScriptRoot(Source fullSource, MaterializedFrame fr
                 int lineIndex = 1;
                 int startLine = lineIndex;
                 StringBuilder sb = new StringBuilder();
+                String nextLineInput = br.readLine();
+                ParseException lastParseException = null;
                 while (true) {
-                    String input = br.readLine();
+                    String input = nextLineInput;
                     if (input == null) {
                         if (sb.length() != 0) {
                             // end of file, but not end of statement => error
-                            statements.add(new SyntaxErrorNode(null, fullSource.createSection(startLine, 1, sb.length())));
+                            statements.add(new SyntaxErrorNode(lastParseException, fullSource.createSection(startLine, 1, sb.length())));
                         }
                         break;
                     }
+                    nextLineInput = br.readLine();
                     sb.append(input);
                     Source src = Source.newBuilder(RRuntime.R_LANGUAGE_ID, sb.toString(), file + "#" + startLine + "-" + lineIndex).uri(uri).build();
                     lineIndex++;
@@ -394,7 +389,10 @@ private EngineRootNode createRScriptRoot(Source fullSource, MaterializedFrame fr
                         RParserFactory.Parser<RSyntaxNode> parser = RParserFactory.getParser();
                         currentStmts = parser.statements(src, fullSource, startLine, new RASTBuilder(), context.getLanguage());
                     } catch (IncompleteSourceException e) {
-                        sb.append('\n');
+                        lastParseException = e;
+                        if (nextLineInput != null) {
+                            sb.append('\n');
+                        }
                         continue;
                     } catch (ParseException e) {
                         statements.add(new SyntaxErrorNode(e, fullSource.createSection(startLine, 1, sb.length())));
@@ -647,8 +645,8 @@ public RNode getBody() {
 
     @TruffleBoundary
     private static boolean checkResult(Object result) {
-        if (FastROptions.CheckResultCompleteness.getBooleanValue() && result instanceof RAbstractVector) {
-            assert RAbstractVector.verify((RAbstractVector) result);
+        if (result instanceof RAbstractVector) {
+            return RAbstractVector.verify((RAbstractVector) result);
         }
         return true;
     }
@@ -678,7 +676,7 @@ private static void printValue(RContext ctx, MaterializedFrame callingFrame, Obj
                 RFunction function = (RFunction) evaluatePromise(printMethod);
                 CallRFunctionNode.executeSlowpath(function, RCaller.createInvalid(callingFrame), callingFrame, new Object[]{resultValue, RArgsValuesAndNames.EMPTY}, null);
             }
-            ShareObjectNode.unshare(resultValue);
+            UnShareObjectNode.unshare(resultValue);
         } else {
             // this supports printing of non-R values (via toString for now)
             String str;

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

@@ -23,7 +23,6 @@
 package com.oracle.truffle.r.engine;
 
 import java.io.ByteArrayOutputStream;
-import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -55,7 +54,6 @@
 import com.oracle.truffle.r.nodes.function.ClassHierarchyNode;
 import com.oracle.truffle.r.nodes.function.FunctionDefinitionNode;
 import com.oracle.truffle.r.nodes.function.RCallNode;
-import com.oracle.truffle.r.nodes.instrumentation.RInstrumentation;
 import com.oracle.truffle.r.nodes.instrumentation.RSyntaxTags.FunctionBodyBlockTag;
 import com.oracle.truffle.r.nodes.instrumentation.RSyntaxTags.LoopTag;
 import com.oracle.truffle.r.runtime.ArgumentsSignature;
@@ -354,20 +352,20 @@ public boolean disableDebug(RFunction func) {
     }
 
     @Override
-    public Object rcommandMain(String[] args, String[] env, boolean intern) {
+    public Object rcommandMain(String[] args, String[] env, boolean intern, int timeoutSecs) {
         IORedirect redirect = handleIORedirect(args, intern);
         assert env == null : "re-enable env arguments";
-        int result = RMain.runR(redirect.args, redirect.in, redirect.out, redirect.err);
+        int result = RMain.runR(redirect.args, redirect.in, redirect.out, redirect.err, timeoutSecs);
         return redirect.getInternResult(result);
     }
 
     @Override
-    public Object rscriptMain(String[] args, String[] env, boolean intern) {
+    public Object rscriptMain(String[] args, String[] env, boolean intern, int timeoutSecs) {
         IORedirect redirect = handleIORedirect(args, intern);
         // TODO argument parsing can fail with ExitException, which needs to be handled correctly in
         // nested context
         assert env == null : "re-enable env arguments";
-        int result = RMain.runRscript(redirect.args, redirect.in, redirect.out, redirect.err);
+        int result = RMain.runRscript(redirect.args, redirect.in, redirect.out, redirect.err, timeoutSecs);
         return redirect.getInternResult(result);
     }
 
@@ -433,7 +431,7 @@ private static IORedirect handleIORedirect(String[] args, boolean intern) {
                     throw RError.error(RError.NO_CALLER, RError.Message.GENERIC, "redirect missing");
                 }
                 try {
-                    in = new FileInputStream(file);
+                    in = RContext.getInstance().getEnv().getTruffleFile(file).newInputStream();
                 } catch (IOException ex) {
                     throw RError.error(RError.NO_CALLER, RError.Message.NO_SUCH_FILE, file);
                 }
@@ -490,11 +488,6 @@ public String encodeComplex(RComplex x, int digits) {
         return ComplexVectorPrinter.encodeComplex(x, digits);
     }
 
-    @Override
-    public void checkDebugRequest(RFunction func) {
-        RInstrumentation.checkDebugRequested(func);
-    }
-
     @Override
     public Class<? extends TruffleRLanguage> getTruffleRLanguage() {
         return TruffleRLanguageImpl.class;

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

@@ -418,6 +418,12 @@ protected Object write(TruffleObject receiver, int idx, Object valueObj) {
             return write(receiver, new Object[]{idx + 1}, valueObj);
         }
 
+        @Specialization
+        protected Object write(TruffleObject receiver, long idx, Object valueObj) {
+            // idx + 1 R is indexing from 1
+            return write(receiver, new Object[]{idx + 1}, valueObj);
+        }
+
         @Specialization
         protected Object write(TruffleObject receiver, String field, Object valueObj) {
             return write(receiver, new Object[]{field}, valueObj);

com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/interop/ListMR.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
@@ -23,6 +23,7 @@
 package com.oracle.truffle.r.engine.interop;
 
 import java.util.List;
+import java.util.function.Supplier;
 
 import com.oracle.truffle.api.CallTarget;
 import com.oracle.truffle.api.CompilerDirectives;
@@ -472,7 +473,16 @@ public Object execute(VirtualFrame frame) {
         });
     }
 
-    static class Check extends RootNode {
+    public static final Supplier<RootNode> CHECK_FACTORY = new CheckFactory();
+
+    private static final class CheckFactory implements Supplier<RootNode> {
+        @Override
+        public RootNode get() {
+            return new Check();
+        }
+    }
+
+    private static final class Check extends RootNode {
 
         Check() {
             super(null);

com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/interop/RAbstractVectorAccessFactory.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
@@ -122,7 +122,7 @@ public ForeignAccess getForeignAccess(RTruffleObject obj) {
         } else if (obj instanceof RInteropNA) {
             return RInteropNAMRForeign.ACCESS;
         } else if (obj instanceof RAbstractAtomicVector) {
-            return ForeignAccess.create(new RAbstractVectorAccessFactory(), new RAbstractVectorAccessFactory.Check());
+            return ForeignAccess.createAccess(new RAbstractVectorAccessFactory(), RAbstractVectorAccessFactory.CHECK_FACTORY);
         } else {
             ForeignAccess access = FFI_RForeignAccessFactoryImpl.getForeignAccess(obj);
             if (access != null) {