Merge commit '9c790b6edb27bd0b41181ba30532308542d6ebd6' into release/graal-vm/1.0

Author: ansalond

.gitattributes

@@ -0,0 +1 @@
+CHANGELOG.md merge=union

CHANGELOG.md

@@ -1,3 +1,29 @@
+# 1.0 RC 14
+
+* all FastR specific options (NOT those GNU-R compatible like `--save`) are experimental except for `--R.PrintErrorStacktracesToFile`,
+which is an option that enables logging of FastR internal errors for bug reporting purposes. Experimental options can be unlocked
+using `--experimental-options` or with `ContextBuilder#allowExperimentalOptions`.
+* the MRAN mirror used by FastR by default instead of CRAN was bumped to 2019-02-13
+* options for the JVM or native image are now passed using `--vm.` prefix in both cases instead of `--jvm.` or `--native.`
+(e.g., `--jvm.Dproperty=false` becomes `--vm.Dproperty=false`)
+
+New features:
+
+* whenever possible, errors are propagated to the FastR embedder
+
+Added missing R builtins and C API
+
+* `Rf_StringBlank`
+
+Bug fixes:
+
+* `C_numeric_deriv` gives wrong results of gradient #54
+* `tcrossprod` with a single vector #56
+* `length<-` would remove attributes from the target even if it was a shared value
+* `length(x) <- N` should not strip attributes if `length(x) == N`, which is not in line with GNU-R documentation,
+but relied upon in the `methods` package #55
+* `as.Date` with invalid date string #56
+
 # 1.0 RC 13
 
 New features:

ci.hocon

@@ -8,7 +8,7 @@ include "ci_common/common.hocon"
 # The standard set of gate builds. N.B. the style/builtin checks are only run on Linux as they are not OS-dependent.
 
 # in case you do not want to enforce a specific overlay commit, comment:
-overlay = "f2f27ae819a1f8ce3398aaf43c79aec358acd0a2"
+overlay = "9fd1ed7dac318a520ffe30b28bde900553950658"
 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"}

ci_common/common.hocon

@@ -27,20 +27,29 @@ java9Downloads : {
 logfiles : [
     "fastr_errors*.log"
     "results.json"
-    "libdownloads/R-*/gnur_configure.log"
-    "libdownloads/R-*/config.log"
-    "libdownloads/R-*/gnur_make.log"
-    "libdownloads/R-*/Makeconf"
-    "com.oracle.truffle.r.native/gnur/tests/log/all.diff"
-    "com.oracle.truffle.r.test.native/embedded/*.output"
-    "com.oracle.truffle.r.test.native/embedded/src/*.output"
+    "**/R-*/gnur_configure.log"
+    "**/R-*/config.log"
+    "**/R-*/gnur_make.log"
+    "**/gnur_configure.log"
+    "**/config.log"
+    "**/gnur_make.log"
+    "**/Makeconf"
+    "fastr/libdownloads/R-*/gnur_configure.log"
+    "fastr/libdownloads/R-*/config.log"
+    "fastr/libdownloads/R-*/gnur_make.log"
+    "../fastr/libdownloads/R-*/gnur_configure.log"
+    "../fastr/libdownloads/R-*/config.log"
+    "../fastr/libdownloads/R-*/gnur_make.log"
+    "**/com.oracle.truffle.r.native/gnur/tests/log/all.diff"
+    "**/com.oracle.truffle.r.test.native/embedded/*.output"
+    "**/com.oracle.truffle.r.test.native/embedded/src/*.output"
     # Uncomment to debug pkgtest issues, produces lot of logs!
-    "test.fastr/**/*.Rout"
-    "test.fastr/**/*.fail"
-    "test.fastr/**/*-tests/*.Rout"
-    "test.gnur/**/*.Rout"
-    "test.gnur/**/*-tests/*.Rout"
-    "test.gnur/**/*.fail"
+    "**/test.fastr/**/*.Rout"
+    "**/test.fastr/**/*.fail"
+    "**/test.fastr/**/*-tests/*.Rout"
+    "**/test.gnur/**/*.Rout"
+    "**/test.gnur/**/*-tests/*.Rout"
+    "**/test.gnur/**/*.fail"
     # Uncomment to debug the event loop hanging issue. It must be accompanied by enabling
     # the logging by setting the TRACE_EVENT_LOOP env var to true.
     # "traceEventLoop.log"
@@ -104,6 +113,7 @@ common : ${java8Downloads} {
     PKG_TEST_ENV_miniUI : "LC_ALL=C"
     PKG_TEST_ENV_compare : "LC_ALL=C"
     FASTR_OPTION_PrintErrorStacktracesToFile: "true"
+    GRAALVM_CHECK_EXPERIMENTAL_OPTIONS : "true"
   }
 }
 

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

@@ -274,13 +274,13 @@ public Object parseAndEval(Source source, MaterializedFrame frame, boolean print
     }
 
     private List<RSyntaxNode> parseSource(Source source) throws ParseException {
-        RParserFactory.Parser<RSyntaxNode> parser = RParserFactory.getParser();
+        RParserFactory.Parser parser = RParserFactory.getParser();
         return parser.script(source, new RASTBuilder(true), context.getLanguage());
     }
 
     @Override
     public ParsedExpression parse(Source source, boolean keepSource) throws ParseException {
-        RParserFactory.Parser<RSyntaxNode> parser = RParserFactory.getParser();
+        RParserFactory.Parser parser = RParserFactory.getParser();
         RASTBuilder builder = new RASTBuilder(true);
         List<RSyntaxNode> script = parser.script(source, builder, context.getLanguage());
         Object[] data = new Object[script.size()];
@@ -388,7 +388,7 @@ private EngineRootNode createRScriptRoot(Source fullSource, MaterializedFrame fr
                     lineIndex++;
                     List<RSyntaxNode> currentStmts = null;
                     try {
-                        RParserFactory.Parser<RSyntaxNode> parser = RParserFactory.getParser();
+                        RParserFactory.Parser parser = RParserFactory.getParser();
                         currentStmts = parser.statements(src, fullSource, startLine, new RASTBuilder(true), context.getLanguage());
                     } catch (IncompleteSourceException e) {
                         lastParseException = e;

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

@@ -140,11 +140,8 @@ public Engine createEngine(RContext context) {
 
     @Override
     public RPairList getSyntaxCaller(RCaller rl) {
-        RCaller call = rl;
-        while (call.isPromise()) {
-            call = call.getParent();
-        }
-        if (call.isValidCaller()) {
+        RCaller call = RCaller.unwrapPromiseCaller(rl);
+        if (call != null && call.isValidCaller()) {
             RSyntaxElement syntaxNode = call.getSyntaxNode();
             return RDataFactory.createLanguage(getOrCreateLanguageClosure(((RSyntaxNode) syntaxNode).asRNode()));
         } else {
@@ -239,19 +236,9 @@ public Object findCaller(RBaseNode call) {
 
     private Object findCallerFromFrame(Frame frame) {
         if (frame != null && RArguments.isRFrame(frame)) {
-            RCaller caller = RArguments.getCall(frame);
-            while (caller.isPromise()) {
-                if (!caller.hasSysParent()) {
-                    // frame created to evaluate promise via CallTarget (i.e. the PIC cache was
-                    // filled and the promise could not be evaluated while in the context of the
-                    // frame that cased its evaluation)
-                    caller = caller.getPromiseCaller();
-                } else {
-                    // NOTE: maybe we should just use the caller as is otherwise...
-                    caller = caller.getParent();
-                }
-            }
-            if (caller.isValidCaller()) {
+            // This finds the next non-artificial frame on the R call stack
+            RCaller caller = RCaller.unwrapPrevious(RArguments.getCall(frame));
+            if (RCaller.isValidCaller(caller)) {
                 // This is where we need to ensure that we have an RLanguage object with a rep that
                 // is an RSyntaxNode.
                 return getSyntaxCaller(caller);

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

@@ -24,7 +24,6 @@
 
 import com.oracle.truffle.api.CompilerAsserts;
 import com.oracle.truffle.api.interop.ForeignAccess;
-import com.oracle.truffle.api.interop.MessageResolution;
 import com.oracle.truffle.r.ffi.impl.interop.FFI_RForeignAccessFactoryImpl;
 import com.oracle.truffle.r.runtime.RInternalError;
 import com.oracle.truffle.r.runtime.conn.RConnection;
@@ -57,8 +56,8 @@
 import com.oracle.truffle.r.runtime.env.frame.ActiveBinding;
 
 /**
- * For most types we use the {@link MessageResolution} facility to automatically generate the
- * factory for creating the {@link ForeignAccess} instance. The exceptions are the (many) subclasses
+ * For most types we use the {@code MessageResolution} facility to automatically generate the
+ * factory for creating the {@code ForeignAccess} instance. The exceptions are the (many) subclasses
  * of {@link RAbstractVector} as these have the same handling but the generator cannot handle
  * abstract classes.
  *

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

@@ -135,7 +135,7 @@ private static void runRmainloop() {
         RContext ctx = RContext.getInstance();
         ctx.completeEmbeddedInitialization();
         ctx.getRFFI().initializeEmbedded(ctx);
-        int status = REPL.readEvalPrint(context, consoleHandler, false, System.err);
+        int status = REPL.readEvalPrint(context, consoleHandler, false);
         context.leave();
         context.close();
         Utils.systemExit(status);

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

@@ -283,7 +283,8 @@ private static Object findVarInFrameHelper(Object envArg, Object symbolArg, bool
         RSymbol name = (RSymbol) symbolArg;
         REnvironment env = (REnvironment) envArg;
         while (env != REnvironment.emptyEnv()) {
-            Object value = env.get(name.getName());
+            String nameKey = name.getName();
+            Object value = env.get(nameKey);
             if (value != null) {
                 if (value instanceof RPromise && ((RPromise) value).isOptimized()) {
                     // From the point of view of RFFI, optimized promises (i.e. promises with null
@@ -297,6 +298,14 @@ private static Object findVarInFrameHelper(Object envArg, Object symbolArg, bool
                 if (value == RMissing.instance || value == REmpty.instance) {
                     return RSymbol.MISSING;
                 }
+                Object v = RRuntime.asAbstractVector(value);
+                if (v instanceof RAbstractVector) {
+                    v = ((RAbstractVector) v).materialize();
+                }
+                if (v != value) {
+                    env.putOverrideLock(nameKey, v);
+                    value = v;
+                }
                 return value;
             }
             if (!inherits) {
@@ -1238,7 +1247,7 @@ public Object R_getGlobalFunctionContext() {
             if (!currentCaller.isPromise() && currentCaller.isValidCaller() && currentCaller != RContext.getInstance().stateInstrumentation.getBrowserState().getInBrowserCaller()) {
                 break;
             }
-            currentCaller = currentCaller.getParent();
+            currentCaller = currentCaller.getPrevious();
         }
         return currentCaller == null || currentCaller == RCaller.topLevel ? RNull.instance : currentCaller;
     }
@@ -1249,7 +1258,7 @@ public Object R_getParentFunctionContext(Object c) {
         Utils.warn("Potential memory leak (parent function context object)");
         RCaller currentCaller = guaranteeInstanceOf(c, RCaller.class);
         while (true) {
-            currentCaller = currentCaller.getParent();
+            currentCaller = currentCaller.getPrevious();
             if (currentCaller == null ||
                             (!currentCaller.isPromise() && currentCaller.isValidCaller() && currentCaller != RContext.getInstance().stateInstrumentation.getBrowserState().getInBrowserCaller())) {
                 break;
@@ -1333,7 +1342,7 @@ public Object R_getContextSrcRef(Object c) {
             SourceSection ss = f.getRootNode().getSourceSection();
             String path = RSource.getPath(ss.getSource());
             // TODO: is it OK to pass "" if path is null?
-            return RSrcref.createLloc(ss, path == null ? "" : path);
+            return RSrcref.createLloc(RContext.getInstance(), ss, path == null ? "" : path);
         }
     }
 

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/interop/package-info.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2018, 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
@@ -21,7 +21,7 @@
  * questions.
  */
 /**
- * A collection of types and {@link com.oracle.truffle.api.interop.MessageResolution} classes that
+ * A collection of types and {@code com.oracle.truffle.api.interop.MessageResolution} classes that
  * support the implementations.
  */
 package com.oracle.truffle.r.ffi.impl.interop;