Merge commit 'ee11fce71b248d77ac4d6d6af75a2a5b33c20035' into release/graal-vm/1.0

Author: ansalond

CHANGELOG.md

@@ -1,8 +1,42 @@
+# 1.0 RC 10
+
+New features:
+
+* interop and tooling: READ and WRITE of ActiveBinding may have side effects. This is communicated via `KEY_INFO` to the tools and other languages (e.g., a debugger may warn before evaluating an ActiveBinding)
+* the MRAN mirror used by FastR as default repo was moved to https://mran.microsoft.com/snapshot/2018-06-20
+* new function `install.fastr.packages` to install FastR rJava replacement and possibly other packages in the future
+* print the whole guest language stacktrace if an exception occurs during an interop call into another language
+
+Added missing R builtins and C API
+
+* `pos.to.env` builtin
+* private `do_fmin` external function from the stats packages used by public R function `optimize`
+* `beta` #33
+
+Bug fixes:
+
+* tooling: top level statements are not marked as functions (e.g., a debugger will not treat them as such anymore)
+* update rpath correctly for redistributed libraries when producing a release build. This issue caused linking problems for MacOS users #26
+* UseMethod caused internal error under some specific circumstances (happens during installation of the R.oo package)
+* fully support indirect use of .Internal, e.g. in `(get('.Internal'))(paste0(list(1,2),','))`
+* `as.character(external-pointer)` does not crash, but prints the pointer address #28
+* `file.path` with `NULL` as one of its arguments gives correct result (empty character vector)
+* `format.POSIXlt` uses the same time zone database as rest of the system #29
+* `dev.control(displaylist = 'inhibit')` caused `ClassCastException`
+* `download.file` follows redirects.
+* static members of Java interop objects are not ignored during printing and deparsing
+* fixed internal error in `on.exit(NULL)`
+* fixed `mget` to accept also non list values for `ifnotfound`
+* updating dimensions of a vector always resets the dimnames. #34
+* `env2list` used in, e.g., `as.list.environment` can handle `...` inside the environment
+
 # 1.0 RC 9
 
 New features
 
 * various improvements in handling of foreign objects in R
+  * [brief overview in the documentation](http://www.graalvm.org/docs/reference-manual/languages/r/#foreign)
+  * [executable specification](https://github.com/oracle/fastr/blob/master/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/library/fastr/R/interop-array-conversion-test.R#L158)
 
 Added missing R builtins and C API
 

README.md

@@ -1,10 +1,21 @@
-A high performance implementation of the R programming language., built on the GraalVM by Oracle Labs.
+[![Join the chat at https://gitter.im/graalvm/graal-core](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/graalvm/graal-core?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+
+A high-performance implementation of the R programming language, built on GraalVM.
 
 FastR aims to be:
-* [efficient](https://medium.com/graalvm/faster-r-with-fastr-4b8db0e0dceb#4ab6): executing R language scripts faster than any other R runtime.
+* [efficient](https://medium.com/graalvm/faster-r-with-fastr-4b8db0e0dceb#4ab6): executing R language scripts faster than any other R runtime
 * [polyglot](https://medium.com/graalvm/faster-r-with-fastr-4b8db0e0dceb#0f5c): allowing [polyglot interoperability](https://www.graalvm.org/docs/reference-manual/polyglot/) with other languages in the GraalVM ecosystem.
-* [compatible](https://medium.com/graalvm/faster-r-with-fastr-4b8db0e0dceb#fff5): providing support for existing packages and the R native interface.
-* [embeddable](https://github.com/graalvm/examples/tree/master/r_java_embedding): allowing integration using the R embedding API or the GraalVM polyglot embedding SDK.
+* [compatible](https://medium.com/graalvm/faster-r-with-fastr-4b8db0e0dceb#fff5): providing support for existing packages and the R native interface
+* [embeddable](https://github.com/graalvm/examples/tree/master/r_java_embedding): allowing integration using the R embedding API or the GraalVM polyglot embedding SDK
+
+
+The screenshot below shows Java application with embedded FastR engine.
+The plot below was generated by `ggplot2` running on FastR and it shows
+peak performance of the [raytracing example](http://www.tylermw.com/throwing-shade/).
+The measurements were [reproduced independently](https://nextjournal.com/sdanisch/fastr-benchmark).
+
+![Java embedding](documentation/assets/javaui.png)
+![Speedup](documentation/assets/speedup.png)
 
  ## Getting Started
 See the documentation on the GraalVM website on how to [get GraalVM](https://www.graalvm.org/docs/getting-started/) and [install and use FastR](http://www.graalvm.org/docs/reference-manual/languages/r/).

ci_common/common.hocon

@@ -36,9 +36,14 @@ logfiles : [
     "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"
+    # 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"
   ]
 
 # This is needed by all (Linux) builds but is specific to the module system employed
@@ -223,7 +228,7 @@ rbcheck : ${common} {
 internalPkgtest: ${common} {
   run : [
     ["mx", "build"]
-    ["mx", "pkgtest", "--repos", "FASTR", "--pkg-filelist", "com.oracle.truffle.r.test.native/packages/pkg-filelist"]
+    ["mx", "pkgtest", "--verbose", "--repos", "FASTR", "--pkg-filelist", "com.oracle.truffle.r.test.native/packages/pkg-filelist"]
   ]
   logs: ${common.logs}
 }

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

@@ -26,6 +26,7 @@
 
 import com.oracle.truffle.api.CompilerDirectives;
 import com.oracle.truffle.api.Truffle;
+import com.oracle.truffle.api.TruffleException;
 import com.oracle.truffle.api.TruffleLanguage.ContextReference;
 import com.oracle.truffle.api.frame.MaterializedFrame;
 import com.oracle.truffle.api.frame.VirtualFrame;
@@ -91,6 +92,9 @@ public Object execute(VirtualFrame frame) {
             throw e;
         } catch (Throwable t) {
             CompilerDirectives.transferToInterpreter();
+            if (t instanceof TruffleException && !((TruffleException) t).isInternalError()) {
+                throw t;
+            }
             // other errors didn't produce an output yet
             RInternalError.reportError(t);
             throw t;

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

@@ -415,7 +415,7 @@ private EngineRootNode createRScriptRoot(Source fullSource, MaterializedFrame fr
 
     @Override
     @TruffleBoundary
-    public Object eval(RExpression exprs, REnvironment envir, RCaller caller) {
+    public Object eval(RExpression exprs, REnvironment envir, Object callerFrame, RCaller caller, RFunction function) {
         Object result = RNull.instance;
         for (int i = 0; i < exprs.getLength(); i++) {
             Object obj = exprs.getDataAt(i);
@@ -427,7 +427,7 @@ public Object eval(RExpression exprs, REnvironment envir, RCaller caller) {
                     throw RError.error(RError.SHOW_CALLER, RError.Message.ARGUMENT_MISSING, identifier);
                 }
             } else if ((obj instanceof RPairList && ((RPairList) obj).isLanguage())) {
-                result = eval((RPairList) obj, envir, caller);
+                result = eval((RPairList) obj, envir, callerFrame, caller, function);
             } else {
                 result = obj;
             }
@@ -437,9 +437,9 @@ public Object eval(RExpression exprs, REnvironment envir, RCaller caller) {
 
     @Override
     @TruffleBoundary
-    public Object eval(RPairList expr, REnvironment envir, RCaller caller) {
+    public Object eval(RPairList expr, REnvironment envir, Object callerFrame, RCaller caller, RFunction function) {
         assert expr.isLanguage();
-        return expr.getClosure().eval(envir, caller);
+        return expr.getClosure().eval(envir, callerFrame, caller, function);
     }
 
     @Override

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

@@ -259,11 +259,16 @@ abstract static class REnvironmentKeyInfoImplNode extends Node {
 
         @Specialization
         protected int access(REnvironment receiver, String identifier) {
-            Object val = receiver.get(identifier);
-            if (val == null) {
-                return 0;
-            }
+            Object val = null;
             int result = KeyInfo.READABLE;
+            if (receiver.isActiveBinding(identifier)) {
+                result |= KeyInfo.READ_SIDE_EFFECTS | KeyInfo.WRITE_SIDE_EFFECTS;
+            } else {
+                val = receiver.get(identifier);
+                if (val == null) {
+                    return 0;
+                }
+            }
             if (!receiver.isLocked() && !receiver.bindingIsLocked(identifier)) {
                 result |= KeyInfo.MODIFIABLE;
             }

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

@@ -133,7 +133,7 @@ private static void runRmainloop() {
         RContext ctx = RContext.getInstance();
         ctx.completeEmbeddedInitialization();
         ctx.getRFFI().initializeEmbedded(ctx);
-        int status = REPL.readEvalPrint(context, consoleHandler, false);
+        int status = REPL.readEvalPrint(context, consoleHandler, false, System.err);
         context.leave();
         context.close();
         Utils.systemExit(status);

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

@@ -75,25 +75,29 @@
 import com.oracle.truffle.r.runtime.data.RComplexVector;
 import com.oracle.truffle.r.runtime.data.RDataFactory;
 import com.oracle.truffle.r.runtime.data.RDoubleVector;
+import com.oracle.truffle.r.runtime.data.REmpty;
 import com.oracle.truffle.r.runtime.data.RExpression;
 import com.oracle.truffle.r.runtime.data.RExternalPtr;
 import com.oracle.truffle.r.runtime.data.RFunction;
 import com.oracle.truffle.r.runtime.data.RIntVector;
-import com.oracle.truffle.r.runtime.data.RPairList;
 import com.oracle.truffle.r.runtime.data.RList;
 import com.oracle.truffle.r.runtime.data.RLogicalVector;
+import com.oracle.truffle.r.runtime.data.RMissing;
 import com.oracle.truffle.r.runtime.data.RNull;
 import com.oracle.truffle.r.runtime.data.RObject;
+import com.oracle.truffle.r.runtime.data.RPairList;
 import com.oracle.truffle.r.runtime.data.RPromise;
-import com.oracle.truffle.r.runtime.data.RRaw;
 import com.oracle.truffle.r.runtime.data.RPromise.EagerPromise;
+import com.oracle.truffle.r.runtime.data.RRaw;
 import com.oracle.truffle.r.runtime.data.RRawVector;
 import com.oracle.truffle.r.runtime.data.RShareable;
 import com.oracle.truffle.r.runtime.data.RStringVector;
 import com.oracle.truffle.r.runtime.data.RSymbol;
 import com.oracle.truffle.r.runtime.data.RTypedValue;
 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.RAbstractListBaseVector;
 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;
@@ -224,7 +228,11 @@ public void Rf_defineVar(Object symbolArg, Object value, Object envArg) {
         REnvironment env = (REnvironment) envArg;
         RSymbol name = (RSymbol) symbolArg;
         try {
-            env.put(name.getName(), value);
+            if (value == RUnboundValue.instance) {
+                env.rm(name.getName());
+            } else {
+                env.put(name.getName(), value);
+            }
         } catch (PutException ex) {
             throw RError.error(RError.SHOW_CALLER2, ex);
         }
@@ -283,7 +291,11 @@ private static Object findVarInFrameHelper(Object envArg, Object symbolArg, bool
                     return ((RPromise) value).getRawValue();
                 }
                 if (value instanceof RArgsValuesAndNames) {
-                    return ((RArgsValuesAndNames) value).toPairlist();
+                    RArgsValuesAndNames argsValsNames = (RArgsValuesAndNames) value;
+                    return argsValsNames.isEmpty() ? RSymbol.MISSING : argsValsNames.toPairlist();
+                }
+                if (value == RMissing.instance || value == REmpty.instance) {
+                    return RSymbol.MISSING;
                 }
                 return value;
             }
@@ -460,6 +472,8 @@ public Object Rf_allocVector(int mode, long n) {
             case LISTSXP:
             case LANGSXP:
                 return RDataFactory.createPairList(ni, type);
+            case NILSXP:
+                return RNull.instance;
             default:
                 throw unimplemented("unexpected SEXPTYPE " + type);
         }
@@ -727,7 +741,7 @@ public Object PRINTNAME(Object x) {
             return x;
         }
         guaranteeInstanceOf(x, RSymbol.class);
-        return CharSXPWrapper.create(((RSymbol) x).getName());
+        return ((RSymbol) x).getWrappedName();
     }
 
     @Override
@@ -1619,8 +1633,7 @@ public int registerRoutines(Object dllInfoObj, int nstOrd, int num, Object routi
     @Override
     @TruffleBoundary
     public int registerCCallable(String pkgName, String functionName, Object address) {
-        DLLInfo lib = DLL.safeFindLibrary(pkgName);
-        lib.registerCEntry(new CEntry(functionName, new SymbolHandle(address)));
+        DLLInfo.registerCEntry(pkgName, new CEntry(functionName, new SymbolHandle(address)));
         return 0;
     }
 
@@ -2399,8 +2412,12 @@ public Object LOGICAL(Object x) {
     }
 
     @Override
+    @TruffleBoundary
     public Object REAL(Object x) {
-        return VectorRFFIWrapper.get(guaranteeVectorOrNull(x, RDoubleVector.class));
+        if ((x instanceof RAbstractStringVector) || (x instanceof RAbstractListBaseVector)) {
+            RFFIUtils.unimplemented("REAL is being called for type " + Utils.getTypeName(x));
+        }
+        return VectorRFFIWrapper.get(guaranteeVectorOrNull(x, RAbstractAtomicVector.class));
     }
 
     @Override
@@ -2433,6 +2450,11 @@ public Object R_forceAndCall(Object e, Object f, int n, Object args) {
         throw implementedAsNode();
     }
 
+    @Override
+    public void R_MakeActiveBinding(Object symArg, Object funArg, Object envArg) {
+        throw implementedAsNode();
+    }
+
     private static TruffleObject guaranteeVectorOrNull(Object obj, Class<? extends TruffleObject> clazz) {
         if (obj == RNull.instance) {
             return RNull.instance;

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

@@ -32,11 +32,10 @@
 import com.oracle.truffle.api.interop.UnsupportedMessageException;
 import com.oracle.truffle.api.nodes.Node;
 import com.oracle.truffle.r.runtime.RInternalError;
+import com.oracle.truffle.r.runtime.Utils;
 import com.oracle.truffle.r.runtime.context.RContext;
 import com.oracle.truffle.r.runtime.data.RObject;
 import com.oracle.truffle.r.runtime.data.RPairList;
-import com.oracle.truffle.r.runtime.data.RSymbol;
-import com.oracle.truffle.r.runtime.data.model.RAbstractVector;
 import com.oracle.truffle.r.runtime.ffi.RFFIContext;
 import com.oracle.truffle.r.runtime.ffi.RFFILog;
 
@@ -121,32 +120,20 @@ private static void printArgs(CallMode mode, StringBuilder sb, Object[] args) {
                 sb.append("null");
                 continue;
             }
-            sb.append(arg.getClass().getSimpleName()).append('(').append(arg.hashCode());
+            sb.append(arg.getClass().getSimpleName()).append('(').append(arg.hashCode()).append(';');
             if (arg instanceof TruffleObject && ForeignAccess.sendIsPointer(getIsPointerNode(), (TruffleObject) arg)) {
                 try {
-                    sb.append(";ptr:").append(String.valueOf(ForeignAccess.sendAsPointer(getAsPointerNode(), (TruffleObject) arg)));
+                    sb.append("ptr:").append(Long.toHexString(ForeignAccess.sendAsPointer(getAsPointerNode(), (TruffleObject) arg)));
                 } catch (UnsupportedMessageException e) {
                     throw RInternalError.shouldNotReachHere();
                 }
-            } else if (arg instanceof RSymbol) {
-                sb.append(';').append("\"" + arg.toString() + "\"");
-            } else if (arg instanceof RAbstractVector) {
-                RAbstractVector vec = (RAbstractVector) arg;
-                if (vec.getLength() == 0) {
-                    sb.append(";empty");
-                } else {
-                    sb.append(";len:" + vec.getLength() + ";data:");
-                    for (int i = 0; i < Math.min(3, vec.getLength()); i++) {
-                        String str = ((RAbstractVector) arg).getDataAtAsObject(0).toString();
-                        str = str.length() > 30 ? str.substring(0, 27) + "..." : str;
-                        sb.append(',').append(str);
-                    }
-                }
+            } else {
+                Utils.printDebugInfo(sb, arg);
             }
             // Note: it makes sense to include native mirrors only once they have been create
             // already
             if (mode.logNativeMirror && arg instanceof RObject) {
-                sb.append(";" + ((RObject) arg).getNativeMirror());
+                sb.append(((RObject) arg).getNativeMirror());
             }
             sb.append(')');
         }

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

@@ -44,6 +44,7 @@
 
 import com.oracle.truffle.api.CallTarget;
 import com.oracle.truffle.api.CompilerDirectives;
+import com.oracle.truffle.api.CompilerDirectives.TruffleBoundary;
 import com.oracle.truffle.api.interop.ForeignAccess;
 import com.oracle.truffle.api.interop.Message;
 import com.oracle.truffle.api.interop.TruffleObject;
@@ -180,6 +181,7 @@ private LLVMArchive(LLVM_IR[] irs, List<String> nativeLibs) {
         }
     }
 
+    @TruffleBoundary
     public static LLVMArchive getZipLLVMIR(String path) {
         List<String> nativeLibs = Collections.emptyList();
         try (ZipInputStream zis = new ZipInputStream(new BufferedInputStream(new FileInputStream(path + "l")))) {
@@ -248,6 +250,7 @@ private static class TruffleLLVM_DLOpenNode extends Node implements DLOpenNode {
          * the IR has not been parsed yet.
          */
         @Override
+        @TruffleBoundary
         public Object execute(String path, boolean local, boolean now) {
             try {
                 LLVMArchive ar = getZipLLVMIR(path);
@@ -365,6 +368,7 @@ private static String getLibName(String path) {
      */
     private LLVM_IR[] libRModules;
 
+    @TruffleBoundary
     private static CallTarget parseLLVM(String libName, LLVM_IR ir) {
         if (ir instanceof LLVM_IR.Binary) {
             LLVM_IR.Binary bir = (LLVM_IR.Binary) ir;