Merge commit 'c04b36087767a5b26d0b84bce40feaa2bb4b416b' into release/…

…graal-vm/1.0

.gitignore

@@ -147,3 +147,12 @@ documentation/.pydevproject
 com.oracle.truffle.r.native/gnur/patch-build
 com.oracle.truffle.r.test.native/embedded/embedded.actual.output
 com.oracle.truffle.r.test.native/embedded/main.actual.output
+f2c
+test.fastr
+test.gnur
+test.diffs
+install.tmp.fastr
+install.tmp.gnur
+lib.install.packages.fastr
+lib.install.packages.gnur
+/com.oracle.truffle.r.release/doc/

CHANGELOG.md

@@ -1,3 +1,25 @@
+# 1.0 RC 15
+
+* `ActiveBinding` objects do not support the `UNBOX` message anymore
+* new Truffle interop converts `double` values to `int` values if they fit in the integer range
+  * see the changes in the [spec tests](https://github.com/oracle/fastr/commit/e08e2b19571479dddb6167d9a1d492a14cb4c7b2#diff-c842fa11097793b19bd410589c36af99)
+
+Added missing R builtins and C APIa
+
+* simple support for the weak reference API functions (`R_MakeWeakRef`, `R_MakeWeakRefC`, `R_WeakRefKey`, `R_WeakRefValue`)
+* `Rf_i1mach`
+* `gzcon` builtin for `url` connections, e.g., `load(url('protocol://path'))` should work now
+* `Sys.localeconv` supports: `decimal_point`, `thousands_sep`, `grouping`, `int_curr_symbol`, `currency_symbol`, `mon_decimal_point`,
+  `mon_thousands_sep`, `mon_grouping`, `int_frac_digits`, `p_cs_precedes`, other fields are fixed to some meaningful but not culture
+  sensitive value for given field
+
+Bug fixes:
+
+* `rep.int` with value argument of length 0 just returns the value argument
+* `tcrossprod` called from `apply` did not give correct result #60
+* `Rf_lengthgets` can accept `NULL` argument
+* FastR does not allow Java interop when not started with `--jvm`
+
 # 1.0 RC 14
 
 * all FastR specific options (NOT those GNU-R compatible like `--save`) are experimental except for `--R.PrintErrorStacktracesToFile`,

LICENSE

@@ -4,7 +4,7 @@ This is a release of GraalVM Community Edition 1.0 R Language Component. This
 particular copy of the software is released under version 3 of GNU General 
 Public License.
 
-Copyright (c) 2015, 2018, Oracle and/or its affiliates. All rights reserved
+Copyright (c) 2015, 2019, Oracle and/or its affiliates. All rights reserved
 
 ===========================================================================
 

ci.hocon

@@ -22,4 +22,6 @@ builds = [
   ${internalPkgtest}          {capabilities : [linux, amd64],  targets : [gate], name: "gate-internal-pkgtest-linux-amd64"}
   ${gateTestJava9Linux}       {capabilities : [linux, amd64, fast],  targets : [gate], name: "gate-test-java9-linux-amd64"}
   # ${gnurTests}                {capabilities : [linux, amd64, fast],  targets : [gate], name: "gate-gnur-tests"}
+
+  ${coverageLinux}            {capabilities : [linux, amd64],  targets : [weekly], name: "coverage-r-linux-amd64"}
 ]

ci_common/common.hocon

@@ -61,8 +61,8 @@ logfiles : [
 
 environmentLinux: {
   environment : {
-    PKG_INCLUDE_FLAGS_OVERRIDE : "-I/cm/shared/apps/zlib/1.2.11/include -I/cm/shared/apps/bzip2/1.0.6/include -I/cm/shared/apps/xz/5.2.2/include -I/cm/shared/apps/pcre/8.38/include -I/cm/shared/apps/curl/7.50.1/include"
-    PKG_LDFLAGS_OVERRIDE : "-L/cm/shared/apps/zlib/1.2.11/lib -L/cm/shared/apps/bzip2/1.0.6/lib -L/cm/shared/apps/xz/5.2.2/lib -L/cm/shared/apps/pcre/8.38/lib -L/cm/shared/apps/curl/7.50.1/lib -L/cm/shared/apps/gcc/4.9.1/lib64"
+    PKG_INCLUDE_FLAGS_OVERRIDE : "-I/cm/shared/apps/zlib/1.2.11/include -I/cm/shared/apps/bzip2/1.0.6/include -I/cm/shared/apps/xz/5.2.2/include -I/cm/shared/apps/pcre/8.42/include -I/cm/shared/apps/curl/7.50.1/include"
+    PKG_LDFLAGS_OVERRIDE : "-L/cm/shared/apps/zlib/1.2.11/lib -L/cm/shared/apps/bzip2/1.0.6/lib -L/cm/shared/apps/xz/5.2.2/lib -L/cm/shared/apps/pcre/8.42/lib -L/cm/shared/apps/curl/7.50.1/lib -L/cm/shared/apps/gcc/4.9.1/lib64"
     TZDIR: "/usr/share/zoneinfo"
   }
 }
@@ -84,7 +84,7 @@ packagesLinux : {
     "pip:ninja_syntax" : "==1.7.2"
     make : ">=3.83"
     gcc-build-essentials : "==4.9.1" # TODO: upgrade to 4.9.2
-    pcre : ">=8.38"
+    pcre : "==8.42"
     zlib : "==1.2.11"
     # these are needed to build GNU-R
     readline : "==6.3"
@@ -96,7 +96,7 @@ packagesDarwin : {
   "pip:astroid" : "==1.1.0"
   "pip:pylint" : "==1.1.0"
   "pip:ninja_syntax" : "==1.7.2"
-  "pcre" : "==8.38"
+  "pcre" : "==8.42"
   "homebrew/gcc" : "==4.9"
 }
 
@@ -141,9 +141,9 @@ gateTestLinux : ${gateTestCommon} ${commonLinux}
 
 gateTestDarwin : ${gateTestCommon} ${commonDarwin} {
   setup : [
-    [set-export, PKG_INCLUDE_FLAGS_OVERRIDE, "-I/cm/shared/apps/pcre/8.38/include -I/cm/shared/apps/bzip2/1.0.6/include -I/cm/shared/apps/xz/5.2.2/include -I/cm/shared/apps/curl/7.50.1/include"]
+    [set-export, PKG_INCLUDE_FLAGS_OVERRIDE, "-I/cm/shared/apps/pcre/8.42/include -I/cm/shared/apps/bzip2/1.0.6/include -I/cm/shared/apps/xz/5.2.2/include -I/cm/shared/apps/curl/7.50.1/include"]
     [set-export, MOD_LIB_PATH, [echo, "${LD_LIBRARY_PATH}", |, tr, "\:", "\\n", |, grep, lib/gcc, |, tail, "-1"]]
-    [set-export, PKG_LDFLAGS_OVERRIDE, "-L/cm/shared/apps/bzip2/1.0.6/lib -L/cm/shared/apps/xz/5.2.2/lib -L/cm/shared/apps/pcre/8.38/lib -L/cm/shared/apps/curl/7.50.1/lib -L${MOD_LIB_PATH} -L/usr/lib"]
+    [set-export, PKG_LDFLAGS_OVERRIDE, "-L/cm/shared/apps/bzip2/1.0.6/lib -L/cm/shared/apps/xz/5.2.2/lib -L/cm/shared/apps/pcre/8.42/lib -L/cm/shared/apps/curl/7.50.1/lib -L${MOD_LIB_PATH} -L/usr/lib"]
   ]
 }
 
@@ -258,3 +258,14 @@ gnurTests: ${commonLinux} {
     ["mx", "gnu-rtests"]
   ]
 }
+
+
+coverageLinux : ${commonLinux}  {
+  run : [
+// cannot run with excluded "GeneratedBy" since that would lead to "command line too long"
+//  ["mx", "--jacoco-whitelist-package", "com.oracle.truffle.r", "--jacoco-exclude-annotation", "@GeneratedBy", "--strict-compliance", "rgate", "-B=--force-deprecation-as-warning", "--strict-mode", "-t", "Versions,JDKReleaseInfo,BuildJavaWithJavac,UnitTests: no specials,UnitTests: with specials,Rembedded", "--jacocout", "html"],
+//  ["mx", "--jacoco-whitelist-package", "com.oracle.truffle.r", "--jacoco-exclude-annotation", "@GeneratedBy", "sonarqube-upload", "-Dsonar.host.url=$SONAR_HOST_URL", "-Dsonar.projectKey=com.oracle.graalvm.r", "-Dsonar.projectName=GraalVM - R", "--exclude-generated"]
+  ["mx", "--jacoco-whitelist-package", "com.oracle.truffle.r", "--strict-compliance", "rgate", "-B=--force-deprecation-as-warning", "--strict-mode", "-t", "Versions,JDKReleaseInfo,BuildJavaWithJavac,UnitTests: no specials,UnitTests: with specials,Rembedded", "--jacocout", "html"],
+  ["mx", "--jacoco-whitelist-package", "com.oracle.truffle.r", "sonarqube-upload", "-Dsonar.host.url=$SONAR_HOST_URL", "-Dsonar.projectKey=com.oracle.graalvm.r", "-Dsonar.projectName=GraalVM - R", "--exclude-generated"]
+  ]
+}

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

@@ -685,7 +685,7 @@ private static void printValue(RContext ctx, MaterializedFrame callingFrame, Obj
             if (result == null) {
                 str = "[polyglot value (null)]";
             } else if (result instanceof CharSequence) {
-                str = "[1] \"" + String.valueOf(result) + "\"";
+                str = "[1] \"" + result + "\"";
             } else {
                 str = String.valueOf(result);
             }

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

@@ -23,21 +23,24 @@
 package com.oracle.truffle.r.engine;
 
 import java.io.IOException;
-import java.nio.file.Path;
-import java.nio.file.spi.FileTypeDetector;
+import java.nio.charset.Charset;
+import com.oracle.truffle.api.TruffleFile;
 
 import com.oracle.truffle.r.runtime.RRuntime;
 
-public final class RFileTypeDetector extends FileTypeDetector {
+public final class RFileTypeDetector implements TruffleFile.FileTypeDetector {
+
     @Override
-    public String probeContentType(Path path) throws IOException {
-        Path fileNamePath = path.getFileName();
-        if (fileNamePath != null) {
-            String fileName = fileNamePath.toString();
-            if (fileName.endsWith(".R") || fileName.endsWith(".r")) {
-                return RRuntime.R_TEXT_MIME;
-            }
+    public String findMimeType(TruffleFile file) throws IOException {
+        String fileName = file.getName();
+        if (fileName != null && (fileName.endsWith(".R") || fileName.endsWith(".r"))) {
+            return RRuntime.R_TEXT_MIME;
         }
         return null;
     }
+
+    @Override
+    public Charset findEncoding(TruffleFile file) throws IOException {
+        return null;
+    }
 }

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

@@ -47,8 +47,9 @@
 import com.oracle.truffle.r.nodes.builtin.base.printer.DoubleVectorPrinter;
 import com.oracle.truffle.r.nodes.builtin.helpers.DebugHandling;
 import com.oracle.truffle.r.nodes.builtin.helpers.TraceHandling;
+import com.oracle.truffle.r.nodes.control.AbstractBlockNode;
 import com.oracle.truffle.r.nodes.control.AbstractLoopNode;
-import com.oracle.truffle.r.nodes.control.BlockNode;
+import com.oracle.truffle.r.nodes.control.BlockNode.HugeBlockRootNode;
 import com.oracle.truffle.r.nodes.control.IfNode;
 import com.oracle.truffle.r.nodes.control.ReplacementDispatchNode;
 import com.oracle.truffle.r.nodes.function.ClassHierarchyNode;
@@ -281,28 +282,29 @@ public boolean isTaggedWith(Node node, Class<?> tag) {
             return node instanceof RCallNode;
         }
         if (tag == FunctionBodyBlockTag.class) {
-            return node instanceof BlockNode && ((BlockNode) node).unwrapParent() instanceof RootBodyNode;
+            return node instanceof AbstractBlockNode && ((AbstractBlockNode) node).unwrapParent() instanceof RootBodyNode;
         }
         if (tag == LoopTag.class) {
             return node instanceof AbstractLoopNode;
         }
         if (tag == StatementTag.class) {
-            if (node instanceof BlockNode) {
+            if (node instanceof AbstractBlockNode) {
                 // so that the stepping location is not the block itself, but the first statement in
                 // the block, note that the FastR's own debugging and tracing mechanism uses
                 // FunctionBodyBlockTag to recognize function bodies.
                 return false;
             }
             // How to recognize statement from some node inside a statement (e.g. expression)?
             Node parent = ((RInstrumentableNode) node).unwrapParent();
-            if (parent instanceof BlockNode) {
+            if (parent instanceof AbstractBlockNode) {
                 // It's in a block of statements
                 return true;
             } else {
                 // single statement block: as function body, if/else body, loop body
                 // note: RepeatingNode is not a RSyntaxElement but the body of a loop is
                 // under the repeating node !
-                return parent instanceof RootBodyNode || parent instanceof IfNode || AbstractLoopNode.isLoopBody(node) || EngineRootNode.isEngineBody(parent);
+                return parent instanceof RootBodyNode || parent instanceof IfNode || AbstractLoopNode.isLoopBody(node) ||
+                                EngineRootNode.isEngineBody(parent) || parent instanceof HugeBlockRootNode;
             }
         }
         // TODO: ExpressionTag: (!statement && !loop && !if && !call && !root)??

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

@@ -61,6 +61,7 @@
 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.RInteropScalar.RInteropNA;
 import com.oracle.truffle.r.runtime.data.RPromise;
 import com.oracle.truffle.r.runtime.data.RTypedValue;
 import com.oracle.truffle.r.runtime.env.REnvironment;
@@ -69,7 +70,7 @@
 import com.oracle.truffle.r.runtime.nodes.RBaseNode;
 import org.graalvm.options.OptionDescriptors;
 
-@TruffleLanguage.Registration(name = "R", id = "R", version = "3.5.1", mimeType = {RRuntime.R_APP_MIME, RRuntime.R_TEXT_MIME}, interactive = true)
+@TruffleLanguage.Registration(name = "R", id = "R", version = "3.5.1", mimeType = {RRuntime.R_APP_MIME, RRuntime.R_TEXT_MIME}, interactive = true, fileTypeDetectors = RFileTypeDetector.class)
 @ProvidedTags({StandardTags.CallTag.class, StandardTags.StatementTag.class, StandardTags.RootTag.class, RSyntaxTags.LoopTag.class, FunctionBodyBlockTag.class})
 public final class TruffleRLanguageImpl extends TruffleRLanguage {
 
@@ -140,6 +141,21 @@ protected void disposeContext(RContext context) {
 
     @Override
     protected String toString(RContext context, Object value) {
+        // primitive values are never produced by FastR so we don't print them as R vectors
+        if (value instanceof Boolean) {
+            // boolean constants are capitalized like in R
+            return (boolean) value ? "TRUE" : "FALSE";
+        }
+        if (value instanceof Number || value instanceof String || value instanceof Character) {
+            return value.toString();
+        }
+
+        // special class designated to exchange NA values with the outside world
+        // this value is a scalar, the only way to get it is via getArrayMember on an R vector
+        if (value instanceof RInteropNA) {
+            return "NA";
+        }
+
         // 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
@@ -155,8 +171,11 @@ protected String toString(RContext context, Object value) {
         if (RMissingHelper.isMissing(unwrapped)) {
             return "missing";
         }
-        Object asVector = RRuntime.asAbstractVector(unwrapped);
-        if (!(asVector instanceof TruffleObject)) {
+
+        // the value unwrapped from an RPromise can be primitive Java type, but now we know that we
+        // are dealing with primitive that is supposed to be treated as R vector
+        unwrapped = RRuntime.asAbstractVector(unwrapped);
+        if (!(unwrapped 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");
@@ -171,9 +190,9 @@ protected String toString(RContext context, Object value) {
         try {
             StringBuilder buffer = new StringBuilder();
             stateStdConnections.setBuffer(buffer);
-            RContext.getEngine().evalFunction((RFunction) printObj, callingFrame, RCaller.topLevel, false, ArgumentsSignature.empty(1), asVector);
+            RContext.getEngine().evalFunction((RFunction) printObj, callingFrame, RCaller.topLevel, false, ArgumentsSignature.empty(1), unwrapped);
             // remove the last "\n", which is useful for REPL, but not here
-            if (buffer.charAt(buffer.length() - 1) == '\n') {
+            if (buffer.length() > 0 && buffer.charAt(buffer.length() - 1) == '\n') {
                 buffer.setLength(buffer.length() - 1);
             }
             return buffer.toString();

com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/interop/ActiveBindingMR.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
@@ -34,15 +34,7 @@ public class ActiveBindingMR {
     @Resolve(message = "IS_BOXED")
     public abstract static class ActiveBindingIsBoxedNode extends Node {
         protected Object access(@SuppressWarnings("unused") ActiveBinding receiver) {
-            return true;
-        }
-    }
-
-    @Resolve(message = "UNBOX")
-    public abstract static class ActiveBindingUnboxNode extends Node {
-
-        protected Object access(ActiveBinding receiver) {
-            return receiver.readValue();
+            return false;
         }
     }
 

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

@@ -365,6 +365,7 @@ public Object execute(VirtualFrame frame) {
     }
 
     public static final Supplier<RootNode> CHECK_FACTORY = new CheckFactory();
+    public static final ForeignAccess ACCESS = ForeignAccess.createAccess(new RAbstractVectorAccessFactory(), RAbstractVectorAccessFactory.CHECK_FACTORY);
 
     private static final class CheckFactory implements Supplier<RootNode> {
         @Override

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

@@ -22,7 +22,6 @@
  */
 package com.oracle.truffle.r.engine.interop;
 
-import com.oracle.truffle.api.CompilerAsserts;
 import com.oracle.truffle.api.interop.ForeignAccess;
 import com.oracle.truffle.r.ffi.impl.interop.FFI_RForeignAccessFactoryImpl;
 import com.oracle.truffle.r.runtime.RInternalError;
@@ -71,7 +70,6 @@ public final class RForeignAccessFactoryImpl implements RForeignAccessFactory {
 
     @Override
     public ForeignAccess getForeignAccess(RTruffleObject obj) {
-        CompilerAsserts.neverPartOfCompilation("getForeignAccess");
         if (obj instanceof RNull) {
             return RNullMRForeign.ACCESS;
         } else if (obj instanceof RList) {
@@ -121,7 +119,7 @@ public ForeignAccess getForeignAccess(RTruffleObject obj) {
         } else if (obj instanceof RInteropNA) {
             return RInteropNAMRForeign.ACCESS;
         } else if (obj instanceof RAbstractAtomicVector) {
-            return ForeignAccess.createAccess(new RAbstractVectorAccessFactory(), RAbstractVectorAccessFactory.CHECK_FACTORY);
+            return RAbstractVectorAccessFactory.ACCESS;
         } else {
             ForeignAccess access = FFI_RForeignAccessFactoryImpl.getForeignAccess(obj);
             if (access != null) {

com.oracle.truffle.r.ffi.codegen/src/com/oracle/truffle/r/ffi/codegen/FFIUpCallsIndexCodeGen.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
@@ -23,6 +23,7 @@
 package com.oracle.truffle.r.ffi.codegen;
 
 import java.lang.reflect.Method;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
 
@@ -47,19 +48,20 @@ private void run(String[] args) {
         out.append("#ifndef RFFI_UPCALLSINDEX_H\n");
         out.append("#define RFFI_UPCALLSINDEX_H\n");
         out.append('\n');
-        Method[] methods = UpCallsRFFI.class.getMethods();
-        Arrays.sort(methods, new Comparator<Method>() {
+        ArrayList<Method> methods = new ArrayList<>(Arrays.asList(UpCallsRFFI.class.getMethods()));
+        methods.removeAll(Arrays.asList(UpCallsRFFI.class.getDeclaredMethods()));
+        methods.sort(new Comparator<Method>() {
             @Override
             public int compare(Method e1, Method e2) {
                 return e1.getName().toString().compareTo(e2.getName().toString());
             }
         });
-        for (int i = 0; i < methods.length; i++) {
-            Method method = methods[i];
+        for (int i = 0; i < methods.size(); i++) {
+            Method method = methods.get(i);
             out.append("#define ").append(method.getName()).append("_x ").append(Integer.toString(i)).append('\n');
         }
         out.append('\n');
-        out.append("#define ").append("UPCALLS_TABLE_SIZE ").append(Integer.toString(methods.length)).append('\n');
+        out.append("#define ").append("UPCALLS_TABLE_SIZE ").append(Integer.toString(methods.size())).append('\n');
         out.append('\n');
         out.append("#endif // RFFI_UPCALLSINDEX_H\n");
     }