Merge commit 'c04b36087767a5b26d0b84bce40feaa2bb4b416b' into release/graal-vm/1.0

Author: ansalond

.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/

3rd_party_licenses.txt

@@ -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`,

CHANGELOG.md

@@ -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
 
 ===========================================================================
 

LICENSE

@@ -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.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"]
+  ]
+}

ci_common/common.hocon

@@ -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/META-INF/services/java.nio.file.spi.FileTypeDetector

@@ -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/REngine.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)??