Merge commit 'cf8b4217b18b3e4539cca46b001c402108a498cb' into release/graal-vm/1.0

Author: ansalond

CHANGELOG.md

@@ -1,3 +1,26 @@
+# 1.0 RC 13
+
+New features:
+
+* new JUL-like logging infrastructure backed by Truffle
+* FastR options backed by Truffle now. New command-line format - i.e. bin/r --R.PerformanceWarning="true". Also configurable via org.graal.polyglot.Context.Builder.
+* script configure_fastr also regenerates etc/Renviron and etc/ldpaths
+* FastR vectors are not writeable from other languages
+  * in order to update FastR vectors from other languages:
+    retrieve reference to the subset assign function `` `[<-` `` and execute it.
+    Note that it will return the new vector with the updated values.
+
+Added missing R builtins and C API
+
+* `polyroot`
+* dummy implementation of `pcre_config`
+
+Bug fixes:
+
+* when using GNU-R graphics (--R.UseInternalGridGraphics=false) FastR would still override the graphics package R functions
+* cannot install RcppParallel #52
+* visibility propagation in `tryCatch`
+
 # 1.0 RC 12
 
 New Features:
@@ -27,6 +50,7 @@ Bug fixes:
 * `unlink` error for paths containing wildcard(s) but no path separator
 *  dims attribute errorneously set to RDoubleVector; exception when retrieving the dims #49
 * issues with the dplyr's `mutate` and `transmute`: #50 and #51
+* fixed promises result visibility propagation eliminating extra `NULL` output of `tryCatch(cat('Hello\n'))`
 
 # 1.0 RC 11
 

ci.hocon

@@ -7,14 +7,14 @@ 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 want to enforce specific overlay commit, uncomment:
-# overlay = "1823c758582f31386f8ba4d89157265a23cebd04"
+# in case you do not want to enforce a specific overlay commit, comment:
+overlay = "f2f27ae819a1f8ce3398aaf43c79aec358acd0a2"
 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"}
   ${gateTestNoSpecialsLinux}  {capabilities : [linux, amd64, fast],  targets : [gate], name: "gate-test-linux-amd64-nospecials"}
   ${gateTestNoDSLCacheNoSpecialsLinux}  {capabilities : [linux, amd64, fast],  targets : [gate], name: "gate-test-linux-amd64-nospecials-no-dsl-cache"}
-  ${gateTestDarwin}           {capabilities : [darwin_sierra, amd64], targets : [gate], name: "gate-test-darwin-amd64"}
+  ${gateTestDarwin}           {capabilities : [darwin, amd64], targets : [gate], name: "gate-test-darwin-amd64"}
   ${gateStyle}                {capabilities : [linux, amd64],  targets : [gate], name: "gate-style-linux-amd64"}
   ${gateBuildWithEcj}         {capabilities : [linux, amd64],  targets : [gate], name: "gate-ecj-linux-amd64"}
   # GR-11799

ci_common/common.hocon

@@ -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 : "8u192-jvmci-0.52", platformspecific: true}
+java8 : {name : labsjdk, version : "8-jvmci-latest", platformspecific: true}
 java9 : {name : oraclejdk, version : "9.0.4+11", platformspecific: true}
 
 java8Downloads : {
@@ -50,26 +50,35 @@ logfiles : [
 # on the CI cluster. Not all of the modules are needed by FastR but all are needed by the
 # embedded GNU R that is built within FastR.
 
-pkgEnvironment: {
+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"""
-	TZDIR: "/usr/share/zoneinfo"
+    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"
+    TZDIR: "/usr/share/zoneinfo"
   }
 }
 
-packagesLinux : ${pkgEnvironment} {
+environmentDarwin : {
+  environment : {
+    PATH : "/usr/local/bin:$JAVA_HOME/bin:$PATH"
+    F77: "/usr/local/bin/gfortran-4.9"
+    TZDIR: "/usr/share/zoneinfo"
+  }
+}
+
+packagesLinux : {
   packages : {
     git : ">=1.8.3"
     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"
+    gcc-build-essentials : "==4.9.1" # TODO: upgrade to 4.9.2
     pcre : ">=8.38"
-    zlib : ">=1.2.11"
+    zlib : "==1.2.11"
+    # these are needed to build GNU-R
+    readline : "==6.3"
     curl : ">=7.50.1"
   }
 }
@@ -79,21 +88,28 @@ packagesDarwin : {
   "pip:pylint" : "==1.1.0"
   "pip:ninja_syntax" : "==1.7.2"
   "pcre" : "==8.38"
+  "homebrew/gcc" : "==4.9"
 }
 
-# Common settings for all builds but note that it uses the Linux package settings,
-# so these must be overridden in any darwin builds
+# Common settings for all builds
 
-common : ${java8Downloads} ${packagesLinux}  {
+common : ${java8Downloads} {
   logs: ${logfiles}
+  catch_files : [
+    "Graal diagnostic output saved in (?P<filename>.+\.zip)"
+  ]
   timelimit : "1:00:00"
   environment : {
-	PKG_TEST_ENV_miniUI : "LC_ALL=C"
-	PKG_TEST_ENV_compare : "LC_ALL=C"
-	FASTR_OPTION_PrintErrorStacktracesToFile: "true"
+    FASTR_TEST_trace_tests : "true"
+    PKG_TEST_ENV_miniUI : "LC_ALL=C"
+    PKG_TEST_ENV_compare : "LC_ALL=C"
+    FASTR_OPTION_PrintErrorStacktracesToFile: "true"
   }
 }
 
+commonLinux: ${common} ${packagesLinux} ${environmentLinux}
+commonDarwin: ${common} ${packagesDarwin} ${environmentDarwin}
+
 # Every "pull request" (PR) is subject to a series of "gate" commands that must pass
 # for the PR to be accepted into the master branch. The gate commands are run under
 # the "mx" tool. This defines a common prefix for all gate commands. The "-t"
@@ -105,17 +121,24 @@ gateCmd : ["mx", "-v", "--strict-compliance", "rgate", "-B=--force-deprecation-a
 
 # The standard set of gate tasks: the actual executable tests are in the "UnitTests" task.
 
-gateTestCommon : ${common} {
+gateTestCommon : {
   run : [
     ${gateCmd} ["Versions,JDKReleaseInfo,BuildJavaWithJavac,UnitTests: with specials,Rembedded"]
   ]
 }
 
-gateTestLinux : ${gateTestCommon}  {
+gateTestLinux : ${gateTestCommon} ${commonLinux}
+
+gateTestDarwin : ${gateTestCommon} ${commonDarwin} {
+  setup : [
+    [set-export, PKG_INCLUDE_FLAGS_OVERRIDE, "-I/cm/shared/apps/pcre/8.38/include -I/cm/shared/apps/bzip2/1.0.6/include -I/cm/shared/apps/xz/5.2.2/include -I/cm/shared/apps/curl/7.50.1/include"]
+    [set-export, MOD_LIB_PATH, [echo, "${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"]
+  ]
 }
 
-gateTestNoDSLCacheLinux : ${common} {
-  environment : ${common.environment} {
+gateTestNoDSLCacheLinux : ${commonLinux} {
+  environment : ${common.environment} ${environmentLinux.environment} {
     FASTR_RELEASE: "true", # release build so that we also tests recommended pkgs installation
     FASTR_OPTION_DSLCacheSizeFactor: "0"
   }
@@ -126,14 +149,14 @@ gateTestNoDSLCacheLinux : ${common} {
   ]
 }
 
-gateTestNoSpecialsLinux : ${common}  {
+gateTestNoSpecialsLinux : ${commonLinux}  {
   run : [
     ${gateCmd} ["Versions,JDKReleaseInfo,BuildJavaWithJavac,UnitTests: no specials"]
   ]
 }
 
-gateTestNoDSLCacheNoSpecialsLinux : ${common} {
-  environment : ${common.environment} {
+gateTestNoDSLCacheNoSpecialsLinux : ${commonLinux} {
+  environment : ${common.environment} ${environmentLinux.environment} {
     FASTR_RELEASE: "true", # release build so that we also tests recommended pkgs installation
     FASTR_OPTION_DSLCacheSizeFactor: "0"
   }
@@ -144,22 +167,8 @@ gateTestNoDSLCacheNoSpecialsLinux : ${common} {
   ]
 }
 
-darwinEnvironment : {
-  environment :  {
-    PATH : "/usr/local/bin:$JAVA_HOME/bin:$PATH"
-    F77: "/usr/local/bin/gfortran-4.9"
-    TZDIR: "/usr/share/zoneinfo"
-	  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"""
-    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/cm/shared/apps/gcc/4.9.1/lib64 -L/usr/local/Cellar/[email protected]/4.9.4/lib/gcc/4.9/ -L/usr/lib"""
-  }
-}
-
-gateTestDarwin : ${gateTestCommon} ${darwinEnvironment}  {
-  packages : ${packagesDarwin}
-}
-
-gateTestLinuxNFI : ${gateTestCommon}  {
-  environment :  {
+gateTestLinuxNFI : ${gateTestLinux} {
+  environment :  ${common.environment} ${environmentLinux.environment} {
       FASTR_RFFI : "nfi"
       TZDIR: "/usr/share/zoneinfo"
   }
@@ -172,10 +181,7 @@ requireGCC: {
     }
 }
 
-gateTestJava9Linux : ${java9Downloads} ${gateTestCommon} {
-  setup: [
-    [export, "FASTR_TEST_trace_tests=true"]
-  ]
+gateTestJava9Linux : ${java9Downloads} ${gateTestLinux} {
   downloads : {
     JAVA_HOME : ${java9Downloads.downloads.JAVA_HOME}
     EXTRA_JAVA_HOMES : ${java9Downloads.downloads.EXTRA_JAVA_HOMES}
@@ -184,33 +190,33 @@ gateTestJava9Linux : ${java9Downloads} ${gateTestCommon} {
 
 # This performs a number of "style" checks on the code to ensure it confirms to the project standards.
 
-gateStyle : ${common} {
+gateStyle : ${commonLinux} {
   # need pyhocon fix
   downloads : {
     JAVA_HOME : ${java8Downloads.downloads.JAVA_HOME}
     EXTRA_JAVA_HOMES : ${java8Downloads.downloads.EXTRA_JAVA_HOMES}
     JDT : {name: ecj, version: "4.5.1", platformspecific: false}
     ECLIPSE : {name: eclipse, version: "4.5.2", platformspecific: true}
   }
-  environment : {
+  environment : ${common.environment} ${environmentLinux.environment} {
     ECLIPSE_EXE : "$ECLIPSE/eclipse"
   }
   run : [
-    ${gateCmd} ["Versions,JDKReleaseInfo,Pylint,Canonicalization Check,BuildJavaWithJavac,IDEConfigCheck,CodeFormatCheck,Checkstyle,Copyright check,UnitTests: ExpectedTestOutput file check"]
+    ${gateCmd} ["Versions,JDKReleaseInfo,Pylint,Canonicalization Check,BuildJavaWithJavac,SpotBugs,IDEConfigCheck,CodeFormatCheck,Checkstyle,Copyright check,UnitTests: ExpectedTestOutput file check"]
     ["mx", "clean", "--no-native"]
     ${gateCmd} ["BuildWithEcj"]
   ]
 }
 
-gateBuildWithEcj : ${common} {
+gateBuildWithEcj : ${commonLinux} {
   # need pyhocon fix
   downloads : {
     JAVA_HOME : ${java8Downloads.downloads.JAVA_HOME}
     EXTRA_JAVA_HOMES : ${java8Downloads.downloads.EXTRA_JAVA_HOMES}
     JDT : {name: ecj, version: "4.5.1", platformspecific: false}
     ECLIPSE : {name: eclipse, version: "4.5.2", platformspecific: true}
   }
-  environment : {
+  environment : ${common.environment} ${environmentLinux.environment} {
     ECLIPSE_EXE : "$ECLIPSE/eclipse"
   }
   run : [
@@ -220,23 +226,23 @@ gateBuildWithEcj : ${common} {
 
 # This check runs diagnostics on the implementation of the R "builtins" in FastR, e.g., that the argument processing is sound.
 
-rbcheck : ${common} {
+rbcheck : ${commonLinux} {
   run : [
     ${gateCmd} ["Versions,JDKReleaseInfo,BuildJavaWithJavac"]
     ["mx", "rbcheck"]
     ["mx", "rbdiag"]
   ]
 }
 
-internalPkgtest: ${common} {
+internalPkgtest: ${commonLinux} {
   run : [
     ["mx", "build"]
     ["mx", "pkgtest", "--verbose", "--repos", "FASTR", "--pkg-filelist", "com.oracle.truffle.r.test.native/packages/pkg-filelist"]
   ]
   logs: ${common.logs}
 }
 
-gnurTests: ${common} {
+gnurTests: ${commonLinux} {
   run : [
     ["mx", "build"]
     ["mx", "gnu-rtests"]

com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/EngineRootNode.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
@@ -68,8 +68,9 @@ class EngineRootNode extends RootNode {
         this.contextReference = context.getLanguage().getContextReference();
     }
 
-    public static EngineRootNode createEngineRoot(REngine engine, RContext context, List<RSyntaxNode> statements, SourceSection sourceSection, MaterializedFrame executionFrame) {
-        return new EngineRootNode(new EngineBodyNode(engine, statements, getPrintResult(sourceSection)), context, sourceSection, executionFrame);
+    public static EngineRootNode createEngineRoot(REngine engine, RContext context, List<RSyntaxNode> statements, SourceSection sourceSection, MaterializedFrame executionFrame,
+                    boolean forcePrintResult) {
+        return new EngineRootNode(new EngineBodyNode(engine, statements, forcePrintResult || getPrintResult(sourceSection)), context, sourceSection, executionFrame);
     }
 
     /**

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

@@ -61,7 +61,7 @@
 import com.oracle.truffle.r.nodes.instrumentation.RInstrumentation;
 import com.oracle.truffle.r.runtime.ArgumentsSignature;
 import com.oracle.truffle.r.runtime.ExitException;
-import com.oracle.truffle.r.runtime.FastROptions;
+import static com.oracle.truffle.r.runtime.context.FastROptions.LoadProfiles;
 import com.oracle.truffle.r.runtime.JumpToTopLevelException;
 import com.oracle.truffle.r.runtime.RArguments;
 import com.oracle.truffle.r.runtime.RCaller;
@@ -161,7 +161,7 @@ private void initializeNonShared() {
         context.getStateRFFI().initializeVariables(context);
         RBuiltinPackages.loadBase(context.getLanguage(), baseFrame);
         RGraphics.initialize(context);
-        if (FastROptions.LoadProfiles.getBooleanValue()) {
+        if (context.getOption(LoadProfiles)) {
             StartupTiming.timestamp("Before Profiles Loaded");
             /*
              * eval the system/site/user profiles. Experimentally GnuR does not report warnings
@@ -313,7 +313,7 @@ public Object execute(VirtualFrame frame) {
             });
         } else {
             List<RSyntaxNode> statements = parseSource(source);
-            EngineRootNode rootNode = EngineRootNode.createEngineRoot(this, context, statements, createSourceSection(source, statements), executionFrame);
+            EngineRootNode rootNode = EngineRootNode.createEngineRoot(this, context, statements, createSourceSection(source, statements), executionFrame, false);
             return Truffle.getRuntime().createCallTarget(rootNode);
         }
     }
@@ -410,7 +410,7 @@ private EngineRootNode createRScriptRoot(Source fullSource, MaterializedFrame fr
         } catch (IOException ex) {
             throw new RuntimeException(ex);
         }
-        return EngineRootNode.createEngineRoot(this, context, statements, createSourceSection(fullSource, statements), frame);
+        return EngineRootNode.createEngineRoot(this, context, statements, createSourceSection(fullSource, statements), frame, true);
     }
 
     @Override

com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/RFileTypeDetector.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
@@ -31,10 +31,12 @@
 public final class RFileTypeDetector extends FileTypeDetector {
     @Override
     public String probeContentType(Path path) throws IOException {
-
-        String fileName = path.getFileName().toString();
-        if (fileName.endsWith(".R") || fileName.endsWith(".r")) {
-            return RRuntime.R_TEXT_MIME;
+        Path fileNamePath = path.getFileName();
+        if (fileNamePath != null) {
+            String fileName = fileNamePath.toString();
+            if (fileName.endsWith(".R") || fileName.endsWith(".r")) {
+                return RRuntime.R_TEXT_MIME;
+            }
         }
         return null;
     }

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

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014, 2018, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2014, 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
@@ -251,7 +251,7 @@ private Object findCallerFromFrame(Frame frame) {
                     caller = caller.getParent();
                 }
             }
-            if (caller != null && caller.isValidCaller()) {
+            if (caller.isValidCaller()) {
                 // This is where we need to ensure that we have an RLanguage object with a rep that
                 // is an RSyntaxNode.
                 return getSyntaxCaller(caller);