Merge branch 'origin/master' into release/graal-vm/1.0

Author: ansalond

.hgtags

@@ -1,15 +1,25 @@
 
 # 1.0 RC 5
 
+New features
+
+* Script that configures FastR for the current system (jre/languages/R/bin/configure_fastr)
+  * allows to pass additional arguments for the underlying configure script
+  * by default uses the following arguments: --with-x=no --with-aqua=no --enable-memory-profiling FFLAGS=-O2
+
 Updates in interop:
 
 * R code evaluated via interop never returns a Java primitive type, but always a vector
 * Vectors of size 1 that do not contain NA can be unboxed
 * Sending the READ message to an atomic R vector (array subscript in most languages) gives
   * Java primitive type as long as the value is not `NA`
-  * a special value that responds to `IS_NULL` with `true`. If this value is passed back to R it behaves as `NA` again
+  * if the value is `NA`, a special value that responds to `IS_NULL` with `true`. If this value is passed back to R it behaves as `NA` again
 * Note that sending the READ message to a list, environment, or other heterogenous data structure never gives atomic Java type but a primitive R vector
 
+Bug fixes:
+
+* Various smaller issues discovered during testing of CRAN packages.
+
 # 1.0 RC 4
 
 # 1.0 RC 3

CHANGELOG.md

@@ -121,6 +121,11 @@ The access point for contributions, issues and questions about FastR is the [Git
 
 ## Troubleshooting
 
+### GNU-R build fails
+
+GNU-R is built as part of the FastR build and therefore all GNU-R dependencies are required.
+The output from GNU-R configuration is logged in `libdownloads/R-3.4.0/gnur_configure.log`.
+
 ### Build fails when generating R grammar
 
 This problem manifests by the following error message in the build output:
@@ -141,3 +146,10 @@ export LANG=en_US.UTF-8
 export LC_ALL=en_US.UTF-8
 export LC_CTYPE=en_US.UTF-8
 ```
+
+Note: you may need to install `locale` and run the following before setting the above env variables:
+
+```
+locale en_US.UTF-8
+```
+

README.md

@@ -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 want to enforce specific overlay commit, uncomment:
-overlay = "1823c758582f31386f8ba4d89157265a23cebd04"
+# overlay = "1823c758582f31386f8ba4d89157265a23cebd04"
 builds = [
   ${gateTestLinux}            {capabilities : [linux, amd64, fast],  targets : [gate], name: "gate-test-linux-amd64"}
   ${gateTestNoSpecialsLinux}  {capabilities : [linux, amd64, fast],  targets : [gate], name: "gate-test-linux-amd64-nospecials"}

Rpkgsource/.project

@@ -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 : "8u172-jvmci-0.46", platformspecific: true}
+java8 : {name : labsjdk, version : "8u172-jvmci-0.47", platformspecific: true}
 java9 : {name : oraclejdk, version : "9.0.4+11", platformspecific: true}
 
 java8Downloads : {
@@ -35,10 +35,10 @@ logfiles : [
     "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/*/*-tests/*.Rout"
-    # "test.gnur/*/*.Rout"
-    # "test.gnur/*/*-tests/*.Rout"
+    "test.fastr/**/*.Rout"
+    "test.fastr/**/*-tests/*.Rout"
+    "test.gnur/**/*.Rout"
+    "test.gnur/**/*-tests/*.Rout"
   ]
 
 # This is needed by all (Linux) builds but is specific to the module system employed
@@ -91,7 +91,7 @@ common : ${java8Downloads} ${packagesLinux}  {
 # the "mx" tool. This defines a common prefix for all gate commands. The "-t"
 # arg indicates the exact set of gate "tasks" that will be run.
 
-gateCmd : ["mx", "-v", "--strict-compliance", "rgate", "--strict-mode", "-t"]
+gateCmd : ["mx", "-v", "--strict-compliance", "rgate", "-B=--force-deprecation-as-warning", "--strict-mode", "-t"]
 
 # currently disabled gate commands: FindBugs,Checkheaders,Distribution Overlap Check
 
@@ -165,6 +165,8 @@ gateStyle : ${common} {
   }
   run : [
     ${gateCmd} ["Versions,JDKReleaseInfo,Pylint,Canonicalization Check,BuildJavaWithJavac,IDEConfigCheck,CodeFormatCheck,Checkstyle,Copyright check,UnitTests: ExpectedTestOutput file check"]
+    ["mx", "clean", "--no-native"]
+    ${gateCmd} ["BuildWithEcj"]
   ]
 }
 

ci.hocon

@@ -47,7 +47,6 @@
 import com.oracle.truffle.r.runtime.context.RContext;
 import com.oracle.truffle.r.runtime.data.RNull;
 import com.oracle.truffle.r.runtime.interop.R2Foreign;
-import com.oracle.truffle.r.runtime.interop.R2ForeignNodeGen;
 import com.oracle.truffle.r.runtime.nodes.RNode;
 import com.oracle.truffle.r.runtime.nodes.RSyntaxNode;
 

ci_common/common.hocon

@@ -146,8 +146,12 @@ public RPairList getSyntaxCaller(RCaller rl) {
         while (call.isPromise()) {
             call = call.getParent();
         }
-        RSyntaxElement syntaxNode = call.getSyntaxNode();
-        return RDataFactory.createLanguage(getOrCreateLanguageClosure(((RSyntaxNode) syntaxNode).asRNode()));
+        if (call.isValidCaller()) {
+            RSyntaxElement syntaxNode = call.getSyntaxNode();
+            return RDataFactory.createLanguage(getOrCreateLanguageClosure(((RSyntaxNode) syntaxNode).asRNode()));
+        } else {
+            return null;
+        }
     }
 
     private static RBaseNode checkBuiltin(RBaseNode bn) {

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

@@ -55,7 +55,6 @@
 import com.oracle.truffle.r.runtime.interop.Foreign2R;
 import com.oracle.truffle.r.runtime.interop.Foreign2RNodeGen;
 import com.oracle.truffle.r.runtime.interop.R2Foreign;
-import com.oracle.truffle.r.runtime.interop.R2ForeignNodeGen;
 
 public class ListMR {
 

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

@@ -66,7 +66,6 @@
 import com.oracle.truffle.r.runtime.interop.Foreign2R;
 import com.oracle.truffle.r.runtime.interop.Foreign2RNodeGen;
 import com.oracle.truffle.r.runtime.interop.R2Foreign;
-import com.oracle.truffle.r.runtime.interop.R2ForeignNodeGen;
 import com.oracle.truffle.r.runtime.nodes.RSyntaxNode;
 
 abstract class InteropRootNode extends RootNode {