[GR-33795] [GR-33589] FIx C_Approx{Test}, .Rprofile loading, update CHANGELOG, set impl. name.

PullRequest: fastr/2655

Author: steve-s

CHANGELOG.md

@@ -1,3 +1,16 @@
+# 21.3.0
+* Upgrade of PCRE to PCRE2 version 10.37.
+  * Some Unicode patterns and texts are still not supported.
+
+Bug fixes:
+
+* Fixed implicit make rule parameters used when building R extensions
+  * Fixes, e.g., installation of maps package version 3.3.0.
+* Fixed unexpected garbage collection of CHARSXP objects in R extensions
+* Option --no-init-file is not ignored anymore
+* Fixed functions `approx` and `approxfun` from the `stats` package
+  * Previously they were always failing with error message "Incorrect number of arguments"
+
 # 21.2.0
 * Support for packages in 2021-02-01 CRAN snapshot:
   * testthat 3.0.1 is partially supported.

com.oracle.truffle.r.launcher/src/com/oracle/truffle/r/launcher/RStartParams.java

@@ -82,7 +82,7 @@ public RStartParams(RCmdOptions options, boolean embedded) {
         this.verbose = options.getBoolean(VERBOSE);
         this.quiet = options.getBoolean(QUIET) || options.getBoolean(SILENT) || options.getBoolean(NO_ECHO);
         this.loadSiteFile = options.getBoolean(NO_SITE_FILE);
-        this.loadInitFile = !embedded && options.getBoolean(NO_INIT_FILE) && !options.getBoolean(VANILLA);
+        this.loadInitFile = !embedded && !options.getBoolean(NO_INIT_FILE) && !options.getBoolean(VANILLA);
         this.noRenviron = embedded || options.getBoolean(NO_ENVIRON) || options.getBoolean(VANILLA);
         this.restoreAction = options.getBoolean(RESTORE) && !(options.getBoolean(NO_RESTORE) || options.getBoolean(NO_RESTORE_DATA) || options.getBoolean(VANILLA));
         this.noReadline = options.getBoolean(NO_READLINE);

com.oracle.truffle.r.launcher/src/com/oracle/truffle/r/launcher/RVersionNumber.java

@@ -50,11 +50,9 @@ public class RVersionNumber {
 
     public static final String VERSION_STRING = "FastR version " + FULL + RELEASE_DATE;
 
-    public static final String COPYRIGHT = "Copyright (c) 2013-19, Oracle and/or its affiliates\n" +
-                    "Copyright (c) 1995-2018, The R Core Team\n" +
-                    "Copyright (c) 2018 The R Foundation for Statistical Computing\n" +
+    public static final String COPYRIGHT = "Copyright (c) 2013-21, Oracle and/or its affiliates\n" +
+                    "Copyright (C) 2020 The R Foundation for Statistical Computing\n" +
                     "Copyright (c) 2012-4 Purdue University\n" +
-                    "Copyright (c) 1997-2002, Makoto Matsumoto and Takuji Nishimura\n" +
                     "All rights reserved.\n";
 
     /**

com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Approx.java

@@ -24,6 +24,7 @@
 import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.emptyDoubleVector;
 import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.missingValue;
 import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.nullValue;
+import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.toBoolean;
 
 import com.oracle.truffle.api.dsl.Specialization;
 import com.oracle.truffle.api.library.CachedLibrary;
@@ -36,7 +37,10 @@
 import com.oracle.truffle.r.runtime.data.VectorDataLibrary.SeqIterator;
 import com.oracle.truffle.r.runtime.ops.na.NACheck;
 
-public abstract class Approx extends RExternalBuiltinNode.Arg7 {
+/**
+ * Transcribed from {@code src/library/stats/src/approx.c:R_approxfun}.
+ */
+public abstract class Approx extends RExternalBuiltinNode.Arg8 {
     private static final NACheck naCheck = NACheck.create();
 
     public static Approx create() {
@@ -52,10 +56,11 @@ public static Approx create() {
         casts.arg(4).asDoubleVector().findFirst();
         casts.arg(5).asDoubleVector().findFirst();
         casts.arg(6).asDoubleVector().findFirst();
+        casts.arg(7).asLogicalVector().findFirst().map(toBoolean());
     }
 
     @Specialization(limit = "getVectorAccessCacheSize()")
-    protected RDoubleVector approx(RDoubleVector x, RDoubleVector y, RDoubleVector v, int method, double yl, double yr, double f,
+    protected RDoubleVector approx(RDoubleVector x, RDoubleVector y, RDoubleVector v, int method, double yl, double yr, double f, boolean naRm,
                     @CachedLibrary("x.getData()") VectorDataLibrary xLib,
                     @CachedLibrary("y.getData()") VectorDataLibrary yLib,
                     @CachedLibrary("v.getData()") VectorDataLibrary vLib) {
@@ -69,6 +74,7 @@ protected RDoubleVector approx(RDoubleVector x, RDoubleVector y, RDoubleVector v
         apprMeth.kind = method;
         apprMeth.ylow = yl;
         apprMeth.yhigh = yr;
+        apprMeth.naRm = naRm;
         naCheck.enable(true);
 
         Object xData = x.getData();
@@ -94,6 +100,8 @@ private static class ApprMeth {
         double f1;
         double f2;
         int kind;
+        // In GNU-R, naRm field is unused.
+        @SuppressWarnings("unused") boolean naRm;
     }
 
     private static double approx1(double v, VectorDataLibrary xLib, Object xData, RandomAccessIterator xIter,

com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/ApproxTest.java

@@ -2,7 +2,7 @@
  * Copyright (c) 1995, 1996, 1997  Robert Gentleman and Ross Ihaka
  * Copyright (c) 1998-2013, The R Core Team
  * Copyright (c) 2003-2015, The R Foundation
- * Copyright (c) 2016, 2020, Oracle and/or its affiliates
+ * Copyright (c) 2016, 2021, Oracle and/or its affiliates
  *
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -27,7 +27,12 @@
 import com.oracle.truffle.r.runtime.data.RDoubleVector;
 import com.oracle.truffle.r.runtime.data.RNull;
 
-public abstract class ApproxTest extends RExternalBuiltinNode.Arg4 {
+import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.toBoolean;
+
+/**
+ * Transcribed from {@code src/library/stats/src/approx.c:R_approxtest}.
+ */
+public abstract class ApproxTest extends RExternalBuiltinNode.Arg5 {
     public static ApproxTest create() {
         return ApproxTestNodeGen.create();
     }
@@ -36,10 +41,11 @@ public static ApproxTest create() {
         Casts casts = new Casts(ApproxTest.class);
         casts.arg(2).asIntegerVector().findFirst();
         casts.arg(3).asDoubleVector().findFirst();
+        casts.arg(4).asLogicalVector().findFirst().map(toBoolean());
     }
 
     @Specialization
-    protected RNull approxtest(RDoubleVector x, RDoubleVector y, int method, double f) {
+    protected RNull approxtest(RDoubleVector x, RDoubleVector y, int method, double f, boolean naRm) {
         int nx = x.getLength();
         switch (method) {
             case 1:
@@ -54,8 +60,16 @@ protected RNull approxtest(RDoubleVector x, RDoubleVector y, int method, double
         }
 
         for (int i = 0; i < nx; i++) {
-            if (RRuntime.isNAorNaN(x.getDataAt(i)) || RRuntime.isNAorNaN(y.getDataAt(i))) {
-                throw error(RError.Message.GENERIC, ("approx(): attempted to interpolate NA values"));
+            if (naRm) {
+                // (x,y) should not have any NA's anymore
+                if (RRuntime.isNAorNaN(x.getDataAt(i)) || RRuntime.isNAorNaN(y.getDataAt(i))) {
+                    throw error(RError.Message.GENERIC, ("approx(): attempted to interpolate NA values"));
+                }
+            } else {
+                // na.rm = FALSE ==> at least y may contain NA's
+                if (RRuntime.isNAorNaN(x.getDataAt(i))) {
+                    throw error(RError.Message.GENERIC, ("approx(x,y, .., na.rm=FALSE): NA values in x are not allowed"));
+                }
             }
         }
 

com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/CONTRIBUTORS

@@ -16,6 +16,7 @@ Prahlad Joshi
 Tomas Kalibera
 Roman Katerinenko
 Petr Maj
+Pavel Marek
 Miloslav Metelka
 Stepan Sindelar
 Zbynek Slajchrt

com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/context/TruffleRLanguage.java

@@ -59,7 +59,7 @@
 import com.oracle.truffle.r.runtime.interop.ConvertForeignObjectNode;
 import com.oracle.truffle.r.runtime.interop.Foreign2R;
 
-@TruffleLanguage.Registration(name = "R", id = "R", version = "4.0.3", characterMimeTypes = {RRuntime.R_APP_MIME,
+@TruffleLanguage.Registration(name = "R", id = "R", version = "4.0.3", implementationName = "FastR", characterMimeTypes = {RRuntime.R_APP_MIME,
                 RRuntime.R_TEXT_MIME}, defaultMimeType = RRuntime.R_APP_MIME, interactive = true, fileTypeDetectors = RFileTypeDetector.class, dependentLanguages = "llvm")
 @ProvidedTags({StandardTags.CallTag.class, StandardTags.StatementTag.class, StandardTags.RootBodyTag.class, StandardTags.RootTag.class, RSyntaxTags.LoopTag.class, FunctionBodyBlockTag.class})
 public final class TruffleRLanguage extends TruffleLanguage<RContext> {