load all default packages (except base) from binary form

.hgignore

@@ -91,3 +91,4 @@ findbugs.html
 com.oracle.truffle.r.native/builtinlibs/lib/*/librfficall.*
 com.oracle.truffle.r.native/builtinlibs/lib/*/libR.dylib
 com.oracle.truffle.r.native/library/*/lib/*/*.*
+com.oracle.truffle.r.native/library/fastr/lib/*

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

@@ -141,12 +141,7 @@ public final class REngine implements RContext.Engine {
              */
             checkAndRunStartupFunction(".First");
             checkAndRunStartupFunction(".First.sys");
-            /*
-             * TODO The following calls will eventually go away as this will be done in the system
-             * profile
-             */
-            REnvironment.packagesInitialize((RStringVector) ROptions.getValue("defaultPackages"));
-            RPackageVariables.initialize(); // TODO replace with R code
+            REnvironment.defaultPackagesInitialized();
             initialized = true;
         }
         registerBaseGraphicsSystem();

com.oracle.truffle.r.native/fficall/jni/src/rfficall.c

@@ -5,7 +5,7 @@
  *
  * Copyright (c) 1995-2012, The R Core Team
  * Copyright (c) 2003, The R Foundation
- * Copyright (c) 2014, Oracle and/or its affiliates
+ * Copyright (c) 2014, 2015, Oracle and/or its affiliates
  *
  * All rights reserved.
  */
@@ -46,6 +46,7 @@ static jmethodID createDoubleArrayMethodID;
 static jmethodID getIntDataAtZeroID;
 static jmethodID getDoubleDataAtZeroID;
 static jmethodID registerRoutinesID;
+static jmethodID registerCCallableID;
 static jmethodID useDynamicSymbolsID;
 static jmethodID forceSymbolsID;
 static jmethodID setDotSymbolValuesID;
@@ -67,6 +68,7 @@ Java_com_oracle_truffle_r_runtime_ffi_jnr_CallRFFIWithJNI_initialize(JNIEnv *env
 	getIntDataAtZeroID = checkGetMethodID(env, CallRFFIHelperClass, "getIntDataAtZero", "(Ljava/lang/Object;)I", 1);
 	getDoubleDataAtZeroID = checkGetMethodID(env, CallRFFIHelperClass, "getDoubleDataAtZero", "(Ljava/lang/Object;)D", 1);
 	registerRoutinesID = checkGetMethodID(env, DLLClass, "registerRoutines", "(Lcom/oracle/truffle/r/runtime/ffi/DLL$DLLInfo;IIJ)V", 1);
+	registerCCallableID = checkGetMethodID(env, DLLClass, "registerCCallable", "(Ljava/lang/String;Ljava/lang/String;J)V", 1);
 	useDynamicSymbolsID = checkGetMethodID(env, DLLClass, "useDynamicSymbols", "(Lcom/oracle/truffle/r/runtime/ffi/DLL$DLLInfo;I)I", 1);
 	forceSymbolsID = checkGetMethodID(env, DLLClass, "forceSymbols", "(Lcom/oracle/truffle/r/runtime/ffi/DLL$DLLInfo;I)I", 1);
 	setDotSymbolValuesID = checkGetMethodID(env, DLLClass, "setDotSymbolValues", "(Ljava/lang/String;JI)Lcom/oracle/truffle/r/runtime/ffi/DLL$DotSymbol;", 1);
@@ -83,7 +85,8 @@ R_registerRoutines(DllInfo *info, const R_CMethodDef * const croutines,
 		   const R_CallMethodDef * const callRoutines,
 		   const R_FortranMethodDef * const fortranRoutines,
 		   const R_ExternalMethodDef * const externalRoutines) {
-	// To avoid callbacks to convert the data in the R_CallMethodDef piece by piece, create it here.
+	// In theory we could create all the data here and pass it up, but in practice there were inexplicable
+	// Hotspot SEGV crashes creating Java arrays and Java objects in this function
 	JNIEnv *thisenv = getEnv();
 	int num;
 	if (croutines) {
@@ -105,6 +108,14 @@ R_registerRoutines(DllInfo *info, const R_CMethodDef * const croutines,
     return 1;
 }
 
+void R_RegisterCCallable(const char *package, const char *name, DL_FUNC fptr) {
+	JNIEnv *thisenv = getEnv();
+//	printf("pkgname %s, name %s\n", package, name);
+	jstring packageString = (*thisenv)->NewStringUTF(thisenv, package);
+	jstring nameString = (*thisenv)->NewStringUTF(thisenv, name);
+	(*thisenv)->CallStaticVoidMethod(thisenv, DLLClass, registerCCallableID, packageString, nameString, fptr);
+}
+
 JNIEXPORT jobject JNICALL
 Java_com_oracle_truffle_r_runtime_ffi_DLL_setSymbol(JNIEnv *env, jclass c, jint nstOrd, jlong routinesAddr, jint index) {
 	const char *name;
@@ -131,6 +142,7 @@ Java_com_oracle_truffle_r_runtime_ffi_DLL_setSymbol(JNIEnv *env, jclass c, jint
 		name = fortranRoutines[index].name;
 		fun = (long) fortranRoutines[index].fun;
 		numArgs = fortranRoutines[index].numArgs;
+		break;
 	}
 	case EXTERNAL_NATIVE_TYPE: {
 		R_ExternalMethodDef * externalRoutines = (R_ExternalMethodDef *) routinesAddr;
@@ -139,7 +151,7 @@ Java_com_oracle_truffle_r_runtime_ffi_DLL_setSymbol(JNIEnv *env, jclass c, jint
 		numArgs = externalRoutines[index].numArgs;
 		break;
 	}
-	default: (*env)->FatalError(env, "NativeSynbolTyope out of range");
+	default: (*env)->FatalError(env, "NativeSymbolType out of range");
 	}
 //	printf("name %s, fun %0lx, numArgs %d\n", name, fun, numArgs);
 	jstring nameString = (*env)->NewStringUTF(env, name);

com.oracle.truffle.r.native/library/Makefile

@@ -23,7 +23,7 @@
 
 .PHONY: all clean libdir make_subdirs clean_subdirs
 
-SUBDIRS = datasets utils grDevices graphics stats methods tools 
+SUBDIRS = datasets utils grDevices graphics stats methods tools fastr
 export FASTR_LIBDIR = $(TOPDIR)/../library
 
 all: libdir make_subdirs

com.oracle.truffle.r.native/library/README

+This directory tree contains the default packages for FastR. Each package directory contains a '.gz' file that was
+created from the corresponding GnuR 'library' directory, plus necessary C source and header files, most notably 'init.c',
+also copied from GnuR. Since these files reference functions in the GnuR implementation, 'init.c' is recompiled
+in the FastR environment and the resulting '.so' replaces the one from the '.gz' file in the FastR 'library' directory.
+Absolutely minimal changes are made to the C source, typically just to define (as empty functions), rather than reference,
+the C functions that are passed to R_registerRoutines. This step is still necesssary in FastR as it causes R symbols that are'
+referenced in the R package code to become defined.
+
+Note that 'datasets' and 'fastr' don't actually have any native code, but it is convenient to store them here. Note also that
+'fastr', obviously, does not originate from GnuR, so its build process is completely different.

com.oracle.truffle.r.native/library/fastr/Makefile

+#
+# Copyright (c) 2015, 2015, 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
+# under the terms of the GNU General Public License version 2 only, as
+# published by the Free Software Foundation.
+#
+# This code is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+# version 2 for more details (a copy is included in the LICENSE file that
+# accompanied this code).
+#
+# You should have received a copy of the GNU General Public License version
+# 2 along with this work; if not, write to the Free Software Foundation,
+# Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+# or visit www.oracle.com if you need additional information or have any
+# questions.
+#
+
+# This "builds" the "fastr" package, which defines functions that can
+# access the internals of the FastR implementation, e.g., print Truffle ASTs.
+# It is a "real" package, and loaded in the same way as any R package.
+
+# We use a 'tar' file of the sources as the sentinel for whether the INSTALL step is needed
+# Since this is just R code, we use GnuR to do the INSTALL
+
+.PHONY: all
+
+PKG_FILES = $(shell find src/ -type f -name '*')
+INSTALL_SENTINEL = $(FASTR_LIBDIR)/fastr/DESCRIPTION
+
+PKG_TAR = lib/fastr.tar
+
+all: $(INSTALL_SENTINEL)
+
+$(PKG_TAR): $(PKG_FILES)
+	mkdir -p lib
+	(cd src; tar cf ../$(PKG_TAR) *)
+
+$(INSTALL_SENTINEL): $(PKG_TAR)
+	R CMD INSTALL --library=$(FASTR_LIBDIR) src
+	
+clean:
+	rm -f $(PKG_TAR)
+

com.oracle.truffle.r.native/library/fastr/src/DESCRIPTION

+Package: fastr
+Type: Package
+Title: Functions for interacting with the FastR implementation
+Version: 1.0
+Date: 2015-02-05
+Author: FastR
+Maintainer: FastR <fastr@yahoogroups.com>
+Description: Functions for interacting with the FastR implementation
+License: GPL-2
+Packaged: 2014-02-05 22:48:32 UTC; 
\ No newline at end of file

com.oracle.truffle.r.native/library/fastr/src/NAMESPACE

+## exported functions
+export(fastr.createcc)
+export(fastr.getcc)
+export(fastr.compile)
+export(fastr.dumptrees)
+export(fastr.source)
+export(fastr.stacktrace)
+export(fastr.syntaxtree)
+export(fastr.seqlengths)
+export(fastr.tree)
+export(fastr.typeof)

com.oracle.truffle.r.native/library/fastr/src/R/fastr.R

+#
+# Copyright (c) 2015, 2015, 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
+# under the terms of the GNU General Public License version 2 only, as
+# published by the Free Software Foundation.
+#
+# This code is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+# version 2 for more details (a copy is included in the LICENSE file that
+# accompanied this code).
+#
+# You should have received a copy of the GNU General Public License version
+# 2 along with this work; if not, write to the Free Software Foundation,
+# Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+# or visit www.oracle.com if you need additional information or have any
+# questions.
+#
+
+fastr.createcc <- function(func) .FastR(.NAME="createcc", func)
+
+fastr.getcc <- function(func) .FastR(.NAME="getcc", func)
+
+fastr.compile <- function(func, background=TRUE) .FastR(.NAME="getcc", func, background)
+
+fastr.dumptrees <- function(func, igvDump=FALSE, verbose=FALSE) .FastR(.NAME="getcc", func, igvDump, verbose)
+
+fastr.source <- function(func) .FastR(.NAME="source", func)
+
+fastr.syntaxtree <- function(func) .FastR(.NAME="syntaxtree", func)
+
+fastr.tree <- function(func, verbose=FALSE) .FastR(.NAME="tree", func, verbose)
+
+fastr.seqlengths <- function(func) .FastR(.NAME="seqlengths", func)
+
+fastr.typeof <- function(x) .FastR(.NAME="typeof", x)
+
+fastr.stacktrace <- function(print.frame.contents=TRUE) .FastR(.NAME="stacktrace", print.frame.contents)
+

com.oracle.truffle.r.native/library/fastr/src/man/fastr-package.Rd

+\name{fastr-package}
+\alias{fastr-package}
+\alias{fastr}
+\docType{package}
+\title{Functions for interacting with the FastR implementation}
+\description{Functions for interacting with the FastR implementation}
+\details{
+\tabular{ll}{
+Package: \tab fastr\cr
+Type: \tab Package\cr
+Version: \tab 1.0\cr
+Date: \tab 2015-02-05\cr
+License: \tab GPL-2\cr
+}
+
+}
+\author{
+The FastR Team
+
+Maintainer: fastr@yahoogroups.com
+}
+\references{
+}
+
+\keyword{ package }
+\seealso{
+
+}
+\examples{
+
+}

com.oracle.truffle.r.native/library/fastr/src/man/fastr.Rd

+\name{fastr}
+\alias{fastr}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+fastr
+}
+\description{
+Functions for interacting with the FastR implementation
+}
+\usage{
+fastr.compile(f)
+}
+
+\details{
+
+}
+\value{
+invisble NULL
+}
+\references{
+
+}
+\author{
+FastR Team
+}
+\note{
+
+}
+
+\seealso{
+%
+}
+\examples{
+fastr.compile(f)
+}

com.oracle.truffle.r.native/library/graphics/src/graphics.h

+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2012   The R Core Team.
+ *
+ *  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
+ *  the Free Software Foundation; either version 2 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+#ifdef ENABLE_NLS
+#include <libintl.h>
+#undef _
+#define _(String) dgettext ("graphics", String)
+#else
+#define _(String) (String)
+#endif
+
+SEXP C_contour(SEXP args) { return NULL; }
+SEXP C_contourDef(void) { return NULL; }
+SEXP C_filledcontour(SEXP args) { return NULL; }
+SEXP C_image(SEXP args) { return NULL; }
+SEXP C_persp(SEXP args) { return NULL; }
+
+SEXP C_abline(SEXP args) { return NULL; }
+SEXP C_arrows(SEXP args) { return NULL; }
+SEXP C_axis(SEXP args) { return NULL; }
+SEXP C_box(SEXP args) { return NULL; }
+SEXP C_clip(SEXP args) { return NULL; }
+SEXP C_convertX(SEXP args) { return NULL; }
+SEXP C_convertY(SEXP args) { return NULL; }
+SEXP C_dend(SEXP args) { return NULL; }
+SEXP C_dendwindow(SEXP args) { return NULL; }
+SEXP C_erase(SEXP args) { return NULL; }
+SEXP C_layout(SEXP args) { return NULL; }
+SEXP C_mtext(SEXP args) { return NULL; }
+SEXP C_path(SEXP args) { return NULL; }
+SEXP C_plotXY(SEXP args) { return NULL; }
+SEXP C_plot_window(SEXP args) { return NULL; }
+SEXP C_polygon(SEXP args) { return NULL; }
+SEXP C_raster(SEXP args) { return NULL; }
+SEXP C_rect(SEXP args) { return NULL; }
+SEXP C_segments(SEXP args) { return NULL; }
+SEXP C_strHeight(SEXP args) { return NULL; }
+SEXP C_strWidth (SEXP args) { return NULL; }
+SEXP C_symbols(SEXP args) { return NULL; }
+SEXP C_text(SEXP args) { return NULL; }
+SEXP C_title(SEXP args) { return NULL; }
+SEXP C_xspline(SEXP args) { return NULL; }
+
+
+SEXP C_par(SEXP call, SEXP op, SEXP args, SEXP rho) { return NULL; }
+SEXP C_plot_new(SEXP call, SEXP op, SEXP args, SEXP rho) { return NULL; }
+SEXP C_locator(SEXP call, SEXP op, SEXP args, SEXP rho) { return NULL; }
+SEXP C_identify(SEXP call, SEXP op, SEXP args, SEXP rho) { return NULL; }
+
+void registerBase(void) { }
+void unregisterBase(void) { }
+SEXP RunregisterBase(void) { return NULL; }
+
+SEXP C_StemLeaf(SEXP x, SEXP scale, SEXP swidth, SEXP atom) { return NULL; }
+SEXP C_BinCount(SEXP x, SEXP breaks, SEXP right, SEXP lowest) { return NULL; }
+
+Rboolean isNAcol(SEXP col, int index, int ncol) { return FALSE; }

com.oracle.truffle.r.native/library/graphics/src/init.c

+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2012   The R Core Team.
+ *
+ *  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
+ *  the Free Software Foundation; either version 2 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <R.h>
+#include <Rinternals.h>
+
+#include "graphics.h"
+#include <R_ext/Rdynload.h>
+
+#define CALLDEF(name, n)  {#name, (DL_FUNC) &name, n}
+
+static const R_CallMethodDef CallEntries[] = {
+    CALLDEF(C_contourDef, 0),
+    CALLDEF(C_StemLeaf, 4),
+    CALLDEF(C_BinCount, 4),
+    CALLDEF(RunregisterBase, 0),
+    {NULL, NULL, 0}
+};
+
+
+#define EXTDEF(name, n)  {#name, (DL_FUNC) &name, n}
+
+static const R_ExternalMethodDef ExtEntries[] = {
+    EXTDEF(C_contour, -1),
+    EXTDEF(C_filledcontour, 5),
+    EXTDEF(C_image, 4),
+    EXTDEF(C_persp, -1),
+
+    EXTDEF(C_abline, -1),
+    EXTDEF(C_axis, -1),
+    EXTDEF(C_arrows, -1),
+    EXTDEF(C_box, -1),
+    EXTDEF(C_clip, -1),
+    EXTDEF(C_convertX, 3),
+    EXTDEF(C_convertY, 3),
+    EXTDEF(C_dend, -1),
+    EXTDEF(C_dendwindow, -1),
+    EXTDEF(C_erase, -1),
+    EXTDEF(C_layout, -1),
+    EXTDEF(C_mtext, -1),
+    EXTDEF(C_par, -1),
+    EXTDEF(C_path, -1),
+    EXTDEF(C_plotXY, -1),
+    EXTDEF(C_plot_window, -1),
+    EXTDEF(C_polygon, -1),
+    EXTDEF(C_raster, -1),
+    EXTDEF(C_rect, -1),
+    EXTDEF(C_segments, -1),
+    EXTDEF(C_strHeight, -1),
+    EXTDEF(C_strWidth, -1),
+    EXTDEF(C_symbols, -1),
+    EXTDEF(C_text, -1),
+    EXTDEF(C_title, -1),
+    EXTDEF(C_xspline, -1),
+
+    EXTDEF(C_plot_new, 0),
+    EXTDEF(C_locator, -1),
+    EXTDEF(C_identify, -1),
+    {NULL, NULL, 0}
+};
+
+
+void
+#ifdef HAVE_VISIBILITY_ATTRIBUTE
+__attribute__ ((visibility ("default")))
+#endif
+R_init_graphics(DllInfo *dll)
+{
+    R_registerRoutines(dll, NULL, CallEntries, NULL, ExtEntries);
+    R_useDynamicSymbols(dll, FALSE);
+    R_forceSymbols(dll, TRUE);
+    registerBase();
+}

com.oracle.truffle.r.native/library/lib.mk

@@ -55,7 +55,11 @@ INCLUDES := $(JNI_INCLUDES) $(FFI_INCLUDES)
 PKGDIR := $(FASTR_LIBDIR)/$(PKG)
 PKGTAR := $(SRC)/$(PKG).tar.gz
 
+ifneq ($(C_SOURCES),)
 all: libcommon $(LIB_PKG)
+else
+all: libcommon
+endif
 
 libcommon: $(PKGDIR)
 

com.oracle.truffle.r.native/library/stats/src/nls.h

@@ -24,7 +24,7 @@
 #define _(String) (String)
 #endif
 
-SEXP nls_iter(SEXP m, SEXP control, SEXP doTraceArg);
-SEXP numeric_deriv(SEXP expr, SEXP theta, SEXP rho, SEXP dir);
+SEXP nls_iter(SEXP m, SEXP control, SEXP doTraceArg) { return NULL; }
+SEXP numeric_deriv(SEXP expr, SEXP theta, SEXP rho, SEXP dir) { return NULL; }
 
 

com.oracle.truffle.r.native/library/utils/src/utils.c

-// Empty file

com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/RBuiltinPackages.java

 /*
- * Copyright (c) 2013, 2014, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2013, 2015, 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
@@ -27,8 +27,6 @@ import java.util.*;
 import com.oracle.truffle.api.*;
 import com.oracle.truffle.api.frame.*;
 import com.oracle.truffle.r.nodes.builtin.base.*;
-import com.oracle.truffle.r.nodes.builtin.fastr.*;
-import com.oracle.truffle.r.nodes.builtin.stats.*;
 import com.oracle.truffle.r.options.*;
 import com.oracle.truffle.r.runtime.*;
 import com.oracle.truffle.r.runtime.data.*;
@@ -49,8 +47,6 @@ public final class RBuiltinPackages implements RBuiltinLookup {
 
     static {
         RBuiltinPackages.add(new BasePackage());
-        RBuiltinPackages.add(new FastRPackage());
-        RBuiltinPackages.add(new StatsPackage());
     }
 
     protected static void add(RBuiltinPackage builtins) {

com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Cor.java

-/*
- * Copyright (c) 2013, 2014, 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
- * under the terms of the GNU General Public License version 2 only, as
- * published by the Free Software Foundation.
- *
- * This code is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
- * version 2 for more details (a copy is included in the LICENSE file that
- * accompanied this code).
- *
- * You should have received a copy of the GNU General Public License version
- * 2 along with this work; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
- * or visit www.oracle.com if you need additional information or have any
- * questions.
- */
-package com.oracle.truffle.r.nodes.builtin.base;
-
-import static com.oracle.truffle.r.runtime.RBuiltinKind.*;
-
-import com.oracle.truffle.api.dsl.*;
-import com.oracle.truffle.r.nodes.*;
-import com.oracle.truffle.r.nodes.access.*;
-import com.oracle.truffle.r.runtime.*;
-import com.oracle.truffle.r.runtime.data.*;
-
-@RBuiltin(name = "cor", kind = SUBSTITUTE, parameterNames = {"x", "y", "use", "method"})
-public abstract class Cor extends Covcor {
-
-    @Override
-    public RNode[] getParameterValues() {
-        // x, y = NULL, use = "everything", method = c("pearson", "kendall", "spearman")
-        return new RNode[]{ConstantNode.create(RMissing.instance), ConstantNode.create(RNull.instance), ConstantNode.create("everything"),
-                        ConstantNode.create(RDataFactory.createStringVector(new String[]{"pearson", "kendall", "spearman"}, true))};
-    }
-
-    @Specialization
-    protected RDoubleVector dimWithDimensions(RDoubleVector vector1, RDoubleVector vector2, @SuppressWarnings("unused") String use, @SuppressWarnings("unused") RStringVector method) {
-        controlVisibility();
-        return corcov(vector1, vector2, false, true);
-    }
-
-    @Specialization
-    @SuppressWarnings("unused")
-    protected RDoubleVector dimWithDimensions(RDoubleVector vector1, RMissing vector2, String use, RStringVector method) {
-        controlVisibility();
-        return corcov(vector1, null, false, true);
-    }
-
-    @Specialization
-    @SuppressWarnings("unused")
-    protected RDoubleVector dimWithDimensions(RDoubleVector vector1, RNull vector2, String use, RStringVector method) {
-        controlVisibility();
-        return corcov(vector1, null, false, true);
-    }
-}

com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Cov.java

-/*
- * Copyright (c) 2013, 2014, 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
- * under the terms of the GNU General Public License version 2 only, as
- * published by the Free Software Foundation.
- *
- * This code is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
- * version 2 for more details (a copy is included in the LICENSE file that
- * accompanied this code).
- *
- * You should have received a copy of the GNU General Public License version
- * 2 along with this work; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
- * or visit www.oracle.com if you need additional information or have any
- * questions.
- */
-package com.oracle.truffle.r.nodes.builtin.base;
-
-import static com.oracle.truffle.r.runtime.RBuiltinKind.*;
-
-import com.oracle.truffle.api.dsl.*;
-import com.oracle.truffle.r.nodes.*;
-import com.oracle.truffle.r.nodes.access.*;
-import com.oracle.truffle.r.runtime.*;
-import com.oracle.truffle.r.runtime.data.*;
-
-@RBuiltin(name = "cov", kind = SUBSTITUTE, parameterNames = {"x", "y", "use", "method"})
-public abstract class Cov extends Covcor {
-
-    @Override
-    public RNode[] getParameterValues() {
-        // x, y = NULL, use = "everything", method = c("pearson", "kendall", "spearman")
-        // TODO Is there a constant for "everyting"?
-        return new RNode[]{ConstantNode.create(RMissing.instance), ConstantNode.create(RNull.instance), ConstantNode.create("everything"),
-                        ConstantNode.create(RDataFactory.createStringVector(new String[]{"pearson", "kendall", "spearman"}, true))};
-    }
-
-    @Specialization
-    protected RDoubleVector dimWithDimensions(RDoubleVector vector1, RDoubleVector vector2) {
-        controlVisibility();
-        return corcov(vector1, vector2, false, false);
-    }
-
-    @Specialization
-    @SuppressWarnings("unused")
-    protected RDoubleVector dimWithDimensions(RDoubleVector vector1, RMissing vector2) {
-        controlVisibility();
-        return corcov(vector1, null, false, false);
-    }
-}