diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/methods/MethodsListDispatch.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/methods/MethodsListDispatch.java
index ec801c5738807ea575b3516daf8418ec46b04bb5..28a93fd8c07ea1f3b3b8c2cd10952f0d4ddef089 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/methods/MethodsListDispatch.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/methods/MethodsListDispatch.java
@@ -51,7 +51,7 @@ public class MethodsListDispatch {
@TruffleBoundary
@Specialization
- protected Object callGetClassFromCache(REnvironment table, Object klass) {
+ protected Object callGetClassFromCache(Object klass, REnvironment table) {
String klassString = RRuntime.asString(klass);
if (klassString != null) {
diff --git a/com.oracle.truffle.r.native/fficall/jni/src/misc.c b/com.oracle.truffle.r.native/fficall/jni/src/misc.c
index fef275f202b61561763e3f3e7b49211cd6e5a227..afbc0e520c3078fad8735763777443f0ce69bb7f 100644
--- a/com.oracle.truffle.r.native/fficall/jni/src/misc.c
+++ b/com.oracle.truffle.r.native/fficall/jni/src/misc.c
@@ -67,6 +67,14 @@ void R_qsort_int_I(int *iv, int *II, int i, int j) {
unimplemented("R_qsort_int_I");
}
+void rsort_with_index(double *a, int *b, int c) {
+ unimplemented("rsort_with_index");
+}
+
+void revsort(double *a, int *b, int c) {
+ unimplemented("revsort");
+}
+
void R_CheckUserInterrupt() {
// TODO (we don't even do this in the Java code)
}
diff --git a/com.oracle.truffle.r.native/fficall/jni/src/rf_functions.c b/com.oracle.truffle.r.native/fficall/jni/src/rf_functions.c
index b2ac82ebab94bb10c6cdffc6aff88f901b000b9c..2c1c41fbb6d518a7daa28e864081413841729f8e 100644
--- a/com.oracle.truffle.r.native/fficall/jni/src/rf_functions.c
+++ b/com.oracle.truffle.r.native/fficall/jni/src/rf_functions.c
@@ -382,6 +382,15 @@ void Rf_unprotect(int x) {
// TODO perhaps we can use this
}
+void R_ProtectWithIndex(SEXP x, PROTECT_INDEX *y) {
+
+}
+
+void R_Reprotect(SEXP x, PROTECT_INDEX y) {
+
+}
+
+
void Rf_unprotect_ptr(SEXP x) {
// TODO perhaps we can use this
}
@@ -467,6 +476,11 @@ void Rf_rPsort(double *x, int n, int k) {
unimplemented("Rf_rPsort");
}
+void Rf_cPsort(Rcomplex *x, int n, int k) {
+ JNIEnv *thisenv = getEnv();
+ unimplemented("Rf_cPsort");
+}
+
SEXP Rf_classgets(SEXP x, SEXP y) {
unimplemented("Rf_classgets");
}
diff --git a/com.oracle.truffle.r.native/fficall/jni/src/rfficall.c b/com.oracle.truffle.r.native/fficall/jni/src/rfficall.c
index b00783dbbf923cce017585dabd3b9e2f89b20109..75589f4a8673b1b252b4c3a17badfa34e8c11455 100644
--- a/com.oracle.truffle.r.native/fficall/jni/src/rfficall.c
+++ b/com.oracle.truffle.r.native/fficall/jni/src/rfficall.c
@@ -36,6 +36,7 @@ Java_com_oracle_truffle_r_runtime_ffi_jnr_CallRFFIWithJNI_initialize(JNIEnv *env
init_typecoerce(env);
init_attrib(env);
init_misc(env);
+ init_rmath(env);
init_rng(env);
init_optim(env);
init_vectoraccess(env);
diff --git a/com.oracle.truffle.r.native/fficall/jni/src/rmathc.c b/com.oracle.truffle.r.native/fficall/jni/src/rmathc.c
new file mode 100644
index 0000000000000000000000000000000000000000..47599d9a21a6432aaca08ff8b82ae4240604503e
--- /dev/null
+++ b/com.oracle.truffle.r.native/fficall/jni/src/rmathc.c
@@ -0,0 +1,31 @@
+/*
+ * 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.
+ */
+#include "rffiutils.h"
+
+void init_rmath(JNIEnv *env) {
+
+}
+
+double Rf_dnorm4(double a, double b, double c , int d) {
+ unimplemented("Rf_dnorm4");
+}
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Format.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Format.java
index 2282d892211616466be0632e643360ca2f34c0f3..2a5b4839cf2c789c2d47850842248632bbd1e1b7 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Format.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Format.java
@@ -236,11 +236,11 @@ public abstract class Format extends RBuiltinNode {
}
@Specialization
- protected RStringVector format(RStringVector value, RLogicalVector trimVec, RIntVector digitsVec, RIntVector nsmallVec, RIntVector widthVec, RIntVector justifyVec, RLogicalVector naEncodeVec,
- RAbstractVector sciVec) {
+ protected RStringVector format(RAbstractStringVector value, RLogicalVector trimVec, RIntVector digitsVec, RIntVector nsmallVec, RIntVector widthVec, RIntVector justifyVec,
+ RLogicalVector naEncodeVec, RAbstractVector sciVec) {
checkArgs(trimVec, digitsVec, nsmallVec, widthVec, justifyVec, naEncodeVec, sciVec);
// TODO: implement full semantics
- return value;
+ return value.materialize();
}
@Specialization
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Structure.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Structure.java
index c8dac4d265fd7721275d3b83f4a9ea54e9d4ce39..0585aaea16a85ebe0117fabf0d45d67f165c5284 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Structure.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Structure.java
@@ -32,6 +32,7 @@ import com.oracle.truffle.r.nodes.builtin.*;
import com.oracle.truffle.r.runtime.*;
import com.oracle.truffle.r.runtime.data.*;
import com.oracle.truffle.r.runtime.data.model.*;
+import com.oracle.truffle.r.runtime.env.REnvironment;
/**
* A temporary substitution to work around bug with {@code list(...)} used in R version.
@@ -71,24 +72,51 @@ public abstract class Structure extends RBuiltinNode {
}
@Specialization
- @TruffleBoundary
+ protected Object structure(RFunction obj, RArgsValuesAndNames args) {
+ return doStructure(obj, args);
+ }
+
+ @Specialization
+ protected Object structure(REnvironment obj, RArgsValuesAndNames args) {
+ return doStructure(obj, args);
+ }
+
+ @Specialization
+ protected Object structure(RSymbol obj, RArgsValuesAndNames args) {
+ return doStructure(obj, args);
+ }
+
+ @Specialization
+ protected Object structure(RExternalPtr obj, RArgsValuesAndNames args) {
+ return doStructure(obj, args);
+ }
+
+ @Specialization
protected Object structure(RAbstractContainer obj, RArgsValuesAndNames args) {
- Object[] values = args.getArguments();
- ArgumentsSignature signature = getSuppliedSignature();
- validateArgNames(signature);
- RAbstractContainer res = obj;
+ RAttributable res = obj;
// TODO: should we consider storing attributes with sequences?
if (res instanceof RSequence) {
res = ((RSequence) res).createVector();
}
+ return doStructure(res, args);
+ }
+
+ // Ideally we would only need this as a specialization, but then we fail due to
+ // lack of auto-translation of, e.g. Double to RAbstractContainer.
+ @TruffleBoundary
+ protected Object doStructure(RAttributable obj, RArgsValuesAndNames args) {
+ Object[] values = args.getArguments();
+ ArgumentsSignature signature = getSuppliedSignature();
+ validateArgNames(signature);
+ RAttributable res = obj;
for (int i = 0; i < values.length; i++) {
Object value = fixupValue(values[i]);
String attrName = fixupAttrName(signature.getName(i + 1));
if (attrName.equals(RRuntime.CLASS_ATTR_KEY)) {
if (value == RNull.instance) {
- res = (RAbstractContainer) res.setClassAttr(null, true);
+ res = res.setClassAttr(null, true);
} else {
- res = (RAbstractContainer) res.setClassAttr((RStringVector) value, true);
+ res = res.setClassAttr((RStringVector) value, true);
}
} else {
if (value == RNull.instance) {
diff --git a/com.oracle.truffle.r.test.cran/r/install.cran.packages.R b/com.oracle.truffle.r.test.cran/r/install.cran.packages.R
index dd7ba22be1d81c78c9f315991f6b6ab493d8e89b..f61643d474353ca638c0f0de71a493a5f437d5a8 100644
--- a/com.oracle.truffle.r.test.cran/r/install.cran.packages.R
+++ b/com.oracle.truffle.r.test.cran/r/install.cran.packages.R
@@ -70,24 +70,31 @@ create.blacklist.iter <- function(blacklist) {
}
# known to be uninstallable
-# uses ++
+# uses C++
cplusplus <- c("Rcpp", "Segmentor3IsBack", "QUIC", "kernlab", "adaptivetau", "geepack", "caTools", "amap", "rgenoud", "stringi", "rjson", "ars",
"e1071", "aylmer")
+# tcltk
+tcltk <- c("AnnotLists", "tcltk2", "aplpack")
# parser bugs
-parserbug <- character()
-# unimplemented feature
-unimplemented <- c("ABCoptim")
+parserbug <- c("R2HTML")
+# e.g., unimplemented builtin, assertion error
+core <- c("ade4", "ABCoptim", "R.methodsS3", "lattice", "aidar", "DBI", "SparseM", "quantreg", "doParallel", "ApacheLogProcessor", "aplore3",
+ "vignettes", "archiDART", "corpcor", "acss.data")
# e.g. complex replacement assignments
-trufflevisitor.nyi <- c("colorspace", "R.methodsS3", "ade4", "lattice")
+trufflevisitor.nyi <- c("colorspace")
# problems with native code
-nativeinstall <- c("Rglpk", "overlap", "adimpro")
+nativeinstall <- c("Rglpk", "overlap", "adimpro", "deSolve")
# S4 anything using S4 objects
-s4 <- c("matrixStats")
+s4 <- c("matrixStats", "AcceptanceSampling", "biglm", "analyz", "RCurl", "anfis", "aod", "ascii")
# graphics
-graphics <- c("Cairo")
+graphics <- c("Cairo", "rgl")
+# incomplete definitions from Rmath.h
+math <- c("mvtnorm")
# serialize
-serialize <- c("actuar", "spam")
-initial.blacklist <- c(cplusplus, parserbug, unimplemented, trufflevisitor.nyi, nativeinstall, s4, graphics, serialize)
+serialize <- c("actuar", "spam", "codetools", "iterators", "apc", "apsrtable", "assertthat")
+# fortran related
+fortran <- c("appell")
+initial.blacklist <- c(cplusplus, tcltk, parserbug, core, math, trufflevisitor.nyi, nativeinstall, s4, graphics, serialize, fortran)
create.blacklist <- function() {
create.blacklist.iter(initial.blacklist)