From 432314a8170498fb44a80a8cdae48d1db1a67837 Mon Sep 17 00:00:00 2001
From: Adam Welc <adam.welc@oracle.com>
Date: Mon, 6 Oct 2014 18:33:22 -0700
Subject: [PATCH] Partial implementation of the "scan" function.
---
.../builtin/base/ConnectionFunctions.java | 7 +-
.../truffle/r/nodes/builtin/base/R/scan.R | 56 +++
.../truffle/r/nodes/builtin/base/Scan.java | 349 ++++++++++++++++++
.../com/oracle/truffle/r/runtime/RError.java | 4 +
.../oracle/truffle/r/runtime/RRuntime.java | 9 +
.../com/oracle/truffle/r/runtime/Utils.java | 4 +
.../r/runtime/data/RComplexVector.java | 6 +
.../r/runtime/data/RDoubleSequence.java | 7 +-
.../truffle/r/runtime/data/RDoubleVector.java | 6 +
.../truffle/r/runtime/data/RIntSequence.java | 8 +-
.../truffle/r/runtime/data/RIntVector.java | 6 +
.../oracle/truffle/r/runtime/data/RList.java | 6 +
.../r/runtime/data/RLogicalVector.java | 6 +
.../truffle/r/runtime/data/RRawVector.java | 6 +
.../truffle/r/runtime/data/RStringVector.java | 6 +
.../truffle/r/runtime/data/RVector.java | 14 +-
.../data/closures/RToVectorClosure.java | 7 +-
.../r/runtime/data/model/RAbstractVector.java | 4 +-
mx.fastr/copyrights/gnu_r_scan.copyright.star | 11 +
.../gnu_r_scan.copyright.star.regex | 1 +
mx.fastr/copyrights/overrides | 1 +
21 files changed, 516 insertions(+), 8 deletions(-)
create mode 100644 com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/R/scan.R
create mode 100644 com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Scan.java
create mode 100644 mx.fastr/copyrights/gnu_r_scan.copyright.star
create mode 100644 mx.fastr/copyrights/gnu_r_scan.copyright.star.regex
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/ConnectionFunctions.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/ConnectionFunctions.java
index 64de1c38f6..403f1b1229 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/ConnectionFunctions.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/ConnectionFunctions.java
@@ -101,8 +101,11 @@ public abstract class ConnectionFunctions {
break;
}
}
- String[] result = new String[lines.size()];
- lines.toArray(result);
+ String[] result = null;
+ if (lines.size() > 0) {
+ result = new String[lines.size()];
+ lines.toArray(result);
+ }
return result;
}
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/R/scan.R b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/R/scan.R
new file mode 100644
index 0000000000..620c6f3074
--- /dev/null
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/R/scan.R
@@ -0,0 +1,56 @@
+# File src/library/base/R/scan.R
+# Part of the R package, http://www.R-project.org
+#
+# Copyright (C) 1995-2014 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.
+#
+# A copy of the GNU General Public License is available at
+# http://www.r-project.org/Licenses/
+
+scan <-
+function(file = "", what = double(), nmax = -1L, n = -1L, sep = "",
+ quote = if(identical(sep, "\n")) "" else "'\"",
+ dec = ".", skip = 0L, nlines = 0L,
+ na.strings = "NA", flush = FALSE, fill = FALSE,
+ strip.white = FALSE, quiet = FALSE, blank.lines.skip = TRUE,
+ multi.line = TRUE, comment.char = "", allowEscapes = FALSE,
+ fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)
+{
+ na.strings <- as.character(na.strings)# allow it to be NULL
+ if(!missing(n)) {
+ if(missing(nmax))
+ nmax <- n / pmax(length(what), 1L)
+ else
+ stop("either specify 'nmax' or 'n', but not both.")
+ }
+ if (missing(file) && !missing(text)) {
+ file <- textConnection(text, encoding = "UTF-8")
+ encoding <- "UTF-8"
+ on.exit(close(file))
+ }
+
+ if(is.character(file))
+ if(file == "") file <- stdin()
+ else {
+ file <- if(nzchar(fileEncoding))
+ file(file, "r", encoding = fileEncoding) else file(file, "r")
+ # TODO: on.exit does not work properly (connection is currently closed in the internal implementation of scan)
+# on.exit(close(file))
+ }
+ # TODO: uncomment once RConnection is more faithful to how connections are implemented in GNU R
+# if(!inherits(file, "connection"))
+# stop("'file' must be a character string or connection")
+ .Internal(scan(file, what, nmax, sep, dec, quote, skip, nlines,
+ na.strings, flush, fill, strip.white, quiet,
+ blank.lines.skip, multi.line, comment.char,
+ allowEscapes, encoding, skipNul))
+}
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Scan.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Scan.java
new file mode 100644
index 0000000000..a95400fdf7
--- /dev/null
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Scan.java
@@ -0,0 +1,349 @@
+/*
+ * This material is distributed under the GNU General Public License
+ * Version 2. You may review the terms of this license at
+ * http://www.gnu.org/licenses/gpl-2.0.html
+ *
+ * Copyright (c) 1995, 1996, Robert Gentleman and Ross Ihaka
+ * Copyright (c) 1998-2013, The R Core Team
+ * Copyright (c) 2014, 2014, Oracle and/or its affiliates
+ *
+ * All rights reserved.
+ */
+
+package com.oracle.truffle.r.nodes.builtin.base;
+
+import static com.oracle.truffle.r.runtime.RBuiltinKind.*;
+
+import java.io.*;
+
+import com.oracle.truffle.api.*;
+import com.oracle.truffle.api.dsl.*;
+import com.oracle.truffle.api.frame.*;
+import com.oracle.truffle.r.nodes.*;
+import com.oracle.truffle.r.nodes.access.*;
+import com.oracle.truffle.r.nodes.builtin.*;
+import com.oracle.truffle.r.nodes.unary.*;
+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.ops.na.*;
+
+@SuppressWarnings("unused")
+@RBuiltin(name = "scan", kind = INTERNAL, parameterNames = {"file", "what", "nmax", "sep", "dec", "quote", "skip", "nlines", "na.strings", "flush", "fill", "strip.white", "quiet", "blank.lines.skip",
+ "multi.line", "comment.char", "allowEscapes", "encoding", "skipNull"})
+public abstract class Scan extends RBuiltinNode {
+
+ private static final int SCAN_BLOCKSIZE = 1000;
+ private static final int NO_COMCHAR = 100000; /* won't occur even in Unicode */
+
+ private final NACheck naCheck = new NACheck();
+
+ private static class LocalData {
+ RAbstractStringVector naStrings = null;
+ boolean quiet = false;
+ String sepchar = null;
+ char decchar = '.';
+ String quoteset = null;
+ int comchar = NO_COMCHAR;
+ // connection-related (currently not supported)
+ // int ttyflag = 0;
+ RConnection con = null;
+ // connection-related (currently not supported)
+ // boolean wasopen = false;
+ boolean escapes = false;
+ int save = 0;
+ boolean isLatin1 = false;
+ boolean isUTF8 = false;
+ boolean atStart = false;
+ boolean embedWarn = false;
+ boolean skipNull = false;
+ }
+
+ @CreateCast({"arguments"})
+ public RNode[] createCastValue(RNode[] children) {
+ RNode file = children[0];
+ RNode what = CastToVectorNodeFactory.create(children[1], false, false, false, false);
+ RNode nmax = CastToVectorNodeFactory.create(CastIntegerNodeFactory.create(children[2], false, false, false), false, false, false, false);
+ RNode sep = CastToVectorNodeFactory.create(children[3], false, false, false, false);
+ RNode dec = CastToVectorNodeFactory.create(children[4], false, false, false, false);
+ RNode quotes = CastToVectorNodeFactory.create(children[5], false, false, false, false);
+ RNode nskip = CastToVectorNodeFactory.create(CastIntegerNodeFactory.create(children[6], false, false, false), false, false, false, false);
+ RNode nlines = CastToVectorNodeFactory.create(CastIntegerNodeFactory.create(children[7], false, false, false), false, false, false, false);
+ RNode naStrings = CastToVectorNodeFactory.create(children[8], false, false, false, false);
+ RNode flush = CastToVectorNodeFactory.create(CastLogicalNodeFactory.create(children[9], false, false, false), false, false, false, false);
+ RNode fill = CastToVectorNodeFactory.create(CastLogicalNodeFactory.create(children[10], false, false, false), false, false, false, false);
+ RNode stripWhite = CastToVectorNodeFactory.create(children[11], false, false, false, false);
+ RNode quiet = CastToVectorNodeFactory.create(CastLogicalNodeFactory.create(children[12], false, false, false), false, false, false, false);
+ RNode blSkip = CastToVectorNodeFactory.create(CastLogicalNodeFactory.create(children[13], false, false, false), false, false, false, false);
+ RNode multiLine = CastToVectorNodeFactory.create(CastLogicalNodeFactory.create(children[14], false, false, false), false, false, false, false);
+ RNode commentChar = CastToVectorNodeFactory.create(children[15], false, false, false, false);
+ RNode allowEscapes = CastToVectorNodeFactory.create(CastLogicalNodeFactory.create(children[16], false, false, false), false, false, false, false);
+ RNode encoding = CastToVectorNodeFactory.create(children[17], false, false, false, false);
+ RNode skipNull = CastToVectorNodeFactory.create(CastLogicalNodeFactory.create(children[18], false, false, false), false, false, false, false);
+
+ return new RNode[]{file, what, nmax, sep, dec, quotes, nskip, nlines, naStrings, flush, fill, stripWhite, quiet, blSkip, multiLine, commentChar, allowEscapes, encoding, skipNull};
+ }
+
+ @Specialization
+ Object doScan(RConnection file, RAbstractVector what, RAbstractIntVector nmaxVec, RAbstractVector sepVec, RAbstractVector decVec, RAbstractVector quotesVec, RAbstractIntVector nskipVec,
+ RAbstractIntVector nlinesVec, RAbstractVector naStringsVec, RAbstractLogicalVector flushVec, RAbstractLogicalVector fillVec, RAbstractVector stripVec,
+ RAbstractLogicalVector dataQuietVec, RAbstractLogicalVector blSkipVec, RAbstractLogicalVector multiLineVec, RAbstractVector commentCharVec, RAbstractLogicalVector escapesVec,
+ RAbstractVector encodingVec, RAbstractLogicalVector skipNullVec) {
+
+ LocalData data = new LocalData();
+
+ int nmax = nmaxVec.getLength() == 0 ? RRuntime.INT_NA : nmaxVec.getDataAt(0);
+
+ if (sepVec.getLength() == 0) {
+ data.sepchar = null;
+ } else if (sepVec.getElementClass() != RString.class) {
+ throw RError.error(RError.Message.INVALID_ARGUMENT, "sep");
+ }
+ // TODO: some sort of character translation happens here?
+ String sep = ((RAbstractStringVector) sepVec).getDataAt(0);
+ if (sep.length() > 1) {
+ throw RError.error(RError.Message.MUST_BE_ONE_BYTE, "'sep' value");
+ }
+ data.sepchar = sep.length() == 0 ? null : sep.substring(0, 1);
+
+ if (decVec.getLength() == 0) {
+ data.decchar = '.';
+ } else if (decVec.getElementClass() != RString.class) {
+ throw RError.error(RError.Message.INVALID_DECIMAL_SEP);
+ }
+ // TODO: some sort of character translation happens here?
+ String dec = ((RAbstractStringVector) decVec).getDataAt(0);
+ if (dec.length() > 1) {
+ throw RError.error(RError.Message.MUST_BE_ONE_BYTE, "decimal separator");
+ }
+ data.decchar = dec.charAt(0);
+
+ if (quotesVec.getLength() == 0) {
+ data.quoteset = "";
+ } else if (quotesVec.getElementClass() != RString.class) {
+ throw RError.error(RError.Message.INVALID_QUOTE_SYMBOL);
+ }
+ // TODO: some sort of character translation happens here?
+ data.quoteset = ((RAbstractStringVector) quotesVec).getDataAt(0);
+
+ int nskip = nskipVec.getLength() == 0 ? RRuntime.INT_NA : nskipVec.getDataAt(0);
+
+ int nlines = nlinesVec.getLength() == 0 ? RRuntime.INT_NA : nlinesVec.getDataAt(0);
+
+ if (naStringsVec.getElementClass() != RString.class) {
+ throw RError.error(RError.Message.INVALID_ARGUMENT, "na.strings");
+ }
+ data.naStrings = (RAbstractStringVector) naStringsVec;
+
+ byte flush = flushVec.getLength() == 0 ? RRuntime.LOGICAL_NA : flushVec.getDataAt(0);
+
+ byte fill = fillVec.getLength() == 0 ? RRuntime.LOGICAL_NA : fillVec.getDataAt(0);
+
+ if (stripVec.getElementClass() != RLogical.class) {
+ throw RError.error(RError.Message.INVALID_ARGUMENT, "strip.white");
+ }
+ if (stripVec.getLength() != 1 && stripVec.getLength() != what.getLength()) {
+ throw RError.error(RError.Message.INVALID_LENGTH, "strip.white");
+ }
+ byte strip = ((RAbstractLogicalVector) stripVec).getDataAt(0);
+
+ data.quiet = dataQuietVec.getLength() == 0 || RRuntime.isNA(dataQuietVec.getDataAt(0)) ? false : dataQuietVec.getDataAt(0) == RRuntime.LOGICAL_TRUE;
+
+ byte blSkip = blSkipVec.getLength() == 0 ? RRuntime.LOGICAL_NA : blSkipVec.getDataAt(0);
+
+ byte multiLine = multiLineVec.getLength() == 0 ? RRuntime.LOGICAL_NA : multiLineVec.getDataAt(0);
+
+ if (commentCharVec.getElementClass() != RString.class || commentCharVec.getLength() != 1) {
+ throw RError.error(RError.Message.INVALID_ARGUMENT, "comment.char");
+ }
+ String commentChar = ((RAbstractStringVector) commentCharVec).getDataAt(0);
+ data.comchar = NO_COMCHAR;
+ if (commentChar.length() > 1) {
+ throw RError.error(RError.Message.INVALID_ARGUMENT, "comment.char");
+ } else if (commentChar.length() == 1) {
+ data.comchar = commentChar.charAt(0);
+ }
+
+ byte escapes = escapesVec.getLength() == 0 ? RRuntime.LOGICAL_NA : escapesVec.getDataAt(0);
+ if (RRuntime.isNA(escapes)) {
+ throw RError.error(RError.Message.INVALID_ARGUMENT, "allowEscapes");
+ }
+ data.escapes = escapes != RRuntime.LOGICAL_FALSE;
+
+ if (encodingVec.getElementClass() != RString.class || encodingVec.getLength() != 1) {
+ throw RError.error(RError.Message.INVALID_ARGUMENT, "encoding");
+ }
+ String encoding = ((RAbstractStringVector) encodingVec).getDataAt(0);
+ if (encoding.equals("latin1")) {
+ data.isLatin1 = true;
+ }
+ if (encoding.equals("UTF-8")) {
+ data.isUTF8 = true;
+ }
+
+ byte skipNull = skipNullVec.getLength() == 0 ? RRuntime.LOGICAL_NA : skipNullVec.getDataAt(0);
+ if (RRuntime.isNA(skipNull)) {
+ throw RError.error(RError.Message.INVALID_ARGUMENT, "skipNull");
+ }
+ data.skipNull = skipNull != RRuntime.LOGICAL_FALSE;
+
+ if (blSkip == RRuntime.LOGICAL_NA) {
+ blSkip = 1;
+ }
+ if (multiLine == RRuntime.LOGICAL_NA) {
+ multiLine = 1;
+ }
+ if (nskip < 0 || nskip == RRuntime.INT_NA) {
+ nskip = 0;
+ }
+ if (nlines < 0 || nlines == RRuntime.INT_NA) {
+ nlines = 0;
+ }
+ if (nmax < 0 || nmax == RRuntime.INT_NA) {
+ nmax = 0;
+ }
+
+ // TODO: quite a few more things happen in GNU R around connections
+ data.con = file;
+
+ Object result = RNull.instance;
+ data.save = 0;
+
+ try {
+ if (nskip > 0) {
+ data.con.readLines(nskip);
+ }
+ if (what.getElementClass() != Object.class) {
+ return scanVector(what, nmax, nlines, flush, strip, blSkip, data);
+ }
+
+ } catch (IOException x) {
+ throw RError.error(RError.Message.CANNOT_READ_CONNECTION);
+ } finally {
+ try {
+ data.con.close();
+ } catch (IOException ex) {
+ }
+ }
+
+ return result;
+ }
+
+ private RVector scanVector(RAbstractVector what, int maxItems, int maxLines, int flush, byte stripWhite, int blSkip, LocalData data) throws IOException {
+ int blockSize = maxItems > 0 ? maxItems : SCAN_BLOCKSIZE;
+ RVector vec = what.createEmptySameType(blockSize, RDataFactory.COMPLETE_VECTOR);
+ naCheck.enable(true);
+
+ int n = 0;
+ int lines = 0;
+ while (true) {
+ // TODO: does not do any fancy stuff, like handling comments
+ String[] str = data.con.readLines(1);
+ if (str == null || str.length == 0) {
+ break;
+ }
+ String[] strItems = data.sepchar == null ? str[0].trim().split("\\s+") : str[0].trim().split(data.sepchar);
+
+ boolean done = false;
+ for (int i = 0; i < strItems.length; i++) {
+
+ Object item = extractItem(what, strItems[i], data);
+
+ if (n == blockSize) {
+ // enlarge the vector
+ blockSize = blockSize * 2;
+ vec.copyResized(blockSize, false);
+ }
+
+ vec.updateDataAtAsObject(n, item, naCheck);
+ n++;
+ if (n == maxItems) {
+ done = true;
+ break;
+ }
+ }
+ if (done) {
+ break;
+ }
+ lines++;
+ if (lines == maxLines) {
+ break;
+ }
+
+ }
+ if (!data.quiet) {
+ RContext.getInstance().getConsoleHandler().printf("Read %d item%s\n", n, (n == 1) ? "" : "s");
+ }
+ // trim vector if necessary
+ return vec.getLength() > n ? vec.copyResized(n, false) : vec;
+ }
+
+ // If mode = 0 use for numeric fields where "" is NA
+ // If mode = 1 use for character fields where "" is verbatim unless
+ // na.strings includes ""
+ private static boolean isNaString(String buffer, int mode, LocalData data) {
+ int i;
+
+ if (mode == 0 && buffer.length() == 0) {
+ return true;
+ }
+ for (i = 0; i < data.naStrings.getLength(); i++) {
+ if (data.naStrings.getDataAt(i).equals(buffer)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private static Object extractItem(RAbstractVector what, String buffer, LocalData data) {
+ if (what.getElementClass() == RLogical.class) {
+ if (isNaString(buffer, 0, data)) {
+ return RRuntime.LOGICAL_NA;
+ } else {
+ return RRuntime.string2logicalNoCheck(buffer);
+ }
+ }
+ if (what.getElementClass() == RInt.class) {
+ if (isNaString(buffer, 0, data)) {
+ return RRuntime.INT_NA;
+ } else {
+ return RRuntime.string2intNoCheck(buffer);
+ }
+ }
+
+ if (what.getElementClass() == RDouble.class) {
+ if (isNaString(buffer, 0, data)) {
+ return RRuntime.DOUBLE_NA;
+ } else {
+ return RRuntime.string2doubleNoCheck(buffer);
+ }
+ }
+
+ if (what.getElementClass() == RComplex.class) {
+ if (isNaString(buffer, 0, data)) {
+ return RRuntime.createComplexNA();
+ } else {
+ return RRuntime.string2complexNoCheck(buffer);
+ }
+ }
+
+ if (what.getElementClass() == RString.class) {
+ if (isNaString(buffer, 0, data)) {
+ return RRuntime.STRING_NA;
+ } else {
+ return buffer;
+ }
+ }
+
+ if (what.getElementClass() == RRaw.class) {
+ if (isNaString(buffer, 0, data)) {
+ return RDataFactory.createRaw((byte) 0);
+ } else {
+ return RRuntime.string2raw(buffer);
+ }
+ }
+
+ throw RInternalError.shouldNotReachHere();
+ }
+
+}
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java
index e73169627c..cc1ecf32a1 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java
@@ -271,6 +271,7 @@ public final class RError extends RuntimeException {
INCORRECT_SUBSCRIPTS("incorrect number of subscripts"),
INCORRECT_SUBSCRIPTS_MATRIX("incorrect number of subscripts on matrix"),
INVALID_SEP("invalid 'sep' specification"),
+ INVALID_LENGTH("invalid '%s' length"),
// below: GNU R gives also expression for the argument
NOT_FUNCTION("argument is not a function, character or symbol"),
NON_NUMERIC_MATH("non-numeric argument to mathematical function"),
@@ -459,6 +460,9 @@ public final class RError extends RuntimeException {
INCORRECT_NUM_PROB("incorrect number of probabilities"),
NA_IN_PROB_VECTOR("NA in probability vector"),
NEGATIVE_PROBABILITY("non-positive probability"),
+ MUST_BE_ONE_BYTE("invalid %s: must be one byte"),
+ INVALID_DECIMAL_SEP("invalid decimal separator"),
+ INVALID_QUOTE_SYMBOL("invalid quote symbol set"),
// below: not exactly GNU-R message
TOO_FEW_POSITIVE_PROBABILITY("too few positive probabilities"),
DOTS_BOUNDS("The ... list does not contain %s elements"),
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RRuntime.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RRuntime.java
index 76099c23be..7ce57708a2 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RRuntime.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RRuntime.java
@@ -374,6 +374,15 @@ public class RRuntime {
return isNA(v) ? createComplexNA() : string2complexNoCheck(v);
}
+ @SlowPath
+ public static RRaw string2raw(String v) {
+ if (v.length() == 2 && (Utils.isIsoLatinDigit(v.charAt(0)) || Utils.isRomanLetter(v.charAt(0))) && (Utils.isIsoLatinDigit(v.charAt(1)) || Utils.isRomanLetter(v.charAt(1)))) {
+ return RDataFactory.createRaw(Byte.parseByte(v, 16));
+ } else {
+ return RDataFactory.createRaw((byte) 0);
+ }
+ }
+
// conversions from int
public static double int2doubleNoCheck(int i) {
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/Utils.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/Utils.java
index 62ea5d8599..afc0941bdd 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/Utils.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/Utils.java
@@ -68,6 +68,10 @@ public final class Utils {
return c >= '\u0030' && c <= '\u0039';
}
+ public static boolean isRomanLetter(char c) {
+ return (/* lower case */c >= '\u00DF' && c <= '\u00FF') || (/* upper case */c >= '\u00C0' && c <= '\u00DE');
+ }
+
public static int incMod(int value, int mod) {
int result = (value + 1);
if (result == mod) {
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RComplexVector.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RComplexVector.java
index 03cf4b7ea3..201a6d22dd 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RComplexVector.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RComplexVector.java
@@ -138,6 +138,12 @@ public final class RComplexVector extends RVector implements RAbstractComplexVec
return this;
}
+ @Override
+ public RComplexVector updateDataAtAsObject(int i, Object o, NACheck naCheck) {
+ return updateDataAt(i, (RComplex) o, naCheck);
+
+ }
+
private double[] copyResizedData(int size, boolean fillNA) {
int csize = size << 1;
double[] newData = Arrays.copyOf(data, csize);
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RDoubleSequence.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RDoubleSequence.java
index 7a277630d2..0d60e8f005 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RDoubleSequence.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RDoubleSequence.java
@@ -102,10 +102,15 @@ public final class RDoubleSequence extends RSequence implements RAbstractDoubleV
}
@Override
- public RAbstractVector copyResized(int size, boolean fillNA) {
+ public RDoubleVector copyResized(int size, boolean fillNA) {
double[] data = new double[size];
populateVectorData(data);
RDoubleVector.resizeData(data, data, getLength(), fillNA);
return RDataFactory.createDoubleVector(data, !(fillNA && size > getLength()));
}
+
+ @Override
+ public RDoubleVector createEmptySameType(int newLength, boolean newIsComplete) {
+ return RDataFactory.createDoubleVector(new double[newLength], newIsComplete);
+ }
}
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RDoubleVector.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RDoubleVector.java
index d45c31d5f1..a158953cc6 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RDoubleVector.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RDoubleVector.java
@@ -168,6 +168,12 @@ public final class RDoubleVector extends RVector implements RAbstractDoubleVecto
return this;
}
+ @Override
+ public RDoubleVector updateDataAtAsObject(int i, Object o, NACheck naCheck) {
+ return updateDataAt(i, (Double) o, naCheck);
+
+ }
+
public static double[] resizeData(double[] newData, double[] oldData, int oldDataLength, boolean fillNA) {
if (newData.length > oldDataLength) {
if (fillNA) {
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RIntSequence.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RIntSequence.java
index cfe868729c..8f6f1a89d4 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RIntSequence.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RIntSequence.java
@@ -103,10 +103,16 @@ public final class RIntSequence extends RSequence implements RAbstractIntVector
}
@Override
- public RAbstractVector copyResized(int size, boolean fillNA) {
+ public RIntVector copyResized(int size, boolean fillNA) {
int[] data = new int[size];
populateVectorData(data);
RIntVector.resizeData(data, data, getLength(), fillNA);
return RDataFactory.createIntVector(data, !(fillNA && size > getLength()));
}
+
+ @Override
+ public RIntVector createEmptySameType(int newLength, boolean newIsComplete) {
+ return RDataFactory.createIntVector(new int[newLength], newIsComplete);
+ }
+
}
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RIntVector.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RIntVector.java
index e1544b49fc..97452f3784 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RIntVector.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RIntVector.java
@@ -156,6 +156,12 @@ public final class RIntVector extends RVector implements RAbstractIntVector {
return this;
}
+ @Override
+ public RIntVector updateDataAtAsObject(int i, Object o, NACheck naCheck) {
+ return updateDataAt(i, (Integer) o, naCheck);
+
+ }
+
public static int[] resizeData(int[] newData, int[] oldData, int oldDataLength, boolean fillNA) {
if (newData.length > oldDataLength) {
if (fillNA) {
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RList.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RList.java
index c1c9a527c8..429d229b60 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RList.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RList.java
@@ -135,6 +135,12 @@ public final class RList extends RVector implements RAbstractVector {
return this;
}
+ @Override
+ public RList updateDataAtAsObject(int i, Object o, NACheck naCheck) {
+ return updateDataAt(i, o, naCheck);
+
+ }
+
@Override
public RList createEmptySameType(int newLength, boolean newIsComplete) {
return RDataFactory.createList(new Object[newLength]);
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RLogicalVector.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RLogicalVector.java
index 4f02a17937..afb3cfb544 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RLogicalVector.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RLogicalVector.java
@@ -103,6 +103,12 @@ public final class RLogicalVector extends RVector implements RAbstractLogicalVec
return this;
}
+ @Override
+ public RLogicalVector updateDataAtAsObject(int i, Object o, NACheck naCheck) {
+ return updateDataAt(i, (Byte) o, naCheck);
+
+ }
+
private byte[] copyResizedData(int size, boolean fillNA) {
byte[] newData = Arrays.copyOf(data, size);
if (size > this.getLength()) {
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RRawVector.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RRawVector.java
index 1e5a1a8430..627023dc61 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RRawVector.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RRawVector.java
@@ -27,6 +27,7 @@ import java.util.*;
import com.oracle.truffle.api.CompilerDirectives.SlowPath;
import com.oracle.truffle.r.runtime.*;
import com.oracle.truffle.r.runtime.data.model.*;
+import com.oracle.truffle.r.runtime.ops.na.*;
public final class RRawVector extends RVector implements RAbstractRawVector {
@@ -132,6 +133,11 @@ public final class RRawVector extends RVector implements RAbstractRawVector {
return this;
}
+ @Override
+ public RRawVector updateDataAtAsObject(int i, Object o, NACheck naCheck) {
+ return updateDataAt(i, (RRaw) o);
+ }
+
private byte[] copyResizedData(int size, boolean fillNA) {
byte[] newData = Arrays.copyOf(data, size);
if (!fillNA) {
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RStringVector.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RStringVector.java
index a2c2aa510a..4f77350ae2 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RStringVector.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RStringVector.java
@@ -118,6 +118,12 @@ public final class RStringVector extends RVector implements RAbstractStringVecto
return this;
}
+ @Override
+ public RStringVector updateDataAtAsObject(int i, Object o, NACheck naCheck) {
+ return updateDataAt(i, (String) o, naCheck);
+
+ }
+
private String[] copyResizedData(int size, String fill) {
String[] newData = Arrays.copyOf(data, size);
if (size > this.getLength()) {
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RVector.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RVector.java
index 56cf5dc211..b68bef7daf 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RVector.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/RVector.java
@@ -29,6 +29,7 @@ import com.oracle.truffle.api.source.*;
import com.oracle.truffle.r.runtime.*;
import com.oracle.truffle.r.runtime.data.RAttributes.RAttribute;
import com.oracle.truffle.r.runtime.data.model.*;
+import com.oracle.truffle.r.runtime.ops.na.*;
import edu.umd.cs.findbugs.annotations.*;
@@ -461,6 +462,17 @@ public abstract class RVector extends RBounded implements RShareable, RAbstractV
protected abstract boolean internalVerify();
+ /**
+ * Update a data item in the vector. Possibly not as efficient as type-specific methods, but in
+ * some cases it likely does not matter (e.g. if used alongside I/O operations).
+ *
+ * @param i index of the vector item to be updated
+ * @param o updated value
+ * @param naCheck NA check used to change vector's mode in case value is NA
+ * @return updated vector
+ */
+ public abstract RVector updateDataAtAsObject(int i, Object o, NACheck naCheck);
+
public final RStringVector toStringVector() {
String[] values = new String[getLength()];
for (int i = 0; i < getLength(); ++i) {
@@ -469,8 +481,6 @@ public abstract class RVector extends RBounded implements RShareable, RAbstractV
return RDataFactory.createStringVector(values, this.isComplete());
}
- public abstract RVector createEmptySameType(int newLength, boolean newIsComplete);
-
public abstract void transferElementSameType(int toIndex, RVector fromVector, int fromIndex);
public final boolean isInBounds(int firstPosition, int secondPosition) {
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/closures/RToVectorClosure.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/closures/RToVectorClosure.java
index 6449f86ce8..dc6c4cae6e 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/closures/RToVectorClosure.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/closures/RToVectorClosure.java
@@ -86,7 +86,7 @@ public abstract class RToVectorClosure implements RAbstractVector {
}
@Override
- public RAbstractVector copyResized(int size, boolean fillNA) {
+ public RVector copyResized(int size, boolean fillNA) {
return vector.copyResized(size, fillNA);
}
@@ -121,4 +121,9 @@ public abstract class RToVectorClosure implements RAbstractVector {
return vector.materialize();
}
+ @Override
+ public RVector createEmptySameType(int newLength, boolean newIsComplete) {
+ return vector.createEmptySameType(newLength, newIsComplete);
+ }
+
}
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/model/RAbstractVector.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/model/RAbstractVector.java
index 262357a893..8b3f6a798e 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/model/RAbstractVector.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/data/model/RAbstractVector.java
@@ -41,12 +41,14 @@ public interface RAbstractVector extends RAbstractContainer {
*/
RAbstractVector copy();
- RAbstractVector copyResized(int size, boolean fillNA);
+ RVector copyResized(int size, boolean fillNA);
RAbstractVector copyWithNewDimensions(int[] newDimensions);
RAbstractVector copyDropAttributes();
+ RVector createEmptySameType(int newLength, boolean newIsComplete);
+
/**
* May throw errors, so needs a {@link VirtualFrame}.
*/
diff --git a/mx.fastr/copyrights/gnu_r_scan.copyright.star b/mx.fastr/copyrights/gnu_r_scan.copyright.star
new file mode 100644
index 0000000000..0a1b1ef591
--- /dev/null
+++ b/mx.fastr/copyrights/gnu_r_scan.copyright.star
@@ -0,0 +1,11 @@
+/*
+ * This material is distributed under the GNU General Public License
+ * Version 2. You may review the terms of this license at
+ * http://www.gnu.org/licenses/gpl-2.0.html
+ *
+ * Copyright (c) 1995, 1996, Robert Gentleman and Ross Ihaka
+ * Copyright (c) 1998-2013, The R Core Team
+ * Copyright (c) 2014, 2014, Oracle and/or its affiliates
+ *
+ * All rights reserved.
+ */
diff --git a/mx.fastr/copyrights/gnu_r_scan.copyright.star.regex b/mx.fastr/copyrights/gnu_r_scan.copyright.star.regex
new file mode 100644
index 0000000000..249eb964ce
--- /dev/null
+++ b/mx.fastr/copyrights/gnu_r_scan.copyright.star.regex
@@ -0,0 +1 @@
+/\*\n \* This material is distributed under the GNU General Public License\n \* Version 2. You may review the terms of this license at\n \* http://www.gnu.org/licenses/gpl-2.0.html\n \*\n \* Copyright \(c\) 1995, 1996, Robert Gentleman and Ross Ihaka\n \* Copyright \(c\) 1997-2013, The R Core Team\n \* Copyright \(c\) (?:(20[0-9][0-9]), )?(20[0-9][0-9]), Oracle and/or its affiliates\n \*\n \* All rights reserved.\n \*/\n.*
diff --git a/mx.fastr/copyrights/overrides b/mx.fastr/copyrights/overrides
index 2fc370c18b..a6fb6a219b 100644
--- a/mx.fastr/copyrights/overrides
+++ b/mx.fastr/copyrights/overrides
@@ -53,6 +53,7 @@ com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/R
com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/RowMeans.java,purdue.copyright
com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/RowSums.java,purdue.copyright
com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Sample.java,gnu_r_sample.copyright
+com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Scan.java,gnu_r_scan.copyright
com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Tabulate.java,purdue.copyright
com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/UnClass.java,purdue.copyright
com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/Unlist.java,gnu_r.copyright
--
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