diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSerialize.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSerialize.java
index 494ff5bb7be0fc08e88a548a7c7c152aaa1720e9..63106513cecf09e4b94c58d17505a8ed7a0844e3 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSerialize.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSerialize.java
@@ -53,7 +53,6 @@ import com.oracle.truffle.r.runtime.data.REmpty;
import com.oracle.truffle.r.runtime.data.RExpression;
import com.oracle.truffle.r.runtime.data.RExternalPtr;
import com.oracle.truffle.r.runtime.data.RFunction;
-import com.oracle.truffle.r.runtime.data.RIntVector;
import com.oracle.truffle.r.runtime.data.RLanguage;
import com.oracle.truffle.r.runtime.data.RList;
import com.oracle.truffle.r.runtime.data.RMissing;
@@ -84,7 +83,6 @@ import com.oracle.truffle.r.runtime.env.frame.FrameSlotChangeMonitor;
import com.oracle.truffle.r.runtime.ffi.DLL;
import com.oracle.truffle.r.runtime.gnur.SEXPTYPE;
import com.oracle.truffle.r.runtime.nodes.RCodeBuilder;
-import com.oracle.truffle.r.runtime.nodes.RSourceSectionNode;
import com.oracle.truffle.r.runtime.nodes.RSyntaxCall;
import com.oracle.truffle.r.runtime.nodes.RSyntaxConstant;
import com.oracle.truffle.r.runtime.nodes.RSyntaxElement;
@@ -1435,7 +1433,6 @@ public class RSerialize {
} else if (type == SEXPTYPE.SYMSXP) {
writeSymbol((RSymbol) obj);
} else {
- SourceSection sourceSection = getSourceSection(obj);
if (type == SEXPTYPE.ENVSXP) {
REnvironment env = (REnvironment) obj;
addReadRef(obj);
@@ -1466,27 +1463,20 @@ public class RSerialize {
}
terminatePairList();
writeItem(RNull.instance); // hashtab
- DynamicObject attributes = env.getAttributes();
- writeAttributes(attributes, sourceSection);
- if (attributes == null && sourceSection == null) {
+ OutAttributes attributes = new OutAttributes(env, type);
+ if (attributes.hasAttributes()) {
+ writeAttributes(attributes);
+ } else {
writeItem(RNull.instance);
}
}
} else {
// flags
- DynamicObject attributes = null;
- SourceSection ss = sourceSection;
- if (obj instanceof RAttributable) {
- RAttributable rattr = (RAttributable) obj;
- attributes = rattr.getAttributes();
- if (attributes != null && attributes.isEmpty()) {
- attributes = null;
- }
- }
+ OutAttributes attributes = new OutAttributes(obj, type);
boolean hasTag = gnuRType == SEXPTYPE.CLOSXP || gnuRType == SEXPTYPE.DOTSXP || (gnuRType == SEXPTYPE.PROMSXP && !((RPromise) obj).isEvaluated()) ||
(type == SEXPTYPE.LISTSXP && !((RPairList) obj).isNullTag());
int gpbits = getGPBits(obj);
- int flags = Flags.packFlags(gnuRType, gpbits, isObject(obj), attributes != null, hasTag);
+ int flags = Flags.packFlags(gnuRType, gpbits, isObject(obj), attributes.hasAttributes(), hasTag);
stream.writeInt(flags);
switch (type) {
case STRSXP: {
@@ -1613,21 +1603,13 @@ public class RSerialize {
stream.writeString(name);
break;
}
- if (type == SEXPTYPE.FUNSXP) {
- RFunction fun = (RFunction) obj;
- RSyntaxFunction body = (RSyntaxFunction) fun.getRootNode();
- ss = body.getLazySourceSection();
- }
tailCall = true;
// attributes written first to avoid recursion on cdr
- writeAttributes(attributes, ss);
+ writeAttributes(attributes);
if (attributes != null) {
attributes = null;
}
- if (ss != null) {
- ss = null;
- }
switch (type) {
case FUNSXP: {
@@ -1698,19 +1680,12 @@ public class RSerialize {
throw RInternalError.unimplemented(type.name());
}
- writeAttributes(attributes, ss);
+ writeAttributes(attributes);
}
}
} while (tailCall);
}
- private static SourceSection getSourceSection(Object obj) {
- if (obj instanceof RSourceSectionNode) {
- return ((RSourceSectionNode) obj).getLazySourceSection();
- }
- return null;
- }
-
private static Object getValueIgnoreActiveBinding(Frame frame, String key) {
FrameDescriptor fd = frame.getFrameDescriptor();
FrameSlot slot = fd.findFrameSlot(key);
@@ -1780,27 +1755,31 @@ public class RSerialize {
}
}
- private void writeAttributes(DynamicObject attributes, SourceSection ss) throws IOException {
- if (ss != null && ss != RSyntaxNode.LAZY_DEPARSE) {
- String path = ss.getSource().getURI().getPath();
- REnvironment createSrcfile = RSrcref.createSrcfile(path);
- Object createLloc = RSrcref.createLloc(ss);
- writePairListEntry(RRuntime.R_SRCREF, createLloc);
- writePairListEntry(RRuntime.R_SRCFILE, createSrcfile);
- }
- if (attributes != null) {
- // have to convert to GnuR pairlist
- Iterator<RAttributesLayout.RAttribute> iter = RAttributesLayout.asIterable(attributes).iterator();
- while (iter.hasNext()) {
- RAttributesLayout.RAttribute attr = iter.next();
- // name is the tag of the virtual pairlist
- // value is the car
- // next is the cdr
- writePairListEntry(attr.getName(), attr.getValue());
+ private void writeAttributes(OutAttributes outAttrs) throws IOException {
+ if (outAttrs != null) {
+ SourceSection ss = outAttrs.getSourceReferenceAttributes();
+ if (ss != null) {
+ String path = ss.getSource().getURI().getPath();
+ REnvironment createSrcfile = RSrcref.createSrcfile(path);
+ Object createLloc = RSrcref.createLloc(ss, createSrcfile);
+ writePairListEntry(RRuntime.R_SRCREF, createLloc);
+ writePairListEntry(RRuntime.R_SRCFILE, createSrcfile);
+ }
+ DynamicObject attributes = outAttrs.getExplicitAttributes();
+ if (attributes != null) {
+ // have to convert to GnuR pairlist
+ Iterator<RAttributesLayout.RAttribute> iter = RAttributesLayout.asIterable(attributes).iterator();
+ while (iter.hasNext()) {
+ RAttributesLayout.RAttribute attr = iter.next();
+ // name is the tag of the virtual pairlist
+ // value is the car
+ // next is the cdr
+ writePairListEntry(attr.getName(), attr.getValue());
+ }
+ }
+ if (outAttrs.hasAttributes()) {
+ terminatePairList();
}
- }
- if (attributes != null || ss != null && ss != RSyntaxNode.LAZY_DEPARSE) {
- terminatePairList();
}
}
@@ -2108,6 +2087,52 @@ public class RSerialize {
}
}
+ /**
+ * An abstraction of implicit and explicit attributes to serialize.
+ */
+ private static class OutAttributes {
+ private DynamicObject explicitAttributes;
+ private SourceSection ss;
+
+ OutAttributes(RAttributable obj, SEXPTYPE type) {
+
+ explicitAttributes = obj.getAttributes();
+ initSourceSection(obj, type);
+ }
+
+ OutAttributes(Object obj, SEXPTYPE type) {
+
+ if (obj instanceof RAttributable) {
+ explicitAttributes = ((RAttributable) obj).getAttributes();
+ }
+ initSourceSection(obj, type);
+ }
+
+ private void initSourceSection(Object obj, SEXPTYPE type) {
+ if (type == SEXPTYPE.FUNSXP) {
+ RFunction fun = (RFunction) obj;
+ RSyntaxFunction body = (RSyntaxFunction) fun.getRootNode();
+ SourceSection lazySourceSection = body.getLazySourceSection();
+ if (lazySourceSection != RSyntaxNode.LAZY_DEPARSE) {
+ ss = lazySourceSection;
+ }
+ }
+ }
+
+ public boolean hasAttributes() {
+ return explicitAttributes != null && !explicitAttributes.isEmpty() || ss != null && ss != RSyntaxNode.LAZY_DEPARSE;
+ }
+
+ public DynamicObject getExplicitAttributes() {
+ return explicitAttributes;
+ }
+
+ public SourceSection getSourceReferenceAttributes() {
+ return ss;
+ }
+
+ }
+
/**
* For {@code lazyLoadDBinsertValue}.
*/
@@ -2418,21 +2443,6 @@ public class RSerialize {
return state.closePairList();
}
- private static Object extractFromList(Object tag, SEXPTYPE expectedType) {
- SEXPTYPE type = SEXPTYPE.typeForClass(tag.getClass());
- if (type == expectedType) {
- return tag;
- } else if (type == SEXPTYPE.LISTSXP) {
- for (RPairList item : (RPairList) tag) {
- Object data = item.car();
- if (SEXPTYPE.typeForClass(data.getClass()) == expectedType) {
- return data;
- }
- }
- }
- return null;
- }
-
/**
* A collection of static functions that will transform a pairlist into an AST using the
* {@link RCodeBuilder}.
@@ -2585,7 +2595,8 @@ public class RSerialize {
} else {
Object srcref = func.getAttr(RRuntime.R_SRCREF);
if (srcref instanceof RAbstractIntVector) {
- handleSrcrefAttr((RAbstractIntVector) srcref, null, elem);
+ SourceSection ss = RSrcref.createSourceSection((RAbstractIntVector) srcref, null);
+ elem.setSourceSection(ss);
}
}
}
@@ -2597,12 +2608,13 @@ public class RSerialize {
private static void handleSrcrefAttr(RAttributable func, RSyntaxCall elem) {
Object srcref = func.getAttr(RRuntime.R_SRCREF);
if (srcref instanceof RAbstractIntVector) {
- handleSrcrefAttr((RAbstractIntVector) srcref, null, elem);
+ SourceSection ss = RSrcref.createSourceSection((RAbstractIntVector) srcref, null);
+ elem.setSourceSection(ss);
} else if (srcref instanceof RList) {
try {
Object srcfile = func.getAttr(RRuntime.R_SRCFILE);
assert srcfile instanceof REnvironment;
- Source source = RSource.fromFile((REnvironment) srcfile);
+ Source source = RSource.fromSrcfile((REnvironment) srcfile);
RList l = (RList) srcref;
RSyntaxElement[] syntaxArguments = elem.getSyntaxArguments();
@@ -2611,10 +2623,11 @@ public class RSerialize {
for (int i = 0; i < l.getLength(); i++) {
Object dataAt = l.getDataAt(i);
assert dataAt instanceof RAbstractIntVector;
+ SourceSection ss = RSrcref.createSourceSection((RAbstractIntVector) dataAt, source);
if (i == 0) {
- handleSrcrefAttr((RAbstractIntVector) dataAt, source, elem);
+ elem.setSourceSection(ss);
} else {
- handleSrcrefAttr((RAbstractIntVector) dataAt, source, syntaxArguments[i - 1]);
+ syntaxArguments[i - 1].setSourceSection(ss);
}
}
} catch (NoSuchFileException e) {
@@ -2624,30 +2637,4 @@ public class RSerialize {
}
}
}
-
- private static void handleSrcrefAttr(RAbstractIntVector srcrefVec, Source sharedSource, RSyntaxElement elem) {
-
- try {
- Source source;
- if (sharedSource != null) {
- source = sharedSource;
- } else {
- Object srcfile = srcrefVec.getAttr(RRuntime.R_SRCFILE);
- assert srcfile instanceof REnvironment;
- source = RSource.fromFile((REnvironment) srcfile);
- }
- int startLine = srcrefVec.getDataAt(0);
- int startColumn = srcrefVec.getDataAt(1);
- int startIdx = source.getLineStartOffset(startLine) + startColumn;
- int length = source.getLineStartOffset(srcrefVec.getDataAt(2)) + srcrefVec.getDataAt(3) - startIdx;
- SourceSection createSection = source.createSection(startLine, startColumn, length);
- elem.setSourceSection(createSection);
- } catch (NoSuchFileException e) {
- RError.warning(RError.SHOW_CALLER, RError.Message.GENERIC, "Missing source file: " + e.getMessage());
- } catch (IOException e) {
- RError.warning(RError.SHOW_CALLER, RError.Message.GENERIC, "Cannot access source file: " + e.getMessage());
- } catch (IllegalArgumentException e) {
- RError.warning(RError.SHOW_CALLER, RError.Message.GENERIC, "Invalid source reference: " + e.getMessage());
- }
- }
}
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSource.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSource.java
index c345c3e30c078a6c9414a8adf556066f1290c62b..e4bdde9ff45ac1d7c3b801028d1081d55d32fcf8 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSource.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSource.java
@@ -27,6 +27,8 @@ import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
+import java.nio.file.Path;
+import java.nio.file.Paths;
import com.oracle.truffle.api.source.Source;
import com.oracle.truffle.api.source.SourceSection;
@@ -192,9 +194,13 @@ public class RSource {
/**
* Create an (external) source from an R srcfile ({@link RSrcref#createSrcfile(String)}).
*/
- public static Source fromFile(REnvironment env) throws IOException {
- String path = (String) RRuntime.r2Java(env.get(SrcrefFields.filename.name()));
- return fromFileName(path, false);
+ public static Source fromSrcfile(REnvironment env) throws IOException {
+ Path filename = Paths.get((String) RRuntime.r2Java(env.get(SrcrefFields.filename.name())));
+ if (filename.isAbsolute()) {
+ return fromFileName(filename.toString(), false);
+ }
+ Path wd = Paths.get((String) RRuntime.r2Java(env.get(SrcrefFields.wd.name())));
+ return fromFileName(wd.resolve(filename).toString(), false);
}
/**
@@ -231,6 +237,18 @@ public class RSource {
return uri.getPath();
}
+ /**
+ * Like {@link #getPath(Source)} but ignoring if {@code source} is "internal".
+ */
+ public static String getPathInternal(Source source) {
+ if (source == null) {
+ return null;
+ }
+ URI uri = source.getURI();
+ assert uri != null;
+ return uri.getPath();
+ }
+
/**
* Always returns a non-null string even for internal sources.
*/
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSrcref.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSrcref.java
index d2a27b63774482b121dc835c85c905c982377e17..247bf965ada4be08ff17f8125e9bf8941f99bbec 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSrcref.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RSrcref.java
@@ -14,7 +14,9 @@ package com.oracle.truffle.r.runtime;
import java.io.IOException;
import java.nio.file.FileSystems;
import java.nio.file.Files;
+import java.nio.file.NoSuchFileException;
import java.nio.file.Path;
+import java.nio.file.Paths;
import java.nio.file.attribute.PosixFileAttributes;
import com.oracle.truffle.api.CompilerDirectives.TruffleBoundary;
@@ -25,9 +27,11 @@ import com.oracle.truffle.r.runtime.data.RDataFactory;
import com.oracle.truffle.r.runtime.data.RIntVector;
import com.oracle.truffle.r.runtime.data.RNull;
import com.oracle.truffle.r.runtime.data.RStringVector;
+import com.oracle.truffle.r.runtime.data.model.RAbstractIntVector;
import com.oracle.truffle.r.runtime.env.REnvironment;
import com.oracle.truffle.r.runtime.env.REnvironment.PutException;
import com.oracle.truffle.r.runtime.ffi.BaseRFFI;
+import com.oracle.truffle.r.runtime.nodes.RSourceSectionNode;
import com.oracle.truffle.r.runtime.nodes.RSyntaxNode;
/**
@@ -50,7 +54,9 @@ public class RSrcref {
timestamp,
filename,
isFile,
- wd;
+ wd,
+ fixedNewlines,
+ lines;
}
private static final RStringVector SRCREF_ATTR = RDataFactory.createStringVectorFromScalar(RRuntime.R_SRCREF);
@@ -66,17 +72,10 @@ public class RSrcref {
@TruffleBoundary
private static REnvironment createSrcfile(Path path) {
// A srcref is an environment
- double mtime;
- try {
- PosixFileAttributes pfa = Files.readAttributes(path, PosixFileAttributes.class);
- mtime = pfa.lastModifiedTime().toMillis();
- } catch (IOException ex) {
- mtime = RRuntime.DOUBLE_NA;
- }
REnvironment env = RDataFactory.createNewEnv("");
env.safePut(SrcrefFields.Enc.name(), "unknown");
env.safePut(SrcrefFields.encoding.name(), "native.enc");
- env.safePut(SrcrefFields.timestamp.name(), mtime);
+ env.safePut(SrcrefFields.timestamp.name(), getTimestamp(path));
env.safePut(SrcrefFields.filename.name(), path.toString());
env.safePut(SrcrefFields.isFile.name(), RRuntime.LOGICAL_TRUE);
env.safePut(SrcrefFields.wd.name(), BaseRFFI.GetwdRootNode.create().getCallTarget().call());
@@ -84,6 +83,17 @@ public class RSrcref {
return env;
}
+ private static double getTimestamp(Path path) {
+ double mtime;
+ try {
+ PosixFileAttributes pfa = Files.readAttributes(path, PosixFileAttributes.class);
+ mtime = pfa.lastModifiedTime().toMillis();
+ } catch (IOException ex) {
+ mtime = RRuntime.DOUBLE_NA;
+ }
+ return mtime;
+ }
+
/**
* Creates an {@code lloc} structure from a {@link SourceSection} and associated {@code srcfile}
* . assert: srcfile was created from the {@link Source} associated with {@code ss} or is
@@ -107,13 +117,18 @@ public class RSrcref {
env = RDataFactory.createNewEnv("src");
env.setClassAttr(RDataFactory.createStringVector(new String[]{"srcfilecopy", RRuntime.R_SRCFILE}, true));
try {
- env.put("filename", source.getPath() == null ? "" : source.getPath());
- env.put("fixedNewlines", RRuntime.LOGICAL_TRUE);
+ Path path = Paths.get(RSource.getPathInternal(source));
+ env.put(SrcrefFields.filename.name(), path.toString());
+ env.put(SrcrefFields.fixedNewlines.name(), RRuntime.LOGICAL_TRUE);
String[] lines = new String[source.getLineCount()];
for (int i = 0; i < lines.length; i++) {
lines[i] = source.getCode(i + 1);
}
- env.put("lines", RDataFactory.createStringVector(lines, true));
+ env.put(SrcrefFields.lines.name(), RDataFactory.createStringVector(lines, true));
+ env.safePut(SrcrefFields.Enc.name(), "unknown");
+ env.safePut(SrcrefFields.isFile.name(), RRuntime.asLogical(Files.isRegularFile(path)));
+ env.safePut(SrcrefFields.timestamp.name(), getTimestamp(path));
+ env.safePut(SrcrefFields.wd.name(), BaseRFFI.GetwdRootNode.create().getCallTarget().call());
} catch (PutException e) {
throw RInternalError.shouldNotReachHere(e);
}
@@ -149,4 +164,38 @@ public class RSrcref {
lloc.setAttr(RRuntime.R_SRCFILE, srcfile);
return lloc;
}
+
+ public static SourceSection createSourceSection(RAbstractIntVector srcrefVec, Source sharedSource) {
+
+ try {
+ Source source;
+ if (sharedSource != null) {
+ source = sharedSource;
+ } else {
+ Object srcfile = srcrefVec.getAttr(RRuntime.R_SRCFILE);
+ assert srcfile instanceof REnvironment;
+ source = RSource.fromSrcfile((REnvironment) srcfile);
+ }
+ int startLine = srcrefVec.getDataAt(0);
+ int startColumn = srcrefVec.getDataAt(1);
+ int startIdx = getLineStartOffset(source, startLine) + startColumn;
+ int length = getLineStartOffset(source, srcrefVec.getDataAt(2)) + srcrefVec.getDataAt(3) - startIdx;
+ return source.createSection(startLine, startColumn, length);
+ } catch (NoSuchFileException e) {
+ RError.warning(RError.SHOW_CALLER, RError.Message.GENERIC, "Missing source file: " + e.getMessage());
+ } catch (IOException e) {
+ RError.warning(RError.SHOW_CALLER, RError.Message.GENERIC, "Cannot access source file: " + e.getMessage());
+ } catch (IllegalArgumentException e) {
+ RError.warning(RError.SHOW_CALLER, RError.Message.GENERIC, "Invalid source reference: " + e.getMessage());
+ }
+ return RSourceSectionNode.LAZY_DEPARSE;
+ }
+
+ private static int getLineStartOffset(Source source, int lineNum) {
+ try {
+ return source.getLineStartOffset(lineNum);
+ } catch (IllegalArgumentException e) {
+ throw new IllegalArgumentException(String.format("line %d does not exist in source %s", lineNum, RSource.getPathInternal(source)), e);
+ }
+ }
}