rJava rewrite - fastr changes:

- removed jri
- removed all native code and replced with fastr interop based impl in R
- some tweaks in original rjava R code
- java build part of install

com.oracle.truffle.r.pkgs/rJava/jri/Makevars.win

-R_HOME=$(RHOME)
-JAVA_HOME=$(JAVAHOME)
-JAVAINC=-I$(JAVAHOME)/include -I$(JAVAHOME)/include/win32
-RINC=-I$(R_HOME)/include
-JNISO=.dll
-JAVA_LIBS=-Lwin32 -ljvm
-JNILD=-shared $(JAVA_LIBS) -L$(RHOME)/src/gnuwin32 -L$(RHOME)/bin$(R_ARCH) -lR -Wl,--kill-at
-CFLAGS+=-DWin32 -D_JNI_IMPLEMENTATION_
-JAVA_PROG=$(JAVAHOME)/bin/java
-JAVA=$(JAVAHOME)/bin/java
-JAVAC=$(JAVAHOME)/bin/javac
-JAVAH=$(JAVAHOME)/bin/javah
-JAR=$(JAVAHOME)/bin/jar
-JRIDEPS=win32/libjvm.dll.a
-JNIPREFIX=
-PLATFORMT=run.bat
-JRILIB=jri.dll

com.oracle.truffle.r.pkgs/rJava/jri/Mutex.java

-package org.rosuda.JRI;
-
-/** This class implements a (not so) simple mutex. The initial state of the mutex is unlocked. */
-public class Mutex {
-    public static boolean verbose=false;
-
-    /** defines the current mutex state */
-    private boolean locked=false;
-
-    /** thread that locked this mutex (used for simple deadlock-detection) */
-    private Thread lockedBy=null;
-
-    /** locks the mutex. If the mutex is already locked, waits until the mutex becomes free. Make sure the same thread doesn't issue two locks, because that will cause a deadlock. Use {@link #safeLock()} instead if you wish to detect such deadlocks. */
-    public synchronized void lock()
-    {
-        while (locked) {
-            if (lockedBy==Thread.currentThread())
-                System.err.println("FATAL ERROR: org.rosuda.JRI.Mutex detected a deadlock! The application is likely to hang indefinitely!");
-            if (verbose)
-                System.out.println("INFO: "+toString()+" is locked by "+lockedBy+", but "+Thread.currentThread()+" waits for release (no timeout)");
-            try {
-                wait();
-            } catch (InterruptedException e) {
-                if (verbose)
-                    System.out.println("INFO: "+toString()+" caught InterruptedException");
-            }
-        }
-        locked=true;
-        lockedBy=Thread.currentThread();
-        if (verbose) System.out.println("INFO: "+toString()+" locked by "+lockedBy);
-    }
-
-    /** locks the mutex. If the mutex is already locked, waits until the mutex becomes free. Make sure the same thread doesn't issue two locks, because that will cause a deadlock.
-        @param to timeout in milliseconds, see {@link #wait()}.
-        @return <code>true</code> if the lock was successful, <code>false</code> if not
-        */
-    public synchronized boolean lockWithTimeout(long to)
-    {
-        if (locked) {
-            if (lockedBy==Thread.currentThread())
-                System.err.println("FATAL ERROR: org.rosuda.JRI.Mutex detected a deadlock! The application is likely to hang indefinitely!");
-            if (verbose)
-                System.out.println("INFO: "+toString()+" is locked by "+lockedBy+", but "+Thread.currentThread()+" waits for release (timeout "+to+" ms)");
-            try {
-                wait(to);
-            } catch (InterruptedException e) {
-                if (verbose)
-                    System.out.println("INFO: "+toString()+" caught InterruptedException");
-            }
-        }
-        if (!locked) {
-            locked=true;
-            lockedBy=Thread.currentThread();
-            if (verbose) System.out.println("INFO: "+toString()+" locked by "+lockedBy);
-            return true;
-        }
-        if (verbose) System.out.println("INFO: "+toString()+" timeout, failed to obtain lock for "+Thread.currentThread());
-        return false;
-    }
-
-    /** attempts to lock the mutex and returns information about its success.
-        @return 0 if the mutex was locked sucessfully<br>1 if the mutex is already locked by another thread<br>-1 is the mutex is already locked by the same thread (hence a call to {@link #lock()} would cause a deadlock). */
-    public synchronized int tryLock()
-    {
-        if (verbose) System.out.println("INFO: "+toString()+" tryLock by "+Thread.currentThread());
-        if (locked) return (lockedBy==Thread.currentThread())?-1:1;
-        locked=true;
-        lockedBy=Thread.currentThread();
-        if (verbose) System.out.println("INFO: "+toString()+" locked by "+lockedBy);
-        return 0;
-    }
-
-    /** Locks the mutex. It works like {@link #lock()} except that it returns immediately if the same thread already owns the lock. It is safer to use this function rather than {@link #lock()}, because lock can possibly cause a deadlock which won't be resolved.
-        @return <code>true</code> is the mutex was successfully locked, <code>false</code> if deadlock was detected (i.e. the same thread has already the lock). */
-    public synchronized boolean safeLock()
-    {
-        if (locked && lockedBy==Thread.currentThread()) {
-            if (verbose) System.out.println("INFO: "+toString()+" unable to provide safe lock for "+Thread.currentThread());
-            return false;
-        }
-        lock();
-        return true;
-    }
-
-    /** Locks the mutex. It works like {@link #lockWithTimeout(long)} except that it returns immediately if the same thread already owns the lock. It is safer to use this function rather than {@link #lockWithTimeout(long)}, because lock can possibly cause a deadlock which won't be resolved.
-        @return <code>true</code> is the mutex was successfully locked, <code>false</code> if deadlock was detected or timeout elapsed. */
-    public synchronized boolean safeLockWithTimeout(long to)
-    {
-        if (locked && lockedBy==Thread.currentThread()) {
-            if (verbose) System.out.println("INFO: "+toString()+" unable to provide safe lock (deadlock detected) for "+Thread.currentThread());
-            return false;
-        }
-        return lockWithTimeout(to);
-    }
-
-    /** unlocks the mutex. It is possible to unlock an unlocked mutex, but a warning may be issued. */
-    public synchronized void unlock()
-    {
-        if (locked && lockedBy!=Thread.currentThread())
-            System.err.println("WARNING: org.rosuda.JRI.Mutex was unlocked by other thread than locked! This may soon lead to a crash...");
-        locked=false;
-        if (verbose) System.out.println("INFO: "+toString()+" unlocked by "+Thread.currentThread());
-
-        // notify just 1 in case more of them are waiting
-        notify();
-    }
-
-    public String toString()
-    {
-        return super.toString()+"["+((locked)?"":"un")+"locked"+((!locked)?"":(", by "+((lockedBy==Thread.currentThread())?"current":"another")+" thread"))+"]";
-    }
-}

com.oracle.truffle.r.pkgs/rJava/jri/NEWS

- NEWS/ChangeLog for JRI
---------------------------
-
-0.5-5	(under development)
-    o	fix compilation in parallel using the -j switch for GNU Make
-    o	some more Win64 fixes
-
-0.5-4	2010-09-17
-    o	added more options to rniStop() on unix and changed the
-	default to use interrupt flags instead of signals since
-	signals cause problems in some JVM implmentations. The
-	previous behavior can be achieved by rniStop(1).
-
-0.5-3	2010-09-02
-    o	fixed changed by the Win64 support which broke some other OSes by
-	using sign extension when converting to long storage.
-
-    o	avoid the use of the sign of pointers for signaling. Note
-	that rniEval() now returns 0 on error and not -1 or -2. The
-	old behavior was undocumented (and dangerous) and thus should
-	not be relied upon. (fixes #172)
-
-0.5-2	2010-04-28
-    o	fixed handling of NAs in strings - they are now correctly
-	converted to <null>s on the Java side.
-
-	IMPORTANT: previously NAs would come as the string "NA"
-	from R which is incorrect since it is not distinguishable from
-	a literal "NA" string. Code that deals with NAs must be prepared
-	to receive nulls in string arrays (note that nulls where
-	correctly converted to NA string, it's just that incoming
-	string were not converted).
-
-	(Thanks to Stephan Wahlbrink for pointing out the inconsistency)
-
-    o	multiple fixes to Windows support: common command line
-	arguments are now correctly processed, sub-architectures are
-	supported, Win64 is now also supported
-
-0.5-1	2010-03-16
-   o	API 1.10: rniAssign now returns boolean to denote success/failure
-
-   o	numerous bug fixes and additions
-
-0.5-0	2009-08-22
-    o	API 1.9: added rniPreserve, rniRelease, rniParentEnv, rniFindVar,
-	         rniListEnv, rniSpecialObject, rniPrintValue,
-		 rniGetRawArray, rniPutRawArray, rniGetAttrNames methods
-		 added jriLoaded field (boolean)
-
-    o	new REngine-based API (org.rosuda.REngine.JRI.JRIEngine)
-	has been created - this allows the same code to interface
-	JRI or Rserve without re-compilation
-
-	Note: the JAR files are currently shipped separately from the JRI
-	installation and can be obtained from
-	http://rforge.net/JRI/files/
-
-    o	proxy references are now preserved until finalized
-
-    o	if jri.ignore.ule=yes property is set, JRI will not abort on
-	failing to load the JRI library (UnsatisfiedLinkException).
-	This can be used by GUIs to display a more meaningful message
-	instead of abort. The jriLoaded flag is false in that case.
-
-
-0.4-2
-    o	declare string encoding as UTF-8 and convert incoming strings
-	to UTF-8 if possible (R >= 2.7.0 required).
-
-0.4-1	(part of rJava 0.5-1 and later)
-    o	fixed configuration to work with multi-arch builds
-
-0.4-0	2007-08-22 (part of rJava 0.5-0)
-    o	adapt to changes in R-devel
-
-    o	add -I. to CFLAGS for compatibility (thanks to BDR)
-
-    o	added RConsoleOuputStream class
-
-    o	API 1.8: added rniPrint, added int oType parameter to the
-	rWriteConsole callback
-
-    o	work around broken MinGW runtimes
-
-    o	allow JRI to hook into a running R process (and thusly provide
-	rJava with callbacks)
-
-    o	added: inMainRThread(), isStandAlone()
-
-    o	include configure in SVN and don't rebuild it on mkdist
-
-0.3-7	2006-01-14
-    o	make sure rniJavaToXref creates a global reference
-
-    o	API 1.7: rniCons can accept two new arguments: tag and lang
-	rniLCons was added
-
-    o	assign now supports raw REXPs (XT_NONE)
-
-    o	createRJavaRef was added to create jobjRef R objects from
-	Java objects
-
-0.3-6	2006-11-29
-    o	adapted to API change in R-devel
-
-    o	fixed double-inclusion of JFLAGS which throws off GIJ
-
-0.3-5	2006-10-06
-    o	remove variadic macros to be compatible with compilers
-	that don't support C99
-
-0.3-4	2006-09-14
-    o	updated Makefiles to force 1.4 target and sources
-
-0.3-3	2006-09-12
-    o	fixed API version in Java sources and added version check
-	to examples
-
-0.3-2	2006-09-11
-    o	New API (1.6): add handling of boolean type
-
-0.3-1	2006-08-31
-
-0.3-0	2006-05-31
-    o	New API (1.5) entries: rniGetTAG, rniInherits,
-	rniGetSymbolName, rniInstallName
-	allows handling of symbols, named lists and inheritance
-
-    o	fixed/improved REXP, RList and RFactor
-
-0.2-5	2006-05-08
-    o	Use configure to detect CStackXXX and R_SignalHandlers
-	set the latter to 0 if present (solves threading issues)
-
-0.2-4	2006-05-03
-    o	added support for pre-configuration passed from rJava
-
-0.2-3	2006-04-20
-    o	fix warnings and issues with R 2.3.0
-
-0.2-2	2006-04-11
-    o	licensed under LGPL
-
-0.2-1	2006-03-07
-    o	fixed Java detection, fixed eval double-unlock,
-	use R shlib flags, added FreeBSD support
-
-0.2-0	2005-12-19
-    o	switched to autoconf process for configuration/installation 
-
-0.1-0
-    o	First JRI release
-

com.oracle.truffle.r.pkgs/rJava/jri/RBool.java

-package org.rosuda.JRI;
-
-// JRclient library - client interface to Rserve, see http://www.rosuda.org/Rserve/
-// Copyright (C) 2004 Simon Urbanek
-// --- for licensing information see LICENSE file in the original JRclient distribution ---
-
-/** Implementation of tri-state logical data type in R.
-    The three states are TRUE, FALSE and NA. To obtain truly boolean
-    value, you'll need to use {@link #isTRUE} or {@link #isFALSE} since there is
-    no canonical representation of RBool in boolean
-
-    @version $Id: RBool.java 2720 2007-03-15 17:35:42Z urbanek $
-*/
-public class RBool extends Object {
-    int val;
-
-    public RBool(boolean b) {
-	val=(b)?1:0;
-    };
-    public RBool(RBool r) {
-	val=r.val;
-    };
-    public RBool(int i) { /* 0=FALSE, 2=NA, anything else = TRUE */
-	val=(i==0||i==2)?i:1;
-    };
-
-    public boolean isNA() { return (val==2); };
-    public boolean isTRUE() { return (val==1); };
-    public boolean isFALSE() { return (val==0); };
-
-    public String toString() { return (val==0)?"FALSE":((val==2)?"NA":"TRUE"); };
-}

com.oracle.truffle.r.pkgs/rJava/jri/RConsoleOutputStream.java

-// RConsoleOutputStream, part of Java/R Interface
-//
-// (C)Copyright 2007 Simon Urbanek
-//
-// For licensing terms see LICENSE in the root if the JRI distribution
-
-package org.rosuda.JRI;
-
-import java.io.OutputStream;
-import java.io.IOException;
-
-/** RConsoleOutputStream provides an OutputStream which causes its output to be written to the R console. It is a pseudo-stream as there is no real descriptor connected to the R console and thusly it is legal to have multiple console streams open. The synchonization happens at the RNI level.<p>Note that stdout/stderr are not connected to the R console by default, so one way of using this stream is to re-route Java output to R console:<pre>
-System.setOut(new PrintStream(new RConsoleOutputStream(engine, 0)));
-System.setErr(new PrintStream(new RConsoleOutputStream(engine, 1)));
-</pre>
-
-@since JRI 0.4-0
-*/
-public class RConsoleOutputStream extends OutputStream {
-	Rengine eng;
-	int oType;
-	boolean isOpen;
-	
-	/** opens a new output stream to R console
-		@param eng R engine
-		@param oType output type (0=regular, 1=error/warning) */
-	public RConsoleOutputStream(Rengine eng, int oType) {
-		this.eng = eng;
-		this.oType = oType;
-		isOpen = true;
-	}
-	
-	public void write(byte[] b, int off, int len) throws IOException {
-		if (!isOpen) throw new IOException("cannot write to a closed stream");
-		if (eng == null) throw new IOException("missing R engine");
-		String s = new String(b, off, len);
-		eng.rniPrint(s, oType);
-	}
-	
-	public void write(byte[] b) throws IOException { write(b, 0, b.length); }
-	public void write(int b) throws IOException { write(new byte[] { (byte)(b&255) }); }
-	public void close() throws IOException { isOpen=false; eng=null; }
-}

com.oracle.truffle.r.pkgs/rJava/jri/REngine/JRI/Makefile

-## there are two ways to compile JRIEngine - either use
-## already installed REngine and JRI and then just
-## compile JRIEngine against those jars or use this
-## Makefile with all org sources checked out
-## in which case the JRIEngine.jar will implicitly
-## contain org.rosuda.JRI classes as well
-## However, that requires both:
-## org/rosuda/JRI
-## org/rosuda/REngine
-
-JRI_MAIN_SRC=$(wildcard ../../*.java)
-JRIENGINE_SRC=JRIEngine.java
-
-JAVAC=javac
-JAR=jar
-JFLAGS=-source 1.6 -target 1.6
-
-all: JRIEngine.jar
-
-JRIEngine.jar: $(JRI_MAIN_SRC) $(JRIENGINE_SRC)
-	rm -rf org
-	$(JAVAC) $(JFLAGS) -classpath ../REngine.jar -d . $^
-	$(JAR) fc $@ org
-
-clean:
-	rm -rf org *~ JRIEngine.jar *.class
-	make -C test clean

com.oracle.truffle.r.pkgs/rJava/jri/REngine/JRI/package-info.java

-/**
- * REngine-based interface to JRI
- *
- * <p>
- * Currently it uses low-level calls from org.rosuda.JRI.Rengine, but
- * all REXP representations are created based on the org.rosuda.REngine API
- */
-package org.rosuda.REngine.JRI ;
-

com.oracle.truffle.r.pkgs/rJava/jri/REngine/LICENSE

-REngine - Java interface to R
-Copyright (C) 2004,5,6,7  Simon Urbanek
-
-This library is free software; you can redistribute it and/or
-modify it under the terms of the GNU Lesser General Public
-License as published by the Free Software Foundation; either
-version 2.1 of the License, or (at your option) any later version.
-
-This library 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
-Lesser General Public License for more details.
-
-You should have received a copy of the GNU Lesser General Public
-License along with this library; if not, write to the Free Software
-Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

com.oracle.truffle.r.pkgs/rJava/jri/REngine/MutableREXP.java

-package org.rosuda.REngine;
-
-public interface MutableREXP {
-	public void setAttribute(String name, REXP value);
-}