 NEWS/ChangeLog for rJava
--------------------------

0.9-9	(released to CRAN)
    o	Work around a bug of Oracle's Java on Linux which caps the stack of
        R at 2M.  The bug leads to segfaults in recursive computations (not
        an R error as R doesn't know the stack size has been reduced).  The
        workaround can be disabled via environment variable
        RJAVA_JVM_STACK_WORKAROUND=0, which may produce better results with
        memory access checkers (ASAN, valgrind), because the workaround
        detects the new stack size by trying to access inaccessible memory. 
        This JVM behavior was a workaround for an issue in old Linux systems
        (JDK-4466587) and is going to be fixed in Java 10.

    o   Java 9 only supports versions >= 1.6, so change many Makefiles to 1.6.

0.9-8	2016-01-07
    o	Work around a bug on Oracle's Java on OS X by pre-loading jli

    o	Work around DYLD_FALLBACK_LIBRARY_PATH being dropped in OS X 10.11


0.9-7	2015-07-27
    o	explicitly set -classpath in configure for getps since the user
	may have set CLASSPATH and thus override the default
	(see #3)

    o	when constructing String references from character vectors,
	treat NA as null on the Java side (see #15)

    o	add .jsimplify(..., promote=TRUE) option to promote int
	to double if integer NAs are to be interpreted literally as
	-2147483648 values. (see #39)

    o	fix .jarray(.jshort(...)) to respect the `jshort` tag (see #40)


0.9-6	2012-12-23
    o	bugfix: the first JVM parameters was shadowed by headless
	mode parameter if enabled (default on OS X).


0.9-5	2012-12-03
    o	add more debugging information in RJavaClassLoader to trace
	cases where class path entries are invalid or discarded

    o	detect support for -Xrs and enable it by default (this prevents
	Java from killing R process on interrupt)

    o	restore locales after Java initialization (some JVMs clobber
	locales with incompatible settings).

    o	add --enable-headless option which sets the java.awt.headless
	to true. In the auto mode this flag is only enabled on Mac OS X.
	Note that it is only set upon initialization, it does not
	affect already running JVMs.

0.9-4	2013-03-11
    o	added support for unboxing of Double[], Integer[] and Boolean[]
	to .jevalArray(.., simplify=TRUE) and thus also to .jcall()

    o	Windows: add Java configuartion paths before existing PATH
	entries

    o	Windows: honor a new option "java.home" to override JAVA_HOME
	environment variable and system settings to allow co-existence
	of other tools that may require differen Java paths.

    o	Windows: fix a buglet in error reporting when no Java is installed

    o	raise an error if the number of arguments to a Java call exceeds
	maxJavaPars. Previously, calls woud be silently truncated.
	Note that maxJavaPars can be raised by compiling rJava, e.g. with:
	PKG_CFLAGS=-DmaxJavaPars=96 R CMD INSTAL rJava_...

0.9-3	2011-12-10
    o	bugfix: .jinit() was failing on Java 1.4 with
	"cannot obtain Class.getSimpleName method ID"
	since the method is only present in Java 1.5+
	This was inadvertent, rJava aims to support Java 1.2+

0.9-2	2011-10-26
    o	When NOAWT is set, rJava will enable headless mode in the JVM
	by setting the java.awt.headless property to true during
	initialization in .jinit()

    o	All C-level entry points are now pre-cached when rJava is
	loaded such that calls can be made much faster since symbols
	don't need to be looked up. This should speed up calls to
	methods that take very little time as well as other parts
	such as checking for exceptions.

0.9-1	2011-06-28
    o	fixed Java detection from registry on Windows (bug introduced
	in 0.9-0)

0.9-0	2011-06-22
    o	fixes issues introduced by several new features in the late
	0.8 series. Most imporantly .jarray() and .jevalArray() behave
	as intended (and as implemented in previous versions). The
	same applies to .jcall() behavior with respect to arrays and
	its evalArray arument. The defaults for some new arguments
	have been changed to reflect the original behavior.

    o	.jevalArray() has an additional argument `simplify' which allows
	multi-dimensional arrays to be converted to native R
	types. Use with care - it may convert more recursive types in
	the future so it should be used preferrably where you have
	control over the types converted.

    o	fixed a bug in .jevalArray that was not simplifying string
	vectors correctly when the array type was not specified
	(.jclass returns dot notation whereas signatures use JNI
	notation so a conversion was necessary)

    o	use install.libs.R in R 2.13.1 to install multi-arch JRI


0.8-8	2010-12-20
    o	Add support for r.arch in RJavaClassLoader on Windows as well

    o   javaImport was only able to import java packages from the system class
        loader (not from additional jars)

0.8-7	2010-10-18
    o	Windows updates to accomodate changes in R 2.12 and layout
	changes in recent Sun Java installations.

0.8-6	2010-09-17
    o	JRI 0.5-4: rniStop() provides several ways to notify R on unix.
	It improves handing of user interrupts via rniStop() by
	allowing to avoid signals (signals can cause problems in some
	recent JVM implementations).

0.8-5	2010-09-02
    o	fix a bug introduced in 0.8-2 where .jclassPath() would not
	show the real class path

    o	if the rJava class loader is used as a primary loader it will
	also register as the context class loader. Some projects
	rely on the thread context class loader instead of
	Class.getClassLoader() [which is still more reliable] 
	so those will now work as well.

    o	JRI 0.5-3 (bugfixes)


0.8-4	2010-04-28
    o	JRI 0.5-2
	IMPORTANT NOTE: handling of NAs in character vectors has been
	fixed, NAs were	incorrectly passed as "NA" from R to Java
	instead of nulls (it was correct the other way round). Any
	code that relies on such incorrect behavior will need to be
	fixed!

	Other changes in JRI are mostly related to Windows support
	(bugfixes R 2.11.0 and Windows 64-bit support)

    o	run.bat is now installed as part of JRI

0.8-3	2010-03-16
    o	REngine and JRIEngine classes are now included in rJava/JRI
	although they are not loaded by default.

    o	.r2j now has convert parameter to allow the creation of
	pure references (convert=FALSE)

    o	toJava() is a new function equivalent to .r2j but resulting
	in REngine API references (instances of REXPReference).
	By default the references are not resolved since the primary
	use is to pass R functions to Java for callbacks.

    o	set text mode for stdin on Windows (thanks to Brian Ripley)

    o	fix support of NULL arguments in new(J("SomeClass"), ...)

    o	fixed issues in with() and within() when used on jobjRef;
	also the evaluation environment is now the parent frame as
	expected

    o	disable AWT tests if NOAWT is set; enable a few more tests


0.8-2	2010-01-22
    o	faster class loader implementation

    o	added support for 64-bit Windows (thanks to Brian Ripley)


0.8-1	2009-10-30
    o	fixed exception handling on Windows: the access to "call"
	was off for Windows builds causing incorrect "call" entries
	in exceptions which broke when encountered in try().

    o	fixed .jcall() which had inadvertently the default for
	use.true.class argument set to TRUE. That is considered
	a bug since it breaks the original behavior and is against the
	idea of .jcall being the low-level interface.


0.8-0	2009-10-27
    o	new exception handling was introduced:

	Java exceptions are mapped to Exception conditions which can
	be used to catch the exception at R level using e.g tryCatch. 
	
	The class name automatically contains "Exception", "error"
	and "condition", as well as all the names (without package path)
	of the classes in the inheritance tree of the actual class of the 
	Exception. This allows targetted handlers:
	tryCatch(.jnew("foo"), NoClassDefFoundError=function(e) ...)

	In addition JNI code now causes an error instead of a warning,
	however, some errors internal to JNI may not have an associated
	Java exception and thus will fire the usual simpleError
	condition.

	As a consequence of the new error handling exception objects
	are now supplied in e$jobj of the handler and .jgetEx()
	becomes obsolete.

    o	added new high-level API using the "J" function. It replaces
	the previously used .J()/.jrnew() and .jrcall().

	New Java objects are created using new(J("class"), ...) and
	static methods and fields are accessed using J("class")$...
	The corresponding implementation uses reflection in all cases.

	An additional class "jclassName" was created to support static
	calls to accessor methods such as $ and calls to new().
	
    o   [RF] arrays are now split in two classes : "jrectRef" for rectangular
        arrays, similar to R arrays, and jarrayRef for rugged arrays. 
        Indexing of all arrays is supported using the double bracket 
        indexer "[[" and "[[<-"
        
        The single indexer "[" is only currently implemented for 
        rectangular arrays. This is experimental. Replacement ([<-) 
        is not supported yet.

    o   [RF] with.jclassName and within.jclassName is added to support
        "with" semantics on static fields and methods of java classes. 
        
        Double <- J("java.lang.Double" )
        with( Double, parseDouble( "10.2" ) )
        

    o   [RF] length.jarrayRef queries the number
        of objects in a java array. An exception is generated if the 
        object is not an array. Also array$length can be used 
        similary to array.length in java
        
    o   [RF] .jcast gains arguments "check" and "convert.array". Their 
             default value is FALSE for backwards compatibility with 
             previous releases of rJava
             
    o   [RF] Binary operators <, >, <=, >= to compare two objects where 
             at least one is a java object reference. 
             d <- new( J("java.lang.Double"), 0.0 )
             d < 1.0
             d < 1L
             Comparison of arrays is not currently supported
             
    o   [RF] lapply and sapply may now be used on Iterable java objects
             such as Vector and java arrays. see ?as.list.jobjRef
             
    o   [RF] The generic "clone" function is added, and an implementation for 
             java objects. an Object must implement the Cloneable 
             interface, otherwise an exception will be raised. 
             Furthermore, careful reading of the java documentation 
             of Object#clone is recommended since this is not standard
             java behaviour. Currently "clone" is not supported on 
             arrays
             
    o   [RF] A mechanism for "attach"ing java packages has been introduced, 
             following the mechanism of the RObjectTables package
             from the OmegaHat project. This allows to "attach" a set of
             java package paths to R's search path: 
             
             > attach( javaImport( "java.util", "java.lang" ) )
             
             and then use classes from this package like this :
             
             > new( Vector )
             > new( HashMap )
             > new( Double, 10.2 )
             > new( Integer, 10L ) 
             > Collections$EMPTY_MAP
             
             This feature is currently __very__ experimental and is as
             dangerous as any other use of attach


0.7-1	(never released)
    o	[RF] added .J high-level java constructor (based on reflection 
	as opposed to complete match as .jnew does)

    o	[RF] added .jinstanceof and instanceof operator

    o	when loaded into another JVM (e.g. via JRI), rJava would crash
	on any call if .jinit() was missing. Now it correctly reports
	the error.

    o	fixed synchronization issues in both JRI and REngine

0.7-0	2009-08-22
    o	fixed bug in $ getter of fields using old .jfield API

    o	fixed a bug in .jevalArray which failed when the signature
	was specified directly (and subsequently .jfield failed in
	most cases)

    o	improve speed of reflection-based API (.jrcall and `$')
	by using native array support in rJava

    o	reflection API now returns NULL invisibly for void results

    o	try to find the best match in reflection-based API
	using internal Java code (code and idea by
	Romain Francois)

    o	added with() method for jobjRef (by Romain Francois), see
	http://romainfrancois.blog.free.fr/index.php?
	post/2009/06/17/with-semantics-for-java-objects-in-rJava

    o	added names() method for jobjRef to facilitate code
	completion (based on code by RF: http://tr.im/w33B)

    o	update to JRI 0.5-0

0.6-3	2009-06-14
    o	update to JRI 0.4-3 (adds REngine API, enhanced support for
	environments and references)

    o	allow signatures longer than 256 bytes

    o	added lib.loc parameter to .jpackage()

0.6-2	2009-01-26
    o	fix --enable-debug to really enable debug code

    o	improve Windows setup (add only paths if they are not already
	listed and check thier presence first) and warn if the system
	suffers from PATH truncation bug (or PATH is truncated in
	general)

[0.6-branch is created as a stable branch -- see trunk for development]


0.6-1	2008-12-23
    o	substitute $(JAVA_HOME) in configuration flags when necessary

    o	flag generated strings as UTF-8 and convert incoming strings
	into UTF-8 (see note in ?.jcall for details)
	This should improve interoperability in non-UTF-8 locales
	(most prominent example is Windows)


0.6-0	2008-09-22
    o	add support for object cache - see .jcache() - based
	on Java serialization


0.5-2	(never released, turned into 0.6-0)
    o	add direct support for raw vectors as method parameters
	(before .jarray(r) had to be used)

    o	add .jserialize() and .junserialize() functions for
	Java-serialization (do not confuse with R serialization!)


0.5-1	2007-11-05
    o	fix crashes in Windows when Java calls the vfprintf hook

    o	enhance Java environment checks, add more specific errors

    o	add support for r.arch system property which allows multi-arch
	support on platforms that don't have fat binaries (e.g. Linux)


0.5-0	2007-08-22
    o	**API CHANGE**
	The order of arguments of .jfield has been changed to match
	the order used in .jcall and the return value is as expected
	and doesn't need .jsimplify anymore.

    o	The implementation of .jfield no longer uses reflection
	it supports static fields and .jfield<-() was added.

    o	Consolidate interface code for static/non-static calls.
	It is now possible to call a static method using a non-static
	object.

    o	Add .jpackage function for initialization of Java packages.
	See documentation for details, packages should no longer
	use .jinit in their initialization code.

    o	Add preliminary JRI support from R (see .jengine)

    o	Prepare hooks for de-serialization

    o	Add support for short Java type

    o	Add support for convertors

    o	Fix R-devel compatibility issues

    o	Fix a memory leak in string array handling

    o	Use Java settings from R for compilation

    o	Add a custom class loader

    o	Fix a bug in .jcastToArray that produced invalid signatures

    o	Added support for [Z in .jevalArray

    o	Fix a bug in .jarray missing [ prefix for native type arrays



0.4 branch has been branched off the trunk, see 0.4-branch for NEWS

0.4-13	2007-01-14
    o	Fix Java-side memory leaks (temporary parameters to methods
	were not propery released, thanks to Erik van Barneveld for
	supplying a reproducible example).

    o	Fix a bug that caused only the first VM parameter to be passed
	on during initialization (thanks to Bernard Rosman for
	reporting).

    o	.jmkref now accepts plain class names (with .)

    o	Fix bug in .jarray (and underlying RcreateArray) that was
	returning wrong class name if the contents class was an array.

    o	Add --enable-callbacks option to configure (disabled by
	default). The callbacks support is currently incomplete and
	experimental.

    o	Update URL to http://www.rforge.net/rJava/

    o	Update to JRI 0.3-7 (LCons, createRJavaRef, assign XT_NONE) 

0.4-12	2006-11-29
    o	Added documentation for .jthrow, .jclear and .jgetEx and
	a bugfix in .jgetEx

    o	rJava now uses a namespace. This is still somewhat experimental,
	because rJava needs to perform some dirty tricks to unseal
	the namespace during initialization. Please test and report!

    o	Update to JRI 0.3-6 (GIJ fix and fix for R-devel interface changes)

0.4-11  2006-10-10
    o	Replace variadic macros with wrappers (for compilers that don't
	support ISO C99).

    o	Modify JNI error reporting - use warnings instead of direct stderr.

    o	Update to JRI 0.3-5

0.4-10	2006-09-14
    o	Removed obsolete JNI 1.1 support that is no longer provided
	in JDK 1.6 and thus prevented rJava from being used with JDK 1.6

    o	Update to JRI 0.3-4 (change compilation to force Java 1.4
	compatibility even when more recent JDK is used)

0.4-9	2006-09-12
    o	Update to JRI 0.3-3 which fixes API version mistake which

0.4-8	2006-09-11
    o	Added --enable-jri=auto option which will build JRI only if R
	shared library is present. It is now the default.

    o	Update to JRI 0.3-2 (added boolean support)

0.4-7	2006-09-05
    o	.jevalArray now works with Java objects that have not been
	cast to a Java array explicitly. The function is now also
	documented properly.

    o	Added .jgetEx and .jclear functions for querying and clearing
	of Java exceptions/throwables.

    o	Added .jthrow to allow throwing of exceptions from R code.

    o	Fixed a typo in .jrcall when handling string return values.

0.4-6	2006-08-20
    o	Fixed bug in initialization on Windows, introduced in 0.4-4

0.4-5	2006-06-24
    o	Added support for scalar bytes as .jbyte (byte arrays are still
	natively represented as RAW vectors)

    o	Added .r2j function which allows to push R objects into Java as
	references. This works only if R is run via JRI, because it
	requires a working Rengine instance.

0.4-4	2006-06-21
    o	Fixed bug that prevented loading into existing VM
	if the classpath contained duplicate items.
	.jmergeClassPath now filters out duplicate paths.

    o	.jcall and .jnew discard all named parameters that are passed
	as `...'. Named parameters are now reserved for future call options

    o	Converted all S3-methods into S4 methods.
	Also `show' is now used instead of `print' and the
	output format was changed.

    o	Protoype for jobjRef is now a valid null-Object

    o	Added .jequals and corresponding ==, != op methods.
	Currently == and != operators feature the same behavior as
	.jequals(...,strict=FALSE), i.e. scalar non-Java objects are
	converted into Java objects if possible and then compared, so
	 s <- .jnew("java/lang/String","foo")
	 s == "foo"  # returns TRUE

    o	Added .jinherits which allows to check Java-side
	inheritance using JNI (= isAssignableTo).

    o   Added .jfindClass and .jclassRef that return Java
	class object

    o	Added check parameter to .jcall and .jnew that allows the caller
	to prevent implicit call to .jcheck
	It is mainly useful in cases where silent operation
	is desired (e.g. in conjunction with try).
	Additionally, silent parameter was added to .jnew

    o	Added is.jnull which is like is.null but also returns
	TRUE if the supplied Java object is a null-reference

    o	Added jlong class and .jlong function. Those were documented in
	the tutorial but never really implemented. Still, they may not
	be supported in all parts of rJava.
	WARNING: conversion between Java's long and R's jlong is lossy!
	R stores jlong in doubles so the conversion implies loss of
	precision.

0.4-3	2006-05-16
    o	improved, documented and fixed handling of fields
	.jfield is dedicated accessor with more options

0.4-2	2006-05-08
    o	Update to JRI 0.2-5 (no change in rJava)

0.4-1	2006-05-05
    o	Fixed bug in Windows initialization

0.4-0	2006-05-03
    o	JRI is now included in rJava

0.3-9	2006-04-20
     o	fixed a minor bug in Rglue.c that may prevent older
	compilers from compiling it.

0.3-8	2006-04-17
     o	.jinit has an additional parameter 'parameters' that allows
	users to pass additional parameters to the VM (such as -X...)

     o	.jinit now uses a hack (defined in .jmergeClassPath) that
	allows us to modify the class path of a running VM. This may
	or may not work for a specific VM, because it is an ugly hack
	exploiting some implementational features of the VM.
	See .jmergeClassPath source for reference and explanation.

     o	.jarray now supports the use of .jarray(x) where x is a Java
	reference. The documentation requires you to use
	.jarray(list(x)), but since the use of .jarray(x) seems to be
	a very common mistake, we may as well silently support it.

     o	.jarray has an optional parameter contents.class which allows
	the global specification of the class type for arrays of
	objects. (Untested, use with care! In most cases .jcast is
	probably what you really want.)

     o	Added some more support for floats, longs and byte arrays.
	(Again, untested)

0.3-7	2006-01-31 (non-public release)
     o	New, experimental feature has been added - JNI cache. This
	feature can be enabled by passing --enable-jni-cache argument
	to configure. Normally, each time we access JVM we retrieve
	new JNI environment to make sure there are no threading
	issues. In single-threaded environment this is superfluous, so
	we may as well cache it. The idea is to reduce the
	overhead. However, the gain is not as huge as expected, so it
	is not enabled by default. Also note that threads and
	jni-cache are mutually exclusive.

     o	Another even more experimental feature has been added -
	support for threads. This feature is enabled by using
	--enable-threads configure argument. When threads support is
	enabled, JVM is started on a thread separate from the main
	thread. Some implementations of AWT classes require
	this. However, it is not always safe to use, because R event
	loop is unaware of the separate thread and can deadlock it.

0.3-6	2006-01-30
0.3-5	2006-01-02
0.3-4	2005-12-28
0.3-3	2005-12-20
0.3	2005-12-19	[finalizers, arrays]
0.2	2005-09-03	[S4 classes]
0.1	2003-08-26	[initial release]
