[R] SJava help
Weiming Zhang
Weiming.Zhang at uchsc.edu
Wed Sep 24 22:15:39 CEST 2003
Hi,
That would be great! I will wait.
Thanks.
Weiming
On Wed, 2003-09-24 at 13:59, Duncan Temple Lang wrote:
>
> Hi.
>
> Over the past few weeks, I have spent some time enhancing the
> SJava package and ironing out some issues (syncrhonization
> and locking of the R evaluator, etc.). Along the way,
> I did encounter the problem you mention about java.lang.Hashtable.
> I can't quite remember what the problem was, but I think it
> may have been a typo in one part of the code.
>
> I will make a new version of the package available in the next
> day or so and hopefully your problem and others will be
> resolved.
>
> D.
>
>
>
> Weiming Zhang wrote:
> > Hi, Henrik,
> >
> > Thank you very much for replying.
> >
> > I actually have the JAVA_HOME environment variable set in a linux shell
> > script .bash_profile which set up all of my development environment
> > before I install this SJava package and it points to the current java
> > cdk I am using. So it is weird that R could not find the common java
> > libraries. Do you think I need to use .Renviron instead of
> > .bash_profile?
> >
> > Weiming
> >
> > On Wed, 2003-09-24 at 12:42, Henrik Bengtsson wrote:
> > > Hi, I do not have Linux myself but looking at your error message
> > >
> > > > > .JavaInit()
> > > > [1] error initializing manager class can't find class
> > > > java/lang/Hashtable Error in .JavaInit() : Couldn't start
> > > > Java Virtual Machine: can't find class java/lang/Hashtable
> > > > >
> > >
> > > it looks like you have not set the JAVA_HOME variable correctly. On a
> > > Windows XP machine you will get the error (together with a popup
> > > dialog):
> > >
> > > > library(SJava)
> > > using JAVA_HOME = /c/Program Files/Java/j2sdk1.4.0_02
> > > Error in dyn.load(x, as.logical(local), as.logical(now)) :
> > > unable to load shared library
> > > "c:/PROGRA~1/R/rw1071/library/SJava/libs/S
> > > Java.dll":
> > > LoadLibrary failure: The specified module could not be found.
> > > Error in library(SJava) : .First.lib failed
> > > >
> > >
> > > See help(.Renviron) how to set the JAVA_HOME environment variable.
> > >
> > > ***Note*** on Windows XP (and maybe on other systems too) you have to
> > > set JAVA_HOME differently if you have i) Java Runtime Edition or the ii)
> > > Java SDK. For Java SDK, which you have, you have to set
> > >
> > > JAVA_HOME=C:/Program Files/Java/j2sdk1.4.0_02/jre/
> > >
> > > and not to
> > >
> > > JAVA_HOME=C:/Program Files/Java/j2sdk1.4.0_02/
> > >
> > > as one would guess. But with Java Runtime Edition you should do
> > >
> > > JAVA_HOME=C:/Program Files/Java/j2re1.4.1_02/
> > >
> > > If you use ~/.Renviron it won't mess with your other settings.
> > >
> > > Again, I'm not sure if this applies to Linux, but it's worth a try.
> > >
> > > Cheers
> > >
> > > Henrik Bengtsson
> > >
> > >
> > > > -----Original Message-----
> > > > From: r-help-bounces at stat.math.ethz.ch
> > > > [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Weiming Zhang
> > > > Sent: den 24 september 2003 19:16
> > > > To: R-help at stat.math.ethz.ch
> > > > Subject: [R] SJava help
> > > >
> > > >
> > > > Hi,
> > > >
> > > > I installed SJava 0.66-1 on my linux RH 7.2 machine. I am
> > > > using R-1.7.1. I set LD_LIBRARY_PATH up then called
> > > > library(SJava) and it was fine. But when I called
> > > > .JavaInit(), I got weird error that states it could not find
> > > > java/lang/Hashtable. The session is below and shows my java
> > > > configuration. I am using j2sdk1.4.2_01 from Sun.
> > > >
> > > > Thank you very much.
> > > >
> > > > Weiming Zhang
> > > >
> > > > > .javaConfig
> > > > $classPath
> > > > [1] "/usr/lib/R/library/SJava/org/omegahat/Jars/Environment.jar"
> > > > [2] "/usr/lib/R/library/SJava/org/.."
> > > > [3] "/usr/lib/R/library/SJava/org/omegahat/Jars/antlr.jar"
> > > > [4] "/usr/lib/R/library/SJava/org/omegahat/Jars/jas.jar"
> > > > [5] "/usr/lib/R/library/SJava/org/omegahat/Jars/jhall.jar"
> > > >
> > > > $properties
> > > >
> > > > EmbeddedInR
> > > >
> > > > "true"
> > > >
> > > > InterfaceManagerClass
> > > >
> > > > "org/omegahat/Interfaces/NativeInterface/OmegaInterfaceManager"
> > > >
> > > > ForeignReferenceBaseClass
> > > >
> > > > "org/omegahat/R/Java/RForeignReference"
> > > >
> > > > java.compiler
> > > >
> > > > "NONE"
> > > >
> > > > OMEGA_HOME
> > > >
> > > > "/usr/lib/R/library/SJava/org/omegahat"
> > > >
> > > > OmegahatSearchPath
> > > > ".,${OMEGA_HOME}/Environment/Scripts/Run,${OMEGA_HOME}/Jars/En
> > > > vironment.jar"
> > > >
> > > > java.library.path
> > > >
> > > > "/usr/lib/R/library/SJava/libs"
> > > >
> > > > $libraryPath
> > > > [1] "/usr/lib/R/library/SJava/libs"
> > > >
> > > > $args
> > > > character(0)
> > > >
> > > > > .JavaInit()
> > > > [1] error initializing manager class can't find class
> > > > java/lang/Hashtable Error in .JavaInit() : Couldn't start
> > > > Java Virtual Machine: can't find class java/lang/Hashtable
> > > > >
> > > >
> > > > The output from installation is here and
> > > > I used R INSTALL -c SJavaPackageName:
> > > >
> > > > * Installing *source* package 'SJava' ...
> > > > creating cache ./config.cache
> > > > checking for java... /opt/lang/java/j2sdk1.4.2_01/bin/java
> > > > Java VM /opt/lang/java/j2sdk1.4.2_01/bin/java
> > > > checking for javah... /opt/lang/java/j2sdk1.4.2_01/bin/javah
> > > > checking for c++... c++
> > > > checking whether the C++ compiler (c++ ) works... yes
> > > > checking whether the C++ compiler (c++ ) is a
> > > > cross-compiler... no checking whether we are using GNU C++...
> > > > yes checking whether c++ accepts -g... yes checking for
> > > > gcc... gcc checking whether the C compiler (gcc ) works...
> > > > yes checking whether the C compiler (gcc ) is a
> > > > cross-compiler... no checking whether we are using GNU C...
> > > > yes checking whether gcc accepts -g... yes checking for
> > > > Rf_initEmbeddedR in -lR... no No R shared library found
> > > > updating cache ./config.cache creating ./config.status
> > > > creating Makevars creating src/Makevars creating
> > > > src/RSJava/Makefile creating Makefile_rules creating
> > > > inst/scripts/RJava.bsh creating inst/scripts/RJava.csh
> > > > creating R/zzz.R creating cleanup creating inst/scripts/RJava
> > > > Copying the cleanup script to the scripts/ directory Building
> > > > libRSNativeJava.so in /tmp/R.INSTALL.30363/SJava/src/RSJava
> > > > if test ! -d /usr/lib/R/library/SJava/libs ; then \
> > > > mkdir /usr/lib/R/library/SJava/libs ; \
> > > > fi
> > > > gcc -g -O2 -D_R_ -I/usr/lib/R/include
> > > > -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux -c CtoJava.c
> > > > gcc -g -O2 -D_R_ -I/usr/lib/R/include
> > > > -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux -c
> > > > ErrorHandling.c gcc -g -O2 -D_R_ -I/usr/lib/R/include
> > > > -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux -c
> > > > ManagerInterfaceUtils.c gcc -g -O2 -D_R_ -I/usr/lib/R/include
> > > > -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux -c References.c
> > > > gcc -g -O2 -D_R_ -I/usr/lib/R/include
> > > > -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux -c JNIUtils.c
> > > > gcc -shared -o libRSNativeJava.so CtoJava.o ErrorHandling.o
> > > > ManagerInterfaceUtils.o References.o JNIUtils.o
> > > > -L/opt/lang/java/j2sdk1.4.2_01/jre/lib/i386/client
> > > > -L/opt/lang/java/j2sdk1.4.2_01/jre/lib/i386
> > > > -L/opt/lang/java/j2sdk1.4.2_01/jre/../lib/i386 -ljvm
> > > > -L/tmp/R.INSTALL.30363/SJava/inst/libs
> > > > -L/opt/lang/java/j2sdk1.4.2_01/jre/lib/i386/client
> > > > -L/opt/lang/java/j2sdk1.4.2_01/jre/lib/i386
> > > > -L/opt/lang/java/j2sdk1.4.2_01/jre/../lib/i386
> > > > -L/usr/lib/R/library/SJava/libs
> > > > if test -n "CtoJava.h ErrorHandling.h JNIUtils.h
> > > > ManagerInterfaceUtils.h References.h" ; then cp CtoJava.h
> > > > ErrorHandling.h JNIUtils.h ManagerInterfaceUtils.h
> > > > References.h /tmp/R.INSTALL.30363/SJava/inst/include ; fi mv
> > > > libRSNativeJava.so /tmp/R.INSTALL.30363/SJava/inst/libs
> > > > Generating JNI header files from Java classes.
> > > > RForeignReference, RManualFunctionActionListener,
> > > > ROmegahatInterpreter & REvaluator
> > > > *************
> > > > Warning:
> > > > At present, to use the library you must set the
> > > > LD_LIBRARY_PATH environment variable
> > > > to
> > > >
> > > > /usr/lib/R/library/SJava/libs:/opt/lang/java/j2sdk1.4.2_01/jre
> > > /lib/i386/client:/opt/lang/java/j2sdk1.4.2_>
> > > 01/jre/lib/i386:/opt/lang/java/j2sdk1.4.2_01/jre/../lib/i386:
> > > > or use one of the RJava.bsh or RJava.csh scripts
> > > > *************
> > > > ** libs
> > > > gcc -I/usr/lib/R/include -D_R_ -I/usr/lib/R/include
> > > > -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include -IRSJava
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux
> > > > -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC
> > > > -O2 -m486 -fno-strength-reduce -g -c ConverterExamples.c -o
> > > > ConverterExamples.o gcc -I/usr/lib/R/include -D_R_
> > > > -I/usr/lib/R/include -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include -IRSJava
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux
> > > > -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC
> > > > -O2 -m486 -fno-strength-reduce -g -c Converters.c -o
> > > > Converters.o gcc -I/usr/lib/R/include -D_R_
> > > > -I/usr/lib/R/include -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include -IRSJava
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux
> > > > -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC
> > > > -O2 -m486 -fno-strength-reduce -g -c Reflectance.c -o
> > > > Reflectance.o gcc -I/usr/lib/R/include -D_R_
> > > > -I/usr/lib/R/include -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include -IRSJava
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux
> > > > -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC
> > > > -O2 -m486 -fno-strength-reduce -g -c REmbed.c -o REmbed.o gcc
> > > > -I/usr/lib/R/include -D_R_ -I/usr/lib/R/include
> > > > -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include -IRSJava
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux
> > > > -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC
> > > > -O2 -m486 -fno-strength-reduce -g -c REmbedWin.c -o
> > > > REmbedWin.o gcc -I/usr/lib/R/include -D_R_
> > > > -I/usr/lib/R/include -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include -IRSJava
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux
> > > > -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC
> > > > -O2 -m486 -fno-strength-reduce -g -c REval.c -o REval.o gcc
> > > > -I/usr/lib/R/include -D_R_ -I/usr/lib/R/include
> > > > -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include -IRSJava
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux
> > > > -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC
> > > > -O2 -m486 -fno-strength-reduce -g -c RFunctionListener.c -o
> > > > RFunctionListener.o gcc -I/usr/lib/R/include -D_R_
> > > > -I/usr/lib/R/include -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include -IRSJava
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux
> > > > -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC
> > > > -O2 -m486 -fno-strength-reduce -g -c RReferenceCall.c -o
> > > > RReferenceCall.o gcc -I/usr/lib/R/include -D_R_
> > > > -I/usr/lib/R/include -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include -IRSJava
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux
> > > > -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC
> > > > -O2 -m486 -fno-strength-reduce -g -c RStoJava.c -o RStoJava.o
> > > > gcc -I/usr/lib/R/include -D_R_ -I/usr/lib/R/include
> > > > -I/usr/lib/R/include/R_ext
> > > > -I/tmp/R.INSTALL.30363/SJava/src/RSJava -I.
> > > > -I/tmp/R.INSTALL.30363/SJava/inst/include -IRSJava
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include
> > > > -I/opt/lang/java/j2sdk1.4.2_01/include/linux
> > > > -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC
> > > > -O2 -m486 -fno-strength-reduce -g -c RtoJava.c -o RtoJava.o
> > > > gcc -shared -L/usr/local/lib -o SJava.so ConverterExamples.o
> > > > Converters.o Reflectance.o REmbed.o REmbedWin.o REval.o
> > > > RFunctionListener.o RReferenceCall.o RStoJava.o RtoJava.o
> > > > -L/tmp/R.INSTALL.30363/SJava/inst/libs
> > > > -L/opt/lang/java/j2sdk1.4.2_01/jre/lib/i386/client
> > > > -L/opt/lang/java/j2sdk1.4.2_01/jre/lib/i386
> > > > -L/opt/lang/java/j2sdk1.4.2_01/jre/../lib/i386
> > > > -L/usr/lib/R/library/SJava/libs -lRSNativeJava -ljvm
> > > > ** R
> > > > ** inst
> > > > ** help
> > > > >>> Building/Updating help pages for package 'SJava'
> > > > Formats: text html latex example
> > > > Array text html latex example
> > > > Dollar text html latex example
> > > > DotJavaSigs text html latex
> > > > DotjavaConfig text html latex
> > > > JClass text html latex example
> > > > Java text html latex example
> > > > JavaConstructor text html latex example
> > > > JavaInit text html latex example
> > > > JavaTerminate text html latex example
> > > > OmegahatExpression text html latex example
> > > > RSJava.symbol text html latex example
> > > > RtoJavaSig text html latex example
> > > > expandClassName text html latex example
> > > > foreignReference text html latex example
> > > > getForeignReferences text html latex example
> > > > getJavaConverterDescriptions text html latex example
> > > > getJavaHandler text html latex example
> > > > getMethods text html latex example
> > > > getNumJavaConverters text html latex example
> > > > interfaceGenerator text html latex example
> > > > isJavaInitialized text html latex example
> > > > javaConfig text html latex example
> > > > javaHandlerGenerator text html latex example
> > > > javaIs text html latex example
> > > > javaMatchFunctions text html latex
> > > > javaSig text html latex example
> > > > jdynamicCompile text html latex example
> > > > mergePath text html latex example
> > > > mergeProperties text html latex example
> > > > omegahatReference text html latex example
> > > > removeJavaConverter text html latex example
> > > > setConvertible text html latex example
> > > > setJavaConverter text html latex example
> > > > setJavaFunctionConverter text html latex example
> > > > setJavaHandler text html latex example
> > > > missing link(s): javaHandlerGenerator()
> > > > Creating the symbolic link for libSJava.so in
> > > > /usr/lib/R/library/SJava/libs/
> > > > * DONE (SJava)
> > > >
> > > > * DONE (INSTALL)
> > > >
> > > > ______________________________________________
> > > > R-help at stat.math.ethz.ch mailing list
> > > > https://www.stat.math.ethz.ch/mailman/listinfo> /r-help
> > > >
> > > >
> > >
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>
> --
> _______________________________________________________________
>
> Duncan Temple Lang duncan at research.bell-labs.com
> Bell Labs, Lucent Technologies office: (908)582-3217
> 700 Mountain Avenue, Room 2C-259 fax: (908)582-3340
> Murray Hill, NJ 07974-2070
> http://cm.bell-labs.com/stat/duncan
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