[R] SJava help
Weiming Zhang
Weiming.Zhang at uchsc.edu
Wed Sep 24 20:54:43 CEST 2003
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
> >
> >
>
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