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)
>
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