[R] SJava help
Weiming Zhang
Weiming.Zhang at uchsc.edu
Wed Sep 24 19:15:50 CEST 2003
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/Environment.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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