Could some pls help with this error message. Pls see below
thanks
Rupak
---------- Forwarded message ----------
From: Rupak Khurana <[EMAIL PROTECTED]>
Date: Jan 31, 2007 2:46 PM
Subject: Unable to load rJava - Undefined Symbol GetCreatedJavaVMs
To: [EMAIL PROTECTED]
Simon
I am unable to load rJava. Pls see the log below. Any help is welcome and
appreciated.
thanks
Rupak
[EMAIL PROTECTED] rkhurana]# uname -a
Linux localhost.localdomain 2.6.18-1.2798.fc6 #1 SMP Mon Oct 16 14:37:32 EDT
2006 i686 i686 i386 GNU/Linux
[EMAIL PROTECTED] rkhurana]# echo $PATH
/usr/kerberos/sbin:/usr/local/jdk1.5.0_11/bin:/usr/lib/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/rkhurana/bin:/usr/local/jdk1.5.0_11/lib:/usr/local/jdk1.5.0_11/jre/lib:/usr/local/jdk1.5.0_11/jre/lib/i386:/usr/local/jdk1.5.0_11/jre/lib/i386/client:/usr/local/jdk1.5.0_11/jre/lib/i386/server:/usr/lib/R/library/rJava/libs:/usr/lib/R/lib
[EMAIL PROTECTED] rkhurana]# echo $LD_LIBRARY_PATH
/usr/local/jdk1.5.0_11/lib:/usr/local/jdk1.5.0_11/jre/lib:/usr/local/jdk1.5.0_11/jre/lib/i386:/usr/local/jdk1.5.0_11/jre/lib/i386/client:/usr/local/jdk1.5.0_11/jre/lib/i386/server:/usr/lib/R/library/rJava/libs:/usr/lib/R/lib:
[EMAIL PROTECTED] rkhurana]#
[EMAIL PROTECTED] rkhurana]# R
R version 2.4.1 (2006-12-18)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
' help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages("rJava")
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.stat.sfu.ca/src/contrib/rJava_0.4-13.tar.gz'
Content type 'application/x-gzip' length 195434 bytes
opened URL
==================================================
downloaded 190Kb
* Installing *source* package 'rJava' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for java... /usr/local/jdk1.5.0_11/bin/java
checking Java environment home... in /usr/local/jdk1.5.0_11/jre
checking for /usr/local/jdk1.5.0_11/jre/include/jni.h... no
checking for /usr/local/jdk1.5.0_11/jre/jni.h... no
checking for /usr/local/jdk1.5.0_11/jre/../include/jni.h... yes
checking for /usr/local/jdk1.5.0_11/jre/../include/./jni_md.h... no
checking for /usr/local/jdk1.5.0_11/jre/../include/linux/jni_md.h... yes
checking whether JNI programs can be compiled... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... yes
checking whether debugging output should be enabled... no
checking whether threads support is requested... no
checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no
checking whether JRI is requested... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status : creating src/config.h
=== configuring in jri (/tmp/R.INSTALL.G32323/rJava/jri)
configure: running /bin/sh ./configure '--prefix=/usr/local'
--cache-file=/dev/null --srcdir=.
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for java... /usr/local/jdk1.5.0_11/jre/bin/java
checking for javac... /usr/local/jdk1.5.0_11/bin/javac
checking for javah... /usr/local/jdk1.5.0_11/bin/javah
checking for jar... /usr/local/jdk1.5.0_11/bin/jar
checking whether Java interpreter works... yes
checking for Java environment... in /usr/local/jdk1.5.0_11/jre
checking for /usr/local/jdk1.5.0_11/jre/include/jni.h... no
checking for /usr/local/jdk1.5.0_11/jre/jni.h... no
checking for /usr/local/jdk1.5.0_11/jre/../include/jni.h... yes
checking for /usr/local/jdk1.5.0_11/jre/../include/./jni_md.h... no
checking for /usr/local/jdk1.5.0_11/jre/../include/linux/jni_md.h... yes
checking whether JNI programs can be compiled... yes
checking whether JNI programs can be run... yes
checking JNI data types... ok
checking whether Rinterface.h exports R_CStackXXX variables... yes
checking whether Rinterface.h exports R_SignalHandlers... yes
configure: creating ./config.status
config.status : creating src/Makefile
config.status: creating Makefile
config.status: creating run
config.status: creating src/config.h
** libs
gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/local/include
-I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fpic -O3 -g -std=gnu99 -c
callback.c -o callback.o
gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/local/include
-I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fpic -O3 -g -std=gnu99 -c
callJNI.c -o callJNI.o
gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/local/include
-I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fpic -O3 -g -std=gnu99 -c
jri_glue.c -o jri_glue.o
gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/local/include
-I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fpic -O3 -g -std=gnu99 -c
Rglue.c -o Rglue.o
gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/local/include
-I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fpic -O3 -g -std=gnu99 -c
rJava.c -o rJava.o
gcc -shared -Bdirect,--hash-stype=both,-Wl,-O1 -o rJava.so callback.o
callJNI.o jri_glue.o Rglue.o
rJava.o-L/usr/local/jdk1.5.0_11/jre/lib/i386/client
-L/usr/local/jdk1.5.0_11/jre/lib/i386
-L/usr/local/jdk1.5.0_11/jre/../lib/i386 -L/usr/lib/R/lib -L
-L/usr/lib/R/lib -L -L/usr/local/jdk1.5.0_11/lib
-L/usr/local/jdk1.5.0_11/jre/lib -L/usr/local/jdk1.5.0_11/jre/lib/i386
-L/usr/local/jdk1.5.0_11/jre/lib/i386/client
-L/usr/local/jdk1.5.0_11/jre/lib/i386/server -L/usr/lib/R/library/rJava/libs
-L/usr/lib/R/lib -L -ljvm -L/usr/lib/R/lib -lR
make -C ../jri/
make[1]: Entering directory `/tmp/R.INSTALL.G32323/rJava/jri'
make -C src JRI.jar
make[2]: Entering directory `/tmp/R.INSTALL.G32323/rJava/jri/src'
/usr/local/jdk1.5.0_11/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java
../RBool.java ../Rengine.java ../REXP.java ../RFactor.java ../RList.java
../RMainLoopCallbacks.java ../RVector.java
/usr/local/jdk1.5.0_11/bin/javah -d . -classpath . org.rosuda.JRI.Rengine
gcc -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK
-DRIF_HAS_RSIGHAND -O3 -g -std=gnu99 -I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fPIC
-I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -I/usr/lib/R/include
-I/usr/lib/R/include -I/usr/lib/R/include
gcc -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O3
-g -std=gnu99 -I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fPIC
-I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -I/usr/lib/R/include
-I/usr/lib/R/include -I/usr/lib/R/include
gcc -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK
-DRIF_HAS_RSIGHAND -O3 -g -std=gnu99 -I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fPIC
-I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -I/usr/lib/R/include
-I/usr/lib/R/include -I/usr/lib/R/include
gcc -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND
-O3 -g -std=gnu99 -I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fPIC -I/usr/lib/R/include
-I/usr/lib/R/include -I/usr/lib/R/include
gcc -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK
-DRIF_HAS_RSIGHAND -O3 -g -std=gnu99 -I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fPIC
-I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux
gcc -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND
-O3 -g -std=gnu99 -I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux -fPIC
-I/usr/local/jdk1.5.0_11/jre/../include
-I/usr/local/jdk1.5.0_11/jre/../include/linux
gcc -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o
-shared -L/usr/local/jdk1.5.0_11/jre/lib/i386/client
-L/usr/local/jdk1.5.0_11/jre/lib/i386
-L/usr/local/jdk1.5.0_11/jre/../lib/i386 -L/usr/lib/R/lib -L
-L/usr/lib/R/lib -L -L/usr/local/jdk1.5.0_11/lib
-L/usr/local/jdk1.5.0_11/jre/lib -L/usr/local/jdk1.5.0_11/jre/lib/i386
-L/usr/local/jdk1.5.0_11/jre/lib/i386/client
-L/usr/local/jdk1.5.0_11/jre/lib/i386/server -L/usr/lib/R/library/rJava/libs
-L/usr/lib/R/lib -L -L/usr/local/jdk1.5.0_11/jre/lib/i386/client
-L/usr/local/jdk1.5.0_11/jre/lib/i386
-L/usr/local/jdk1.5.0_11/jre/../lib/i386 -L/usr/lib/R/lib -L
-L/usr/lib/R/lib -L -L/usr/local/jdk1.5.0_11/lib
-L/usr/local/jdk1.5.0_11/jre/lib -L/usr/local/jdk1.5.0_11/jre/lib/i386
-L/usr/local/jdk1.5.0_11/jre/lib/i386/client
-L/usr/local/jdk1.5.0_11/jre/lib/i386/server -L/usr/lib/R/library/rJava/libs
-L/usr/lib/R/lib -L -ljvm -L/usr/lib/R/lib -lR
/usr/local/jdk1.5.0_11/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java
../RBool.java ../Rengine.java ../REXP.java ../RFactor.java ../RList.java
../RMainLoopCallbacks.java ../RVector.java
/usr/local/jdk1.5.0_11/bin/jar fc JRI.jar org libjri.so
make[2]: Leaving directory `/tmp/R.INSTALL.G32323/rJava/jri/src'
rm -f libjri.so
cp src/libjri.so libjri.so
/usr/local/jdk1.5.0_11/bin/javac -target 1.4 -source 1.4 -classpath
src/JRI.jar -d examples examples/rtest2.java
Note: examples/rtest2.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
/usr/local/jdk1.5.0_11/bin/javac -target 1.4 -source 1.4 -classpath
src/JRI.jar -d examples examples/rtest.java
Note: examples/rtest.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
make[1]: Leaving directory `/tmp/R.INSTALL.G32323/rJava/jri'
** R
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'rJava'
Formats: text html latex example
accessOp text html latex example
jarray text html latex example
jarrayRef-class text html latex
jcall text html latex example
jcast text html latex example
jcastToArray text html latex example
jcheck text html latex example
jequals text html latex example
jfield text html latex example
jfloat-class text html latex
jfloat text html latex
jinit text html latex example
jnew text html latex example
jnull text html latex example
jobjRef-class text html latex
jreflection text html latex example
jsimplify text html latex example
show text html latex
** building package indices ...
* DONE (rJava)
The downloaded packages are in
/tmp/RtmpVfFdOr/downloaded_packages
> library(rJava)
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'/usr/lib/R/library/rJava/libs/rJava.so':
/usr/lib/R/library/rJava/libs/rJava.so: undefined symbol:
JNI_GetCreatedJavaVMs
Error: .onLoad failed in 'loadNamespace' for 'rJava'
Error: package/namespace load failed for 'rJava'
[[alternative HTML version deleted]]
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