Rupak Khurana
2007-Jan-31 20:05 UTC
[Rd] Fwd: Unable to load rJava - Undefined Symbol GetCreatedJavaVMs
Could some pls help with this error message. Pls see below thanks Rupak ---------- Forwarded message ---------- From: Rupak Khurana <khurana.rupak@gmail.com> Date: Jan 31, 2007 2:46 PM Subject: Unable to load rJava - Undefined Symbol GetCreatedJavaVMs To: simon.urbanek@r-project.org Simon I am unable to load rJava. Pls see the log below. Any help is welcome and appreciated. thanks Rupak [root@localhost 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 [root@localhost 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 [root@localhost 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: [root@localhost rkhurana]# [root@localhost 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]]
Possibly Parallel Threads
Wisdom of the Ancients
