rJava Error
On Jun 27, 2012, at 12:16 AM, fabin.ittiachan wrote:
Hi, I'm receiving an error when I am trying to install rJava. I have posted the error below.
Your R was not compiled with --enable-R-shlib so you can't use JRI (see http://rforge.net/rJava). You can either disable JRI (if you don't need it) or have to use R compiled with shlib support. NB: stats-rosuda-devel mailing list is the proper list for rJava questions. Cheers, Simon
RHive_0.0-6.tar.gz rJava_0.9-3.tar.gz RJDBC_0.2-0.tar.gz Rserve_0.6-8.tar.gz [root at localhost Package]# R CMD INSTALL rJava_0.9-3.tar.gz * installing to library ?/usr/local/lib64/R/library? * installing *source* package ?rJava? ... ** package ?rJava? successfully unpacked and MD5 sums checked checking for gcc... gcc -std=gnu99 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 -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -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 configure: checking whether gcc -std=gnu99 supports static inline... yes checking whether setjmp.h is POSIX.1 compatible... yes checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking Java support in R... present: interpreter : '/usr/local/Java/jre/bin/java' archiver : '/usr/local/Java/jre/../bin/jar' compiler : '/usr/local/Java/jre/../bin/javac' header prep.: '/usr/local/Java/jre/../bin/javah' cpp flags : '-I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux' java libs : '-L/usr/local/Java/jre/lib/amd64 -L/usr/local/Java/jre/lib/amd64/server -ljvm' 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 memory profiling is desired... 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/RtmpUyYk4N/R.INSTALL6645c827c46/rJava/jri) configure: running /bin/sh ./configure '--prefix=/usr/local' --cache-file=/dev/null --srcdir=. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for gcc... gcc -std=gnu99 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 -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -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 whether Java interpreter works... 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 -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c Rglue.c -o Rglue.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c arrayc.c -o arrayc.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c callJNI.c -o callJNI.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c callback.c -o callback.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c fields.c -o fields.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c jri_glue.c -o jri_glue.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c loader.c -o loader.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c otables.c -o otables.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c rJava.c -o rJava.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG -I. -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c tools.c -o tools.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o tools.o -L/usr/local/Java/jre/lib/amd64 -L/usr/local/Java/jre/lib/amd64/server -ljvm (cd ../jri && make) make[1]: Entering directory `/tmp/RtmpUyYk4N/R.INSTALL6645c827c46/rJava/jri' make -C src JRI.jar make[2]: Entering directory `/tmp/RtmpUyYk4N/R.INSTALL6645c827c46/rJava/jri/src' /usr/local/Java/jre/../bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.java warning: [options] bootstrap class path not set in conjunction with -source 1.4 1 warning /usr/local/Java/jre/../bin/javah -d . -classpath . org.rosuda.JRI.Rengine gcc -std=gnu99 -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -fpic -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include gcc -std=gnu99 -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -fpic -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include gcc -std=gnu99 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -fpic -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include gcc -std=gnu99 -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -fpic -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include gcc -std=gnu99 -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -fpic -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux gcc -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux -fpic -I/usr/local/Java/jre/../include -I/usr/local/Java/jre/../include/linux gcc -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared -L/usr/local/Java/jre/lib/amd64 -L/usr/local/Java/jre/lib/amd64/server -ljvm /usr/local/lib64/R/lib/libR.a -L/usr/local/lib64/R/lib -lRblas -lgfortran -lm -lreadline -lrt -ldl -lm /usr/bin/ld: /usr/local/lib64/R/lib/libR.a(attrib.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/local/lib64/R/lib/libR.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [libjri.so] Error 1 make[2]: Leaving directory `/tmp/RtmpUyYk4N/R.INSTALL6645c827c46/rJava/jri/src' make[1]: *** [src/JRI.jar] Error 2 make[1]: Leaving directory `/tmp/RtmpUyYk4N/R.INSTALL6645c827c46/rJava/jri' make: *** [jri] Error 2 ERROR: compilation failed for package ?rJava? * removing ?/usr/local/lib64/R/library/rJava? [root at localhost Package]# I am working on CentOS which is running on top of a VM. I did not get the error when I installed rJava normally but this happens when I had complied R with shared library enabled. Appreciate the help. Regards, Fabin -- View this message in context: http://r.789695.n4.nabble.com/rJava-Error-tp4634572.html Sent from the R help mailing list archive at Nabble.com.
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