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@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@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. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
