[R] rJava Error

Simon Urbanek simon.urbanek at r-project.org
Wed Jan 9 17:28:23 CET 2013 

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 
> 
> --
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