g *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... /usr/bin/grep checking for egrep... /usr/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/sap/jdk1.6.0_18//jre/bin/java' archiver : '/usr/sap/jdk1.6.0_18//bin/jar' compiler : '/usr/sap/jdk1.6.0_18//bin/javac' header prep.: '/usr/sap/jdk1.6.0_18//bin/javah' cpp flags : '-I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux' java libs : '-L/usr/sap/jdk1.6.0_18/jre/lib/amd64/server -L/usr/sap/jdk1.6.0_18/jre/lib/amd64 -L/usr/sap/jdk1.6.0_18/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -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/RtmplI0Fwh/R.INSTALL25603707d3d6a/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... /usr/bin/grep checking for egrep... /usr/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/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c Rglue.c -o Rglue.o Rglue.c:831: warning: 'new_jrectRef' defined but not used gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c arrayc.c -o arrayc.o arrayc.c: In function 'RgetShortArrayCont': arrayc.c:161: warning: 'o' may be used uninitialized in this function arrayc.c: In function 'RgetCharArrayCont': arrayc.c:124: warning: 'o' may be used uninitialized in this function arrayc.c: In function 'RgetBoolArrayCont': arrayc.c:87: warning: 'o' may be used uninitialized in this function arrayc.c: In function 'RgetSimpleClassNames': arrayc.c:420: warning: 'jobj' may be used uninitialized in this function arrayc.c: In function 'RgetLongArrayCont': arrayc.c:294: warning: 'o' may be used uninitialized in this function arrayc.c: In function 'RgetFloatArrayCont': arrayc.c:260: warning: 'o' may be used uninitialized in this function arrayc.c: In function 'RgetDoubleArrayCont': arrayc.c:229: warning: 'o' may be used uninitialized in this function arrayc.c: In function 'RgetIntArrayCont': arrayc.c:56: warning: 'o' may be used uninitialized in this function arrayc.c: In function 'RgetByteArrayCont': arrayc.c:198: warning: 'o' may be used uninitialized in this function arrayc.c: In function 'RgetObjectArrayCont': arrayc.c:12: warning: 'o' may be used uninitialized in this function gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c callJNI.c -o callJNI.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c callback.c -o callback.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c fields.c -o fields.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c init.c -o init.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c jri_glue.c -o jri_glue.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c loader.c -o loader.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c otables.c -o otables.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c rJava.c -o rJava.o gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I. -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -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/sap/jdk1.6.0_18/jre/lib/amd64/server -L/usr/sap/jdk1.6.0_18/jre/lib/amd64 -L/usr/sap/jdk1.6.0_18/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm -L/usr/lib64/R/lib -lR (cd ../jri && make) make[1]: Entering directory `/tmp/RtmplI0Fwh/R.INSTALL25603707d3d6a/rJava/jri' make -C src JRI.jar make[2]: Entering directory `/tmp/RtmplI0Fwh/R.INSTALL25603707d3d6a/rJava/jri/src' /usr/sap/jdk1.6.0_18//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 /usr/sap/jdk1.6.0_18//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 -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -fpic -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/lib64/R/include -I/usr/lib64/R/include gcc -std=gnu99 -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -fpic -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/lib64/R/include -I/usr/lib64/R/include gcc -std=gnu99 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -fpic -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -I/usr/lib64/R/include -I/usr/lib64/R/include gcc -std=gnu99 -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -fpic -I/usr/lib64/R/include -I/usr/lib64/R/include gcc -std=gnu99 -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -fpic -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux gcc -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux -fpic -I/usr/sap/jdk1.6.0_18//include -I/usr/sap/jdk1.6.0_18//include/linux rjava.c: In function 'RJava_request_lock': rjava.c:22: warning: ignoring return value of 'write', declared with attribute warn_unused_result rjava.c: In function 'RJava_clear_lock': rjava.c:30: warning: ignoring return value of 'write', declared with attribute warn_unused_result rjava.c: In function 'RJava_request_callback': rjava.c:39: warning: ignoring return value of 'write', declared with attribute warn_unused_result rjava.c: In function 'RJava_init_ctrl': rjava.c:51: warning: ignoring return value of 'write', declared with attribute warn_unused_result rjava.c:52: warning: ignoring return value of 'read', declared with attribute warn_unused_result gcc -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared -L/usr/sap/jdk1.6.0_18/jre/lib/amd64/server -L/usr/sap/jdk1.6.0_18/jre/lib/amd64 -L/usr/sap/jdk1.6.0_18/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm -L/usr/lib64/R/lib -lR /usr/sap/jdk1.6.0_18//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 /usr/sap/jdk1.6.0_18//bin/jar fc JRI.jar org libjri.so make[2]: Leaving directory `/tmp/RtmplI0Fwh/R.INSTALL25603707d3d6a/rJava/jri/src' rm -f libjri.so cp src/libjri.so libjri.so /usr/sap/jdk1.6.0_18//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. /usr/sap/jdk1.6.0_18//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. make[1]: Leaving directory `/tmp/RtmplI0Fwh/R.INSTALL25603707d3d6a/rJava/jri' installing via 'install.libs.R' to /usr/lib64/R/library/rJava ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'rJava', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/usr/lib64/R/library/rJava/libs/rJava.so': /usr/lib64/R/library/rJava/libs/rJava.so: undefined symbol: R_BadLongVector Error: loading failed Execution halted ERROR: loading failed * removing '/usr/lib64/R/library/rJava' The downloaded source packages are in '/tmp/Rtmpl00eIq/downloaded_packages' Updating HTML index of packages in '.Library' Making packages.html ... done Warning message: In install.packages("rJava") : installation of package 'rJava' had non-zero exit status