Jiiindo wrote: > Colleagues, > How i can solve this error when i install SJava package
A more recent version of SJava is available with > source('http://bioconductor.org/biocLite.R') > biocLite('SJava') rJava is an alternative. Martin > Thanks > ---------------- > R CMD INSTALL -c /usr/local/lib/R/SJava_0.69-0.tar.gz > > * installing to library ‘/usr/local/lib/R/site-library’ > * installing *source* package ‘SJava’ ... > checking for java... /usr/lib/jvm/java-6-sun/bin/java > Java VM /usr/lib/jvm/java-6-sun/bin/java > checking for javah... /usr/lib/jvm/java-6-sun/bin/javah > Looking in /usr/lib/jvm/java-6-sun/include > Looking in /usr/lib/jvm/java-6-sun/include/linux > checking for g++... g++ > checking for C++ compiler default output... 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 g++ accepts -g... yes > checking for gcc... gcc > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ANSI C... none needed > checking for Rf_initEmbeddedR in -lR... no > No R shared library found > configure: creating ./config.status > config.status: creating Makevars > config.status: creating src/Makevars > config.status: creating src/RSJava/Makefile > config.status: creating Makefile_rules > config.status: creating inst/scripts/RJava.bsh > config.status: creating inst/scripts/RJava.csh > config.status: creating R/zzz.R > config.status: creating cleanup > config.status: creating inst/scripts/RJava > Copying the cleanup script to the scripts/ directory > Building libRSNativeJava.so in > /tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava > if test ! -d /usr/local/lib/R/site-library/SJava/libs ; then \ > mkdir /usr/local/lib/R/site-library/SJava/libs ; \ > fi > gcc -std=gnu99 -g -O2 -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -c CtoJava.c > CtoJava.cweb:148: error: expected '=', ',', ';', 'asm' or '__attribute__' > before 'vm1_args' > CtoJava.cweb:215: error: static declaration of 'std_env' follows non-static > declaration > CtoJava.cweb:195: error: previous declaration of 'std_env' was here > CtoJava.cweb: In function 'create_Java_vm': > CtoJava.cweb:256: error: 'vm1_args' undeclared (first use in this function) > CtoJava.cweb:256: error: (Each undeclared identifier is reported only once > CtoJava.cweb:256: error: for each function it appears in.) > make: *** [CtoJava.o] Error 1 > Generating JNI header files from Java classes. > RForeignReference, RManualFunctionActionListener, ROmegahatInterpreter & > REvaluator > ************* > Warning: > At present, to use the library you must set the > LD_LIBRARY_PATH environment variable > to > > /usr/local/lib/R/site-library/SJava/libs:/usr/lib/jvm/java-6-sun-1.6.0.14/jre/lib/i386/server:/usr/lib/jvm/java-6-sun-1.6.0.14/jre/lib/i386:/usr/lib/jvm/java-6-sun-1.6.0.14/jre/../lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib > or use one of the RJava.bsh or RJava.csh scripts > ************* > ** libs > gcc -std=gnu99 -I/usr/local/lib/R/include -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include -IRSJava > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -I/usr/local/include -fpic -g -O2 -c ConverterExamples.c -o > ConverterExamples.o > ConverterExamples.cweb: In function ‘RS_JAVA_setFunctionConverter’: > ConverterExamples.cweb:213: warning: assignment discards qualifiers from > pointer target type > ConverterExamples.cweb: In function ‘RS_JAVA_toJavaFunctionConverter’: > ConverterExamples.cweb:312: warning: passing argument 1 of > ‘getOmegahatReferenceValue’ discards qualifiers from pointer target type > gcc -std=gnu99 -I/usr/local/lib/R/include -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include -IRSJava > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -I/usr/local/include -fpic -g -O2 -c Converters.c -o Converters.o > Converters.cweb: In function ‘RS_JAVA_removeConverter’: > Converters.cweb:399: warning: assignment discards qualifiers from pointer > target type > gcc -std=gnu99 -I/usr/local/lib/R/include -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include -IRSJava > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -I/usr/local/include -fpic -g -O2 -c REmbed.c -o REmbed.o > gcc -std=gnu99 -I/usr/local/lib/R/include -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include -IRSJava > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -I/usr/local/include -fpic -g -O2 -c REmbedWin.c -o REmbedWin.o > gcc -std=gnu99 -I/usr/local/lib/R/include -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include -IRSJava > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -I/usr/local/include -fpic -g -O2 -c REval.c -o REval.o > REval.cweb: In function > ‘Java_org_omegahat_Interfaces_NativeInterface_OmegaInterfaceManager_nativeSetup’: > REval.cweb:249: warning: implicit declaration of function ‘setJNIEnv’ > REval.cweb:250: warning: implicit declaration of function ‘computeJavaVM’ > gcc -std=gnu99 -I/usr/local/lib/R/include -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include -IRSJava > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -I/usr/local/include -fpic -g -O2 -c RFunctionListener.c -o > RFunctionListener.o > RFunctionListener.cweb: In function ‘RFunctionConverter’: > RFunctionListener.cweb:133: warning: assignment discards qualifiers from > pointer target type > RFunctionListener.cweb:140: warning: implicit declaration of function > ‘s_catch_exception’ > gcc -std=gnu99 -I/usr/local/lib/R/include -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include -IRSJava > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -I/usr/local/include -fpic -g -O2 -c RReferenceCall.c -o > RReferenceCall.o > gcc -std=gnu99 -I/usr/local/lib/R/include -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include -IRSJava > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -I/usr/local/include -fpic -g -O2 -c RStoJava.c -o RStoJava.o > RStoJava.cweb: In function ‘s_to_java_basic’: > RStoJava.cweb:798: warning: cast from pointer to integer of different size > RStoJava.cweb: In function ‘RS_genericJavaCall’: > RStoJava.cweb:274: warning: assignment discards qualifiers from pointer > target type > RStoJava.cweb: In function ‘argsToArray’: > RStoJava.cweb:623: warning: passing argument 3 of ‘s_to_java_basic’ discards > qualifiers from pointer target type > RStoJava.cweb: In function ‘userReferenceToJava’: > RStoJava.cweb:1615: warning: assignment discards qualifiers from pointer > target type > gcc -std=gnu99 -I/usr/local/lib/R/include -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include -IRSJava > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -I/usr/local/include -fpic -g -O2 -c Reflectance.c -o Reflectance.o > gcc -std=gnu99 -I/usr/local/lib/R/include -D_R_ -I/usr/local/lib/R/include > -I/usr/local/lib/R/include/R_ext > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/src/RSJava -I. > -I/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/include -IRSJava > -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux > -I/usr/local/include -fpic -g -O2 -c RtoJava.c -o RtoJava.o > gcc -std=gnu99 -shared -L/usr/local/lib -o SJava.so ConverterExamples.o > Converters.o REmbed.o REmbedWin.o REval.o RFunctionListener.o > RReferenceCall.o RStoJava.o Reflectance.o RtoJava.o > -L/tmp/RtmpdcTvTv/R.INSTALL327b23c6/SJava/inst/libs > -L/usr/lib/jvm/java-6-sun-1.6.0.14/jre/lib/i386/server > -L/usr/lib/jvm/java-6-sun-1.6.0.14/jre/lib/i386 > -L/usr/lib/jvm/java-6-sun-1.6.0.14/jre/../lib/i386 > -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib > -L/usr/local/lib/R/site-library/SJava/libs -lRSNativeJava -ljvm > -L/usr/local/lib/R/lib -lR > /usr/bin/ld: cannot find -lRSNativeJava > collect2: ld returned 1 exit status > make: *** [SJava.so] Error 1 > ERROR: compilation failed for package ‘SJava’ > * removing ‘/usr/local/lib/R/site-library/SJava’ -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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