[R] trouble with installing SJava
Martin Morgan
mtmorgan at fhcrc.org
Tue Jan 12 21:46:51 CET 2010
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.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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