attempting to install rJava on R-2.7.0, x86_64 platform, config.log shows the
following error:
configure:3880: checking whether JNI programs can be compiled
configure:3898: gcc -m64 -std=gnu99 -o conftest -g -O2
-I/path/to/x86-64-linux/jdk-1.6.0_06/jre/../include conftest.c
-L/path/to/x86-64-linux/jdk-1.6.0_06/jre/lib/amd64/server
-L/path/to/x86-64-linux/jdk-1.6.0_06/jre/lib/amd64
-L/path/to/x86-64-linux/jdk-1.6.0_06/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm 5
/path/to/x86-64-linux/bin/ld: skipping incompatible /usr/lib/libc.so
when
searching for -lc /usr/lib/libc.a: could not read symbols: File format
is
ambiguous collect2: ld returned 1 exit status
It looks like the command above could use /lib64/libc.so.6, but running R CMD
javareconf shows that JNI linker flags don't contain any entry similar to
'-L/lib64':
-bash-3.00$ /path/to/noarch/bin/statcomp R-2.7.0 CMD javareconf
Java interpreter : /path/to/x86-64-linux/bin/java
Java version : 1.6.0_06
Java home path : /path/to/x86-64-linux/jdk-1.6.0_06/jre Java
compiler : /path/to/x86-64-linux/bin/javac
Java headers gen.: /path/to/x86-64-linux/bin/javah
Java archive tool: /path/to/x86-64-linux/bin/jar
Java library path:
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server
-L$(JAVA_HOME)/lib/amd64
-L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/lib
-L/usr/lib -ljvm JNI cpp flags: -I$(JAVA_HOME)/../include
Suggests on the root of the problem or best workarounds?
--
Nathan
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