[R] R-2.7.0 rJava installation failure on x86_64

From: Nathan Coulter <org.r-project_at_pooryorick.com>
Date: Tue, 03 Jun 2008 17:46:42 +0000


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

______________________________________________
R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Received on Tue 03 Jun 2008 - 19:51:07 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Tue 03 Jun 2008 - 20:30:45 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive