[R] Installing rJava fails on Gentoo (amd64) with Sun JDK - checking JNI data types... error
Anthony Staines
anthony.staines at dcu.ie
Sat Aug 14 00:31:57 CEST 2010
Installing rJava fails consistently, whether installed via
the command line as below, or through "install.packages(
'rJava' )", and whether 0.84 or 0.85 is used, with the
message :-
"checking JNI data types... configure: error: One or more
JNI types differ from the corresponding native type. You may
need to use non-standard compiler flags or a different
compiler in order to fix this."
I've tried to fix it using suggestions from the r-help list,
and the Gentoo java documentation, but had no joy so far.
Other Java stuff works fine on this box.
# R CMD INSTALL rJava_0.8-5.tar.gz
* installing to library ‘/usr/lib64/R/library’
* installing *source* package ‘rJava’ ...
checking for gcc... x86_64-pc-linux-gnu-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 x86_64-pc-linux-gnu-gcc -std=gnu99 accepts
-g... yes
checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to
accept ISO C89... none needed
checking how to run the C preprocessor...
x86_64-pc-linux-gnu-gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 x86_64-pc-linux-gnu-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/bin/java'
archiver : '/usr/bin/jar'
compiler :
'/home/astaines/.gentoo/java-config-2/current-user-vm/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/opt/sun-jdk-1.6.0.20/jre/../include
-I/opt/sun-jdk-1.6.0.20/jre/../include/linux'
java libs : '-L/opt/sun-jdk-1.6.0.20/jre/lib/amd64/server
-L/opt/sun-jdk-1.6.0.20/jre/lib/amd64
-L/opt/sun-jdk-1.6.0.20/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... configure: error: One or more JNI
types differ from the corresponding native type. You may
need to use non-standard compiler flags or a different
compiler in order to fix this.
ERROR: configuration failed for package ‘rJava’
* removing ‘/usr/lib64/R/library/rJava’
# R --version
R version 2.11.1 (2010-05-31)
# java -showversion
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) 64-Bit Server VM (build 16.3-b01, mixed mode)
The compiler mentioned in the R output :-
/home/astaines/.gentoo/java-config-2/current-user-vm
is a link pointing to
/usr/lib/jvm/sun-jdk-1.6
which in turn is a link pointing to
/opt/sun-jdk-1.6.0.20
however, any of the three will work.
# R CMD javareconf
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version : 1.6.0_20
Java home path : /opt/sun-jdk-1.6.0.20/jre
Java compiler :
/home/astaines/.gentoo/java-config-2/current-user-vm/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path:
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server
-L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib
-L/usr/lib -ljvm
JNI cpp flags : -I$(JAVA_HOME)/../include
-I$(JAVA_HOME)/../include/linux
Updating Java configuration in /usr/lib64/R
Done.
JAVA_HOME is unset by default on my system. As suggested, by
Godmar Back, on the list I've tried setting it. The Gentoo
way is to use
JAVA_HOME=$(java-config --jdk-home)
and this produces what I think is the desired result
#printenv | grep -i JAVA_HOME
JAVA_HOME=/opt/sun-jdk-1.6.0.20
BUT
# env JAVA_HOME=/opt/sun-jdk-1.6.0.20/ R CMD javareconf
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version : 1.6.0_20
Java home path : /opt/sun-jdk-1.6.0.20/jre
Java compiler :
/home/astaines/.gentoo/java-config-2/current-user-vm/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path:
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server
-L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib
-L/usr/lib -ljvm
JNI cpp flags : -I$(JAVA_HOME)/../include
-I$(JAVA_HOME)/../include/linux
Updating Java configuration in /usr/lib64/R
Done.
AND
Kitchen ~ # env JAVA_HOME=/opt/sun-jdk-1.6.0.20/ R CMD
INSTALL rJava_0.8-5.tar.gz
* installing to library ‘/usr/lib64/R/library’
* installing *source* package ‘rJava’ ...
checking for gcc... x86_64-pc-linux-gnu-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 Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler :
'/home/astaines/.gentoo/java-config-2/current-user-vm/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/opt/sun-jdk-1.6.0.20/jre/../include
-I/opt/sun-jdk-1.6.0.20/jre/../include/linux'
java libs : '-L/opt/sun-jdk-1.6.0.20/jre/lib/amd64/server
-L/opt/sun-jdk-1.6.0.20/jre/lib/amd64
-L/opt/sun-jdk-1.6.0.20/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... configure: error: One or more JNI
types differ from the corresponding native type. You may
need to use non-standard compiler flags or a different
compiler in order to fix this.
ERROR: configuration failed for package ‘rJava’
* removing ‘/usr/lib64/R/library/rJava’
All advice gratefully received
--
Anthony Staines, Professor of Health Systems Research,
School of Nursing, Dublin City University, Dublin 9,Ireland.
Tel:- +353 1 700 7807. Mobile:- +353 86 606 9713
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