It seems that you are not alone with that error (
http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing).
Defining only JAVA_HOME he would find everything else.
Backup your /etc/R before do this.
Running the R CMD javareconf is to place variables like this in
/etc/R/Makeconf (hope the experts corect me)
JAR = /usr/bin/jar
JAVA = /usr/bin/java
JAVAC = /usr/bin/javac
JAVAH = /usr/bin/javah
JAVA_HOME = /usr/lib/jvm/java-6-sun-1.6.0.24/jre
JAVA_LD_LIBRARY_PATH =
$(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib
JAVA_LIBS = -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/lib/i386
-L$(JAVA_HOME)/../lib/i386 -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib
-ljvm
JAVA_CPPFLAGS = -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
Add it manually. Pay attention the amd64 versus my i386. Place on variable
sections
Edit /etc/R/ldpahs place before if test -n...
: ${JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.24/jre}
:
${R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/i386/server:${JAVA_HOME}/lib/i386:${JAVA_HOME}/../lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib}
Again correct with your paths.
And try to install rJava.
Caveman
On Fri, Mar 18, 2011 at 7:30 PM, jcheng liu <jcheng....@gmail.com> wrote:
> Dear Orvalho Augusto,
> Thank so much for you response!
> We had run R CMD javareconf -e, and even R CMD javareconf in administrator.
>
> Actually, we had install the JDK. And in the output, only the item of JNI
> cpp flages could not be detected(I listed output below). What does the item
> mean? What need we install?
>
> Thanks,
> Jiacheng
>
> R CMD javareconf -e
>
> Java interpreter : /usr/bin/java
> Java version : 1.6.0_24
> Java home path : /usr/java/jre1.6.0_24
> Java compiler : /usr/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/usr/java/packages/lib/amd64 -L/usr/lib64
> -L/lib64 -L/lib -L/usr/lib -ljvm
> JNI cpp flags :
>
> The following Java variables have been exported:
> JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS JAVA_LD_LIBRARY_PATH
> Runnig: /bin/tcsh
>
>
>
> On 3/18/2011 12:53 PM, Orvalho Augusto wrote:
>
> Run
> R CMD javareconf -e
>
> as the being suggest by the output. That will try to guess where is Java.
> Or you can install the JDK_HOME and JAVA_HOME variables.
>
> Good luck.
> Caveman
>
>
> On Fri, Mar 18, 2011 at 4:39 PM, jcheng liu <jcheng....@gmail.com> wrote:
>
>> Dear all,
>> Installing rJava fails. The message was listed below. I wonder why cpp
>> flag
>> could not be detected, although I had installed. Thanks!!!
>> -Jiacheng
>>
>> R CMD INSTALL rJava_0.9-0.tar.gz
>> * installing to library
>> /data1/mri_researchers/wexler_data/jiacheng/R-2.12.0/library
>> * installing *source* package rJava ...
>> checking for gcc... 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 gcc -std=gnu99 accepts -g... yes
>> checking for gcc -std=gnu99 option to accept ISO C89... none needed
>> checking how to run the C preprocessor... 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 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 : '/usr/bin/javac'
>> header prep.: '/usr/bin/javah'
>> cpp flags : ''
>> java libs : '-L/usr/java/jre1.6.0_24/lib/amd64/server
>> -L/usr/java/jre1.6.0_24/lib/amd64 -L/usr/java/jre1.6.0_24/../lib/amd64
>> -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib
>> -ljvm'
>> configure: error: One or more Java configuration variables are not set.
>> Make sure R is configured with full Java support (including JDK). Run
>> R CMD javareconf
>> as root to add Java support to R.
>>
>> If you don't have root privileges, run
>> R CMD javareconf -e
>> to set all Java-related variables and then install rJava.
>>
>> ERROR: configuration failed for package rJava
>> * removing /R-2.12.0/library/rJava
>>
>> [[alternative HTML version deleted]]
>>
>>
>> ______________________________________________
>> R-help@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.
>>
>>
>
>
>
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