[R] can't get rJava to install on Linux

Wed Jul 8 04:07:48 CEST 2009

Switching to Sun definitely did not help, still no build with rJava,
below is the output of  R CMD javareconf.

mkimpel-m90 /home/mkimpel/bin# ./R CMD javareconf
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version     : 1.6.0_14
Java home path   : /usr/lib/jvm/java-6-sun-1.6.0.14/jre
/home/mkimpel/R_HOME/R-2.9.1/R-build/lib64/R/bin/javareconf: line 150:
/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javac: No such file
or directory
Java compiler    : not functional
Java headers gen.: /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javah
Java archive tool: /usr/bin/jar
Java library path: /usr/lib/../lib/gcj-4.3-90:/usr/lib/jni
JNI linker flags : -L/usr/lib/../lib/gcj-4.3-90 -L/usr/lib/jni -ljvm
JNI cpp flags    :

Updating Java configuration in /home/mkimpel/R_HOME/R-2.9.1/R-build/lib64/R
Done.

------------------------------------------------------------
Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail

"The real problem is not whether machines think but whether men do."
-- B. F. Skinner
******************************************************************

On Tue, Jul 7, 2009 at 9:43 PM, Godmar Back<godmar at gmail.com> wrote:
> This is just a guess: looks like you have GNU's Java version in your
> path (aka "gcj").
> Perhaps rJava relies on Sun's Java version.
>
> If so, install Sun's Java first. apt-get install sun-java6-jdk might do it.
>
>  - Godmar
>
>
> On Tue, Jul 7, 2009 at 9:28 PM, Mark Kimpel<mwkimpel at gmail.com> wrote:
>> Having difficulties getting rJava to install on my Debian Squeeze box.
>> Perused the R-help list and tried some things that have worked for
>> others but not for me. Below is the output of my attempted build, R
>> CMD javareconf -e, and sessionInfo(). Note I tried the R CMD
>> javareconf also as root, restarted R after each of these, all no help.
>>
>>
>> * 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 Java support in R... present:
>> interpreter : '/usr/bin/java'
>> archiver    : '/usr/bin/jar'
>> compiler    : '/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javac'
>> header prep.: '/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javah'
>> cpp flags   : ''
>> java libs   : '-L/usr/lib/../lib/gcj-4.3-90 -L/usr/lib/jni -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 ‘/home/mkimpel/R_HOME/site-library-2.9.0/rJava’
>>
>> The downloaded packages are in
>>        ‘/tmp/Rtmpfp9kiG/downloaded_packages’
>> Warning message:
>> In install.packages("rJava") :
>>  installation of package 'rJava' had non-zero exit status
>>
>>  ./R CMD javareconf -e
>> Java interpreter : /usr/bin/java
>> Java version     : 1.5.0
>> Java home path   : /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre
>> Java compiler    : /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javac
>> Java headers gen.: /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javah
>> Java archive tool: /usr/bin/jar
>> Java library path: /usr/lib/../lib/gcj-4.3-90:/usr/lib/jni
>> JNI linker flags : -L/usr/lib/../lib/gcj-4.3-90 -L/usr/lib/jni -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
>>
>>> sessionInfo()
>> R version 2.9.1 (2009-06-26)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices datasets  utils     methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] tcltk_2.9.1 tools_2.9.1
>> ------------------------------------------------------------
>> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
>> Indiana University School of Medicine
>>
>> 15032 Hunter Court, Westfield, IN  46074
>>
>> (317) 490-5129 Work, & Mobile & VoiceMail
>>
>> "The real problem is not whether machines think but whether men do."
>> -- B. F. Skinner
>>
>> ______________________________________________
>> 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.
>>
>