Can't install rJava 0.9 on Ubuntu 10.04

Question

I use R 2.13 from the CRAN apt repo for Ubuntu 10.04, and I'm trying to install Deducer, which requires JGR/rJava, but rJava refuses to build/install, complaining about being unable to build a JNI app. I tried sudo R CMD javareconf as suggested but that only led to a different error about the configuration being unset. I found R: rJava package install failing, so I tried the suggestions there of installing r-cran-rjava (but that's 0.8 and Deducer/JGR seem to insist on installing 0.9) and fiddling with my $JAVA_HOME, all to no avail. Any ideas?

Here's a more complete transcript of what happened:

$ sudo aptitude install r-cran-rjava
...
$ R

R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages(c('JGR','Deducer'))
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’
(as ‘lib’ is unspecified)
also installing the dependencies ‘rJava’, ‘JavaGD’, ‘iplots’

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz'
Content type 'application/x-gzip' length 527197 bytes (514 Kb)
opened URL
==================================================
downloaded 514 Kb

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/JavaGD_0.5-4.tar.gz'
Content type 'application/x-gzip' length 102242 bytes (99 Kb)
opened URL
==================================================
downloaded 99 Kb

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/iplots_1.1-4.tar.gz'
Content type 'application/x-gzip' length 330323 bytes (322 Kb)
opened URL
==================================================
downloaded 322 Kb

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/JGR_1.7-7.tar.gz'
Content type 'application/x-gzip' length 536564 bytes (523 Kb)
opened URL
==================================================
downloaded 523 Kb

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/Deducer_0.4-4.tar.gz'
Content type 'application/x-gzip' length 5325794 bytes (5.1 Mb)
opened URL
==================================================
downloaded 5.1 Mb

* installing *source* package ‘rJava’ ...
checking for gcc... gcc
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
c    hecking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -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 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   : '-I/usr/lib/jvm/java-6-openjdk/jre/../include'
java libs   : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details.

Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.

ERROR: configuration failed for package ‘rJava’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’
* installing *source* package ‘JavaGD’ ...
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -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
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking return type of signal handlers... void
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for select... yes
checking for socket... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
cpp flags   : '-I/usr/lib/jvm/java-6-openjdk/jre/../include'
java libs   : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details.
ERROR: configuration failed for package ‘JavaGD’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/JavaGD’
ERROR: dependency ‘rJava’ is not available for package ‘iplots’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/iplots’
ERROR: dependencies ‘rJava’, ‘JavaGD’, ‘iplots’ are not available for package ‘JGR’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/JGR’
ERROR: dependencies ‘rJava’, ‘JGR’ are not available for package ‘Deducer’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/Deducer’

The downloaded packages are in
        ‘/tmp/RtmpCSITmm/downloaded_packages’
Warning messages:
1: In install.packages(c("JGR", "Deducer")) :
  installation of package 'rJava' had non-zero exit status
2: In install.packages(c("JGR", "Deducer")) :
  installation of package 'JavaGD' had non-zero exit status
3: In install.packages(c("JGR", "Deducer")) :
  installation of package 'iplots' had non-zero exit status
4: In install.packages(c("JGR", "Deducer")) :
  installation of package 'JGR' had non-zero exit status
5: In install.packages(c("JGR", "Deducer")) :
  installation of package 'Deducer' had non-zero exit status
>


R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('rJava')
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’
(as ‘lib’ is unspecified)
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz'
Content type 'application/x-gzip' length 527197 bytes (514 Kb)
opened URL
==================================================
downloaded 514 Kb

* installing *source* package ‘rJava’ ...
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -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 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   : '-I/usr/lib/jvm/java-6-openjdk/jre/../include'
java libs   : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details.

Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.

ERROR: configuration failed for package ‘rJava’
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’

The downloaded packages are in
        ‘/tmp/RtmpTk0ftk/downloaded_packages’
Warning message:
In install.packages("rJava") :
  installation of package 'rJava' had non-zero exit status
>
$ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.6.0_20
Java home path   : /usr/lib/jvm/java-6-openjdk/jre
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:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm
JNI cpp flags    :

Updating Java configuration in /etc/R
Done.

$ R

R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('rJava')
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’
(as ‘lib’ is unspecified)
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz'
Content type 'application/x-gzip' length 527197 bytes (514 Kb)
opened URL
==================================================
downloaded 514 Kb

* installing *source* package ‘rJava’ ...
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -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
c    hecking 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 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/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -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 ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’

The downloaded packages are in
        ‘/tmp/RtmpsJBxfe/downloaded_packages’
Warning message:
In install.packages("rJava") :
  installation of package 'rJava' had non-zero exit status
>

Answer 1

Here's another option:

before running R, do this

export LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk/jre/lib/amd64/server

(for path above, substitute location of your particular libjvm.so, if you have a different configuration). To find libjvm.so, you can do

sudo updatedb && locate libjvm.so

Answer 2

DWright is right..an alternative instead export it every time than you start R is locate your java path

 sudo locate libjvm.so

and add ir to ldpaths

 sudo gedit /etc/R/ldpaths 

i.e 
${JAVA_HOME=/usr/java/jdk1.7.0_07/jre} 

Answer 3

Dah, not long after posting I found the answer here:

http://r-interface.blogspot.com/2012/04/install-r-jgr-and-deducer-in-ubuntu.html

Although I already had Sun Java installed, the key was to run update-java-alternatives to actually switch to Sun Java first before running javareconf:

sudo update-java-alternatives -s java-6-sun
sudo R CMD javareconf

Answer 4

One other (relatively obvious) warning: don't do what I did and install both java6 and java7. That led to a conflict I was unable to 'fix' via specifying paths and environment variables. Removing both and reinstalling java6 led to successful installation of JGR. ( This under ubuntu precise, on an Apple G4 powerbook)