From lmramba at gmail.com  Sat Oct 10 05:40:10 2009
From: lmramba at gmail.com (lmramba at gmail.com)
Date: Sat, 10 Oct 2009 05:40:10 +0200 (CEST)
Subject: [Rd] rJava downloads but cannot load,
	when I run R as root (PR#13994)
Message-ID: <20091010034010.9AACC282EF2D@mail.pubhealth.ku.dk>

> library(rJava)
Error in library(rJava) : there is no package called 'rJava'
> install.packages("rJava")
Warning in install.packages("rJava") :
  argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.uk.r-project.org/src/contrib/rJava_0.7-0.tar.gz'
Content type 'application/x-gzip' length 249486 bytes (243 Kb)
opened URL
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
downloaded 243 Kb

* Installing *source* package =91rJava=92 ...
checking for gcc... gcc -std=3Dgnu99
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=3Dgnu99 accepts -g... yes
checking for gcc -std=3Dgnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=3Dgnu99 -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=3Dgnu99 supports static inline...
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/i386/server
-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386
-L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 -L
-L/usr/java/packages/lib/i386 -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 =91rJava=92
* Removing =91/usr/local/lib/R/site-library/rJava=92

The downloaded packages are in
    =91/tmp/RtmpOjM9hY/downloaded_packages=92
Warning message:
In install.packages("rJava") :
  installation of package 'rJava' had non-zero exit status
>


I went ahead and did this:

root at lmramba-laptop:/home/lmramba# R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.6.0_0
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:
$(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386=
::/usr/java/packages/lib/i386:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/lib/i386
-L$(JAVA_HOME)/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib
-L/usr/lib -ljvm
JNI cpp flags    :

Updating Java configuration in /etc/R
Done.


But still installing rJava fails


Plz help

Regards,
Lazarus

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[Rd] rJava downloads but cannot load, when I run R as root (PR#13994)
lmramba at gmail.com