From Christian.Kohler at klinik.uni-regensburg.de  Wed Oct 29 16:51:16 2008
From: Christian.Kohler at klinik.uni-regensburg.de (Christian Kohler)
Date: Wed, 29 Oct 2008 16:51:16 +0100
Subject: [Rd] problems installing rJava with R-2.8.0
Message-ID: <49088674.6090407@klinik.uni-regensburg.de>

Dear R-developers,

I am having trouble installing rJava on R 2.8.0 / debian etch.

What goes wrong?

I am happy for every advice.

Best,
Christian



> install.packages("rJava")
Warning in install.packages("rJava") :
  argument 'lib' is missing: using
'/nfs/compdiag/package/R/lib/bioconductor/release_2.3/x86_64'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.rakanu.com/src/contrib/rJava_0.6-0.tar.gz'
Content type 'application/x-gzip' length 234704 bytes (229 Kb)
opened URL
==================================================
downloaded 229 Kb

* 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/lib/jvm/java-1.5.0-sun/jre/bin/java'
archiver    : '/usr/lib/jvm/java-1.5.0-sun/bin/jar'
compiler    : '/usr/lib/jvm/java-1.5.0-sun/bin/javac'
header prep.: '/usr/lib/jvm/java-1.5.0-sun/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.5.0-sun/include
-I/usr/lib/jvm/java-1.5.0-sun/include/linux'
java libs   :
'-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64/server
-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64
-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/../lib/amd64
-L/usr/local/lib64 -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
'/nfs/compdiag/package/R/lib/bioconductor/release_2.3/x86_64/rJava'

The downloaded packages are in
        /nfs/scratch/Rtmp/RtmpUMDzVa/downloaded_packages
Warning message:
In install.packages("rJava") :
  installation of package 'rJava' had non-zero exit status


> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tcltk_2.8.0 tools_2.8.0









-- 

Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg (BioPark I)
D-93147 Regensburg (Germany)

Tel. +49 941 943 5055
Fax  +49 941 943 5020
christian.kohler at klinik.uni-regensburg.de



[Rd] problems installing rJava with R-2.8.0
Christian Kohler