[Rd] problems installing rJava with R-2.8.0

[Simon Urbanek]

On Oct 29, 2008, at 11:51 , Christian Kohler wrote:

> Dear R-developers,
>
> I am having trouble installing rJava on R 2.8.0 / debian etch.
>
> What goes wrong?
>

Please send me the config.log. Also make sure you have configured R  
with Java support (sudo R CMD javareconf).

Cheers,
S


>
>> 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
>
>
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>
> -- 
>
> 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
>
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