[BioC] Problem with ljava when I run update.packages2

[Martin Morgan]

Hi Marcelo --

Sounds like the library libjava is installed on your system, but that
R doesn't know where. Also sounds like you are using a command like R
CMD INSTALL <pkgname> to install packages.

Try setting the environment variable LD_LIBRARY_PATH to include the
path to libjava, e.g.,

export LD_LIBRARY_PATH=/usr/lib/jrel.5.0/lib/i386:$LD_LIBRARY_PATH
R CMD INSTALL <pkgname>

You can also specify the library path on the command line. Look into
the --configure-args and --configure-vars options of R CMD INSTALL, e.g.,

R CMD INSTALL --help

Hope that helps,

Martin

Marcelo Luiz de Laia <mlaia at fcav.unesp.br> writes:

> Hi Bioconductor Users!
>
> I am doing a update in my librarys and I have this error message:
>
> /usr/bin/ld: cannot find -ljava
>
> The steps more complete are:
>
> ** libs
> gcc -I/usr/lib/R/include -I/include -I/include/linux     -fPIC  -g -O2 
> -c rmageml.c -o rmageml.o
> gcc -shared  -o RMAGEML.so rmageml.o -L/jre/lib/i386 -ljava 
> -L/jre/lib/i386/client -ljvm  -L/usr/lib/R/lib -lR
> /usr/bin/ld: cannot find -ljava
> collect2: ld returned 1 exit status
> make: ** [RMAGEML.so] Erro 1
> ERROR: compilation failed for package 'RMAGEML
>
> But, I have the libjava installed:
>
> root at lbmsala4b:/# ls -al /usr/lib/jre1.5.0/lib/i386/libj*
> -rw-r--r--  1 root root  67848 2004-09-15 08:31 
> /usr/lib/jre1.5.0/lib/i386/libj2pkcs11.so
> -rwxr-xr-x  1 root root   5184 2004-09-15 09:13 
> /usr/lib/jre1.5.0/lib/i386/libjaas_unix.so
> -rwxr-xr-x  1 root root  22317 2004-09-15 08:37 
> /usr/lib/jre1.5.0/lib/i386/libjava_crw_demo.so
> -rwxr-xr-x  1 root root  77584 2004-09-15 09:46 
> /usr/lib/jre1.5.0/lib/i386/libjavaplugin_jni.so
> -rwxr-xr-x  1 root root 330648 2004-09-15 09:46 
> /usr/lib/jre1.5.0/lib/i386/libjavaplugin_nscp_gcc29.so
> -rwxr-xr-x  1 root root 268312 2004-09-15 09:46 
> /usr/lib/jre1.5.0/lib/i386/libjavaplugin_nscp.so
> -rwxr-xr-x  1 root root 140760 2004-09-15 08:34 
> /usr/lib/jre1.5.0/lib/i386/libjava.so
> -rwxr-xr-x  1 root root   3824 2004-09-15 09:10 
> /usr/lib/jre1.5.0/lib/i386/libjawt.so
> -rwxr-xr-x  1 root root 246407 2004-09-15 09:21 
> /usr/lib/jre1.5.0/lib/i386/libjdwp.so
> -rwxr-xr-x  1 root root 195104 2004-09-15 09:05 
> /usr/lib/jre1.5.0/lib/i386/libjpeg.so
> -rwxr-xr-x  1 root root   8343 2004-09-15 08:31 
> /usr/lib/jre1.5.0/lib/i386/libjsig.so
> -rwxr-xr-x  1 root root  66612 2004-09-15 08:44 
> /usr/lib/jre1.5.0/lib/i386/libjsoundalsa.so
> -rwxr-xr-x  1 root root 268428 2004-09-15 08:44 
> /usr/lib/jre1.5.0/lib/i386/libjsound.so
> root at lbmsala4b:/#
>
> How I solve this one???
>
> I use Debian testing.
>
> Thanks in advanced.
>
> -- 
> Marcelo Luiz de Laia
> Ph.D Student in Genetics and Plant Breeding
> São Paulo State University (http://www.unesp.br/eng/)
> School of Agricultural and Veterinary Sciences
> Department of  Technology
> Via de Acesso Prof.Paulo Donato Castellane s/n
> 14884-900   Jaboticabal - SP - Brazil
> Fone: +55-016-3209-2675
>
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