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 S?o 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

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 > S?o 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor