hi all, please ignore my last post. I have found it out. Rookie mistake. just updated the R configuration with $ R CMD javareconf Thnaks anyway. regards, Mamun -------- Original Message -------- Subject: Problem installing RMAGEML Date: Tue, 29 Sep 2009 16:38:46 +0100 From: Md.Mamunur Rashid <mamunur.rashid@kcl.ac.uk> To: bioconductor <bioconductor@stat.math.ethz.ch> Dear Bioc members, I ran in to a problem while trying to install RMAGEML package. /usr/bin/ld: cannot find -ljava . (please look at the bottom for details of the error) I have set the following in ~/.bashrc file. export JAVA_HOME=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64 export LD_LIBRARY_PATH=/home/mamun/R-2.9.0/lib64/R/library/rJava/jri:/ home/mamun/R-2.9.0/lib64/R/lib:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0 .x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/j re/lib/amd64/native_threads My system details: linux version - Fedora 11, java version - java-1.6.0-openjdk-1.6.0.0.x86_64 R-version - 2.9.0 Any suggestion is welcome. thanks in advance. regards, Mamun Details of the problem : rmageml.c: In function updateMAGEML: rmageml.c:599: warning: cast from pointer to integer of different size gcc -std=gnu99 -shared -L/usr/local/lib64 -o RMAGEML.so rmageml.o -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/jre/lib/amd64 -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/jre/lib/i386 -ljava -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/jre/lib/amd64/ser ver -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/jre/lib/i386/clie nt -ljvm -L/home/mamun/R-2.9.0/lib64/R/lib -lR /usr/bin/ld: cannot find -ljava collect2: ld returned 1 exit status make: *** [RMAGEML.so] Error 1 ERROR: compilation failed for package RMAGEML * Removing /home/mamun/R-2.9.0/lib64/R/library/RMAGEML [[alternative HTML version deleted]]