[BioC] Problem installing RMAGEML

Md.Mamunur Rashid mamunur.rashid at kcl.ac.uk
Tue Sep 29 17:38:46 CEST 2009

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-
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-

My system details:

linux version -  Fedora 11,
java version - java-1.6.0-openjdk-
R-version - 2.9.0

Any suggestion is welcome.

thanks in advance.


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- -ljava
-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

More information about the Bioconductor mailing list