Hi,all,
I have a problem about launching SJava in R from external application
(Cytoscape).
My R version is 2.1.0 and Sjava version is 0.68. R is installed by issuing
1. configure --enable-R-shlib
2. make
3. make check
4. make install
SJava is installed by issuing "R CMD INSTALL -c
SJava_version_.tar.gz".
The LD_LIBRARY_PATH is set in .bash_profile by
"LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib/R/library/SJava/libs:/usr/java/j2sdk1.4.2_08/jre/lib/i386/client:/usr/java/j2sdk1.4.2_08/jre/lib/i386:/usr/java/j2sdk1.4.2_08/jre/../lib/i386:
export LD_LIBRARY_PATH"
After installation, type the following command
* library(SJava)
* .JavaInit()
* .Java("java.lang.System", "getProperty",
"java.class.path")
* names(.Java("java.lang.System", "getProperties"))
Get the correct output (omitted here) .
Now the question is:
I am using R to interact with Cytoscape ( a visualization tool), which
has a plugin called "Cytotalk" that can let R and Cytoscape talk to
each other. I successfully ran a R script which need SJava and got the
right output in Cytoscape.
But when I tried to run the R script from the cytoscape menu ( the
plugin enabled a menu in which you can choose a R file to execute it
and display the output in Cytoscape ), the terminal give me the
following error:
Accepting clients from localhost> port <- 8082
> library(SJava)
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'/usr/local/lib/R/library/SJava/libs/SJava.so':
libRSNativeJava.so: cannot open shared object file: No such file or directory
Error in library(SJava) : .First.lib failed for 'SJava'
Execution halted
RESULT: 1
I googled around and found it was a common error when people trying to
install SJava. But I installed SJava correctly and it seems work fine,
I can not figure out why it comes up with this error.
To give you some background information, I guess Cytoscape and R talk
with each other via various java stuff. The fact that I can interact
with Cytoscape from within R showing that the .jar directory should be
fine.
The first few lines of the R code is like :
library(SJava)
#Warning message:
#The Java machine is no longer initialized automatically. You must
explicitly load it in: f(libname, pkgname)
a=javaConfig(classPath="/usr/local/bio/cytoscape/plugins/cytoTalk.jar")
.JavaInit(config=a)
#.Java("System","getProperty","java.class.path")
#[1]
":/usr/local/bio/cytoscape/plugins/cytoTalk.jar:/usr/local/lib/R/library/SJava/org/omegahat/Jars/Environment.jar:/usr/local/lib/R/library/SJava/org/..:/usr/local/lib/R/library/SJava/org/omegahat/Jars/antlr.jar:/usr/local/lib/R/library/SJava/org/omegahat/Jars/jas.jar:/usr/local/lib/R/library/SJava/org/omegahat/Jars/jhall.jar"
source("CytoTalkClient-v2.R")
cy <- .JNew("CytoTalkClient","http://localhost:8082")
And by the way, my OS is Redhat Linux. I really appreciate it if
someone has an clue of the problem. Thanks.
Xiao
