First, make sure you have JDK 1.7 or higher installed.
To install RBioFormats use the biocLite
installation script in order to resolve the dependency on the Bioconductor package EBImage.
source("https://bioconductor.org/biocLite.R")
biocLite("aoles/RBioFormats") # You might need to first run `install.packages("devtools")`
Mac OS comes with a legacy Apple Java 6. In order to use RBioFormats, you will need to update your Java installation to a newer version provided by Oracle.
-
Install Oracle JDK.
-
Update R Java configuration by executing from the command line (you might have to run it as a super user by prepending
sudo
depending on your installation).
R CMD javareconf
- Re-install rJava from sources in order to properly link to the non-system Java installation.
install.packages("rJava", type="source")
You can verify your configuration by running the following commands. This should return the Java version string corresponding to the one downloaded and installed in step 1.
library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
## [1] "1.8.0_112-b16"
For example use, see the package vignette.
See my answers on Stack Overflow.
If you get the java.lang.OutOfMemoryError: Java heap space
error, try increasing the maximum heap size by supplying the -Xmx parameter before the Java Virtual Machine is initialized. For example, use
options( java.parameters = "-Xmx4g" )
library( "RBioFormats" )
to override the default setting and assign 4 gigabytes of heap space to the Java environment.
Each R process needs a separate JVM instance. For this, load the package in the parallelized function, e.g.,
bplapply (files, function(f) {
library(RBioFormats)
...
})
Run mvn install
to build and test with Renjin
Run renjin:repl
to open a Renjin REPL with the package on the classpath.