Name Mode Size
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java 040000
man-roxygen 040000
man 040000
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vignettes 040000
.Rbuildignore 100644 0 kb
DESCRIPTION 100644 1 kb
Makefile 100644 1 kb
NAMESPACE 100644 1 kb 100644 3 kb
# R interface to Bio-Formats *RBioFormats* is an R package which provides an interface to the OME [Bio-Formats]( Java library. It facilitates reading of proprietary image data and metadata in R. ## Installation First, make sure you have [JDK]( 1.8 or higher installed. To install *RBioFormats* use the `biocLite` installation script in order to resolve the dependency on the Bioconductor package *[EBImage](*. ```r if (!require("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("aoles/RBioFormats") ``` ### Mac OS X 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. 1. Install [Oracle JDK]( 2. 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 ``` 3. Re-install *rJava* from sources in order to properly link to the non-system Java installation. ```r 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. ```r library(rJava) .jinit() .jcall("java/lang/System", "S", "getProperty", "java.runtime.version") ## [1] "1.8.0_112-b16" ``` ## Documentation To get started with using *RBioFormats* have a look at the package vignette. ### FAQ See my [answers on Stack Overflow]( for solutions to some common and less common questions. ### Caveats #### The `java.lang.OutOfMemoryError` error 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 ```r options( java.parameters = "-Xmx4g" ) library( "RBioFormats" ) ``` to override the default setting and assign 4 gigabytes of heap space to the Java environment. Information about the current Java heap space limit can be retrieved by `checkJavaMemory()`. #### Use with BiocParallel Each R process needs a separate JVM instance. For this, load the package in the parallelized function, e.g., ```r bplapply (files, function(f) { library(RBioFormats) ... }) ```