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This page lists known recurring issues. If you have a problem with the app, check also the [repository issue tracker](https://git.embl.de/meechan/image-data-explorer/-/issues) and eventually file a new issue there.
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### **Installation Problems**
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**rJava** :
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rJava is an R package that allows R to use libraries written in Java. It requires a Java Development Kit (JDK) installed and findable by R. If you experience issues installing rJava, first make sure that Java is installed. Open a terminal and enter:
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```
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> java -version
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```
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The output should be similar to:
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```
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openjdk version "1.8.0_265"
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OpenJDK Runtime Environment (build 1.8.0_265-8u265-b01-0ubuntu2~16.04-b01)
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OpenJDK 64-Bit Server VM (build 25.265-b01, mixed mode)
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```
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If the output is different, Java is probably not installed. Install it using the procedure appropriate for your system. For example, on Ubuntu and related Linux distributions:
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```
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sudo apt-get install openjdk-8-jdk
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```
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After installing Java, the JDK needs to be registered with R. In a terminal, run:
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```
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> R CMD javareconf
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```
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This command may also need to be run after an update of R or Java.
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Then install rJava from the R console:
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```
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> install.packages("rjava")
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```
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Alternatively, issues may be resolved by installing rJava using your system package manager, e.g. on Ubuntu-like systems:
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```
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> sudo apt-get install r-cran-rjava
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```
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To allocate more memory to Java, find and uncomment the following line towards the top of image_data_explorer.R:
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```
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option(java-parameters= "-Xmx8g)
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```
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Replace the value of 8 by the number of GB you want to allocate.
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**RBioFormats**:
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This package is the R interface to the Bioformats Java library and therefore depends on rJava. However, it also uses other packages such as fftwtools and tiff that depend on system libraries. Inspect any error message for clues as to which library might be missing. For example, if missing, libfftw and libtiff can be installed on Ubuntu-like systems with:
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```
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>sudo apt install libfftw3-dev libtiff5-dev
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```
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