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README.md
# RGMQL API for calling interactively the GMQL Engine from R-Bioconductor [RGMQL on Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/RGMQL.html) ## Requirements The library requires the following: * R version 3.4.2 or higher * Java version 1.8 or higher * The JAVA_HOME enviroment variable set It is recommended the use ot the latest version of RStudio. ## OSX Settings #### before Catalina Edit the `.bash_profile` and add the `JAVA_HOME` environment variable: `export JAVA_HOME = <java_path>` `export PATH=$PATH` #### after Catalina Since on macOS Catalina the default shell is Zsh we need to edit or create the .zsh file: Edit the `.zsh` and add the `JAVA_HOME` environment variable: `export JAVA_HOME = <java_path>` `export PATH=$PATH` At the end, in both cases, edit the `/etc/paths` and add: `$JAVA_HOME/bin` ## Windows Settings Create environment variable `JAVA_HOME`: * Right click on _This PC_. * click on _Advanced system settings_ * go to _Advanced_ tab an click on _evnironment variables_ * create a `JAVA_HOME` variable the jdk path ### Errors Be aware that during a local-processing execution an error message ```{ Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 7.0 failed 1 times, most recent failure: Lost task 0.0 in stage 7.0 (TID 59, localhost, executor driver): java.io.IOException: (null) entry in command string: null chmod 0644 ``` may arise. This happens because some Hadoop binary files are missing in Windows 64Bits. In this case we need to: * Open [DownGit](https://minhaskamal.github.io/DownGit/#/home) * Paste the url `https://github.com/steveloughran/winutils/tree/master/hadoop-2.8.1` and download the **winutil-hadoop2.8.1** * Create a directory (for example at ```C:\Program Files\hadoop\bin```. Use a path you wish * Copy the files from the repository folder **hadoop-2.8.1** into the folder earlier created. * Create environment variable HADOOP_HOME with value equal to the folder path you copied the binaries. or * Go to [https://github.com/steveloughran/winutils](https://github.com/steveloughran/winutils), download the repository * Create a directory (for example at ```C:\Program Files\hadoop\bin```. Use a path you wish * Copy the files from the repository folder **hadoop-2.8.1** into the folder earlier created. * Create environment variable HADOOP_HOME with value equal to the folder path you copied the binaries.