# 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.