# 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.
