updated readme, add solution for java.io.IOException: (null) entry in command string: null chmod 0644` error n windows
Sim1Pall8a authored on 24/10/2020 13:59:07
• GitHub committed on 24/10/2020 13:59:07
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# RGMQL |
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+API for calling interactively the GMQL Engine from R-Bioconductor |
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-This package works with java 1.8 |
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+[RGMQL on Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/RGMQL.html) |
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-## Settings OSX |
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+## Requirements |
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-edit .bash_profile, add environment variable |
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+The library requires the following: |
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+* R version 3.4.2 or higher |
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+* Java version 1.8 or higher |
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+* The JAVA_HOME enviroment variable set |
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-export JAVA_HOME="<java_path>" |
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+It is recommended the use ot the latest version of RStudio. |
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-export PATH=$PATH |
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+## OSX Settings |
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-edit /etc/paths add these |
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+#### before Catalina |
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-$JAVA_HOME/bin |
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+Edit the `.bash_profile` and add the `JAVA_HOME` environment variable: |
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+`export JAVA_HOME = <java_path>` |
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-## Settings Windows |
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+`export PATH=$PATH` |
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-create environment variable JAVA_HOME |
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+#### after Catalina |
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+Since on macOS Catalina the default shell is Zsh we need to edit or create the .zsh file: |
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+ |
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+Edit the `.zsh` and add the `JAVA_HOME` environment variable: |
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+ |
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+`export JAVA_HOME = <java_path>` |
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+ |
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+`export PATH=$PATH` |
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+ |
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+At the end, in both cases, edit the `/etc/paths` and add: |
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+ |
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+`$JAVA_HOME/bin` |
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+ |
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+ |
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+## Windows Settings |
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+ |
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+Create environment variable `JAVA_HOME`: |
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+ |
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+* Right click on _This PC_. |
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+* click on _Advanced system settings_ |
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+* go to _Advanced_ tab an click on _evnironment variables_ |
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+* create a `JAVA_HOME` variable the jdk path |
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+ |
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+### Errors |
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+ |
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+be aware that during execution a message |
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+ |
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+`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`
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+ |
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+may arise in some circustances . |
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+ |
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+This happens because some binary files are missing for Windows, in this case we need to: |
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+ |
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+* Open [DownGit](https://minhaskamal.github.io/DownGit/#/home) |
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+* Paste the url `https://github.com/steveloughran/winutils/tree/master/hadoop-2.8.1` in above website, and download the **winutil-hadoop2.8.1** |
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+ |
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+or |
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+ |
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+* Go to https://github.com/steveloughran/winutils and download the repo and use **winutil-hadoop2.8.1** |
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+ |
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+ |
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+* Create a directory (example `C:\Program Files\hadoop`) with a folder inside named `bin` |
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+* Get those files and copy them inside the bin subfolder, (copy on `C:\Program Files\hadoop\bin`) |
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+* Create environment variable `HADOOP_HOME` with the path containing those files. |
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