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update readme and vignette with windows issue

Simone authored on 25/10/2020 15:42:21
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@@ -48,24 +48,29 @@ Create environment variable `JAVA_HOME`:
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 ### Errors
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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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+Be aware that during a local-processing execution an error message
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+```{
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+Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, 
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+: org.apache.spark.SparkException: Job aborted due to stage failure: 
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+Task 0 in stage 7.0 failed 1 times, most recent failure: 
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+Lost task 0.0 in stage 7.0 (TID 59, localhost, executor driver): 
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+java.io.IOException: (null) entry in command string: null chmod 0644
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+```
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+may arise.
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+
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+This happens because some Hadoop binary files are missing in Windows 64Bits.
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+In this case we need to:
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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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+* Paste the url `https://github.com/steveloughran/winutils/tree/master/hadoop-2.8.1` and download the **winutil-hadoop2.8.1**
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+* Create a directory (for example at ```C:\Program Files\hadoop\bin```. Use a path you wish
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+* Copy the files from the repository folder **hadoop-2.8.1** into the folder earlier created.
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+* Create environment variable HADOOP_HOME with value equal to the folder path you copied the binaries.
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 or
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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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-
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+* Go to [https://github.com/steveloughran/winutils](https://github.com/steveloughran/winutils), download the repository
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+* Create a directory (for example at ```C:\Program Files\hadoop\bin```. Use a path you wish
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+* Copy the files from the repository folder **hadoop-2.8.1** into the folder earlier created.
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+* Create environment variable HADOOP_HOME with value equal to the folder path you copied the binaries.
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@@ -815,5 +815,24 @@ a$S_00000[which(names(a$S_00000) %in% "disease")]
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 ```
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+# Windows OS Issues
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+
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+Be aware that during a [local processing](#local-processing) execution an error message
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+```{
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+Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, 
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+: org.apache.spark.SparkException: Job aborted due to stage failure: 
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+Task 0 in stage 7.0 failed 1 times, most recent failure: 
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+Lost task 0.0 in stage 7.0 (TID 59, localhost, executor driver): 
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+java.io.IOException: (null) entry in command string: null chmod 0644
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+```
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+may arise.
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+
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+This happens because some Hadoop binary files are missing in Windows 64Bits.
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+In this case we need to:
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+
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+* Go to [https://github.com/steveloughran/winutils](https://github.com/steveloughran/winutils), download the repository
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+* Create a directory (for example at ```C:\Program Files\hadoop\bin```. Use a path you wish
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+* Copy the files from the repository folder **hadoop-2.8.1** into the folder earlier created.
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+* Create environment variable HADOOP_HOME with value equal to the folder path you copied the binaries.
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 # References