@@ -42,9 +42,9 @@ RGMQL/

 - [Examples of workflows](Example%20of%20workflows)/ folder containing various use cases

 - [R](R)/ folder containing all the script files

-- [inst](inst)/ folder containing all files that should be copied into the installed R package folder.

-- [inst/example](inst/example) folder containing the datasets and other files in order to run correctly all the test.

-- [inst/NEWS](inst/NEWS) file report the feature/changes/bugfix for each version. 

+- [inst](inst)/ folder containing all files that should be copied into the installed R package folder

+- [inst/example](inst/example) folder containing the datasets and other files in order to run correctly all the test

+- [inst/NEWS](inst/NEWS) file report the feature/changes/bugfix for each version 

 - [man](man)/ folder containing R documentation files

 - [vignettes](vignettes)/ folder containing all the files used to generate correctly the vignette

 - [vignettes/RGMQL-vignette.R](vignettes/RGMQL-vignette.R) long-form guide to your package

@@ -52,8 +52,8 @@ RGMQL/

 - [vignettes/RGMQL-vignette.html](vignettes/RGMQL-vignette.html) vignettes in html

 - [vignettes/bibliography.bib](vignettes/bibliography.bib) the bibliographic file with list of references used in vignettes

 - [vignettes/american-medical-association-no-et-al.csl](vignettes/american-medical-association-no-et-al.csl) the citation style language used in vignettes

-- [DESCRIPTION](DESCRIPTION) this file stores important/mandatory metadata about RGMQL package.

-- [NAMESPACE](NAMESPACE) this file makes your packages self-contained, ensuring that other packages do not interfere with your code, that your code does not interfere with other packages, and that your package works regardless of the environment in which it is running.

+- [DESCRIPTION](DESCRIPTION) this file stores important/mandatory metadata about RGMQL package

+- [NAMESPACE](NAMESPACE) this file makes your packages self-contained, ensuring that other packages do not interfere with your code, that your code does not interfere with other packages, and that your package works regardless of the environment in which it is running

 - [README](README.md) the current file

@@ -3,6 +3,13 @@ API for calling interactively the GMQL Engine from R-Bioconductor

 [RGMQL on Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/RGMQL.html)

+## About

+

+RGMQL is a R/Bioconductor package conceived to provide a set of specialized functions to extract, combine, process

+and compare omics datasets and their metadata from different and differently localized sources. 

+RGMQL is built over the GenoMetric Query Language (GMQL) data management and computational engine, and can leverage its open curated

+repository as well as its cloud-based resources, with the possibility of outsourcing computational tasks to GMQL remote services. Furthermore, it overcomes the limits of the GMQL declarative syntax, by guaranteeing a procedural approach in dealing with omics data within the R/Bioconductor environment. But mostly, it provides full interoperability with other packages of the R/Bioconductor framework and extensibility over the most used genomic data structures and processing functions.

+

 ## Requirements

 The library requires the following:

@@ -33,7 +40,7 @@ RGMQL/

 |-- README.md

 ```

-- [Example of workflows](Example%20of%20workflows)/ folder containig various use cases

+- [Examples of workflows](Example%20of%20workflows)/ folder containing various use cases

 - [R](R)/ folder containing all the script files

 - [inst](inst)/ folder containing all files that should be copied into the installed R package folder.

 - [inst/example](inst/example) folder containing the datasets and other files in order to run correctly all the test.

@@ -41,12 +48,13 @@ RGMQL/

 - [man](man)/ folder containing R documentation files

 - [vignettes](vignettes)/ folder containing all the files used to generate correctly the vignette

 - [vignettes/RGMQL-vignette.R](vignettes/RGMQL-vignette.R) long-form guide to your package

-- [vignettes/RGMQL-vignette.Rmd](vignettes/RGMQL-vignette.Rmd) the vignettes in markup language

-- [vignettes/RGMQL-vignette.html](vignettes/RGMQL-vignette.html) the vignettes in html

-- [vignettes/bibliography.bib](vignettes/bibliography.bib) the bibliographic or list of reference file used in vignette

-- [vignettes/american-medical-association-no-et-al.csl](vignettes/american-medical-association-no-et-al.csl) the citation style language used in vignette

-- [DESCRIPTION](DESCRIPTION) this file store important/mandatory metadata about RGMQL package.

-- [NAMESPACE](NAMESPACE) this file make your packages self-contained, ensuring that other packages won’t interfere with your code, that your code won’t interfere with other packages, and that your package works regardless of the environment in which it’s run.

+- [vignettes/RGMQL-vignette.Rmd](vignettes/RGMQL-vignette.Rmd) vignettes in markup language

+- [vignettes/RGMQL-vignette.html](vignettes/RGMQL-vignette.html) vignettes in html

+- [vignettes/bibliography.bib](vignettes/bibliography.bib) the bibliographic file with list of references used in vignettes

+- [vignettes/american-medical-association-no-et-al.csl](vignettes/american-medical-association-no-et-al.csl) the citation style language used in vignettes

+- [DESCRIPTION](DESCRIPTION) this file stores important/mandatory metadata about RGMQL package.

+- [NAMESPACE](NAMESPACE) this file makes your packages self-contained, ensuring that other packages do not interfere with your code, that your code does not interfere with other packages, and that your package works regardless of the environment in which it is running.

+- [README](README.md) the current file

 ## OSX Settings

@@ -12,6 +12,43 @@ The library requires the following:

 It is recommended the use ot the latest version of RStudio.

+## Structure

+```

+RGMQL/

+|-- Example of workflows/

+|-- R/

+|-- inst/

+|   |-- example/

+|   |-- NEWS

+|-- man/

+|-- vignettes/

+|   |-- RGMQL-vignette.R

+|   |-- RGMQL-vignette.Rmd

+|   |-- RGMQL-vignette.html

+|   |-- american-medical-association-no-et-al.csl

+|   |-- bibliography.bib

+|   |-- ....

+|-- DESCRIPTION

+|-- NAMESPACE

+|-- README.md

+```

+

+- [Example of workflows](Example%20of%20workflows)/ folder containig various use cases

+- [R](R)/ folder containing all the script files

+- [inst](inst)/ folder containing all files that should be copied into the installed R package folder.

+- [inst/example](inst/example) folder containing the datasets and other files in order to run correctly all the test.

+- [inst/NEWS](inst/NEWS) file report the feature/changes/bugfix for each version. 

+- [man](man)/ folder containing R documentation files

+- [vignettes](vignettes)/ folder containing all the files used to generate correctly the vignette

+- [vignettes/RGMQL-vignette.R](vignettes/RGMQL-vignette.R) long-form guide to your package

+- [vignettes/RGMQL-vignette.Rmd](vignettes/RGMQL-vignette.Rmd) the vignettes in markup language

+- [vignettes/RGMQL-vignette.html](vignettes/RGMQL-vignette.html) the vignettes in html

+- [vignettes/bibliography.bib](vignettes/bibliography.bib) the bibliographic or list of reference file used in vignette

+- [vignettes/american-medical-association-no-et-al.csl](vignettes/american-medical-association-no-et-al.csl) the citation style language used in vignette

+- [DESCRIPTION](DESCRIPTION) this file store important/mandatory metadata about RGMQL package.

+- [NAMESPACE](NAMESPACE) this file make your packages self-contained, ensuring that other packages won’t interfere with your code, that your code won’t interfere with other packages, and that your package works regardless of the environment in which it’s run.

+

+

 ## OSX Settings

 #### before Catalina

@@ -59,7 +59,7 @@ 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:

+In this case you 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**

old mode 100644

new mode 100755

@@ -48,24 +48,29 @@ Create environment variable `JAVA_HOME`:

 ### Errors

-be aware that during execution a 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 in some circustances .

-

-This happens because some binary files are missing for Windows, in this case we need to:

+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` in above website, and download the **winutil-hadoop2.8.1**

+* 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 and download the repo and use **winutil-hadoop2.8.1**

-

-

-* Create a directory (example `C:\Program Files\hadoop`) with a folder inside named `bin`

-* Get those files and copy them inside the bin subfolder, (copy on `C:\Program Files\hadoop\bin`)

-* Create environment variable `HADOOP_HOME` with the path containing those files.

-

+* 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.

@@ -1,23 +1,71 @@

 # RGMQL

+API for calling interactively the GMQL Engine from R-Bioconductor

-This package works with java 1.8

+[RGMQL on Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/RGMQL.html)

-## Settings OSX

+## Requirements

-edit .bash_profile, add environment variable

+The library requires the following:

+* R version 3.4.2 or higher

+* Java version 1.8 or higher

+* The JAVA_HOME enviroment variable set

-export JAVA_HOME="<java_path>"

+It is recommended the use ot the latest version of RStudio.

-export PATH=$PATH

+## OSX Settings

-edit /etc/paths add these

+#### before Catalina

-$JAVA_HOME/bin

+Edit the `.bash_profile` and add the `JAVA_HOME` environment variable:

+`export JAVA_HOME = <java_path>`

-## Settings Windows

+`export PATH=$PATH`

-create environment variable JAVA_HOME 

+#### 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 execution a 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 in some circustances .

+

+This happens because some binary files are missing for Windows, 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` in above website, and download the **winutil-hadoop2.8.1**

+

+or

+

+* Go to https://github.com/steveloughran/winutils and download the repo and use **winutil-hadoop2.8.1**

+

+

+* Create a directory (example `C:\Program Files\hadoop`) with a folder inside named `bin`

+* Get those files and copy them inside the bin subfolder, (copy on `C:\Program Files\hadoop\bin`)

+* Create environment variable `HADOOP_HOME` with the path containing those files.

@@ -19,18 +19,5 @@ $JAVA_HOME/bin

 create environment variable JAVA_HOME 

-this settings prevents warning in RStudio when creating scala interpreter object

-

-cat: /no such file or directory

-

-in Rstudio after create interpreter and call info function in R we got this warning

-

-> rscala::scalaInfo(verbose = T)

-

-Searching for a suitable Scala installation.

-* FAILURE: 'scala.home' argument is NULL

-* FAILURE: SCALA_HOME () environment variable

-* ATTEMPT: Found a candidate (/usr/local/scala-2.11.8/bin/scala)

-* SUCCESS: 'scala' in the shell's search path

@@ -1,27 +1,23 @@

 # RGMQL

-This package works with java 1.8 and scala 2.11.8

+This package works with java 1.8

 ## Settings OSX

 edit .bash_profile, add environment variable

-export SCALA_HOME="<scala_path>"

-

 export JAVA_HOME="<java_path>"

 export PATH=$PATH

 edit /etc/paths add these

-$SCALA_HOME/bin

-

 $JAVA_HOME/bin

 ## Settings Windows

-create environment variable JAVA_HOME and SCALA_HOME

+create environment variable JAVA_HOME 

 this settings prevents warning in RStudio when creating scala interpreter object

@@ -7,12 +7,15 @@ This package works with java 1.8 and scala 2.11.8

 edit .bash_profile, add environment variable

 export SCALA_HOME="<scala_path>"

+

 export JAVA_HOME="<java_path>"

+

 export PATH=$PATH

 edit /etc/paths add these

 $SCALA_HOME/bin

+

 $JAVA_HOME/bin

@@ -20,8 +23,6 @@ $JAVA_HOME/bin

 create environment variable JAVA_HOME and SCALA_HOME

-

-

 this settings prevents warning in RStudio when creating scala interpreter object

 cat: /no such file or directory

@@ -36,5 +37,4 @@ Searching for a suitable Scala installation.

 * ATTEMPT: Found a candidate (/usr/local/scala-2.11.8/bin/scala)

 * SUCCESS: 'scala' in the shell's search path

-don-t worry is ok!

@@ -1,26 +1,28 @@

 # RGMQL

-## Settings

+This package works with java 1.8 and scala 2.11.8

-put scala in folder OSX /usr/local/

-create symbolic links as instruction below

+## Settings OSX

-sudo ln -s /usr/local/scala-2.11.8 /usr/local/scala

-sudo ln -s /usr/local/scala-2.11.8 /usr/local/share/scala

+edit .bash_profile, add environment variable

-edit .bash_profile, add these

-

-export SCALA_HOME=/usr/local/share/scala

-export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_79.jdk/Contents/Home

+export SCALA_HOME="<scala_path>"

+export JAVA_HOME="<java_path>"

 export PATH=$PATH

 edit /etc/paths add these

-/usr/local/scala/bin

 $SCALA_HOME/bin

 $JAVA_HOME/bin

-this setting prevents warning in RStudio when creating scala interpreter object

+

+## Settings Windows

+

+create environment variable JAVA_HOME and SCALA_HOME

+

+

+

+this settings prevents warning in RStudio when creating scala interpreter object

 cat: /no such file or directory

@@ -36,17 +38,3 @@ Searching for a suitable Scala installation.

 don-t worry is ok!

-(I don't know what happen with other R "editor" or using R through command line)

-

-## for local "compiling"

-

-I didn't put the jar file in repository cause are ~ 100MB

-after cloned or downloaded the git create a folder "inst" inside GMQL then create folder "java" inside it

-we should have this structure:

-

-GMQL

- |-->inst

-      |-->java

-

-then copy the "uber-GMQL-R-1.0.jar" file inside "java".

-rename it to GMQL.jar or create a symbolic link GMQL.jar

@@ -40,12 +40,13 @@ don-t worry is ok!

 ## for local "compiling"

-I don't put the jar file in repository cause are ~ 100MB

+I didn't put the jar file in repository cause are ~ 100MB

 after cloned or downloaded the git create a folder "inst" inside GMQL then create folder "java" inside it

 we should have this structure:

 GMQL

- |__ inst

-       |__ java

+ |-->inst

+      |-->java

-then copy the jar file inside "java" or create a symbolic link

+then copy the "uber-GMQL-R-1.0.jar" file inside "java".

+rename it to GMQL.jar or create a symbolic link GMQL.jar

@@ -1 +1,51 @@

-# RGMQL

\ No newline at end of file

+# RGMQL

+

+## Settings

+

+put scala in folder OSX /usr/local/

+create symbolic links as instruction below

+

+sudo ln -s /usr/local/scala-2.11.8 /usr/local/scala

+sudo ln -s /usr/local/scala-2.11.8 /usr/local/share/scala

+

+edit .bash_profile, add these

+

+export SCALA_HOME=/usr/local/share/scala

+export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_79.jdk/Contents/Home

+export PATH=$PATH

+

+edit /etc/paths add these

+

+/usr/local/scala/bin

+$SCALA_HOME/bin

+$JAVA_HOME/bin

+

+this setting prevents warning in RStudio when creating scala interpreter object

+

+cat: /no such file or directory

+

+in Rstudio after create interpreter and call info function in R we got this warning

+

+> rscala::scalaInfo(verbose = T)

+

+Searching for a suitable Scala installation.

+* FAILURE: 'scala.home' argument is NULL

+* FAILURE: SCALA_HOME () environment variable

+* ATTEMPT: Found a candidate (/usr/local/scala-2.11.8/bin/scala)

+* SUCCESS: 'scala' in the shell's search path

+

+don-t worry is ok!

+

+(I don't know what happen with other R "editor" or using R through command line)

+

+## for local "compiling"

+

+I don't put the jar file in repository cause are ~ 100MB

+after cloned or downloaded the git create a folder "inst" inside GMQL then create folder "java" inside it

+we should have this structure:

+

+GMQL

+ |__ inst

+       |__ java

+

+then copy the jar file inside "java" or create a symbolic link

new file mode 100644

@@ -0,0 +1 @@

+# RGMQL

\ No newline at end of file