Name Mode Size
Example of workflows 040000
R 040000
inst 040000
man 040000
vignettes 040000
.BBSoptions 100755 0 kb
.Rbuildignore 100755 0 kb
.gitignore 100755 0 kb
DESCRIPTION 100644 3 kb
NAMESPACE 100755 2 kb
README.md 100755 4 kb
README.md
# 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. ## 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 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 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** * 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.