About

This is an example R package project that uses code written in Java.

For a concise introduction to rJava, read "Documentation" section on the webpage of the rJava project .

Goal

The goal of this project is to show the following things.

• How to make and use Java code embedded in R package.
• How to call Java code from R by
  • creating Java class instance and calling its method,
  • calling static method of a class.
• How to manage the project using a buildsystem based on Makefiles and Maven.
• How to distribute R code that uses Java code (using R package system).
• How to document code (using Roxygen2).
• How to test code (using testthat package).
• How to mark functions that should be accessible by users of the package with @export annotation.
• How to follow conventions from the excellent "R packages" 2015 book by Hadley Wickham.

Installation

Note that in order to be able to build the project, you need to have all R packages listed in the Imports section of the DESCRIPTION file installed in the system.

Some issues

• Note that the name of the project is repeated many times.
  • In the source files we have:
    • *.Rproj file: its name
    • DESCRIPTION file
    • usage_example_of_installed_package.R file: library statement
    • tests/testthat.R file: library statement and as an argument to test_check call
  • This is against the DRY principle; however, trying to deal with it would be probably too complex.
• When running devtools::check() two NOTEs are printed related to the following things.
  • The first one is that the paths in the Java project are too long (messages like "storing paths of more than 100 bytes is not portable"). This is unfortunate, because Java projects tend to contain files with long paths. I haven't found a good way of solving this problem.
  • The second one is that GNU make is a system requirement of the package (as defined in the DESCRIPTION file). This is required, because in the java/number-adder/Makefile file we use ifndef construction which is GNU make extension with regards to POSIX make. Using GNU Make is discouraged because it is not completely portable as noted in "Writing R Extensions" document, section "Writing-portable-packages".
• Note that the philosophy of this code is that the derived files are not included in the version control system. As such, automatically generated file NAMESPACE and directory man are entered in .gitignore file. Hadley Wickham disapproves of this in his book (see chapter "Git and GitHub", paragraph starting from "Some developers never commit derived files").

Troubleshooting

If you get a cryptic error message while running the tests similar to the one below:

Error in ._jobjRef_dollar(x[["jobj"]], name) :
  no field, method or inner class called 'calls'
Calls: <Anonymous> ... expectation_error -> $ -> $.Throwable -> ._jobjRef_dollar

this might mean that the version of Java that the source files were compiled for is incompatible with the Java version configured in R environment. The version of Java for the source files is set in java/number-adder/pom.xml while version of Java used in R environment is set using R CMD javareconf command.