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R-Server-Template

Harlan D. Harris
harlan @ harris.name

This template is CC0 1.0 Universal licensed, meaning it is released into the public domain.

Description

This application framework demonstrates how you can write an R application that runs continuously as a server. For example, you could extend this application to periodically read data from a file or database, perform some statistical tests or analyses, and put the results in another file or database. This framework will work on unix-alike (Linux, Mac OS X) machines, but not under Windows.

Features include:

  • configuration -- filenames specified on the command line will be sourced, over-riding default parameters, such as the location of a log file

  • logging -- demonstrates John Myles White's handy log4r package

  • error handling -- captures runtime errors cleanly and logs them

  • continuous execution -- loops until dies or shuts down

  • clean shutdown -- captures the SIGKILL (^C) signal and performs a clean shutdown, complete with logging

  • packaging -- includes a Makefile that creates a package suitable for installation on a server, separate from the source tree

  • versioning -- uses version and tag information from a github repository to tag the application's version number

  • testing -- uses Hadley Wickham's testthat package to test the NA2x functions (see below)

  • status via web service -- using R 2.13.0's new web server and Jeffrey Horner's Rook package, exposes a web page that reports the application

The actual application does nothing useful, outputting a (parameterized) string to stdout every second, until killed or dies (due to a statistically rare event).

Running

  • First, from the main directory, make test to see that all tests pass.

  • Second, make snapshot to build an installation archive. If you'd like, copy that to where you'd like to run the server and extract it with tar xvfz testapp-whatever.tgz.

  • Third, set up the testapp-config.R file as you prefer.

  • Fourth, install the log4r and Rook R libraries and their dependencies.

  • Fifth, run the application: ./testapp.R /path/to/testapp-config.R /path/to/testapp-config-local.R in a terminal window.

  • Sixth, verify that the application is running. Watch the dots appear. Look at the log file. Hit the web server.

  • Seventh, hit ctrl-C to kill the application. Look at the log file again to see the clean shutdown.

Library Functions

The testapp-fns.R file includes several useful functions.

QuitWithErr exits the application with a specified (default is 10) exit status.

LibraryQuiet wraps the library() function to suppress startup messages.

NA2F, NA20, NA2Inf, and NA2mean implement handy vectorized functions that replace NAs in a vector (or list) with appropriate replacements. Tested by the runtests.R script. Note that these return reasonably typed results even with 1-length or 0-length inputs, which the wrapped ifelse() function does not consistently do.

TestAppStatus is a Rook applet that provides information about the status of the application to an administrator.

Directories

The scripts directory contains the Rscript scripts that make up the application.

The scripts/tests subdirectory contains testthat scripts.

Makefile

Targets are as follows:

  • test -- to run tests. Note that the current version of testthat does not support simultaneously quitting with an exit status and printing the output. Therefore, the runtests.R script runs the tests once, outputting to the screen, then if the --quitonerr flag is provided, runs the tests again quietly, quitting if there's a problem. As a result, runtests.R exits with a non-zero exit status if any tests fail.

  • reversion -- to tag the app with a git version tag

  • snapshot -- to build a snapshot release, with the filename based on the git SHA of the current branch.

  • release -- to build a versioned release. Throws warnings if not on an up-to-date master branch, and tags the application and the archive file based on the most recent tag.