emuR - Main package of the EMU Speech Database Management System

Out of funding

Unfortunately, the EMU-SDMS is currently out of funding.

We at the IPS will do what we can to fix bugs, security issues or necessary adjustments to new versions of R; but we cannot currently work on new features or performance improvements.

We would be very glad if funding in academia allowed for more technical staff to maintain software used by the research community.

Introduction

The emuR package provides the next iteration of the EMU Speech Database Management System (EMU-SDMS) with database management, data extraction, data preparation and data visualization facilities. It also contains a server that is intended to host databases in the emuDB format (see vignette('emuDB_intro')) to the EMU-webApp (http://ips-lmu.github.io/EMU-webApp/). The querying of annotations is performed using EMU’s own EQL2 (EMU Query Language Version 2).

This package is part of the next iteration of the EMU Speech Database Management System which aims to be as close to an all-in-one solution for generating, manipulating, querying, analyzing and managing speech databases as possible. For an overview of the system please see http://ips-lmu.github.io/EMU.html and/or https://doi.org/10.1016/j.csl.2017.01.002 .

Installation

• to install the current CRAN release simply call:

install.packages("emuR")

As this also installs all of the dependencies (incl.  the wrassp package) this is the only installation step necessary to install the EMU-SDMS on your system. The only other requirement of the EMU-SDMS is a modern web browser (Chrome (recommended!) / Firefox / …) which most people should already have on their systems.

Quick start

For more information see the The EMU-SDMS Manual

For Beta Testers

Installation (two alternative methods)

• Either install the latest development version from GitHub using the devtools package (preferred method):

library(devtools)
install_github("IPS-LMU/emuR", build_vignettes = TRUE)

• Or download the package from GitHub manually, then install it with the following command:

install.packages("path/to/emuR", repos = NULL, type="source")

For Developers

Prerequisite: Docker is installed on your machine

Build and check package using Docker image rocker/r-devel

• Pull current r-devel image: docker pull rocker/r-devel
• Check if pull worked: docker images
• Check R version in image: docker run --rm rocker/r-devel:latest R --version
• Check R-devel version in image: docker run --rm rocker/r-devel:latest RD --version
• Run a container with an interactive shell, mounting the emuR project folder (that is, the current directory) and a named docker volume for the output tarball: docker run --name emuR-checks -ti -v $(pwd):/source -v r_packages:/output rocker/r-devel:latest bash

In the interactive shell you just started:

• Manually install OS dependencies (this might need a bit of tweaking): apt update && apt install --yes r-cran-tidyverse r-cran-uuid r-cran-base64enc r-cran-shiny r-cran-rsqlite r-cran-dbi r-cran-httpuv r-cran-mime r-cran-v8 r-cran-tidyselect r-cran-mass r-cran-testthat r-cran-knitr r-cran-rmarkdown
• Manually install R dependencies (this might also need a bit of tweaking): RD -e "install.packages(c('wrassp', 'compare', 'matlabr', 'R.matlab'))" Most R packages are actually installed as OS dependency via apt to save compilation time
• Build: RD CMD build --resave-data source/
• Check: R_LIBS_SITE="/usr/lib/R/site-library" RD CMD check --as-cran emuR_*.tar.gz
• Copy the built package to the named docker volume, so it can be shared with other containers that might, for example, run additional checks: cp emuR_*.tar.gz /output