OMERO R Gateway

R wrapper around the OMERO Java Gateway, to enable access to OMERO via R using rJava.

Prerequisites

Users

• R
• Java
• R package: rJava
• R package: jpeg
• R package: httr

Developers

Need additionally:

• R package: devtools
• R package: testthat (optional)
• Git

Install the romero.gateway R package

Download the latest romero.gateway version which is compatible with your OMERO server version from the Release page

OMERO version	romero.gateway version
5.6, 5.5	>= 0.4.8
5.5	0.4.7
5.4	<= 0.4.7

Windows

Download the zip package.

In RStudio "Install Packages" use option "Install from:" "Package Archive File" and select the romero.gateway zip file.

Alternatively: In R console run install.packages("https://github.com/ome/rOMERO-gateway/releases/download/vx.x.x/romero.gateway_x.x.x.zip", repos = NULL)

See Tips for Windows users section if you are running into difficulties.

Unix / OSX

Download the tar.gz package.

In RStudio "Install Packages" use option "Install from:" "Package Archive File" and select the romero.gateway tar.gz file.

Alternatively: In R console run install.packages("https://github.com/ome/rOMERO-gateway/releases/download/vx.x.x/romero.gateway_x.x.x.tar.gz", type='source', repos = NULL)

See Tips for Unix users section if you are running into difficulties.

Docker / Jupyter

With Docker and Jupyter there is a quick and easy way to get an R OMERO enviroment set up and running in your browser. Ideal to quickly try out some snippets. Go to jupyter directory and see the instructions there.

Usage

• Like any other R package load the package library(romero.gateway)
• Try some examples from the examples directory
• Another potential source of examples is the unit tests directory: tests/testthat

Build from source

install.R script

This allows you to install a custom version or build from a custom branch.

Use the install.R script:

  curl -o install.R https://raw.githubusercontent.com/ome/rOMERO-gateway/master/install.R 
  Rscript install.R

This will build and install the current master branch by default. But you can specify a particular branch or version to build or perform a local build of the cloned repository. Run Rscript install.R --help to see more details.

Manually

• Clone this Github repository git clone https://github.com/ome/rOMERO-gateway.git
• Cd into the directory and start R console cd rOMERO-gateway R
• Load devtools library library(devtools)
• Build the package devtools::build()

Unit tests

• Install testthat
• Spin up an OMERO server to test against
• Adjust and run test-data script to populate the test server
• Adjust setup.csv to match your test server setup (mostly omero.host etc; the various ids should be ok if you used the test-data script to populate the server)
• Run devtools::test()

Troubleshooting rJava

The latest R/rJava packages usually don't cause any problems. But older versions have been known for troubles. In these cases try this:

Unix users

Installing rJava

Before installing the rJava package you probably have to set up Java for R first:

# as root
export $JAVA_HOME=[path to JDK/JRE]
R CMD javareconf

Additional dependencies

In order to build/install some necessary R packages, additional system libraries may have to be installed first. E.g. the R packages httr and xml2 need the development libraries for curl and xml2, so for example on a Debian system you probably have to install libcurl4-dev and libxml2-dev first. If you can't install an R package due to compile errors, most likely you are missing a development package of some dependent library on your system.

Windows users

Installing rJava

You need to have a Java SDK installed. Latest version which is supported is 11. Download for example the Adopt OpenJDK 11 from https://adoptopenjdk.net/

Make sure that the java executable is on your Path and JAVA_HOME is set, see 'Environment Variables' settings:

Then install rJava as well as the additional dependencies for the R gateway httr and jpeg from CRAN. Finally install the romero-gateway from the zip file.