R wrapper around the OMERO Java Gateway, to enable access to OMERO via R using rJava.
Need additionally:
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
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.
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.
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.
library(romero.gateway)
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.
git clone https://github.com/ome/rOMERO-gateway.git
cd rOMERO-gateway
R
library(devtools)
devtools::build()
omero.host
etc; the various ids should be ok if you used the test-data
script
to populate the server)devtools::test()
The latest R/rJava packages usually don't cause any problems. But older versions have been known for troubles. In these cases try this:
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
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.
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.
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