R for photobiology repository

A CRAN-like repository

Pedro J. Aphalo


What is stored here?

Binary and source versions of R packages ‘rOmniDriver’ and ‘ooacquire’ as well as some old R packages of my authorship are stored here. The remaining packages are available through CRAN. Sources for all my R packages are available in Git repositories at (https://github.com/aphalo?tab=repositories).


Installation in principle differs from instalaltion from CRAN only in the need to add this repository to those known to R. In practice things are not as simple because the Ocean Optics/Ocean Insight OmniDriver runtime and Java need to be first installed. Consequently, please read before attempting to install ‘rOmniDriver’ or ‘ooacquire’ their README files where you will find up-to-date installation instructions at (https://docs.r4photobiology.info/rOmniDriver/) and (https://docs.r4photobiology.info/ooacquire/).

If we are using a current version of R, we can set an R option, either at the command prompt or in file .Rprofile.

  repos = 
    list(CRAN = "https://cran.rstudio.com/",
         r4photobiology = "https://r.r4photobiology.info"))

If we are using a current version of R, and also use the Bioconductor or other repositories, or a local mirror of CRAN, we can include them in the list, or even fetch the current setting of the option and append the r4photobiology repository to the fetched list and set the option with this list.

If you are using an old version of R, the following code run at the command prompt (in an interactive session) makes this repository known to your R installation for the current session.

# set repositories
  graphics = FALSE,
  addURLs = c(r4photobiology = "https://r.r4photobiology.info")