Failing to deploy shinyapp depending on Bioconductor packages

shiny shinyapps.io
2

What is the value of getOption("repos")?

Do you have this configured to point to BioConductor?

Although the publishing process for Shiny Server and RStudio Connect uses packrat, the miniCRAN vignette demonstrates how to extract the repository values for BioConductor:

bioc <- local({
  env <- new.env()
  on.exit(rm(env))
  evalq(source("http://bioconductor.org/biocLite.R", local = TRUE), env)
  biocinstallRepos()
})

The resulting object bioc looks something like this:

> bioc

                                               BioCsoft 
           "https://bioconductor.org/packages/3.5/bioc" 
                                                BioCann 
"https://bioconductor.org/packages/3.5/data/annotation" 
                                                BioCexp 
"https://bioconductor.org/packages/3.5/data/experiment" 
                                              BioCextra 
          "https://bioconductor.org/packages/3.5/extra" 
                                                   CRAN 
                         "https://cloud.r-project.org/" 
                                              CRANextra 
                  "https://www.stats.ox.ac.uk/pub/RWin"

You can use this information to configure your repos settings.

For more information, the support article Package management in RStudio Connect may help.

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