Bioconductor packages on shinyapps.io

[RyanK]

I have a stable shiny that works great on my localhost, but having issues deploying to the shinyapps.io due to bioconductor. While this problem isn't new to shinyapps, some of the previous solutions are outdated (biocLite.R) or are pretty vague in how it was solved.

According to the shinyapp documentation, we have to:

the repos option must be configured, either directly or by using setRepositories() , to include the BioConductor repositories in addition to CRAN

But how does one do this? When I use setRepositories such as other posts have done, I get the error: "Error in value[3L] : cannot set repositories non-interactively" and I'm not sure how to use the repos option... or not sure how to get it to work (I can't find a valid url)

I just have one BioConductor package: TCGAbiolinks that I would like to get running. What's a good syntax to use BioConductor for future users to follow?

library(tidyverse)
library(BiocManager)
library(TCGAbiolinks)
ui <- fluidPage( titlePanel("Getting BioConductor to work")  )
server <- function(input, output, session){ # just being generic }
shinyApp(ui = ui, server = server)

Thanks!

[RyanK]

Found the solution: options(repos = BiocManager::repositories()) before calling library with the bioconductor package. My personal issue was using a function using !require(), which of course tried installing it on the write protected sever.

options(repos = BiocManager::repositories())
library(TCGAbiolinks)
library(tidyverse)

ui <- fluidPage( titlePanel("Getting BioConductor to work")  )
server <- function(input, output, session){ # just being generic }
shinyApp(ui = ui, server = server)