Error in deploying shiny app

Question

I wrote a shiny app,it depend on some packages from CRAN,bioconductor and Github. I want to deploy it on shinyapps.io,but get some error. Firstly, I use the guide on shinyapp.io user guide. Just using R package "rsconnect",and set account using setAccountInfo and then use rsconnect::deployApp to deploy my app, but get the following error.

And then I add options(repos = BiocInstaller::biocinstallRepos()) It allowed me to install packages on bioconductor,but my app also depend on packages from Github, so get the following Error.

add some example code to reproduce your problem. That might give you more answers ;) — 5th

user5249203 user5249203 · Accepted Answer · 2018-09-11T18:18:51

Please don't post images. It does not help with fonts sizes and does not communicate your issue properly. Try posting the code you entered and the error and finally, sessionInfo().

As per your error, you probably missed in the documentation Using your R packages in the cloud.

In order for BioConductor packages to install successfully on shinyapps.io, the repos option must be configured...`

Check what the repos your session is using

getOption("repos")

by default, you should see. Where the Bioconductor is missing.

                                            CRAN 
"https://mran.microsoft.com/snapshot/2018-08-01" 
                                       CRANextra 
            "http://www.stats.ox.ac.uk/pub/RWin"

You can make a global change in .Rprofile (R root directory). or create a new .Rprofile. I would prefer the second way, where you have better control.

The steps are detailed here Package management in RStudio Connect.

Add .Rprofile in the app directory which you intend to deploy. copy paste the following.

# A sample .Rprofile file with two different package repositories

local({
  r <- getOption("repos")  
    r["BioCsoft"] <- "https://bioconductor.org/packages/3.7/bioc" 
    r["BioCann"]  <- "https://bioconductor.org/packages/3.7/data/annotation" 
    r["BioCexp"]  <- "https://bioconductor.org/packages/3.7/data/experiment" 
r["BioCworkflows"]<- "https://bioconductor.org/packages/3.7/workflows"            
    r["CRAN"]     <- "https://cran.rstudio.com" 
  options(repos = r)
})

Error in deploying shiny app

1 Answers