My phrasing may have not been so clear.
Please allow me to elaborate.
Running a package though the Shiny server should not be an issue in general, nor should fileInputbe problematic.
I think It's just that the solution in my case would entail altering my R package code.
The app runs via the CRAN version of my package, which contains the line
seqs <- ape::read.dna(file = file.choose(), format = "fasta").
The above line of course does not work on the server, but does work locally.
I do intend to include a launchApp() function through my package for users to run the app locally. However, a fully online version is also nice to have.
I could have a shiny = FALSE argument within my package's main function and then simply set this to TRUE for the app. Something like
if (shiny == TRUE) {
...
} else {
seqs <- ape::read.dna(file = file.choose(), format = "fasta")
}
I'll continue to investigate.