A minimal example:

library(shiny)
ui <- fluidPage(plotly::plot_ly())
server <- function(input, output) {}
shinyApp(ui, server)

Results in the JS error: Shiny.setInputValue is not a function

In the long-term, shiny & htmlwidgets should do better to make the methods registered when initShiny executes available to htmlwidgets; but as a short-term fix, plotly should only call Shiny.setInputValue if it's available