Sys.getenv() returns empty in Shiny Apps

Question

NOTE I edited the question, since the use of PG_HOST was causing confussion, but the spirit is the same

I am running a shiny app that needs read some environment variables.

That variables are defined before the shiny server starts. For example

export APPLE=apple
export PENCIL=pencil

In the global.R (or at the beggining of server.R is the same) I wrote the following code:

manzana <- Sys.getenv('APPLE')
lapiz <- Sys.getenv('PENCIL')

but those variables are empty.

If I run that code in the R console, both returns the correct value.

Whay this is not working? Whay is different the R console and the shiny app? How I can get the real environment variables (in this fake example $APPLE and $PENCIL)? Which is the correct way of configuring the shiny app?

Answer 1

For those who, like me, are finding this question years later, the secret of getting this to work depends on two things:

• Setting the environment variable permanently
• Making it available to the user shiny on the server computer

So, for example, the app:

library(shiny)

ui <- fluidPage(
  h1(paste("Run by", Sys.getenv("USER"))),
  textInput("name", "What is your name?", value = "Friendly User"),
  actionButton("greet", "Greet"),
  textOutput("greeting")
)


server <- function(input, output, session) {
  output$greeting <- renderText({
    req(input$greet)
    paste0(Sys.getenv("greeting"), " ", isolate(input$name), "!")
  })
}

shinyApp(ui, server)

Run after the command export greeting='Hello' should say "Hello Friendly User!" if it's finding the correct environment variable, but:

The export statement only sets the environment variable for that session (when you have the terminal open). Even with shiny as user, the session you set the variable in will differ from the session the server is running (which, I think, is constant whilst the server is up). However, see that Sys.getenv("USER") is correctly discovering the system environment variable specifying that the user running the server is shiny.

There are a number of ways of setting environment variables for a shiny server, most of which would require the restarting of the server after running the command (not always possible). If you set it in /etc/environment then it should allow all users (including shiny) to access it whenever it's requested without requiring a restart:

echo greeting='Hello' >> /etc/environment

gives:

For further details, and to try out various options, here's a docker image of the above app, created from this Dockerfile which runs the setting environment variable command.

Answer 2

First step is to understand reactivity. Check out the shiny tutorials.

using your example..kind of..heres an app the updates and sets variables that can be called numerous ways....

shiny_example <- function(){

  server <- shinyServer(function(session,input,output){
    the_slots <- list(Apple = 'apple',Green = 'green')

    make_globs <- function(new_var = NULL){
      if(!is.null(new_var)){
        the_slots <<- append(the_slots,new_var)
      }
    }

    glob_vals <- the_slots

    glob_vals <- eventReactive(input$saver, {
      set_new_vars <- list(input$new_var)
      names(set_new_vars) <- input$new_var_name
      the_slots <<- make_globs(new_var = set_new_vars)
      lapply(list('new_var','new_var_name'),function(i)updateTextInput(session,i, value = ""))
      return(the_slots)

    })

    output$envs <- renderPrint({

      glob_vals()

    })

    output$sels <- renderUI({
      vals <- 1:length(glob_vals())
      Opts <- unlist(lapply(vals,function(i)sprintf('<option value="%s">%s</option>',i,names(glob_vals()[i])))) %>% HTML
      HTML(
        paste(
          "<div class='shiny-input-container'>",
          "<label class='control-label' for='the_ups'></label>",
          "<div><select id='the_ups'>",Opts,"</select></div>",
          "</div>",sep=""))
    })

    output$sel_vals <- renderPrint({
      ref_cards <- lapply(1:length(glob_vals()),function(i)
        data.frame(the_names = names(glob_vals()[i]),the_vals = glob_vals()[[i]]))%>%
        rbind.pages

      ref_cards[input$the_ups,'the_vals']


    })

  })


  ui <- shinyUI(
    bootstrapPage(
      tags$div(class="container",
               fluidRow(
                 tags$h4(HTML('These inputs will update the variable list \n like a variable in Sys.getenv()')),
                 column(6,textInput(inputId = "new_var_name",label = "variable name")),
                 column(6,textInput(inputId = "new_var",label = 'variable value'))
               ),
               fluidRow(

                 column(6,
                        tags$h4(
                          HTML('Pressing the `add_new` button will load the variables and display the corresponding values below'),
                          actionButton(inputId = "saver",label = "add_new")
                        )),
                 column(6,tags$h4("You can even dynamically update a selection input with newly created paths or environment variables"),
                        uiOutput('sels'))
               ),
               fluidRow(
                 column(6,verbatimTextOutput('envs')),
                 column(6,verbatimTextOutput('sel_vals')))
      )))

  shinyApp(ui,server)

}

And the result: