Packages missing in shiny-server

Question

I am trying to create a web application using shiny. It requires me to load a package I have installed on my computer. For example:

## Contents ui.R:
library(shiny)
library(plyr)

shinyUI(pageWithSidebar(

  headerPanel("Hello Shiny!"),

  sidebarPanel(
    sliderInput("obs", 
                "Number of observations:", 
                min = 0, 
                max = 1000, 
                value = 500)
  ),

  mainPanel(
    plotOutput("distPlot")
  )
))

## Contents server.R:
library(shiny)
library(plyr)

shinyServer(function(input, output) {

  output$distPlot <- renderPlot({

    # generate an rnorm distribution and plot it
    dist <- rnorm(input$obs)
    hist(dist)
  })
})

This works fine if I run it locally (using runApp) but when I try to run it via my server (same computer) I get the error that the plyr package (or any other package I try to use this way) is not installed. How could I use extra packages in shiny server?

score 9 · Answer 1 · edited May 23 '17 at 12:08

9

The problem is that shiny-server cannot find the packages that you install because it runs them as a different user which is called shiny. This user is created upon installation of shiny-server

The easiest (and safest IMHO) way to solve this is to just install the packages as the shiny user, using the following steps.

Set a password for the user using sudo passwd shiny, now enter and confirm a password
Switch to the shiny account using: su - shiny
Call up R using $ R (without sudo)
Install the required packages, in this case: install.packages("plyr")

Note that if you have rstudio-server installed on the same machine then you can perform steps 2-4 using that interface. Simply go the same domain/ip and use :8787 for the rstudio-server interface instead of :3838 for shiny-server.

Adapted from my answer here.

edited May 23 '17 at 12:08

Community

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answered Oct 07 '15 at 15:43

Bastiaan Quast

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Trying Step 1, I get "passwd: Unknown user name 'shiny'." - any solutions? – maia Dec 07 '15 at 01:12
@maia, this account should have been created when you installed `shiny-server`, however, you can manually do so using: `useradd shiny` . I hope that works. – Bastiaan Quast Dec 07 '15 at 07:43
you do not need to add a password for the user. Just start with step 2, `su - shiny`. – nycynik Sep 10 '17 at 20:41
agreed, but if you are going to be using the user, it would be a good idea – Bastiaan Quast Sep 11 '17 at 05:45

score 8 · Accepted Answer · answered Apr 17 '13 at 16:56

8

Compare the output of .libPaths() in both cases and adjust accordingly in the server instance / your script.

You may for example have the packages in "your" R package directory which the server cannot access. System-wide package installations are preferable in cases like this -- and are e.g. the default on Debian / Ubuntu.

answered Apr 17 '13 at 16:56

Dirk Eddelbuettel

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An easy way to check is actually to `sudo R` and then have a look (`library(myPotentiallyMissingPackage)` for instance). If needed, you can also install your missing packages from there. – Antoine Lizée Oct 17 '13 at 01:53
4

Do. Not. Start. R. As. Sudo. Ever. – Dirk Eddelbuettel Oct 17 '13 at 01:57
9

Well, it seems to be very bad, but could I ask: why? :-) – Antoine Lizée Oct 25 '13 at 04:34
1

You really do not want to run anything as root because if that program is compromised for any reason, your entire server is now compromised. So, if there are any security holes in R, when running as root, you now allow those threats to have your machine taken over by a bad process/person/etc. – nycynik Sep 10 '17 at 20:40

score 2 · Answer 3 · answered Dec 05 '17 at 16:33

Here might be a solution that doesn't mess up with the system library. Put the following code at the beginning of the server.R.

user <- unname(Sys.info()["user"])
if (user == "shiny") {

  # Set library locations
  .libPaths(c(
    "/path/to/your/own/library"
  )
  )

}

This lets Shiny look for packages installed in your own library preferentially and also keeps the packages you use to develop the app and the packages used when the app is deployed in sync.

Note that you may need to tweak permissions of your library folder for the shiny user to see it properly. Otherwise it will fail to look into your specified location without any error message.

score 0 · Answer 4 · answered Sep 04 '17 at 07:11

0

I have upgraded from R 3.2 to 3.4 and faced the same issue, then i have created a folder named 3.4 in R/x86_64-pc-linux-gnu-library/ and copied everything from 3.2 folder (which is already there in the same location).

answered Sep 04 '17 at 07:11

Venkataramana

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score 0 · Answer 5 · answered Aug 11 '19 at 11:06

If the package is installed in your R library. The easiest way to make it run on shiny-server is to indicate to Shiny the library directory where the package is. Something like: library(plyr, lib.loc="/usr/local/lib/R/site-library") . If you have R-Studio installed, you can view the directory with .libPaths()

score -2 · Answer 6 · answered Jul 23 '13 at 00:44

-2

Why do you need Plyr? nothing in your code is using it; but anyway, you can install packages on Linux R installation by running R , then, install.packages('plyr');

answered Jul 23 '13 at 00:44

gpc

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Packages missing in shiny-server

6 Answers6

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