Shiny application not loading with graphics

Question

I have shiny app, which works perfectly fine on my local machine. I deployed the app on shiny-server running on centos-release-6-9.el6.12.3.x86_64. The content of the application is loaded without any graphics as shown below:

And I get the following message in JS consol.

Loading failed for the <script> with source “http://mamged:3838/v01/shared/bootstrap/shim/respond.min.js”. v01:18:1
ReferenceError: Shiny is not defined[Learn More] v01:21:1
Loading failed for the <script> with source “http://mamged:3838/v01/shinyjs/shinyjs-default-funcs.js”. v01:38:1
ReferenceError: shinyjs is not defined[Learn More] v01:39:1
Loading failed for the <script> with source “http://mamged:3838/v01/message-handler.js”. v01:40:1
ReferenceError: jQuery is not defined[Learn More]
    [Exception... "Favicon at "http://mamged:3838/favicon.ico" failed to load: Not Found." nsresult: "0x80004005 (NS_ERROR_FAILURE)" location: "JS frame :: resource:///modules/FaviconLoader.jsm :: onStopRequest :: line 156" data: no]

I am not sure what is going wrong.

EDIT

I have put some sample code to reproduce the example on the server.

server.r

# clear console
cat("\014")


# Defining the size of file to be accepted. -1 to accept any size.
options(shiny.maxRequestSize = -1) 


# Clear workspace environment
rm(list = ls())    

# set locale
Sys.setlocale('LC_ALL','C') 

# main function
shinyServer(function(input, output,session) {

})

ui.r

library(shiny)
library(shinyjs)


filenames <- list.files(path = "data",pattern="\\.txt$")
names(filenames) <- gsub(pattern = "\\.txt$", "", filenames)
shinyUI(fluidPage(theme = "bootstrap.css",
                  (navbarPage("MAMGEDCDE",
                              position = c("fixed-top"),
                              fluid = TRUE, selected = "none", 
                              navbarMenu("Help", icon = icon("fa fa-infocircle"),

                                         tabPanel(
                                           list(
                                             a("Reference Manual", 
                                               target="_blank", href = "MAMGEDManual.pdf"),

                                             a("GPLs Supported",
                                               target="_blank", href="gpl.pdf"),

                                             a("Video Tutorials",
                                               downloadLink("AbsoluteExpression", " Absolute Expression", class=" fa fa-cloud-download"),
                                               downloadLink("DifferentialExpression", " Differential Expression", class=" fa fa-cloud-download")
                                               )
                                             ))
                                         ),

                              navbarMenu("Sample Data",
                                         tabPanel(
                                           list(
                                             downloadLink("AffymetrixData", " Affymetrix", class=" fa fa-cloud-download"),
                                             downloadLink("CodelinkData", " Codelink", class=" fa fa-cloud-download"),
                                             downloadLink("IlluminaData", " Illumina", class=" fa fa-cloud-download")
                                             ))
                                         ),

                              navbarMenu("Stand-Alone Version", icon = icon("fa fa-infocircle"),
                                         tabPanel(
                                           list(
                                             downloadLink("CodeandData", " MAMGED", class=" fa fa-cloud-download"),
                                             a("Stand-alone Manual", target = "_blank", href= "Stand-alone.pdf")
                                             )
                                           )
                                         )
                              )
                   ),

                  br(),
                  br(),
                  useShinyjs(),  ## initialize shinyjs to reset input files.
                  sidebarLayout(
                    sidebarPanel(
                      br(),

                      width = 4,
                      tabsetPanel(id = "tabs",
                                  tabPanel(id = "tab1", value = "tab1",
                                           h5("Upload Data Files"),
                                           br(),
                                           br(),

                                           fileInput("files", label = "Upload Data Files",
                                                     multiple = "TRUE",
                                                     accept=c('text/csv','text/comma-separated-values,
                                                              text/plain', '.csv','.cel','.TXT','.txt', '.zip')),

                                           uiOutput('Display_source_data'),
                                           br(),

                                           textInput("mailid", "Enter Email ID", placeholder = "Enter your email id")
                                           ),

                                  tabPanel(id = "tab2", value= "tab2",
                                           h5("Download Data",style="bold"),
                                           br(),
                                           br(),
                                           br(),
                                           textInput("jobid", "Enter Job ID", placeholder = "Enter your job id")
                                           )),
                      br(),
                      br(),

                      tags$head(tags$script(src = "message-handler.js")),
                      fluidRow(
                        conditionalPanel(
                          condition = "input.tabs == 'tab1'",
                          column(4,
                                 actionButton("Submit", label = "Submit"))
                          ),
                        conditionalPanel(
                          condition = "input.tabs == 'tab2'",
                          br(),
                          column(4,
                                 uiOutput("button")
                                 )),

                        column(4,
                               actionButton("Reset_Input", label = "Reset"))
                        ),
                      br()

                      ),

                    mainPanel(
                      titlePanel(
                        headerPanel( 
                          h2( "Analysis of Microarray Gene Expression Data",
                              align="center", style="bold"
                              )
                          )
                        ),
                      h5("test page")
                      )
                    )
                  ))

It works fine on the local machine.

One more thing, do I need to install r packages by using sudo -i R to make it work. I installed all the packages without sudo.

Answer 1

Probably the shiny-server is running as a special user.
Assume the username is like on other servers "www-data".
The problem now is that the files in the web-directory perhaps can be accessed by the shiny-server itself, but not by the clients.
Long story short: adjust the Unix-file-rights for all the files, so that a common client can access the files. This must be done for all files that shall be public available like images, css-files and js-files. Surely it can include any other files too you want to serve like PDF, Office-files, etc.
The unix-rights have to be 0744 for being readable, the last digit is for the public and in your case probably to change with chmod.
For a detailed explanation concerning chmod you can show the man-page on commandline with man chmod.

In some environments it's common that all "public" files are sorted in folders named "public" or "Public", then just the file-rights of these folders have to be changed recursive. Even for the public folders here I use plural, as there can be several folders always with the same name in different directories. On your server the shared folder seems having the same functionality but not all public files are sorted in it. If you prefer the folder name shared over public, you never have to change but only to adjust the rights accordingly.

The reason that I mentioned about the server-user "www-data" above is that the files in the web-directory should have this user as owner, but are not required to be public. All you r-files should be private excepted the files which should be called directly in the browser. So all the files are separated in public and private. The file-owner can be adjusted with chown which can be called on commandline recursive too and with man chown you also can show the detailed description.

About public r-files I don't know if they have to be executable on shiny-servers, if so then the file-rights for these files have to be 0755.

Update
Also assure that all files are existent in your www-directory and that the domain is linked to the right folder.

Answer 2

Seems your application is missing a package. Check your application log by default located in /var/log/shiny-server. Also you can add the following option to your config file /etc/shiny-server/shiny-server.conf:

preserve_logs true; (at the top level)

After a restart of Shiny Server check your log file again. Look for missing packages or libraries. Hope it helps.