I try to rebuild my application as in the link. I have a multitematic dashboard and I would like to have each topic in separate ui and server files to have better control of the code.
The main file (app.R) is contacting with other files eg UI using source(file.path("ui", "tab1.R"), local = TRUE)$value
tab1.R looks like:
tabPanel("Tab 1", uiOutput("content1")) (content1 is in server file).
I would like to have possibility to put more then on tabPanel in one file. I thought that i can do something like that:
tab1.R looks like:
aaa <- tabPanel("Tab 2", uiOutput("content2"))
bbb <- tabPanel("Tab 1", uiOutput("content1"))
And then contact with them using:
source(file.path("ui", "tab1.R"), local = TRUE)$aaa
source(file.path("ui", "tab1.R"), local = TRUE)$bbb
But i get ERROR:
Error in attr(x, "selected") <- TRUE :
attempt to set an attribute on NULL
I could not find answer for that anywhere so I disated to write here for help
I found imo the best way, I just used the functions:
aaa <- function(){tabPanel("Tab 2", uiOutput("content2"))}
bbb <- function(){tabPanel("Tab 1", uiOutput("content1"))}
And then on the top on file I upload source:
source(file.path("ui", "tab1.R"), local = TRUE)
Now I can normally use functions in code:
aaa()
bbb()
Related
I have a bash script that i'm running using shiny and system. It takes a long time to run so I'd like to provide feedback to the user about progress. In the bash script I have messages that periodically updates the user and I'm trying to find a way to have them printed in the UI.
Here is a minimal working example for which I'd like to have "Output 1" and "Output 2" returned to the user as they appear in the console.
Any help is greatly appreciated.
library(shiny)
ui <- fluidPage(
actionButton("run", "Print to Console")
)
server <- function(input, output, session) {
observeEvent(input$run,{
system(c("echo output 1; sleep 2; echo output 2"))
})
}
shinyApp(ui, server)
I'd suggest to run your system command asynchronously and redirect the output to a log file. In parallel you can continuously read in the logfile via reactiveFileReader.
In contrast, when intern = TRUE the R session (and shiny) is blocked while the command is executed.
Please check the following:
library(shiny)
file.create("commands.sh", "output.log")
Sys.chmod("commands.sh", mode = "0777", use_umask = TRUE)
writeLines(c("#!/bin/bash", "echo output 1","sleep 2", "echo output 2"), con = "commands.sh")
ui <- fluidPage(
actionButton("run_intern", "Run intern"),
textOutput("myInternTextOutput"),
hr(),
actionButton("run_extern", "Run extern"),
textOutput("myExternTextOutput")
)
server <- function(input, output, session) {
systemOutputIntern <- eventReactive(input$run_intern,{
system(command = "echo output 1; sleep 2; echo output 2", intern = TRUE)
})
output$myInternTextOutput <- renderText(systemOutputIntern())
observeEvent(input$run_extern,{
system(command = "./commands.sh 2>&1 | tee output.log", intern = FALSE, wait = FALSE)
})
log <- reactiveFileReader(200, session, filePath = "output.log", readLines)
output$myExternTextOutput <- renderText(log())
}
shinyApp(ui, server)
PS: As an alternative you might want to check AsyncProgress from library(ipc).
I am getting an error
The application failed to start: exited unexpectedly with code 1
Error in enforcePackage(name, curVersion) :
The shiny package was not found in the library.
Calls: local ... eval -> eval -> eval -> -> enforcePackage
Execution halted
when I try to deploy shiny app. I found similar problem that claimed that having library(shiny) solves it, it didn't help. I also tried lib=("path/to/shiny"), no effect.
Here is my code
library(shiny)
library(DT)
library(rmarkdown)
###
ui <- fluidPage(fluidRow(column(10, div(dataTableOutput("dataTable")))))
server <- function(input, output, session) {
data <- reactiveFileReader(100, session, 'excel.csv', read.csv)
output$dataTable <- renderDT(
data(),
class = "display nowrap compact",
filter = "top",
options = list(
scrollX = TRUE,
searchCols = default_search_columns,
search = list(regex = FALSE, caseInsensitive = FALSE, search = default_search)
)
)
}
shinyApp(ui, server)
rsconnect::deployApp('C:/path//app1.Rmd')
Any help is appreciated.
The error indicates that Shiny is not installed in the environment you are deploying to.
If deploying to a server you own, first install Shiny Server, and confirm that the examples work as expected.
Then consult with the Administrator's Guide to set it up as you like it.
I am quite new to Docker and need to host an R Shiny App on Docker. Any help would be appreciated. Please let me know if I need to change something in the DOckerFile.
R ShinyApp works perfectly fine on a local computer but it crashes while using Docker to host it.I suspect something wrong with the fileInput$datapath and Windows/Docker interaction. Do I need to specify the PATH in the DockerFile?
I have used rocker/verse image from Docker Hub,installed the libraries manually and stored the image locally on my computer as 'r_all_libraries_july2'
This is the image I have used in my DockerFile.
The Shiny Code works well in a Linux environment. But, crashes while running docker in Windows Environment. A temporary file is also getting created in the production environment when a file is input in the Shiny App using fileInput.
library(shiny)
library(DT)
library(dplyr)
library(shinycssloaders)
library(readxl)
library(shinyjs)
library(ggplot2)
library(png)
library(spatstat)
require(tibble)
require(magrittr)
require(dplyr)
require(multcomp)
require(emmeans)
require(readxl)
library(httr)
require(ggfortify)
library(shinyjs)
library(shinyBS)
ui <-navbarPage(title="RShinyApp", windowTitle = "Data Visualization", theme = shinythemes::shinytheme("cerulean"),selected = "Load Data",
tabPanel(title="Load Data", #3rd Tab Panel Start,
fluidPage(useShinyjs(),
sidebarLayout(
sidebarPanel(
wellPanel(checkboxGroupInput("filetype", "Choose filetype to upload:",
choices = c("CSV"="csv", "Excel"="excel"))),
conditionalPanel(condition = "(input.filetype=='csv')|(input.filetype=='excel')",
wellPanel(checkboxInput(inputId = 'header', label = 'Header', value = FALSE)),
fileInput(inputId = "file", label = "Upload File", accept = c(".csv",".xlsx"))
),#End of conditional panel
uiOutput("sheetnames")
#conditionalPanel(condition = "(input.filetype=='excel')&(!is.null(input.file))",uiOutput("sheetnames")),
),#sidebarpanel
mainPanel(
# h3("Data Table"),
withSpinner(tableOutput("contents"))
)
)#SideBarLayout
)#FluidPage End
) #3rd Tab Panel End
)#navbarpage
server <-function(input,output,session){
###########Load Data Tab#######################
rv<-reactiveValues(data=NULL,xlorcsv=NULL,head=FALSE,sheet=NULL,features=NULL)
observeEvent(input$filetype,{if(input$filetype=='csv'){rv$xlorcsv<-'csv'}
else if(input$filetype=='excel'){rv$xlorcsv<-'excel'}})
observeEvent(input$header, rv$head<-input$header)
observeEvent(input$sheetnames,rv$sheet<-input$sheetnames)
observeEvent(input$file,
{if((!is.null(rv$xlorcsv))&(!is.null(input$file))){
#####THIS IS WHERE THE SHINY APP IS CRASHING IN DOCKER--my guess is datapath ###########needs to be defined here
if(rv$xlorcsv=='csv'){rv$data<-read.csv(input$file$datapath, header = rv$head, na.strings = "")
rv$features<-colnames(rv$data)}
}
})
output$sheetnames<-renderUI({
if((is.null(rv$xlorcsv))|(is.null(input$file))){return(NULL)}
if((rv$xlorcsv=='excel')&(!is.null(input$file))){selectInput("sheetnames","Select sheet to load",choices = excel_sheets(path = input$file$datapath))}
})
output$contents<-renderTable({rv$data})
}
shinyApp(server=server, ui=ui)
DockerFile:
FROM r_all_libraries:latest
EXPOSE 80
COPY r_shiny_code_working11.R /home/rstudio/r_shiny_code_working11.R
CMD ["/home/rstudio/r_shiny_code_working11.R"]
This is the error on the console:
standard_init_linux.go:207: exec user process caused "no such file or directory"
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.
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.
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.
I have a shiny app which works just fine. Now, I want to display a static image as a logo on top of the page. Problem is the logo does not show up when I run the app, it just shows a missing file icon..
Top of my ui function looks like this:
ui = fluidPage(
img(heigth = 100, width = 100, src = "logo.png", align = "right"),
pageWithSidebar(
headerPanel(title = "ABC", windowTitle = "ABC"),
sidebarPanel(...
I run the app as follows:
# --------------------------------------------------------------------------------------------------------------------------------------
# Settings:
dir = "C:/app/";
folder_code = "r/";
# --------------------------------------------------------------------------------------------------------------------------------------
# Main:
# Libraries:
library(shiny);
library(plotly);
# Includes:
source(file=paste(dir, folder_code, "analysis.r", sep=""));
source(file=paste(dir, folder_code, "plotlib.r", sep=""));
source(file=paste(dir, folder_code, "ui.r", sep=""));
source(file=paste(dir, folder_code, "server.r", sep=""));
# Run app:
shinyApp(ui = ui, server = server, options=list(launch.browser = TRUE))
The directory where the app code and image is placed looks like this:
|r
|www [<- my image is stored in this folder]
analysis.r
app.r
ui.r
server.r
plotlib.r
EDIT:
With the following changes, it now works:
I create a file app.R with just this line of code:
app = shinyApp(ui = ui, server = server)
In my main code displayed above, I replace
shinyApp(...)
by
shinyAppFile(appFile = paste(dir, folder_code, "app.r", sep=""),
options=list(launch.browser = TRUE))
No clue however why it works like that and not as I had it previously..
You might want to check the permissions on your www directory and image- the directory should be drwxrwxr-x and image -rw-rw-r--.