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$dataTable <- renderDT(
data(),
class = "display nowrap compact",
filter = "top",
options = list(
scrollX = TRUE,
searchCols = default_search_columns,
search = list(regex = FALSE, caseInsensitive = FALSE, search = default_search)
)
)
}
shinyApp(ui, server)
rsconnect::deployApp('C:/path//app1.Rmd')
Any help is appreciated.
The error indicates that Shiny is not installed in the environment you are deploying to.
If deploying to a server you own, first install Shiny Server, and confirm that the examples work as expected.
Then consult with the Administrator's Guide to set it up as you like it.
Related
I am trying to deploy shiny app, that uses reticulate and keras packages. I do not have any problem to run it locally, but real troubles appear, when I try to deploy it to shinyapps.io. My app.r file is as follows:
virtualenv_dir = Sys.getenv("VIRTUALENV_NAME")
python_path = Sys.getenv("PYTHON_PATH")
reticulate::virtualenv_create(envname = virtualenv_dir, python = python_path)
reticulate::virtualenv_install(virtualenv_dir, packages = c("numpy", "h5py", "scipy", "scikit-image", "pyyaml", "pillow"), ignore_installed = TRUE)
reticulate::use_virtualenv(virtualenv = virtualenv_dir)
library(shiny)
library(keras)
library(reticulate)
library(magick)
library(raster)
library(EBImage)
library(rdrop2)
library(plotly)
np <- import("numpy", convert=FALSE)
ndi <- import("scipy.ndimage", convert=FALSE)
segment <- import("skimage.segmentation", convert=FALSE)
feature <- import("skimage.feature", convert=FALSE)
model = load_model_hdf5("model_v02122020.h5")
ui <-
tagList(
fluidPage(
sidebarLayout(sidebarPanel(
fileInput("upload", "Choose a file", accept = c('image/png', 'image/jpeg')),
actionButton('click', 'Start')
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel("Input image", plotOutput("InputImagePlot", height="100%")),
tabPanel("Output image", plotOutput("OutputImagePlot", height="100%")),
)
)
)
)
)
server <-
function(input, output, session) {
observeEvent(input$click, {
## some code for image processing
})
}
shinyApp(ui = ui, server = server)
My .Rprofile file is as follows (credit to this source):
VIRTUALENV_NAME = "virt_tf"
if (Sys.info()[["user"]] == "shiny"){
# Running on shinyapps.io
Sys.setenv(PYTHON_PATH = 'python3')
Sys.setenv(VIRTUALENV_NAME = VIRTUALENV_NAME) # Installs into default shiny virtualenvs dir
Sys.setenv(RETICULATE_PYTHON = paste0('/home/shiny/.virtualenvs/', VIRTUALENV_NAME, '/bin/python'))
} else if (Sys.info()[["user"]] == "rstudio-connect"){
# Running on remote server
Sys.setenv(PYTHON_PATH = '/opt/python/3.7.6/bin/python')
Sys.setenv(VIRTUALENV_NAME = paste0(VIRTUALENV_NAME, '/')) # include '/' => installs into rstudio-connect/apps/
Sys.setenv(RETICULATE_PYTHON = paste0(VIRTUALENV_NAME, '/bin/python'))
} else {
# Running locally
options(shiny.port = 7450)
Sys.setenv(PYTHON_PATH = 'python 3.6.12')
Sys.setenv(VIRTUALENV_NAME = VIRTUALENV_NAME) # exclude '/' => installs into ~/.virtualenvs/
# RETICULATE_PYTHON is not required locally, RStudio infers it based on the ~/.virtualenvs path
}
The deployment process seems to run completely according to R log:
rsconnect::deployApp()
Preparing to deploy application...Update application currently deployed at
https://name.shinyapps.io/appname/? [Y/n] y
DONE
Uploading bundle for application: 3428026...DONE
Deploying bundle: 4035381 for application: 3428026 ...
Waiting for task: 846214175
building: Parsing manifest
building: Building image: 4594673
building: Installing system dependencies
building: Fetching packages
building: Installing packages
building: Installing files
building: Pushing image: 4594673
deploying: Starting instances
terminating: Stopping old instances
Application successfully deployed to https://name.shinyapps.io/appname/
The error I get from the bottom of the log:
Error in value[[3L]](cond) : Installation of TensorFlow not found.
Python environments searched for 'tensorflow' package:
You can install TensorFlow using the install_tensorflow() function.
/home/shiny/.virtualenvs/virt_tf/bin/python3
Calls: local ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
When I try to include tensorflow into the list of packages required to be installed into my virtualenvironment I get the following error message:
Downloading tensorflow-2.3.1-cp35-cp35m-manylinux2010_x86_64.whl (320.4 MB)
Collecting tensorflow
Killed
Calls: local ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Error in value[[3L]](cond) :
Error installing package(s): 'numpy', 'h5py', 'scipy', 'scikit-image', 'pyyaml', 'pillow', 'tensorflow'
Execution halted
Out of memory!
As far as I understand, shinyapps.io pushes me to install tensorflow package into virtualenvironment. However, I guess, it should be in the list of available packages. But how to force using it?
This looks like an issue that might require changes to shinyapps or rsconnect. Please file an issue on github if you're still experiencing this.
Here is my code for a simple test app:
library(shiny)
library(shinydashboard)
library(googlesheets4)
library(googledrive)
library(DT)
drive_auth(email = "xxxx")
shinyws1<-gs4_create("WS1")
#table<-read_sheet("xxx")
# Define UI for application
ui <- fluidPage(
# Application title
titlePanel("Test App"),
# Sidebar with a slider input for number of bins
sidebarLayout(
sidebarPanel(
numericInput("bins",
"Number of friends:",
min = 1,
max = 100,
value = 50),
actionButton("submit","Submit",class="btn-success")
),
# Show a plot of the generated distribution
mainPanel(
#blank so far
)
)
)
# Define server logic required to draw a histogram
server <- function(input, output) {
#results<-reactive(input$bins)
observeEvent(input$submit,{
shinyws1 %>% sheet_append(as.data.frame(input$bins))
})
}
# Run the application
shinyApp(ui = ui, server = server)
It works okay in my local server. But deployment fails.
Here is the error message generated after deployment in Shinyio server:
Error in value[[3L]](cond) : Can't get Google credentials.
Are you running googledrive in a non-interactive session? Consider:
* `drive_deauth()` to prevent the attempt to get credentials.
* Call `drive_auth()` directly with all necessary specifics.
* Read more in: https://gargle.r-lib.org/articles/non-interactive-auth.html
Calls: local ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Does anyone know how to fix it? I've tried every workaround I found online, but it didn't work.
I am quite new to Docker and need to host an R Shiny App on Docker. Any help would be appreciated. Please let me know if I need to change something in the DOckerFile.
R ShinyApp works perfectly fine on a local computer but it crashes while using Docker to host it.I suspect something wrong with the fileInput$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'm posting this because I have not managed to get the solutions posted other places working. I'm trying to re-deploy a shiny dash, but it is failing to install a package at deploy.
It's the BioConductor error, but the package it claims to fail for is a CRAN package, and so I have no idea what to do.
MRE:
library(ggseg); library(shiny); library(tidyverse); library(plotly)
# Define UI ----
ui <- fluidPage(
# Application title
titlePanel("Demonstration of ggseg package"),
# Sidebar with a slider input for number of bins
sidebarLayout(
sidebarPanel(
radioButtons(inputId = "atlasChoice", label="Choose atlas",
choiceValues = c("dkt_3d","yeo7_3d",),
choiceNames = c("DKT", "Yeo7"),
inline = FALSE, width = NULL),
radioButtons(inputId = "positionChoice", label="Choose position",
choices = c("LCBC left","LCBC right"),
inline = FALSE, width = NULL)
),
# Show a plot of the generated distribution
mainPanel(
uiOutput("plotUI")
)
)
)
# Define server ----
server <- function(input, output) {
output$plotUI <- renderUI({
plotlyOutput("plotlyPlot")
})
output$plotlyPlot <- renderPlotly({
cc = strsplit(input$positionChoice, " ")[[1]]
ggseg3d(atlas=input$atlasChoice,
surface=cc[1],
hemisphere=cc[2]
)
})
}
# Run the application
shinyApp(ui = ui, server = server)
My repos are set as so:
getOption("repos")
BioCsoft
"https://bioconductor.org/packages/3.7/bioc"
BioCann
"https://bioconductor.org/packages/3.7/data/annotation"
BioCexp
"https://bioconductor.org/packages/3.7/data/experiment"
BioCworkflows
"https://bioconductor.org/packages/3.7/workflows"
CRAN
"https://cran.rstudio.com"
And the error is as following:
Preparing to deploy document...DONE
Uploading bundle for document: 619289...DONE
Deploying bundle: 1770029 for document: 619289 ...
Waiting for task: 573690766
building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 573690767 failed:
Error parsing manifest: Unable to determine package source for Bioconductor package oompaBase: Repository must be specified
Execution halted
I don't know if Athanasia's solved this in the end, but I had a similar problem today, so here's what worked for me, in case it's useful for someone else :)
My app uses biomaRt, which I think depends on Biobase. When I tried to deploy, I had the error:
Error: Unhandled Exception: Child Task 601909864 failed: Error parsing manifest: Unable to
determine package source for Bioconductor package Biobase: Repository must be specified
I changed my repos settings based on instructions I found here. This alone also didn't work for me.
Once I reinstalled Biomart using BiocInstaller::biocLite(), my app deployed successfully :)
I would like to know how to load packages reading a text file in shiny. I have put the text file containing package list in www directory of the shiny application. The application loads the packages and works fine locally, however when I deploy it on shiny server, it does not load the packages and gives error of not finding the packages.
Error in library(simpleaffy) : there is no package called ‘simpleaffy’
The example code is below.
server.R
shinyServer(function(input, output, session) {
withProgress(message = "Please wait", value = 0, expr = {
for (i in 1:15) {
source(textConnection(readLines("www/packages.txt", warn = FALSE)[i]))
incProgress(amount = 1/15, detail = paste0("Loading package ", i, "/15"))
Sys.sleep(time = 0.1)
}
})
})