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)
}
})
})
Related
I am trying to use a python package inside shiny app to extract the maintext from a webpage: https://newspaper.readthedocs.io/en/latest/
what I mean by main text is the body of the article, without any adds, links, etc... (very similar to the "reader view" in safari on iphone).
To my knowledge, there is no similar package in r, if you know one please let me know.
The goal of this app is to allow the user to insert a web address, click submit and get the clean text as output.
please find the code below as well as the error message. I am using rstudio cloud.
This is the error:
Using virtual environment 'python3_env' ...
Warning in system2(python, c("-c", shQuote(command)), stdout = TRUE, stderr = TRUE) :
running command ''/cloud/project/python3_env/bin/python' -c 'import sys; import pip; sys.stdout.write(pip.__version__)' 2>&1' had status 1
Warning in if (idx != -1) version <- substring(version, 1, idx - 1) :
the condition has length > 1 and only the first element will be used
Warning: Error in : invalid version specification ‘’, ‘ ’
52: stop
51: .make_numeric_version
50: numeric_version
49: pip_version
48: reticulate::virtualenv_install
47: server [/cloud/project/python in shiny.R#42]
Error : invalid version specification ‘’, ‘ ’
and this is the code:
# Python webpage scraper followed by r summary:
library(shiny)
library(reticulate)
ui <- fluidPage(
sidebarLayout(
sidebarPanel(
textInput("web", "Enter URL:"),
actionButton("act", "Submit")
),
mainPanel(br(),
tags$head(tags$style(HTML("pre { white-space: pre-wrap; word-break: keep-all; }"))),
verbatimTextOutput("nText"),
br()
)
)
)
server <- function(input, output){
#1) Add python env and packages:
reticulate::virtualenv_install('python3_env', packages = c('newspaper3k', 'nltk'))
py_run_string("from newspaper import Article")
py_run_string("import nltk")
py_run_string("nltk.download('punkt')")
#2) Pull the webpage url:
webad <- eventReactive(input$act, {
req(input$web)
input$web
})
observe({
py$webadd = webad
py_run_string("article = Article('webadd')")
py_run_string("article.download()")
py_run_string("article.parse()")
py_run_string("article.nlp()")
py_run_string("ztext =article.text")
py_run_string("r.ntexto = ztext")
output$nText <- renderPrint({
r.ntexto
})
})
}
shinyApp(ui = ui, server = server)
I am getting an error
The application failed to start: exited unexpectedly with code 1
Error in enforcePackage(name, curVersion) :
The shiny package was not found in the library.
Calls: local ... eval -> eval -> eval -> -> enforcePackage
Execution halted
when I try to deploy shiny app. I found similar problem that claimed that having library(shiny) solves it, it didn't help. I also tried lib=("path/to/shiny"), no effect.
Here is my code
library(shiny)
library(DT)
library(rmarkdown)
###
ui <- fluidPage(fluidRow(column(10, div(dataTableOutput("dataTable")))))
server <- function(input, output, session) {
data <- reactiveFileReader(100, session, 'excel.csv', read.csv)
output$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'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 am new to R and I am actually developing a page where a directory (string characters like "xx/xx") is given in the server and I want to take back this directory to include it in the source of my ui app.
UI:
library(shiny)
file<-textOutput("paramfile")
source(file(file), local = TRUE, encoding = 'UTF-8')
SERVER :
filedir<-renderText({
"entries/5429_param.R"
})
output$paramfile<-renderText({
filedir()
})
I then have an error :
"Warning in file(filename, "r", encoding = encoding) : cannot open
file '< div id="paramfile" class="shiny-text-output">< /div>':
Invalid argument
Error in file(filename, "r", encoding = encoding) :
cannot open the connection"
Do you know how can I remove those tags or if there is another function that can allow me to take a string in the server and to include it into a source.
Here is a basic example of a ShinyApp:
# Example of UI with fluidPage
ui <- fluidPage(
sidebarLayout(
sidebarPanel(
textInput("dir", label = "Enter a directory")
),
mainPanel(
verbatimTextOutput("dirPrint"),
verbatimTextOutput("lsFiles")
)
)
)
# Server logic
server <- function(input, output) {
output$dirPrint <- renderPrint({
print(input$dir)
})
output$lsFiles <- renderPrint({
fls <- list.files(input$dir)
print(fls)
})
}
# Complete app with UI and server components
shinyApp(ui, server)
If you enter the path of a directory in the textinput, the second renderPrint function is showing all files, that are found at that path.
I would suggest you go over the Shiny-Tutorials, as there seem to be some syntax-problems in your code and I am not sure what exactly you want to achieve.
I made a portable shiny app with portable chrome and R. I launch rscript with vbs script in which stdout is redirected to a logfile with:
RScriptFile & " 1> " & logfile & " 2>&1"
What I want to do is to read in the log file so that the user has feedback about the calculation progress. The following reactivePoll works if the "main" shiny script is writing to the console, but it does not if a sourced function writes. Note that both are displayed in the log file, therefore the fault is surely not in the redirection, but somewhere in my logic or in shiny.
If I set bool_for_testing = T the test button works, on the other hand if I set it False not even the first "Go!" is printed on the console until the script is finished, but both are displayed real time in the logfile:
library(shiny)
bool_for_testing = F # note its use below!
logfile_name = "some_log_file_that_exists" # this is created by the vbs (command line) script!
ui = shinyUI(fluidPage(
actionButton("btn_test", "push meh!"),
fluidRow(
column(12, wellPanel(style = "overflow-y:scroll; max-height: 600px",
tags$b(paste("log file is this one:", logfile_name)),
verbatimTextOutput("logText")
))
)
)
) # end UI
server = shinyServer(function(input, output, session) {
observe({
if(input$btn_test > 0){
if(bool_for_testing) {
# this works!
print("Go!")
} else {
# not a letter on log here
print("Go!")
source("some_barely_interesting_function.R")
some_barely_interesting_function()
}
}
})
logFile <- reactivePoll(1000, session,
checkFunc = function() {
if (file.exists(logfile_name))
# should always refresh
runif(1) # Sys.time() does not work either
else
""
},
valueFunc = function() {
readLines(logfile_name)
}
)
# # this does not work either
# fileReaderData <- reactiveFileReader(500, session,
# logfile_name, readLines)
output$logText <- renderText({
text <- logFile()
paste(text, collapse = '\n')
})
session$onSessionEnded(function() {
# for portable R and chrome application
stopApp()
q("no")
})
})
shinyApp(ui = ui, server = server)
If I manually open the log file it shows the progress continuously, therefore I think the GUI thread is held up until the sourced calculation is finished (if I open a new shiny window only for reading the log file, it will work well, too). Is this truly the case, and is there a workaround for this?