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.exec-shiny-app.R
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.exec-shiny-app.R
#!/usr/bin/env Rscript
# Title : Execute Shiny App
# Objective : Initialize Plumber and run Shiny app as "future" (background) worker as defined by local app.R or server.R/ui.R
# Created by: John Hall
library("future")
library("httr")
library("httpuv")
library("magrittr")
library("plumber")
library("shiny")
library("stringr")
library("uuid")
library("websocket")
library("withr")
library("R6")
args <- commandArgs(trailingOnly = TRUE)
appDir <- getwd()
local_lib <- .libPaths()[1]
local_port <- as.numeric("3000")
# shiny_port <- httpuv::randomPort()
shiny_port <- if (randomPort(min = 1220L, max = 1221L, host = "127.0.0.1", n = 1)) {
1221L
} else {
httpuv::randomPort(host = "127.0.0.1", n = 20)
}
if (exists("args") && !is.null(args) && !is.na(args[1])) {
if (!grepl("install", args[1])) {
# Update path to app and lib
if (!grepl("/", args[1])) {
if (grepl("local", args[1])) {
local_lib <- paste0(getwd(), "/lib")
.libPaths(c(.libPaths(), local_lib))
} else if (dir.exists(paste0(getwd(), "/", args[1]))) {
appDir <- paste0(getwd(), "/", args[1])
}
# } else {
# appDir <- args[1]
# setwd(appDir)
} else if (dir.exists(paste0(getwd(), "/", args[1]))) {
appDir <- paste0(getwd(), "/", args[1])
} else if (dir.exists(args[1])) {
appDir <- args[1]
} else {
message(paste0("Cannot find app direcotry: ", args[1]))
stop()
}
}
if (!is.na(args[2]) && grepl("local", args[2])) {
# Install packages to ./lib instead of user library
local_lib <- paste0(getwd(), "/lib")
.libPaths(c(.libPaths(), local_lib))
} else if (!is.na(args[2]) && !grepl("install", args[2])) {
# Change server port from 3000 to ...
local_port <- switch(
as.character(as.numeric(args[2])),
"NA" = 3000,
as.numeric(args[2])
)
}
}
if (!dir.exists(local_lib)) {
dir.create(local_lib)
}
if (dir.exists("renv")) {
local_lib <- paste0("renv/library/R-", version$major, ".", substr(version$minor,1,1), "/", version$platform)
print(paste0("Use lib: ", local_lib))
if (!require("renv")) {
install.packages("renv")
}
renv::restore(library = local_lib, prompt = FALSE)
} else if (dir.exists("packrat")) tryCatch(
withr::with_libpaths(local_lib, {
if (!grepl("local", args[2]))
try({
print("Packrat config detected!")
local_lib <- paste0("packrat/lib/", version$platform, "/", version$major, ".", version$minor)
if (!file.exists(".Rprofile")) packrat::init()
system(paste0("rm -rf ", local_lib, "/00LOCK-*"))
packrat::restore(overwrite.dirty = TRUE)
})
}),
error = function(e) {
install.packages("withr")
# DEBUG
message(e)
print("Packrat config detected!")
local_lib <- paste0("packrat/lib/", version$platform, "/", version$major, ".", version$minor)
if (!file.exists(".Rprofile") && dir.exists("packrat")) packrat::init()
system(paste0("rm -rf ", local_lib, "/00LOCK-*"))
packrat::restore(overwrite.dirty = TRUE)
},
finally = print(paste0("Use lib: ", local_lib))
)
install_package_deps <- function () {
library(devtools)
no_error <- FALSE
if (any(nzchar(Sys.getenv("GITHUB_TOKEN")))) {
auth_token <- Sys.getenv("GITHUB_TOKEN")
if (!any(nzchar(Sys.getenv("GITHUB_PAT")))) {
Sys.setenv(GITHUB_PAT = auth_token)
}
} else {
auth_token <- Sys.getenv("GITHUB_PAT")
}
print(paste0("GITHUB_PAT: ", Sys.getenv("GITHUB_PAT")))
if (file.exists(paste0(appDir, "/package.csv")) || file.exists(paste0(getwd(), "/package.csv"))) {
if (!require("hrbrthemes")) {
install.packages("hrbrthemes", lib = local_lib)
hrbrthemes::import_roboto_condensed()
}
packages <- read.csv(
switch(
as.character(file.exists(paste0(appDir, "/package.csv"))),
"TRUE" = paste0(appDir, "/package.csv"),
"FALSE" = paste0(getwd(), "/package.csv")
),
header = FALSE, sep = ",", as.is = TRUE, col.names = c("package", "path_version"))
for (p in rownames(packages)) {
package_idx <- as.numeric(p)
package <- packages$package[package_idx]
print(paste0(package, ": ", packages$path_version[package_idx]))
try({
if (grepl("/", packages$path_version[package_idx])) {
github_path <- trimws(packages$path_version[package_idx])
if (!require(as.character(package[1]), character.only = TRUE)) {
message(sprintf(
'devtools::install_github("%s", lib = "%s", upgrade = "never", auth_token = "%s")',
github_path, local_lib, auth_token))
devtools::install_github(github_path, lib = local_lib, upgrade = "never", auth_token = auth_token)
}
} else {
version_string <- trimws(packages$path_version[package_idx])
if (!require(as.character(package[1]), character.only = TRUE) || version_string != as.character(packageVersion(package[1]))) {
message(sprintf(
'devtools::install_version("%s", lib = "%s", upgrade = "never", auth_token = "%s", version = "%s")',
package, local_lib, auth_token, version_string))
devtools::install_version(package, lib = local_lib, upgrade = "never", version = version_string)
}
}
})
if (!require(package[1], character.only = TRUE)) {
if (dir.exists(paste0(local_lib, "/", package[1]))) {
devtools::install_deps(paste0(local_lib, "/", package[1]), lib = local_lib, upgrade = "never", dependencies = TRUE)
}
install.packages(package, lib = local_lib)
}
}
no_error <- TRUE
}
no_error
}
no_error <- FALSE
while (!no_error) tryCatch(
withr::with_libpaths(local_lib, {
if (exists("args") && !is.null(args) && (grepl("install", args[1]) || grepl("install", args[2]))) {
if (!require("devtools") || !require("stringi") || !require("stringr")) {
install.packages(c("cli", "glue", "devtools", "stringr", "tidyverse", "usethis"), lib = local_lib)
}
no_error <- install_package_deps()
if (dir.exists("packrat") && !grepl("local", args[2])) {
if (!file.exists(".Rprofile")) packrat::init()
print("Before taking a new packrat snapshot, try to remove LOCK dirs: ")
system("mkdir -p del")
print(paste0("mv ", local_lib, "/00LOCK-* del/"))
system(paste0("mv ", local_lib, "/00LOCK-* del/"))
system("ls -l del/*")
print("rm -rf del")
system("rm -rf del")
packrat::snapshot(ignore.stale = TRUE)
print("Snapshot saved.")
print("Replace lib-R linked directory with actual libraries:")
print('for f in $(find packrat/lib-R/x86_64-pc-linux-gnu/3.5.1/ -name "[A-Za-z]*"); do lib_path=$(ls -l $f | grep -oP "(\\/var\\/.+)"); if [ $lib_path ]; then rm $f && cp -ar $lib_path packrat/lib-R/x86_64-pc-linux-gnu/3.5.1/; fi; done;')
system('for f in $(find packrat/lib-R/x86_64-pc-linux-gnu/3.5.1/ -name "[A-Za-z]*"); do lib_path=$(ls -l $f | grep -oP "(\\/var\\/.+)"); if [ $lib_path ]; then rm $f && cp -ar $lib_path packrat/lib-R/x86_64-pc-linux-gnu/3.5.1/; fi; done;')
print("Attempting bundle...")
packrat::bundle(file = "packrat.tar.gz")
if (file.exists("packrat.tar.gz")) {
print("Bundle saved.")
}
}
print("Installation finished.")
} else {
future_cluster <- future::makeClusterPSOCK(2) #future::availableCores())
parallelly::autoStopCluster(future_cluster)
for (cl_idx in seq_along(future_cluster)) {
parallel:::sendCall(future_cluster[[cl_idx]], fun = Sys.getpid, args = list())
cl_pid <- parallel:::recvResult(future_cluster[[cl_idx]])
attr(future_cluster[[cl_idx]]$host, "pid") <- cl_pid
}
future::plan(future::cluster, workers = future_cluster)
options(shiny.host = "0.0.0.0") # listen on all available network interfaces
options(shiny.port = shiny_port)
#options(shiny.launch.browser = .rs.invokeShinyWindowExternal)
print(paste0("Run Shiny app: ", appDir))
print(paste0("Use local dir: ", getwd()))
print(list.files(appDir))
print(paste0("Use local lib: ", local_lib))
print(.libPaths())
shiny_fallback_app <- shiny::shinyApp(
ui = function() { shiny::fluidPage(h1("This is a test app")) },
server = function(input, output, session) {}
)
if (grepl("/", appDir)) {
print(paste0("Launching Shiny app (http://127.0.0.1:", shiny_port, ") in future worker cluster..."))
shiny_app_future <- future::future({
shiny_app <- shiny::runApp(
app = if (file.exists(paste0(appDir, "/server.R"))) {
print(paste0("With ", appDir, "/server.R: ", file.exists(paste0(appDir, "/server.R"))))
appDir
} else if (file.exists(paste0(appDir, "/app.R"))) {
print(paste0("With ", appDir, "/app.R: ", file.exists(paste0(appDir, "/app.R"))))
appDir
} else {
shiny_fallback_app
},
host = "0.0.0.0",
port = shiny_port,
launch.browser = FALSE
)
return(NULL)
})
} else {
print(paste0("Launching Shiny app (http://127.0.0.1:", shiny_port, ") in future worker cluster..."))
shiny_app_future <- future::future({
shiny_app <- shiny::runApp(
app = if (file.exists("server.R")) {
print(paste0("With server.R: ", file.exists("server.R")))
getwd()
} else if (file.exists("app.R")) {
print(paste0("With app.R: ", file.exists("app.R")))
getwd()
} else if (file.exists("src/app.R")) {
setwd("src")
print(paste0("With app.R: ", file.exists("app.R")))
getwd()
} else {
shiny_fallback_app
},
host = "0.0.0.0",
port = shiny_port,
launch.browser = FALSE
)
return(NULL)
})
}
# From https://gabrielcp.medium.com/going-real-time-in-r-plumber-with-websockets-93547c767412
PlumberWebSocket <- R6::R6Class(
"PlumberWebSocket",
inherit = plumber::Plumber,
public = list(
onWSOpen = function(ws) {
if (is.function(private$ws_open)) {
private$ws_open(ws)
}
invisible(self)
},
websocket = function(open = NULL) {
if (!is.null(open)) stopifnot(is.function(open))
private$ws_open <- open
}
),
private = list(
ws_open = NULL
)
)
plumbr <- PlumberWebSocket$new()
plumbr$onWSOpen()
ws_clients <- list()
addWebSocketClient <- function(ws_client, message) {
ws_client$request$uuid <- UUIDgenerate()
print(ws_clients)
for(client in ws_clients) {
print(ws_clients)
print("\n")
}
print(ws_client$request$uuid %in% names(ws_clients))
if (!(ws_client$request$uuid %in% names(ws_clients))) {
ws_clients[[ws_client$request$uuid]] <<- ws_client #<<- modifies ws_clients globally
ws_client$onClose(function() {
removeWebSocketClient(ws_client$request$uuid)
})
ws_client$request$ws_shiny <- websocket::WebSocket$new(paste0("ws://127.0.0.1", ":", shiny_port, "/"))
ws_client$request$ws_shiny$connect()
ws_client$request$ws_shiny$onMessage(function(event) {
# print("Relay Shiny server event message to websocket client...")
print(event)
ws_client$send(event$data)
})
}
return(ws_clients)
}
removeWebSocketClient <- function(uuid) {
ws_clients[[uuid]] <<- NULL
}
handleWebSocketEvent <- function(pr) {
pr$websocket(
function (ws_client) {
addWebSocketClient(ws_client)
print("New user connected!")
ws_client$onMessage(function(binary, event) {
if ("ws_shiny" %in% names(ws_client$request)) {
# print("Relay websocket message to Shiny server...")
# print(event)
Sys.sleep(0.0125)
ws_client$request$ws_shiny$send(as.character(event))
}
})
}
)
pr
}
handleFileRequests <- function (req, res) {
cat(paste0("http://", req$REMOTE_ADDR, ":", shiny_port, req$PATH_INFO, "\n"))
file_path <- stringr::str_replace_all(req$PATH_INFO, "/www", "")
cat(paste0(file_path, "\n"))
# httr_target <- httr::GET(paste0("http://", req$REMOTE_ADDR, ":", shiny_port, file_path))
httr_target <- httr::GET(paste0("http://127.0.0.1:", shiny_port, file_path))
# print(names(req$HEADERS))
print(req$HEADERS["accept"])
if (
grepl("gif", req$HEADERS["accept"]) ||
grepl("jpeg", req$HEADERS["accept"]) ||
grepl("png", req$HEADERS["accept"]) ||
grepl("woff", req$HEADERS["accept"])
) {
httr_result <- httr::content(httr_target, as = "raw")
print("requesting binary file")
# print(as.character(httr_result))
} else {
httr_result <- httr::content(httr_target, as = "text", encoding ="UTF-8")
# print(httr_result)
}
httr_result
}
plumbr %>%
handleWebSocketEvent %>%
plumber::pr_filter("globalFilter", function (req, res) {
cat(as.character(Sys.time()), "-",
req$REQUEST_METHOD, req$PATH_INFO, "-",
req$HTTP_USER_AGENT, "@", req$REMOTE_ADDR, "\n"
)
## API && Swagger Filter ----
if (as.character(req$PATH_INFO) != "/" &&
!grepl("/__api__", as.character(req$PATH_INFO)) &&
!grepl("/__docs__", as.character(req$PATH_INFO)) &&
!grepl("/openapi", as.character(req$PATH_INFO))
) {
# Process file request as if it had the static file prefix ("www/")
req$PATH_INFO <- paste0("/www", as.character(req$PATH_INFO))
} # else { Let default plumber handlers process API and/or Swagger __docs__ request }
## CORS access
res$setHeader("Access-Control-Allow-Origin", "*")
if (req$REQUEST_METHOD == "OPTIONS") {
res$setHeader("Access-Control-Allow-Methods","*")
res$setHeader("Access-Control-Allow-Headers", req$HTTP_ACCESS_CONTROL_REQUEST_HEADERS)
res$status <- 200
return(list())
} else {
plumber::forward()
}
}) %>%
plumber::pr_mount("/__api__", pr("modules/plumber.R")) %>% # <- mount additional routes under "/__api__" %>%
(function (pr) {
## Proxy routes to files served by Shiny app ----
pr %>%
plumber::pr_handle(c("GET", "POST"), "/", function (req, res) {
# "<html>
# <h1>Hello, World!</h1>
# </html>"
handleFileRequests(req, res)
}, serializer = plumber::serializer_html()) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<file>.css", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_text(
serialize_fn = as.character,
type = "text/css"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<file>.js", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_text(
serialize_fn = as.character,
type = "application/javascript"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<file>.svg", function (file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_text(
serialize_fn = as.character,
type = "image/svg+xml"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<file>.woff2", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_octet(
serialize_fn = as.raw,
type = "application/font-woff2"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<file>", function (file, req, res) {
handleFileRequests(req, res)
}) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<file>.css", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_text(
serialize_fn = as.character,
type = "text/css"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<file>.gif", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_png(
serialize_fn = as.raw,
type = "image/gif"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<file>.jpeg", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_jpeg(
serialize_fn = as.raw,
type = "image/jpeg"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<file>.jpg", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_jpeg(
serialize_fn = as.raw,
type = "image/jpeg"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<file>.js", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_text(
serialize_fn = as.character,
type = "application/javascript"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<file>.pdf", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_pdf(
serialize_fn = as.raw,
type = "application/pdf"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<file>.png", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_png(
serialize_fn = as.raw,
type = "image/png"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<file>.svg", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_text(
serialize_fn = as.character,
type = "image/svg+xml"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<file>.woff2", function (path1, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_octet(
serialize_fn = as.raw,
type = "application/font-woff2"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<file>", function (path1, file, req, res) {
handleFileRequests(req, res)
}) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<path2>/<file>.css", function (path1, path2, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_text(
serialize_fn = as.character,
type = "text/css"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<path2>/<file>.js", function (path1, path2, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_text(
serialize_fn = as.character,
type = "application/javascript"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<path2>/<file>", function (path1, path2, file, req, res) {
handleFileRequests(req, res)
}) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<path2>/<path3>/<file>.css", function (path1, path2, path3, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_text(
serialize_fn = as.character,
type = "text/css"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<path2>/<path3>/<file>.js", function (path1, path2, path3, file, req, res) {
handleFileRequests(req, res)
}, serializer = plumber::serializer_text(
serialize_fn = as.character,
type = "application/javascript"
)) %>%
plumber::pr_handle(c("GET", "POST"), "/www/<path1>/<path2>/<path3>/<file>", function (path1, path2, path3, file, req, res) {
handleFileRequests(req, res)
}) %>%
plumber::pr_static("/www/", "www/")
# return(pr)
})() %>%
plumber::pr_hook("exit", function(){
print("Stop the future cluster (bg workers)...")
try({
tryCatch(
{
future_host <- shiny_app_future$workers[[shiny_app_future$node]]$host
print(future_host)
pid <- attr(future_host, "pid")
print(pid)
tools::pskill(pid)
},
finally = function () {
parallel::stopCluster(future_cluster)
}
)
})
print("Done!")
}) %>%
plumber::pr_run(
host = "0.0.0.0",
port = local_port
)
}
no_error <- TRUE
}),
error = function(e) {
# DEBUG
message(e)
#if (!no_error) {
if (!is.null(e) && !is.na(e$message) && grepl("package", e$message))
withr::with_libpaths(local_lib, {
print(sprintf("ERROR: %s", e$message))
str_pattern <- paste0("(?:package\\scalled|namespace) ['|‘]([\\w]+)")
package_match <- stringr::str_match(e$message, str_pattern)[,2]
print(paste0("Missing package match: ", package_match))
if (!is.null(package_match) && !is.na(package_match) && !require(package_match[1], character.only = TRUE)) {
if (dir.exists(paste0(local_lib, "/", package_match))) {
if (!require("devtools") || !require("stringi") || !require("stringr")) {
install.packages(c("cli", "glue", "devtools", "stringr", "tidyverse", "usethis"))
}
devtools::install_deps(paste0(local_lib, "/", package_match), lib = local_lib, upgrade = "never", dependencies = TRUE)
}
install.packages(package_match, lib = local_lib)
}
install_package_deps()
})
else quit(save = "no", status = 1, runLast = FALSE)
},
finally = "Shiny app terminated."
)
Raw
.gitignore
*.bak
*.env*
*.idea
.R*
*.Rproj*
renv/lib*
rsconnect
# History files
.Rhistory
.Rapp.history
# Session Data files
.RData
# User-specific files
.Ruserdata
# Example code in package build process
*-Ex.R
# Output files from R CMD build
/*.tar.gz
# Output files from R CMD check
/*.Rcheck/
# RStudio files
.Rproj.user/
# produced vignettes
vignettes/*.html
vignettes/*.pdf
# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth
# knitr and R markdown default cache directories
*_cache/
/cache/
# Temporary files created by R markdown
*.utf8.md
*.knit.md
# R Environment Variables
.Renviron
.CARTOenv
# data
*.csv
*.gpkg
*.shp
*.RDS
*.rds
*.Rds
app/
backend/
bcat/
build/
dashboard/
dist/
frontend/
logs/
modules/
node_modules/
packrat/
renv/
rom-scrollytelling-article/
Raw
.gitmodules
[submodule "shiny-server"]
path = shiny-server
url = https://github.com/dancingfrog/cori-app-reprex.git
Raw
README.Rmd
---
title: "README"
author: John Hall
date: 3/29/2021
output: md_document
---
Use the `.exec-shiny-app.R` script to launch a Shiny app anywhere on local disk. If you need to install packages to a local library, make sure to set/export `GITHUB_PAT` in the system environment with a token from Github (R command: `usethis::create_github_token()`) before running this script:
Rscript .exec-shiny-app.R <optional:path-to-shiny-app-dir> <optional:port>
If either the target app directory or the current working directory contain a `package.csv` file and `install` is specified as either the first or secondary argument (instead of the port number), the script can install the dependencies listed in that file. If the script initially fails to run the target Shiny app, it will also attempt to install dependencies. A `package.csv` file has been provided as an example.
This script now comes with a minimal set of dependency packages, defined by `renv.lock`. After initially cloning the repository, start an interactive R session in the root directory and run:
renv::activate()
Raw
Dockerfile
FROM public.ecr.aws/l2v0f2h3/rocker/shiny-verse:latest as base
ARG gh_token
ENV GITHUB_TOKEN=$gh_token
ARG gh_token
ENV GITHUB_PAT=$gh_token
RUN apt update -y && \
apt purge -y ca-certificates-java && apt install -y ca-certificates-java \
&& apt install -y ca-certificates libgdal-dev libharfbuzz-dev libfribidi-dev libv8-dev libjq-dev \
libmagick++-dev libprotobuf-dev protobuf-compiler libudunits2-dev procps libsodium-dev libudunits2-dev \
&& update-ca-certificates -f -v
RUN Rscript -e '\
local({ r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r); }); \
update.packages(ask = FALSE, checkBuilt = TRUE); \
install.packages(c( \
"R6", "cli", "devtools", "future", "geojsonio", "hrbrthemes", "httr", "httpuv", "leaflet", "magick", "packrat", "plumber", \
"remoter", "remotes", "renv", "sf", "shiny", "stringi", "stringr", "tidyverse", "tools", "uuid", "websocket", "withr" \
));'
RUN chmod -R ga+rw /srv/shiny-server/*
RUN chmod +x /srv/shiny-server/.exec-shiny-app.R
#CMD /usr/bin/bash
CMD /usr/bin/shiny-server
## ^ #FROM public.ecr.aws/l2v0f2h3/rocker/shiny-verse
#
#WORKDIR /srv/shiny-server
#
#COPY renv.lock renv.lock
#
#RUN Rscript -e '\
# version; \
# print(paste0("GITHUB_PAT: ", Sys.getenv("GITHUB_PAT"))); \
# renv::activate(); \
# renv::restore(clean = FALSE); \
#'
#
#COPY .exec-shiny-app.R .exec-shiny-app.R
### Fix incorrect (windows) line-ending that keep this script from running on linux
#RUN bash -c "cp .exec-shiny-app.R .exec-shiny-app.R.bak && \
# sed $'s/\r$//' .exec-shiny-app.R.bak > .exec-shiny-app.R && \
# chmod +x .exec-shiny-app.R; \
#"
#
#RUN chmod -R ga+rw /srv/shiny-server/*
#RUN chmod +x /srv/shiny-server/.exec-shiny-app.R
#
##CMD /usr/bin/bash
##CMD /usr/bin/shiny-server
#CMD /srv/shiny-server/.exec-shiny-app.R
#
#ENTRYPOINT [ "Rscript" ]
EXPOSE 3000
EXPOSE 3838
# ^ #FROM 312512371189.dkr.ecr.us-east-1.amazonaws.com/coriverse/shinyapps:latest
Raw
locate-the-rprofile-file-generating-default-options.R
# https://stackoverflow.com/questions/13735745/locate-the-rprofile-file-generating-default-options
candidates <- c( Sys.getenv("R_PROFILE"),
file.path(Sys.getenv("R_HOME"), "etc", "Rprofile.site"),
Sys.getenv("R_PROFILE_USER"),
file.path(getwd(), ".Rprofile"),
file.path(Sys.getenv("HOME"), ".Rprofile"))
Filter(file.exists, candidates)
Raw
package.csv
dplyr 1.0.7
ellipsis 0.3.2
geojson 0.3.4
geojsonio 0.9.4
gert 1.4.3
ggfittext 0.6.0
gh 1.3.0
glue 1.5.0
nanotime 0.1.2
pkgload 1.2.3
readr 1.4.0
remotes 2.4.1
shinyWidgets 0.5.4
treemapify 2.5.2
vctrs 0.3.8
usethis 2.1.3
R.utils HenrikBengtsson/R.utils
htmltools rstudio/htmltools
hrbrthemes hrbrmstr/hrbrthemes
janitor sfirke/janitor
jobbR dashee87/jobbR
shiny rstudio/shiny
colourpicker daattali/colourpicker
DT rstudio/DT
forecast robjhyndman/forecast
knitr yihui/knitr
tidyverse tidyverse/tidyverse
shinyBS ebailey78/shinyBS
shinydashboard rstudio/shinydashboard
shinycssloaders daattali/shinycssloaders
shinycustomloader emitanaka/shinycustomloader
shinyjs daattali/shinyjs
shinylogs dreamRs/shinylogs
shinythemes rstudio/shinythemes
kableExtra haozhu233/kableExtra
rmarkdown rstudio/rmarkdown
scales r-lib/scales
sf r-spatial/sf
spatstat.utils spatstat/spatstat.utils
spatstat spatstat/spatstat
spatstat spatstat/spatstat
coriverse ruralinnovation/coriverse@cea7d0393a9b680e02414dec0e5a6f11761647eb
geojsonsf SymbolixAU/geojsonsf
leaflet rstudio/leaflet
leaflet.extras bhaskarvk/leaflet.extras
plotly ropensci/plotly
r2d3 rstudio/r2d3
polyclip https://cran.r-project.org/src/contrib/polyclip_1.10-0.tar.gz
protolite jeroen/protolite
rmapshaper ateucher/rmapshaper
shinymaptool ruralinnovation/shinymaptool@21c506b274d55b026bbc1ba80b92e1d222e064ea
yaml viking/r-yaml
zoo r-forge/zoo
Raw
package.json
{
"name": "exec-scripts",
"private": true,
"version": "0.0.1",
"scripts": {
"start": "Rscript .exec-shiny-app.R . 5174"
},
"devDependencies": {
"node-fetch": "^3.3.1"
}
}
Raw
renv.lock
{
"R": {
"Version": "4.1.2",
"Repositories": [
{
"Name": "CRAN",
"URL": "http://cran.rstudio.com"
}
]
},
"Packages": {
"AsioHeaders": {
"Package": "AsioHeaders",
"Version": "1.22.1-1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "57ed34bcad0158fafd9cbdd85bd26881",
"Requirements": []
},
"DBI": {
"Package": "DBI",
"Version": "1.1.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b2866e62bab9378c3cc9476a1954226b",
"Requirements": []
},
"MASS": {
"Package": "MASS",
"Version": "7.3-55",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "c5232ffb549f6d7a04a152c34ca1353d",
"Requirements": []
},
"Matrix": {
"Package": "Matrix",
"Version": "1.4-0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "130c0caba175739d98f2963c6a407cf6",
"Requirements": [
"lattice"
]
},
"R.methodsS3": {
"Package": "R.methodsS3",
"Version": "1.8.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "278c286fd6e9e75d0c2e8f731ea445c8",
"Requirements": []
},
"R.oo": {
"Package": "R.oo",
"Version": "1.25.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a0900a114f4f0194cf4aa8cd4a700681",
"Requirements": [
"R.methodsS3"
]
},
"R.utils": {
"Package": "R.utils",
"Version": "2.12.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "325f01db13da12c04d8f6e7be36ff514",
"Requirements": [
"R.methodsS3",
"R.oo"
]
},
"R6": {
"Package": "R6",
"Version": "2.5.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "470851b6d5d0ac559e9d01bb352b4021",
"Requirements": []
},
"RColorBrewer": {
"Package": "RColorBrewer",
"Version": "1.1-3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "45f0398006e83a5b10b72a90663d8d8c",
"Requirements": []
},
"Rcpp": {
"Package": "Rcpp",
"Version": "1.0.9",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e9c08b94391e9f3f97355841229124f2",
"Requirements": []
},
"Rttf2pt1": {
"Package": "Rttf2pt1",
"Version": "1.3.11",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "60818466bde87943f750b33b5ef5217b",
"Requirements": []
},
"askpass": {
"Package": "askpass",
"Version": "1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e8a22846fff485f0be3770c2da758713",
"Requirements": [
"sys"
]
},
"assertthat": {
"Package": "assertthat",
"Version": "0.2.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "50c838a310445e954bc13f26f26a6ecf",
"Requirements": []
},
"backports": {
"Package": "backports",
"Version": "1.4.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "c39fbec8a30d23e721980b8afb31984c",
"Requirements": []
},
"base64enc": {
"Package": "base64enc",
"Version": "0.1-3",
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"Repository": "CRAN",
"Hash": "543776ae6848fde2f48ff3816d0628bc",
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},
"bit": {
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"Hash": "d242abec29412ce988848d0294b208fd",
"Requirements": []
},
"bit64": {
"Package": "bit64",
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"Hash": "9fe98599ca456d6552421db0d6772d8f",
"Requirements": [
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]
},
"blob": {
"Package": "blob",
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"Hash": "10d231579bc9c06ab1c320618808d4ff",
"Requirements": [
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"vctrs"
]
},
"brew": {
"Package": "brew",
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"Hash": "d69a786e85775b126bddbee185ae6084",
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},
"brio": {
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},
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"Hash": "c90ff735b7812b60f067a3f7a3b4de63",
"Requirements": [
"backports",
"dplyr",
"ellipsis",
"generics",
"ggplot2",
"glue",
"purrr",
"rlang",
"stringr",
"tibble",
"tidyr"
]
},
"bslib": {
"Package": "bslib",
"Version": "0.4.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "89a0cd0c45161e3bd1c1e74a2d65e516",
"Requirements": [
"cachem",
"htmltools",
"jquerylib",
"jsonlite",
"memoise",
"rlang",
"sass"
]
},
"cachem": {
"Package": "cachem",
"Version": "1.0.6",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "648c5b3d71e6a37e3043617489a0a0e9",
"Requirements": [
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"rlang"
]
},
"callr": {
"Package": "callr",
"Version": "3.7.3",
"Source": "Repository",
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"Hash": "9b2191ede20fa29828139b9900922e51",
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]
},
"cellranger": {
"Package": "cellranger",
"Version": "1.1.0",
"Source": "Repository",
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"Hash": "f61dbaec772ccd2e17705c1e872e9e7c",
"Requirements": [
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"tibble"
]
},
"cli": {
"Package": "cli",
"Version": "3.4.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0d297d01734d2bcea40197bd4971a764",
"Requirements": []
},
"clipr": {
"Package": "clipr",
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"Source": "Repository",
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"Hash": "3f038e5ac7f41d4ac41ce658c85e3042",
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},
"codetools": {
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"Source": "Repository",
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},
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"cpp11": {
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"Hash": "ed588261931ee3be2c700d22e94a29ab",
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"Source": "Repository",
"Repository": "CRAN",
"Hash": "e8a1e41acf02548751f45c718d55aa6a",
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},
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"Source": "Repository",
"Repository": "CRAN",
"Hash": "93762d0a34d78e6a025efdbfb5c6bb41",
"Requirements": [
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"curl",
"jsonlite",
"openssl",
"sys"
]
},
"curl": {
"Package": "curl",
"Version": "4.3.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0eb86baa62f06e8855258fa5a8048667",
"Requirements": []
},
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"Hash": "aecef50008ea7b57c76f1cb5c127fb02",
"Requirements": []
},
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"Package": "dbplyr",
"Version": "2.2.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f6c7eb9617e4d2a86bb7182fff99c805",
"Requirements": [
"DBI",
"R6",
"assertthat",
"blob",
"cli",
"dplyr",
"glue",
"lifecycle",
"magrittr",
"pillar",
"purrr",
"rlang",
"tibble",
"tidyselect",
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]
},
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]
},
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"Requirements": [
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"desc",
"ellipsis",
"fs",
"lifecycle",
"memoise",
"miniUI",
"pkgbuild",
"pkgdown",
"pkgload",
"profvis",
"rcmdcheck",
"remotes",
"rlang",
"roxygen2",
"rversions",
"sessioninfo",
"testthat",
"urlchecker",
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"withr"
]
},
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"fansi",
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]
},
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"Requirements": [
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"glue",
"lifecycle",
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]
},
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"Requirements": [
"crayon",
"data.table",
"dplyr",
"ellipsis",
"glue",
"lifecycle",
"rlang",
"tibble",
"tidyselect",
"vctrs"
]
},
"ellipsis": {
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"Hash": "bb0eec2fe32e88d9e2836c2f73ea2077",
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]
},
"evaluate": {
"Package": "evaluate",
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]
},
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},
"fansi": {
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"Hash": "83a8afdbe71839506baa9f90eebad7ec",
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"fastmap": {
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"cli",
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"glue",
"lifecycle",
"magrittr",
"rlang",
"tibble",
"withr"
]
},
"fs": {
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]
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"httr",
"jsonlite",
"rappdirs",
"rlang",
"rstudioapi",
"withr"
]
},
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]
},
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"Source": "Repository",
"Repository": "CRAN",
"Hash": "15e9634c0fcd294799e9b2e929ed1b86",
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},
"gert": {
"Package": "gert",
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"Source": "Repository",
"Repository": "CRAN",
"Hash": "9a091a6d2fb91e43afd4337e2dcef2e7",
"Requirements": [
"askpass",
"credentials",
"openssl",
"rstudioapi",
"sys",
"zip"
]
},
"ggplot2": {
"Package": "ggplot2",
"Version": "3.4.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "fd2aab12f54400c6bca43687231e246b",
"Requirements": [
"MASS",
"cli",
"glue",
"gtable",
"isoband",
"lifecycle",
"mgcv",
"rlang",
"scales",
"tibble",
"vctrs",
"withr"
]
},
"gh": {
"Package": "gh",
"Version": "1.3.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b6a12054ee13dce0f6696c019c10e539",
"Requirements": [
"cli",
"gitcreds",
"httr",
"ini",
"jsonlite"
]
},
"gitcreds": {
"Package": "gitcreds",
"Version": "0.1.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ab08ac61f3e1be454ae21911eb8bc2fe",
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},
"globals": {
"Package": "globals",
"Version": "0.16.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "baa9585ab4ce47a9f4618e671778cc6f",
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@dancingfrog
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dancingfrog commented Apr 1, 2021

start run-shiny-app.R

@dancingfrog
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dancingfrog commented Apr 2, 2021

change script name to .exec-shiny-app.R

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