Error in source(global_r, local = FALSE)

[liaojiahui-r]

Suddenly encountered this ERROR!

Loading required package: shiny Error in source(global_r, local = FALSE) : attempt to use zero-length variable name Calls: <Anonymous> -> do.call -> <Anonymous> -> <Anonymous> -> source Execution halted

This appeared just after I created a new .Rmd file (with Rstudio notebook). I copied exactly the same old app‘s code to this new notebook, it failed to run (what's more the old .Rmd now failed too).

I did some search it seems very few people run into this problem, but its very annoying and I can‘t fix it.

Any help will be highly appreciate!

---

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

[cderv]

Hi! Thanks for the report.

I can't reproduce this error only with the information you gave. However, we get a hint from the error message.

Do you have a file called global.R (or with a different case) ?
If this file is found it will be source which seems to happen according to the error message you have. (Which contains source(global_r, local = FALSE))

If you have that file as I believe, can you check the content ? This is where the error comes from it seems.

If it is expected that this file is sourced and the content is correct, can you share your issue as a reproducible example ? Or at least with more detail about the content.

Thank you.

[liaojiahui-r]

I now realized my .Rmd file name "global XXX.Rmd" could be true problem!

Maybe we should not use any thing contains "global" as file name?

I'm not so good at R and flexdashboard is so user-friendly for people like me! Many thanks!

[cderv]

I now realized my .Rmd file name "global XXX.Rmd" could be true problem!

No it should be only with a global.R file. But what is odd after

Let's take a step back in debugging.

1. You did not share your session info. Are you running last versions of packages ? If not you can try to update to last CRAN version.
2. Can you then run rmarkdown::run("<path to your Rmd file>") ? It should error as you shown. Then can you run traceback() (or better rlang::last_trace() if you have rlang installed) and post the result here ?
   Thank you!

[liaojiahui-r]

Here I tried to reproducing the issue with minimum code.

We need 2 .Rmd files and 1 .R file (for sourcing) to reproducing the issue.

If there is ohter .Rmd file named [global r***.Rmd] (here I use “global reproducing flex template.Rmd” as an example) in the SAME Folder then here comes the issue!

Information of

traceback() AND
rlang::last_trace() just after run rmarkdown::run("<my .Rmd>") AND
R session

is pasted on the bottom.

——————————————————————————————

1st "NEW flex template.Rmd"

---

title: "if there is ohter .Rmd file named [global r***.Rmd] in the same folder then comes the issue!"
output:
flexdashboard::flex_dashboard:
orientation: columns
vertical_layout: fill
runtime: shiny

if there is a .Rmd file named [global r***.Rmd] in the same folder then comes the issue!

library(shiny)
library(flexdashboard)

Column {data-width=300}

Give me a number:

sliderInput(
  "a_number",
  label = "Give me a number:",
  min = 5,
  max = 10,
  value = 5,
  step = 1
)

Column {data-width=300}

Now reproducing the bug

source("plot something.R")

renderPlot({
  plot_sth(give_me_a_munber = input$a_number)
})

——————————————————————————————

2nd "global reproducing flex template.Rmd"

---

title: "if .Rmd file name is [global r***.Rmd] then the issue comes!"
output:
flexdashboard::flex_dashboard:
orientation: columns
vertical_layout: fill
runtime: shiny

library(shiny)
library(flexdashboard)

Column {data-width=650}

Give me a number:

sliderInput(
  "a_number",
  label = "Give me a number:",
  min = 5,
  max = 10,
  value = 5,
  step = 1
)

Column {data-width=350}

Now reproducing the bug

source("plot something.R")

renderPlot({
  plot_sth(give_me_a_munber = input$a_number)
})

——————————————————————————————

3rd "plot something.R" file to source

library(ggplot2)

plot_sth <- function(give_me_a_munber) {
  ggplot(
    data.frame(x = 1:give_me_a_munber, y = rep(1, give_me_a_munber)),
    aes(x, y, size = x)
  ) +
    geom_point(show.legend = FALSE) +
    scale_size_continuous(range = c(1, 20)) +
    theme_void()
}

———————————————————————————————

if I Run rmarkdown::run("~/Downloads/NEW flex template.Rmd")

rmarkdown::run("~/Downloads/NEW flex template.Rmd")
Loading required package: shiny
Error in source(global_r, local = FALSE) :
attempt to use zero-length variable name

rlang::last_trace()

<error/rlang_error>
Can't show last error because no error was recorded yet
Backtrace:
█

1. └─rlang::last_trace()
2. └─rlang::last_error()

———————————————————————————————

traceback()

5: source(global_r, local = FALSE)
4: appParts$onStart()
3: (function (appDir = getwd(), port = getOption("shiny.port"),
launch.browser = getOption("shiny.launch.browser", interactive()),
host = getOption("shiny.host", "127.0.0.1"), workerId = "",
quiet = FALSE, display.mode = c("auto", "normal", "showcase"),
test.mode = getOption("shiny.testmode", FALSE))
{
on.exit({
handlerManager$clear()
}, add = TRUE)
if (.globals$running) {
stop("Can't call runApp() from within runApp(). If your ",
"application code contains runApp(), please remove it.")
}
.globals$running <- TRUE
on.exit({
.globals$running <- FALSE
}, add = TRUE)
oldOptionSet <- .globals$options
on.exit({
.globals$options <- oldOptionSet
}, add = TRUE)
shinyOptions(appToken = createUniqueId(8))
ops <- options(warn = max(1, getOption("warn", default = 1)),
pool.scheduler = scheduleTask)
on.exit(options(ops), add = TRUE)
if (is.null(getShinyOption("cache"))) {
shinyOptions(cache = MemoryCache$new())
}
appParts <- as.shiny.appobj(appDir)
appOps <- appParts$options
findVal <- function(arg, default) {
if (arg %in% names(appOps))
appOps[[arg]]
else default
}
if (missing(port))
port <- findVal("port", port)
if (missing(launch.browser))
launch.browser <- findVal("launch.browser", launch.browser)
if (missing(host))
host <- findVal("host", host)
if (missing(quiet))
quiet <- findVal("quiet", quiet)
if (missing(display.mode))
display.mode <- findVal("display.mode", display.mode)
if (missing(test.mode))
test.mode <- findVal("test.mode", test.mode)
if (is.null(host) || is.na(host))
host <- "0.0.0.0"
workerId(workerId)
if (inShinyServer()) {
ver <- Sys.getenv("SHINY_SERVER_VERSION")
if (utils::compareVersion(ver, .shinyServerMinVersion) <
0) {
warning("Shiny Server v", .shinyServerMinVersion,
" or later is required; please upgrade!")
}
}
setShowcaseDefault(0)
.globals$testMode <- test.mode
if (test.mode) {
message("Running application in test mode.")
}
if (is.character(appDir)) {
desc <- file.path.ci(if (tolower(tools::file_ext(appDir)) ==
"r")
dirname(appDir)
else appDir, "DESCRIPTION")
if (file.exists(desc)) {
con <- file(desc, encoding = checkEncoding(desc))
on.exit(close(con), add = TRUE)
settings <- read.dcf(con)
if ("DisplayMode" %in% colnames(settings)) {
mode <- settings[1, "DisplayMode"]
if (mode == "Showcase") {
setShowcaseDefault(1)
if ("IncludeWWW" %in% colnames(settings)) {
.globals$IncludeWWW <- as.logical(settings[1,
"IncludeWWW"])
if (is.na(.globals$IncludeWWW)) {
stop("In your Description file, IncludeWWW ",
"must be set to True (default) or False")
}
}
else {
.globals$IncludeWWW <- TRUE
}
}
}
}
}
if (is.null(.globals$IncludeWWW) || is.na(.globals$IncludeWWW)) {
.globals$IncludeWWW <- TRUE
}
display.mode <- match.arg(display.mode)
if (display.mode == "normal") {
setShowcaseDefault(0)
}
else if (display.mode == "showcase") {
setShowcaseDefault(1)
}
require(shiny)
if (is.null(port)) {
for (i in 1:20) {
if (!is.null(.globals$lastPort)) {
port <- .globals$lastPort
.globals$lastPort <- NULL
}
else {
while (TRUE) {
port <- p_randomInt(3000, 8000)
if (!port %in% c(3659, 4045, 6000, 6665:6669,
6697)) {
break
}
}
}
tmp <- try(startServer(host, port, list()), silent = TRUE)
if (!inherits(tmp, "try-error")) {
stopServer(tmp)
.globals$lastPort <- port
break
}
}
}
on.exit({
.globals$onStopCallbacks$invoke()
.globals$onStopCallbacks <- Callbacks$new()
}, add = TRUE)
unconsumeAppOptions(appParts$appOptions)
if (!is.null(appParts$onStop))
on.exit(appParts$onStop(), add = TRUE)
if (!is.null(appParts$onStart))
appParts$onStart()
server <- startApp(appParts, port, host, quiet)
shinyOptions(server = server)
on.exit({
stopServer(server)
}, add = TRUE)
if (!is.character(port)) {
browseHost <- host
if (identical(host, "0.0.0.0")) {
browseHost <- "127.0.0.1"
}
else if (identical(host, "::")) {
browseHost <- "::1"
}
if (httpuv::ipFamily(browseHost) == 6L) {
browseHost <- paste0("[", browseHost, "]")
}
appUrl <- paste("http://", browseHost, ":", port, sep = "")
if (is.function(launch.browser))
launch.browser(appUrl)
else if (launch.browser)
utils::browseURL(appUrl)
}
else {
appUrl <- NULL
}
callAppHook("onAppStart", appUrl)
on.exit({
callAppHook("onAppStop", appUrl)
}, add = TRUE)
.globals$reterror <- NULL
.globals$retval <- NULL
.globals$stopped <- FALSE
..stacktraceoff..(captureStackTraces({
while (!.globals$stopped) {
..stacktracefloor..(serviceApp())
}
}))
if (isTRUE(.globals$reterror)) {
stop(.globals$retval)
}
else if (.globals$retval$visible)
.globals$retval$value
else invisible(.globals$retval$value)
})(appDir = structure(list(httpHandler = function (req)
{
if (!identical(req$REQUEST_METHOD, "GET"))
return(NULL)
if (!isTRUE(grepl(uiPattern, req$PATH_INFO)))
return(NULL)
textConn <- file(open = "w+")
on.exit(close(textConn))
showcaseMode <- .globals$showcaseDefault
if (.globals$showcaseOverride) {
mode <- showcaseModeOfReq(req)
if (!is.null(mode))
showcaseMode <- mode
}
testMode <- .globals$testMode %OR% FALSE
bookmarkStore <- getShinyOption("bookmarkStore", default = "disable")
if (bookmarkStore == "disable") {
restoreContext <- RestoreContext$new()
}
else {
restoreContext <- RestoreContext$new(req$QUERY_STRING)
}
withRestoreContext(restoreContext, {
uiValue <- NULL
if (is.function(ui)) {
if (length(formals(ui)) > 0) {
uiValue <- ..stacktraceon..(ui(req))
}
else {
uiValue <- ..stacktraceon..(ui())
}
}
else {
if (getCurrentRestoreContext()$active) {
warning("Trying to restore saved app state, but UI code must be a function for this to work! See ?enableBookmarking")
}
uiValue <- ui
}
})
if (is.null(uiValue))
return(NULL)
renderPage(uiValue, textConn, showcaseMode, testMode)
html <- paste(readLines(textConn, encoding = "UTF-8"), collapse = "\n")
return(httpResponse(200, content = enc2utf8(html)))
}, serverFuncSource = function ()
{
server
}, onStart = function ()
{
global_r <- file.path.ci(dir, "global.R")
if (file.exists(global_r)) {
source(global_r, local = FALSE)
}
shiny::addResourcePath("rmd_resources", pkg_file("rmd/h/rmarkdown"))
}, options = list(), appOptions = list(appDir = "/Users/liaojiahui/Downloads",
bookmarkStore = NULL)), class = "shiny.appobj"), launch.browser = function (url)
{
url <- paste(url, file_rel, sep = "/")
browser <- getOption("shiny.launch.browser")
if (is.function(browser)) {
browser(url)
}
else {
utils::browseURL(url)
}
})
2: do.call(shiny::runApp, shiny_args)
1: rmarkdown::run("~/Downloads/NEW flex template.Rmd")

———————————————————————————————

———————————————————————————————

R session

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils
[5] datasets methods base

other attached packages:
[1] shiny_1.5.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 digest_0.6.27
[3] later_1.1.0.1 mime_0.9
[5] R6_2.5.0 xtable_1.8-4
[7] jsonlite_1.7.2 magrittr_2.0.1
[9] evaluate_0.14 rlang_0.4.10
[11] promises_1.1.1 rmarkdown_2.6
[13] flexdashboard_0.5.2 tools_4.0.3
[15] tinytex_0.28 fastmap_1.0.1
[17] httpuv_1.5.5 xfun_0.20
[19] yaml_2.2.1 compiler_4.0.3
[21] htmltools_0.5.1 knitr_1.30

[cderv]

Thanks a lot for this ! It explains the error !

There is indeed a bug because global.R is seen a a regex pattern when no global.R filename found. And that is why it matches your Rmd file.

This is a very specific bug because you have a file with name containing global.r, with . being any character (in your case a space)

Thanks for this investigation. Glad we found this !

I'll submit a fix

[cderv]

This should be fixed now in the dev version of rmarkdown.

You can install with

remotes::install_github("rstudio/rmarkdown")

[cderv]

@rich-iannone I think you maintain this project now. You can close this issue (I can't so the closes PR did not close this issue)