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Error: C stack usage is too close to the limit at R startup

Time:03-29

Everytime I open a new session in RStudio, I'm greeted with the error message:

Error: C stack usage  7953936 is too close to the limit

Based on suggestions for similar issues posted here and here, I tried using the ulimit command in terminal, but get the following error.

Isabels-MacBook-Pro ~ % ulimit -s
8176

Isabels-MacBook-Pro ~ % R --slave -e 'Cstack_info()["size"]'
Error: C stack usage  7954496 is too close to the limit
Execution halted

Yet, when I run ulimit on it's own, I get:

Isabels-MacBook-Pro ~ % ulimit
unlimited

Just to double-check, I try setting it to unlimited again:

Isabels-MacBook-Pro ~ % ulimit -s unlimited

but then get a new error:

Isabels-MacBook-Pro ~ % R --slave -e 'Cstack_info()["size"]'
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted

I have no clue what this means in this context. Is the Cstack_info() the bit getting stuck on infinite recursion?? I'd love to get this figured out, as it's getting in the way of installing some necessary packages!

In case it's helpful, here's my session info

R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1

And contents of .Rprofile

# REMEMBER to restart R after you modify and save this file!

# First, execute the global .Rprofile if it exists. You may configure blogdown
# options there, too, so they apply to any blogdown projects. Feel free to
# ignore this part if it sounds too complicated to you.
if (file.exists("~/.Rprofile")) {
  base::sys.source("~/.Rprofile", envir = environment())
}

# Now set options to customize the behavior of blogdown for this project. Below
# are a few sample options; for more options, see
# https://bookdown.org/yihui/blogdown/global-options.html
options(
  # to automatically serve the site on RStudio startup, set this option to TRUE
  blogdown.serve_site.startup = FALSE,
  # to disable knitting Rmd files on save, set this option to FALSE
  blogdown.knit.on_save = TRUE,
  # build .Rmd to .html (via Pandoc); to build to Markdown, set this option to 'm$
  blogdown.method = 'html'
)

# fix Hugo version
options(blogdown.hugo.version = "0.82.0")

Here are the contents from /Library/Frameworks/R.framework/Resources/library/base/R/Rprofile

### This is the system Rprofile file. It is always run on startup.
### Additional commands can be placed in site or user Rprofile files
### (see ?Rprofile).

### Copyright (C) 1995-2020 The R Core Team

### Notice that it is a bad idea to use this file as a template for
### personal startup files, since things will be executed twice and in
### the wrong environment (user profiles are run in .GlobalEnv).

.GlobalEnv <- globalenv()
attach(NULL, name = "Autoloads")
.AutoloadEnv <- as.environment(2)
assign(".Autoloaded", NULL, envir = .AutoloadEnv)
T <- TRUE
F <- FALSE
R.version <- structure(R.Version(), class = "simple.list")
version <- R.version            # for S compatibility

## for backwards compatibility only
R.version.string <- R.version$version.string

## NOTA BENE: options() for non-base package functionality are in places like
##            --------- ../utils/R/zzz.R

options(keep.source = interactive())
options(warn = 0)
# options(repos = c(CRAN="@CRAN@"))
# options(BIOC = "http://www.bioconductor.org")

## setting from an env variable added in 4.0.2
local({to <- as.integer(Sys.getenv("R_DEFAULT_INTERNET_TIMEOUT", 60))
    if (is.na(to) || to <= 0) to <- 60L
    options(timeout = to)
})
options(encoding = "native.enc")
options(show.error.messages = TRUE)
## keep in sync with PrintDefaults() in  ../../main/print.c :
options(show.error.messages = TRUE)
## keep in sync with PrintDefaults() in  ../../main/print.c :
options(scipen = 0)
options(max.print = 99999)# max. #{entries} in internal printMatrix()
options(add.smooth = TRUE)# currently only used in 'plot.lm'

if(isFALSE(as.logical(Sys.getenv("_R_OPTIONS_STRINGS_AS_FACTORS_",
                                 "FALSE")))) {
    options(stringsAsFactors = FALSE)
} else {
    options(stringsAsFactors = TRUE)
}

if(!interactive() && is.null(getOption("showErrorCalls")))
    options(showErrorCalls = TRUE)

local({dp <- Sys.getenv("R_DEFAULT_PACKAGES")
       if(identical(dp, "")) ## it fact methods is done first
           dp <- c("datasets", "utils", "grDevices", "graphics",
                   "stats", "methods")
       else if(identical(dp, "NULL")) dp <- character(0)
       else dp <- strsplit(dp, ",")[[1]]
       dp <- sub("[[:blank:]]*([[:alnum:]] )", "\\1", dp) # strip whitespace
       options(defaultPackages = dp)
    })

## Expand R_LIBS_* environment variables.
Sys.setenv(R_LIBS_SITE =
           .expand_R_libs_env_var(Sys.getenv("R_LIBS_SITE")))
Sys.setenv(R_LIBS_USER =
           .expand_R_libs_env_var(Sys.getenv("R_LIBS_USER")))

local({
    if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_CPU")))
        setSessionTimeLimit(cpu = tl)
    if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_ELAPSED")))
        setSessionTimeLimit(elapsed = tl)
})

        setSessionTimeLimit(elapsed = tl)
})

.First.sys <- function()
{
    for(pkg in getOption("defaultPackages")) {
        res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE,
                       character.only = TRUE)
        if(!res)
            warning(gettextf('package %s in options("defaultPackages") was not found', sQuote(pkg)$
                    call. = FALSE, domain = NA)
    }
}

## called at C level in the startup process prior to .First.sys
.OptRequireMethods <- function()
{
    pkg <- "methods" # done this way to avoid R CMD check warning
    if(pkg %in% getOption("defaultPackages"))
        if(!require(pkg, quietly = TRUE, warn.conflicts = FALSE,
                    character.only = TRUE))
            warning('package "methods" in options("defaultPackages") was not found',
                    call. = FALSE)
}

if(nzchar(Sys.getenv("R_BATCH"))) {
    .Last.sys <- function()
    {
        cat("> proc.time()\n")
        print(proc.time())
    }
    ## avoid passing on to spawned R processes
    ## A system has been reported without Sys.unsetenv, so try this
    try(Sys.setenv(R_BATCH=""))
}

local({
    if(nzchar(rv <- Sys.getenv("_R_RNG_VERSION_")))

local({
    if(nzchar(rv <- Sys.getenv("_R_RNG_VERSION_")))
        suppressWarnings(RNGversion(rv))
})

.sys.timezone <- NA_character_
.First <- NULL
.Last <- NULL
###-*- R -*- Unix Specific ----

.Library <- file.path(R.home(), "library")
.Library.site <- Sys.getenv("R_LIBS_SITE")
.Library.site <- if(!nzchar(.Library.site)) file.path(R.home(), "site-library") else unlist(strspl$
.Library.site <- .Library.site[file.exists(.Library.site)]

invisible(.libPaths(c(unlist(strsplit(Sys.getenv("R_LIBS"), ":")),
                      unlist(strsplit(Sys.getenv("R_LIBS_USER"), ":")
                      ))))
local({
    popath <- Sys.getenv("R_TRANSLATIONS", "")
    if(!nzchar(popath)) {
        paths <- file.path(.libPaths(), "translations", "DESCRIPTION")
        popath <- dirname(paths[file.exists(paths)][1])
    }
    bindtextdomain("R", popath)
    bindtextdomain("R-base", popath)
    assign(".popath", popath, .BaseNamespaceEnv)
})
local({
## we distinguish between R_PAPERSIZE as set by the user and by configure
papersize <- Sys.getenv("R_PAPERSIZE_USER")
if(!nchar(papersize)) {
    lcpaper <- Sys.getlocale("LC_PAPER") # might be null: OK as nchar is 0
    papersize <- if(nchar(lcpaper))
        if(length(grep("(_US|_CA)", lcpaper))) "letter" else "a4"
    else Sys.getenv("R_PAPERSIZE")
}
options(papersize = papersize,

}
options(papersize = papersize,
        printcmd = Sys.getenv("R_PRINTCMD"),
        dvipscmd = Sys.getenv("DVIPS", "dvips"),
        texi2dvi = Sys.getenv("R_TEXI2DVICMD"),
        browser = Sys.getenv("R_BROWSER"),
        pager = file.path(R.home(), "bin", "pager"),
        pdfviewer = Sys.getenv("R_PDFVIEWER"),
        useFancyQuotes = TRUE)
})

## non standard settings for the R.app GUI of the macOS port
if(.Platform$GUI == "AQUA") {
    ## this is set to let RAqua use both X11 device and X11/TclTk
    if (Sys.getenv("DISPLAY") == "")
        Sys.setenv("DISPLAY" = ":0")

    ## this is to allow gfortran compiler to work
    Sys.setenv("PATH" = paste(Sys.getenv("PATH"),":/usr/local/bin",sep = ""))
}## end "Aqua"

## de-dupe the environment on macOS (bug in Yosemite which affects things like PATH)
if (grepl("^darwin", R.version$os)) local({
    ## we have to de-dupe one at a time and re-check since the bug affects how
    ## environment modifications propagate
    while(length(dupes <- names(Sys.getenv())[table(names(Sys.getenv())) > 1])) {
        env <- dupes[1]
        value <- Sys.getenv(env)
        Sys.unsetenv(env)             ## removes the dupes, good
        .Internal(Sys.setenv(env, value)) ## wrapper requries named vector, a pain, hence internal
    }
})

local({
    tests_startup <- Sys.getenv("R_TESTS")
    if(nzchar(tests_startup)) source(tests_startup)
})

Is there anything glaring here that could be causing the issue?

CodePudding user response:

Your user .Rprofile file is loading itself recursively for some reason:

if (file.exists("~/.Rprofile")) {
  base::sys.source("~/.Rprofile", envir = environment())
}

From your comments it seems that these lines are inside ~/.Rprofile (~ expands to the user home directory, i.e. /Users/mycomputer in your case, assuming mycomputer is your user name).

Delete these lines (or comment them out), they don’t belong here. In fact, the file looks like it’s a template for a project-specific .Rprofile configuration. It would make sense inside a project directory, but not as the profile-wide user .Rprofile.

The logic for these files is as follows:

  • If there is an .Rprofile file in the current directory, R attempts to load that.
  • Otherwise, if the environment variable R_PROFILE_USER is set to the path of a file, R attempts to load this file.
  • Otherwise, if the file ~/.Rprofile exists, R attempts to load that.

Now, this implies that ~/.Rprofile is not loaded automatically if a projects-specific (= in the current working directory) .Rprofile exists. This is unfortunate, therefore many projects add lines similar to the above to their project-specific .Rprofile files to cause the user-wide ~/.Rprofile to be loaded as well. However, the above implementation ignores the R_PROFILE_USER environment variable. A better implementation would therefore look as follows:

rprofile = Sys.getenv('R_PROFILE_USER', '~/.Rprofile')
if (file.exists(rprofile)) {
  base::sys.source(rprofile, envir = environment())
}
rm(rprofile)

CodePudding user response:

Success! Thank you to everyone in the comment. The issue was resolved by deleting /Library/Frameworks/R.framework/Resources/library/base/R/Rprofile and re-installing R and Rstudio.

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