Error: C Stack Usage Is Too Close to The Limit in R

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

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)

C stack usage 7970960 is too close to the limit

You almost certainly have a bogus function called exp in your search path somewhere, which calls itself. It may be in your workspace (global environment), or (less likely but possible) in a package you have loaded. (It's also possible that the infinite recursion is defined in a more complicated way, i.e. rather than exp() calling itself, it calls something that calls it back ...)

The normal, expected result of find("exp") is

[1] "package:base"

Suppose you have defined a recursive exp function in your workspace:

exp <- function(x) exp(x)

Then exp(1) will give

Error: C stack usage 7969716 is too close to the limit

and find("exp") will give

[1] ".GlobalEnv" "package:base"

i.e. there is an exp in the global environment that R will see before it sees the built-in function in the base package.

If you do have something like this going on, starting a new R session will help (unless the object is in a saved workspace that gets restored when the session starts), or rm("exp").

GenomicRanges: C stack usage ... is too close to the limit

It turned out to be due to some outdated packages. I did not notice that they were not updated because RStudio's 'update packages functionality' ignores packages one does not have write permission to (thus not informing you they are outdated at all). Thus, it turned out to be due a subtle permissions problem see. See this answer.

Error: C stack usage 15924224 is too close to the limit?

runApp(".") would source Shiny app files under the current app folder. It searches files named app.R or ui.R/server.R combined. If you have code runApp(".") in your file, following recursion will happen:

runApp -> source app.R -> find runApp() in code ->

execute runApp -> source app.R -> -> find runApp() in code ->

execute runApp -> ...

One guideline is to never write runApp in your app.R. This function is only to be used on the console. Usually Shiny would return an error and prevent you to be trapped in the loop. Not sure why the error message is not given in your case.

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