4

A few days ago, I was having an error running models in R using 'brms', which said that my posterior samples didn't exist. Upon reading further, these links (1, 2, 3, 4) led me to think it was an rstan problem playing with my macOS (Catalina 10.15.6). I followed their instructions, namely:

-updated packages Rcpp, rstan, arm, and brms

-followed these workaround instructions to alter the 'parallel' settings for stan: https://github.com/rstudio/rstudio/issues/6692

-updated R and RStudio, since this problem was supposedly fixed a few months ago with R 4.0

-updated XCode 11, Quartz 11, GNU Fortran 8.2

-updated latest macOS Catalina bug fixes

-ran sudo rm -rf [path to R] to uninstall R

-tried to do a thorough uninstall of all R and RStudio files, including deleting files in my Library/Frameworks folder, any .plist files in Library/Preferences, and any .Rprofile, .Rscript, .Rapp, .Rhistory, or .Renvirons files

-reinstalled R and RStudio after restart

Now, instead of having a "blank slate" to start from, I am experiencing some super weird behaviors. First, RStudio opens on a completely white blank screen and never loads. Second, when I try to open R directly either via terminal or with R Console, I get stuck in a loop for nearly 20 min that says:

Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE,  : 
  file descriptor is too large for select()
Calls: <Anonymous> ... makePSOCKcluster -> newPSOCKnode -> socketConnection
Execution halted
Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE,  : 
  cannot open the connection
Calls: <Anonymous> ... makePSOCKcluster -> newPSOCKnode -> socketConnection
In addition: Warning message:
In socketConnection("localhost", port = port, server = TRUE, blocking = TRUE,  :
  port 11537 cannot be opened
Execution halted

At the very end, when it finally stops looping forever, it says:

/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R: cannot make pipe for command substitution: Too many open files
ERROR: option '-e' requires a non-empty argument
rm: /var/folders/54/km__8z8x78x8_ct1pw8w8bbh0000gn/T//RtmpVORdTy: Too many open files

I can't access a console or enter anything in R to try to troubleshoot. Moreover, it causes a massive slowdown to my computer and Activity Monitor shows more than 150 'R' processes running, which don't go away after quitting R, only after using 'killall R' in Terminal.

However, someone in IT helped me determine that it's something in my Mac user library or preferences, because we created a brand new user on my machine, installed R and RStudio, and had no problems loading them.

I am just a psychology grad student, so I really don't understand the back end that makes R work and I am totally baffled by these symptoms.

I suspect that these links (5, 6, 7) might help, but I don't know how to execute the solutions because right now I can't enter or run anything in R without triggering that endless loop of 'Execution halted.'

I could really use a hand, thanks!

mthebee
  • 41
  • 1
  • Update: Resolved. I resolved the issue by reinstalling RStudio via anaconda, and then opening my .Renvirons file and deleting this line (which I had added based on this thread - https://github.com/rstudio/rstudio/issues/6692): cl <- parallel::makeCluster(1) – mthebee Aug 21 '20 at 05:30
  • The source of the line of code which I ended up deleting from .Renvirons was a line (cl <- parallel::makeCluster(2, setup_strategy = "sequential") ) suggested in a comment here: https://discourse.mc-stan.org/t/dealing-with-r-4-0/14586 – mthebee Aug 21 '20 at 23:04

0 Answers0