xbarber
September 21, 2020, 7:34am
1
I’m using OS X Catalina and Windows 10 in three different computers. Last R version 4.0.2 and last RSTUDIO version 1.3.1073
I install stan following the “https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started ” Vignette instructions.
I try to use the “schools.stan” example and I obtain “Error in unserialize(socklist[[n]]) : error reading from connection” in chain 2.
I try this code also:
library(rstan)x + sigma rnorm(n)
And I obtain the same error in 3 different computer:2 2 with OS X and 1 with Windows
Thanks in advanced
I try to use m.cores=1 or chain=1 and I obtain a R crash
Probably I’m doing somnething wrong, but as my first “shoot” I can solve it!!!
Hi Xavier,
I can help troubleshoot your Windows installation, then we can tag someone to help with the Catalina installation.
Can you run the following on your Windows machine and post the output:
Sys.getenv("PATH")
Sys.getenv("BINPREF")
readLines("~/.R/Makevars.win")
readLines("~/.Rprofile")
readLines("~/.Renviron")
devtools::session_info("rstan")
xbarber
September 21, 2020, 11:33am
3
On windows 10 computer:
Sys.getenv(“PATH”)
Sys.getenv(“BINPREF”)
readLines(“~/.R/Makevars.win”)
readLines(“~/.Rprofile”)
readLines(“~/.Renviron”)
devtools::session_info(“rstan”)
Session info ------------------------------------------------------------------------------------
Packages ----------------------------------------------------------------------------------------
[1] C:/estadistica/R/library
D – DLL MD5 mismatch, broken installation.
Thanks! It looks like you missed a step when installing RTools4: https://cran.r-project.org/bin/windows/Rtools/
Can you run:
writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
And then restart R/RStudio and try again?
It looks like it didn’t copy correctly, you need the double backspace before the usr and bin paths (i.e. \\usr\\bin)
1 Like
Great! That warning is safe to ignore.
Let’s get someone to have a look at your Catalina installation(s) now!
@jonah This user is on Catalina with R 4.0.2 and getting Error in unserialize(socklist[[n]]) : error reading from connection when running a model
1 Like
jonah
September 21, 2020, 8:49pm
9
I’ve only seen rare instances of this on Mac. I think the most recent encounter with this error on Catalina was in the thread Some models run without problems, but more complex give error: Error in unserialize(socklist[[n]]) : error reading/writing from connection - #12 by torkar . @torkar said that he was able to fix it by removing -march=native from the Makevars file (in this case Makevars and not Makevars.win):
@jonah , I experienced the same error, i.e., “unserialize”, on OS X. Removing -march=native works for me too.
On my Catalina setup I haven’t had problems with this so my Makevars file looks like:
CXX14FLAGS=-O3 -march=native -mtune=native
CXX14FLAGS += -arch x86_64 -ftemplate-depth-256
but following @torkar ’s recommendation you could drop -march=native and try just
CXX14FLAGS=-O3 -mtune=native
CXX14FLAGS += -arch x86_64 -ftemplate-depth-256
You can open that file for editing using file.edit(file.path(Sys.getenv("HOME"), ".R", "Makevars")).
2 Likes
xbarber
September 22, 2020, 7:51am
10
After some uninstall-install and reboot with yours recomentation WORKS in mac too!!!
THANKS!!
1 Like
xbarber
September 22, 2020, 10:09am
12
yes, but then I obtained prep_call_sampler error, after that I Uninstall-install and reboot and then it works.
Thanks
t-anton
September 22, 2021, 9:59am
13
Check Repository for distributing (some) stan-dev R packages | r-packages
and try
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
I had an old version of rstan (version 2.21.2 from CRAN), and It was showing the error.
1 Like
Hello,
Here is my:
setting value
─ Packages ──────────────────────────────────────────────────────────────────────────────────────
Do you get a more helpful error message if you run just a single chain?
with 1 chain and 2 cores R crashes. Tried with 1 core too and R crashes. (I get a pop up message saying R needs to abort, restart session).
1 Like
I have the same problem. When I run any brms code, I either get the error “Error in unserialize(socklist[[n]]) : error reading from connection” or “R session aborted”.
When I run the foollowing code, I get either “R session aborted” as well:
example(stan_model, package = “rstan”, run.dontrun = TRUE)
Session information:
R version 4.3.0 (2023-04-21)
Matrix products: default
locale:
time zone: Asia/Seoul
attached base packages:
other attached packages:
I have the same issue. Is there any fix for this? Please help
I am getting this same error message: