segfault "memory not mapped" example(stan_model) Ubuntu 20.04
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Description
Summary:
On a bare install of Ubuntu 20.04 + R, the example code example(stan_model, package = "rstan", run.dontrun = TRUE) produces a segfault.
Description:
The only additional information I can provide is that it only happens when exiting the R session - so possibly somewhere at or during garbage collection/cleanup?
I have also tried github releases and compiling directly from the tarball here
In hunting for similar issues I'm come across recommendations to
reinstall Rcpp and that their is a potential compiler conflict. If this is the case I still have not come across a set of MAKEVARS that satisfies this.
Reproducible Steps:
Dockerfile
FROM ubuntu:20.04
ENV DEBIAN_FRONTEND noninteractive
RUN apt update && apt install -yqq --no-install-recommends libcurl4-openssl-dev r-base-dev
RUN R -e 'install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))'
CMD ["tail", "-f", "/dev/null"]
docker build -t stan_segfault .
docker run -d --name stan_segfault stan_segfault
docker exec stan_segfault R -e 'example(stan_model, package = "rstan", run.dontrun = TRUE)'
Current Output:
*** caught segfault ***
address 0x18, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Expected Output:
Not to segfault.
RStan Version:
2.26.13
R Version:
4.2.1 (have reproduced with all of 4.1.x - latest)
Operating System:
Ubuntu 20.04
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Research direction
Start with the Dockerfile and the example(stan_model, package = "rstan", run.dontrun = TRUE) command to reproduce the crash on Ubuntu 20.04. Investigate the failure that occurs when the R session exits, using the reported RStan 2.26.13 and R 4.2.1 environment. Done means the example exits without a segfault.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, r, ubuntu
- Domain
- backend, devops
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100