stan-dev / stan-dev/rstan

"double free or corruption (out)" error on using previously working code using dordlogit function in "rethinking" library (Rstan 2.21.2)

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Description

Summary:

"double free or corruption (out)" error on using previously working code using dordlogit function in "rethinking" library (Rstan 2.21.2)

Description:

In trying to use the dordlogit function from the rethinking package (version 2.13), I’m getting an error after reinstalling Rstan to a more recent version (2.21.2, GitRev: 2e1f913d3ca3). The code used to run fine previously.

Reproducible Steps:

To reproduce it, please use (code essentially from McElreath, R. Statistical Rethinking, 2nd Edition, New York: CRC Press, 2020, p. 385, just slightly adapted):

library(rethinking)
library(rstan)
data(Trolley)
d <- Trolley

## R code 12.16
m12.4 <- ulam(
    alist(
        R ~ dordlogit( 0 , cutpoints ),
        cutpoints ~ dnorm( 0 , 1.5 )
    ) , data=list( R=d$response ), chains=1 )
Current Output:

source("~/test.r")
Loading required package: rstan
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Loading required package: parallel
rethinking (Version 2.13)

Attaching package: 'rethinking'

The following object is masked from 'package:stats':

rstudent

Error in open.connection(con, open = mode) :
Could not resolve host: github.com

SAMPLING FOR MODEL 'fbca4c7b48ba5e5074b8d9463e3ca10c' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.004117 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 41.17 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
double free or corruption (out)
Aborted (core dumped)

Rstan version:

rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)

Rethinking version

2.13

R Version:

R version 4.1.1 (2021-08-10)

Operating System:

Ubuntu 20.04.3 LTS

The code used to run despite the github.com connection error, which does not seem to be relevant here.

Thank you.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Begin with the reproducible code in ~/test.r, focusing on the ulam call using dordlogit, then run it with RStan 2.21.2, rethinking 2.13, R 4.1.1, and Ubuntu 20.04. Compare the result with earlier working versions and investigate the github.com connection error separately. Done means the compatibility cause is identified and the crash has a verified resolution or clear upstream diagnosis.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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