Error in sampler$call_sampler
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Description
When running rstan::sampling() I have just started getting the following error message:
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
error occurred during calling the sampler; sampling not done
Please see the comment below for more details
Our stan code hasn't changed in the last 6 months so assume this is related to an updated version of stan / rstan / local compiler change ? The following below is a minimal example code that I was able to use to create the problem, that being said it is super inconsistant, 80% of the time it works fine and 20% of the time it kicks up the above error. Once its kicked up the error it won't fix itself until I restart R. The issue seems to be related to loading our R package via rstantools but I've not been able to consistently reproduce the problem nor diagnose whats triggering it.
Any help / advice would be appreciated.
Version Information
- OS Version: Mac OS Big Sur 11.6.2
- RStan Version: 2.21.3
- No Makevars file exists
- Output of
devtools::session_info("rstan"):
> devtools::session_info("rstan")
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.1.2 (2021-11-01)
os macOS Big Sur 10.16
system x86_64, darwin17.0
ui X11
language (EN)
collate en_GB.UTF-8
ctype en_GB.UTF-8
tz Europe/London
date 2022-03-10
pandoc 2.17.1.1 @ /usr/local/bin/pandoc
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.0)
BH 1.78.0-0 2021-12-15 [1] CRAN (R 4.1.0)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0)
cli 3.2.0 2022-02-14 [1] CRAN (R 4.1.2)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.1.2)
crayon 1.5.0 2022-02-14 [1] CRAN (R 4.1.2)
desc 1.4.1 2022-03-06 [1] CRAN (R 4.1.2)
digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
fansi 1.0.2 2022-01-14 [1] CRAN (R 4.1.2)
farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.0)
ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.1.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
inline 0.3.19 2021-05-31 [1] CRAN (R 4.1.0)
isoband 0.2.5 2021-07-13 [1] CRAN (R 4.1.0)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.0)
lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.2)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.0)
loo 2.4.1 2020-12-09 [1] CRAN (R 4.1.0)
magrittr 2.0.2 2022-01-26 [1] CRAN (R 4.1.2)
MASS 7.3-54 2021-05-03 [1] CRAN (R 4.1.2)
Matrix 1.3-4 2021-06-01 [1] CRAN (R 4.1.2)
matrixStats 0.61.0 2021-09-17 [1] CRAN (R 4.1.0)
mgcv 1.8-38 2021-10-06 [1] CRAN (R 4.1.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
nlme 3.1-153 2021-09-07 [1] CRAN (R 4.1.2)
pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.2)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0)
Rcpp 1.0.8 2022-01-13 [1] CRAN (R 4.1.2)
RcppEigen 0.3.3.9.1 2020-12-17 [1] CRAN (R 4.1.0)
RcppParallel 5.1.5 2022-01-05 [1] CRAN (R 4.1.2)
rlang 1.0.2 2022-03-04 [1] CRAN (R 4.1.2)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0)
rstan 2.21.3 2021-12-19 [1] CRAN (R 4.1.0)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0)
StanHeaders 2.21.0-7 2020-12-17 [1] CRAN (R 4.1.0)
tibble * 3.1.6 2021-11-07 [1] CRAN (R 4.1.0)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0)
viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.0)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.2)
[1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the minimal example using rstan::sampling() and the supplied devtools::session_info("rstan") output, then compare successful and failing runs across R restarts. No repository file or test is named; done would require a reproducible cause and a verified resolution for the intermittent sampler error.
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
- Needs clarification
- Newbie friendliness
- 25/100