stan-dev
Error when running MCMC with CmdStanR
Im getting a new error which im not sure the source of, this is with script that had previously worked fine, but now i’ve installed CmdStanR on a new device and am not sure the parameters or source of this error message, the MCMC does converge and all chains finish successfully but before saving the output it gives this error.
#parameters fit<-model$sample( data = data, seed = 123, chains = 4, parallel_chains = 4, refresh = 500) Error in if (any(efbmi_per_chain < threshold)) { : missing value where TRUE/FALSE needed UPDATE: Im able to have it run and save the output without an error when I tinker with the model parameter in a specific way.
#only way it works!!! fit<-model$sample( data = data, seed = 123456, chains = 1, refresh = 500) Anyone help or advice would be really appreciated
here is the link of the original question
https://discourse.mc-stan.org/t/error-when-running-mcmc-with-rstan/28271
im using Windows 11 R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000)
and
cmdstan_version() [1] “2.30.0”
and
writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars.win"))) CXX14=$(BINPREF)g++ CXX14FLAGS=-O3 -march=native -mtune=native CXX11FLAGS=-O3 -march=native -mtune=native …and…
devtools::session_info('rstan') ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.2.1 (2022-06-23 ucrt) os Windows 10 x64 (build 22000) system x86_64, mingw32 ui RStudio language (EN) collate English_United Kingdom.utf8 ctype English_United Kingdom.utf8 tz Asia/Taipei date 2022-07-21 rstudio 2022.02.3+492 Prairie Trillium (desktop) pandoc NA
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0) BH 1.78.0-0 2021-12-15 [1] CRAN (R 4.2.0) callr 3.7.0 2021-04-20 [1] CRAN (R 4.2.0) checkmate 2.1.0 2022-04-21 [1] CRAN (R 4.2.1) cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.0) colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0) crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0) desc 1.4.1 2022-03-06 [1] CRAN (R 4.2.0) digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0) farver 2.1.0 2021-02-28 [1] CRAN (R 4.2.0) ggplot2 3.3.6 2022-05-03 [1] CRAN (R 4.2.0) glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.2.0) inline 0.3.19 2021-05-31 [1] CRAN (R 4.2.1) isoband 0.2.5 2021-07-13 [1] CRAN (R 4.2.0) labeling 0.4.2 2020-10-20 [1] CRAN (R 4.2.0) lattice 0.20-45 2021-09-22 [2] CRAN (R 4.2.1) lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0) loo 2.5.1 2022-03-24 [1] CRAN (R 4.2.1) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) MASS 7.3-57 2022-04-22 [2] CRAN (R 4.2.1) Matrix 1.4-1 2022-03-23 [2] CRAN (R 4.2.1) matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.2.1) mgcv 1.8-40 2022-03-29 [2] CRAN (R 4.2.1) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0) nlme 3.1-157 2022-03-25 [2] CRAN (R 4.2.1) pillar 1.7.0 2022-02-01 [1] CRAN (R 4.2.0) pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.1) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0) processx 3.6.1 2022-06-17 [1] CRAN (R 4.2.0) ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0) Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.2.0) RcppEigen 0.3.3.9.2 2022-04-08 [1] CRAN (R 4.2.0) RcppParallel 5.1.5 2022-01-05 [1] CRAN (R 4.2.1) rlang 1.0.3 2022-06-27 [1] CRAN (R 4.2.1) rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0) rstan 2.21.5 2022-04-11 [1] CRAN (R 4.2.1) scales 1.2.0 2022-04-13 [1] CRAN (R 4.2.0) StanHeaders 2.21.0-7 2020-12-17 [1] CRAN (R 4.2.1) tibble 3.1.7 2022-05-03 [1] CRAN (R 4.2.0) utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0) viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.2.0) withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
[1] C:/Users/Users/AppData/Local/R/win-library/4.2 [2] C:/Program Files/R/R-4.2.1/library
I've seen that error myself and it's definitely a bug. But now I'm confused about whether it's coming from RStan or CmdStanR. The title says "RStan", but the example has model$sample(...), which is CmdStanR. Could you please clarify, ideally with a reproducible example?
Just transferred this to the cmdstanr repo. @Jamin-R12, can you share a reproducible example so that we can debug?
I think this issue was fixed recently in https://github.com/stan-dev/cmdstanr/pull/659.
@Jamin-R12 you haven't listed the cmdstanr version, but my assumption is that you are using an older version.
Please update to the latest by either running:
remove.packages("cmdstanr")
install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
or
remotes::install_github("stan-dev/cmdstanr")
