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`csv_contents$metadata$save_warmup` is "true" (character), not `TRUE` (logical)
Summary
Update: This error does not occur with cmdstan v2.33.1.
Running cmdstan v2.34.1 (23 January 2024) and cmdstanr v0.7.1. Reprex follows.
Attempting to fit a trivial model:
library(brms)
dat <- data.frame(y = rnorm(1000))
mod <- brm(y ~ 1, data = dat, backend = "cmdstanr")
... fails with:
Error in !is.null(csv_contents$metadata$save_warmup) && csv_contents$metadata$save_warmup: invalid 'y' type in 'x && y'
Debugging with options(error = recover), it seems that csv_contents$metadata$save_warmup is "true" (character), not TRUE (logical), when we reach lines 1437-1438 of fit.R.
Reprex
library(brms)
#> Loading required package: Rcpp
#> Loading 'brms' package (version 2.21.0). Useful instructions
#> can be found by typing help('brms'). A more detailed introduction
#> to the package is available through vignette('brms_overview').
#>
#> Attaching package: 'brms'
#> The following object is masked from 'package:stats':
#>
#> ar
dat <- data.frame(y = rnorm(1000))
mod <- brm(y ~ 1, data = dat, backend = "cmdstanr")
#> Start sampling
#> Running MCMC with 4 sequential chains...
#>
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#> Chain 4 finished in 0.1 seconds.
#>
#> All 4 chains finished successfully.
#> Mean chain execution time: 0.1 seconds.
#> Total execution time: 1.0 seconds.
#> Error in !is.null(csv_contents$metadata$save_warmup) && csv_contents$metadata$save_warmup: invalid 'y' type in 'x && y'
Created on 2024-04-24 with reprex v2.0.2
Session info
sessioninfo::session_info()
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Got the same error fitting the example in the startup guide. Like the previous commenter, I was able to verify that csv_contents$metadata$save_warmup is a character string and not a logical.
Got the same error fitting the example in the startup guide. Like the previous commenter, I was able to verify that
csv_contents$metadata$save_warmupis a character string and not a logical.
Do you get the same error if you install cmdstanr from github?
remotes::install_github("stan-dev/cmdstanr")
I can't replicate the error locally
I get the same error @andrjohns. Have attached all the code I ran from re-downloading and re-building to fitting.
install.packages("rstan") # version 2.32.6
remotes::install_github("stan-dev/cmdstanr")
library(cmdstanr)
rebuild_cmdstan()
cmdstan_version() # 2.35.0
file <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan")
mod <- cmdstan_model(file)
data_list <- list(N = 10, y = c(0,1,0,0,0,0,0,0,0,1))
fit <- mod$sample(
data = data_list,
seed = 123,
chains = 4,
parallel_chains = 4,
refresh = 500
)
stanfit <- rstan::read_stan_csv(fit$output_files())
# Error in if (max(save_warmup) == 0L) { :
# missing value where TRUE/FALSE needed
# In addition: Warning messages:
# 1: In parse_stancsv_comments(comments) : NAs introduced by coercion
# 2: In parse_stancsv_comments(comments) : NAs introduced by coercion
# 3: In parse_stancsv_comments(comments) : NAs introduced by coercion
# 4: In parse_stancsv_comments(comments) : NAs introduced by coercion
Session info
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cmdstanr_0.8.1.9000 rstan_2.32.6 StanHeaders_2.32.10
loaded via a namespace (and not attached):
[1] tensorA_0.36.2.1 utf8_1.2.4 generics_0.1.3 magrittr_2.0.3
[5] grid_4.4.1 jsonlite_1.8.8 processx_3.8.4 pkgbuild_1.4.4
[9] backports_1.5.0 ps_1.7.7 gridExtra_2.3 fansi_1.0.6
[13] QuickJSR_1.3.0 scales_1.3.0 codetools_0.2-20 abind_1.4-5
[17] cli_3.6.3 rlang_1.1.4 munsell_0.5.1 withr_3.0.0
[21] tools_4.4.1 inline_0.3.19 parallel_4.4.1 checkmate_2.3.1
[25] dplyr_1.1.4 colorspace_2.1-0 ggplot2_3.5.1 curl_5.2.1
[29] vctrs_0.6.5 posterior_1.6.0 R6_2.5.1 matrixStats_1.3.0
[33] stats4_4.4.1 lifecycle_1.0.4 V8_4.4.2 pkgconfig_2.0.3
[37] RcppParallel_5.1.8 pillar_1.9.0 gtable_0.3.5 loo_2.8.0
[41] glue_1.7.0 data.table_1.15.4 Rcpp_1.0.12 xfun_0.45
[45] tibble_3.2.1 tidyselect_1.2.1 rstudioapi_0.16.0 knitr_1.48
[49] compiler_4.4.1 distributional_0.4.0
I'm guessing it's related to this issue https://github.com/stan-dev/rstan/pull/1131. There's an open PR to fix it that I'm reviewing at the moment.
