stan-dev
cmdstanr::sample() saves incorrect path to csv files, Windows
When output_dir is set to a full directory path including the drive letter e.g., cmdstanr::sample(..., output_dir = "c:/output"), and using wsl (install_cmdstan(..., wsl = TRUE)), the function does not save the correct path.
It seems to mangle the beginning of the path by adding "/mnt/" and dropping the colon separator.
To Reproduce
Running the example from ?cmdstanr::sample().
library(cmdstanr)
This is cmdstanr version 0.9.0
- CmdStanR documentation and vignettes: mc-stan.org/cmdstanr
- CmdStan path: //wsl$/ECCC-WSL-UBUNTU-24/home/acsmith/.cmdstan/cmdstan-2.36.0
- CmdStan version: 2.36.0
file <- file.path(cmdstan_path(), "examples/bernoulli/bernoulli.stan")
mod <- cmdstan_model(file)
Model executable is up to date!
# Data as a named list (like RStan)
stan_data <- list(N = 10, y = c(0,1,0,0,0,0,0,0,0,1))
# Running example model with output_dir set as full path to drive
drive <- "c:/gitHub"
dir.exists(drive)
[1] TRUE
fit_mcmc <- mod$sample(
+ data = stan_data,
+ seed = 123,
+ chains = 2,
+ parallel_chains = 2,
+ output_dir = drive
+ )
Running MCMC with 2 parallel chains...
Chain 1 Iteration: 1 / 2000 [ 0%] (Warmup)
Chain 1 Iteration: 100 / 2000 [ 5%] (Warmup)
Chain 1 Iteration: 200 / 2000 [ 10%] (Warmup)
Chain 1 Iteration: 300 / 2000 [ 15%] (Warmup)
Chain 1 Iteration: 400 / 2000 [ 20%] (Warmup)
Chain 1 Iteration: 500 / 2000 [ 25%] (Warmup)
Chain 1 Iteration: 600 / 2000 [ 30%] (Warmup)
Chain 1 Iteration: 700 / 2000 [ 35%] (Warmup)
Chain 1 Iteration: 800 / 2000 [ 40%] (Warmup)
Chain 1 Iteration: 900 / 2000 [ 45%] (Warmup)
Chain 1 Iteration: 1000 / 2000 [ 50%] (Warmup)
Chain 1 Iteration: 1001 / 2000 [ 50%] (Sampling)
Chain 1 Iteration: 1100 / 2000 [ 55%] (Sampling)
Chain 1 Iteration: 1200 / 2000 [ 60%] (Sampling)
Chain 1 Iteration: 1300 / 2000 [ 65%] (Sampling)
Chain 1 Iteration: 1400 / 2000 [ 70%] (Sampling)
Chain 1 Iteration: 1500 / 2000 [ 75%] (Sampling)
Chain 1 Iteration: 1600 / 2000 [ 80%] (Sampling)
Chain 2 Iteration: 1 / 2000 [ 0%] (Warmup)
Chain 2 Iteration: 100 / 2000 [ 5%] (Warmup)
Chain 2 Iteration: 200 / 2000 [ 10%] (Warmup)
Chain 2 Iteration: 300 / 2000 [ 15%] (Warmup)
Chain 2 Iteration: 400 / 2000 [ 20%] (Warmup)
Chain 2 Iteration: 500 / 2000 [ 25%] (Warmup)
Chain 2 Iteration: 600 / 2000 [ 30%] (Warmup)
Chain 2 Iteration: 700 / 2000 [ 35%] (Warmup)
Chain 2 Iteration: 800 / 2000 [ 40%] (Warmup)
Chain 2 Iteration: 900 / 2000 [ 45%] (Warmup)
Chain 2 Iteration: 1000 / 2000 [ 50%] (Warmup)
Chain 2 Iteration: 1001 / 2000 [ 50%] (Sampling)
Chain 2 Iteration: 1100 / 2000 [ 55%] (Sampling)
Chain 2 Iteration: 1200 / 2000 [ 60%] (Sampling)
Chain 2 Iteration: 1300 / 2000 [ 65%] (Sampling)
Chain 2 Iteration: 1400 / 2000 [ 70%] (Sampling)
Chain 1 Iteration: 1700 / 2000 [ 85%] (Sampling)
Chain 1 Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 1 Iteration: 1900 / 2000 [ 95%] (Sampling)
Chain 1 Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2 Iteration: 1500 / 2000 [ 75%] (Sampling)
Chain 2 Iteration: 1600 / 2000 [ 80%] (Sampling)
Chain 2 Iteration: 1700 / 2000 [ 85%] (Sampling)
Chain 2 Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 1 finished in 0.3 seconds.
Chain 2 Iteration: 1900 / 2000 [ 95%] (Sampling)
Chain 2 Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2 finished in 0.3 seconds.
Both chains finished successfully.
Mean chain execution time: 0.3 seconds.
Total execution time: 0.7 seconds.
output_file_saved <- fit_mcmc$output_files()
file.exists(output_file_saved)
[1] FALSE FALSE
output_file_saved
[1] "/mnt/c/gitHub/bernoulli-202508281056-1-58343f.csv"
[2] "/mnt/c/gitHub/bernoulli-202508281056-2-58343f.csv"
Operating system
Windows 10,
sysname release version
"Windows" "10 x64" "build 26100"
CmdStanR version number
- CmdStan path: //wsl$/ECCC-WSL-UBUNTU-24/home/acsmith/.cmdstan/cmdstan-2.36.0
- CmdStan version: 2.36.0
Additional context Not sure if this is something new related to a recent Windows or WSL update. This error only started showing up for me recently. I have recreated this error on three machines, each running a different wsl version, but all running the same Windows 10 version.
Thanks for reporting. Tagging @andrjohns, who knows a lot more about WSL than I do.
One of my colleagues pointed out that it may be just a small bug in output_files().
save_object() still works.
Perhaps it's a simple as ensuring that when using wsl, output_files() needs to translate the path into a format suitable for Windows.