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Description
Apologies if this is a duplicate of #550 or #687, but I have a case where include_paths is not recognized for a pre-compiled model in a subdirectory. Users of instantiate are having trouble building packages with pre-compiled models split over multiple Stan files (c.f. wlandau/instantiate#28).
Here's the full context. With these files:
fs::dir_tree("bin")
bin
└── stan
├── bernoulli.stan
└── utils
└── silly.stanbin/stan/bernoulli.stan:
#include utils/silly.stan
data {
int<lower=0> N;
array[N] int<lower=0,upper=1> y;
}
parameters {
real<lower=0,upper=1> theta;
}
model {
theta ~ beta(1,1); // uniform prior on interval 0,1
y ~ bernoulli(theta);
}
generated quantities {
real theta_lin;
theta_lin = silly_logit(theta);
}and bin/stan/utils/silly.stan:
functions {
real silly_logit(real x) {
real out;
out = logit(x);
return out;
}
}and R code to compile and reuse the model:
library(cmdstanr)
#> This is cmdstanr version 0.9.0
#> - CmdStanR documentation and vignettes: mc-stan.org/cmdstanr
#> - CmdStan path: /Users/C240390/.cmdstan/cmdstan-2.36.0
#> - CmdStan version: 2.36.0
model <- cmdstan_model(
stan_file = "bin/stan/bernoulli.stan",
exe_file = "bin/stan/bernoulli",
compile = TRUE,
include_paths = "bin/stan"
)
rstudioapi::restartSession()
library(cmdstanr)
model <- cmdstan_model(
stan_file = "bin/stan/bernoulli.stan",
exe_file = "bin/stan/bernoulli",
compile = FALSE,
include_paths = "bin/stan"
)
y <- c(0, 1, 1, 0, 1, 0)
samples <- model$sample(data = list(N = length(y), y = y))I get this error:
Error in `(function (command = NULL, args = character(), error_on_status = TRUE, …`:
! System command 'stanc' failed
---
Exit status: 1
Stderr (last 10 lines, see `$stderr` for more):
34: */
35:
36: #include utils/silly.stan
^
37: data {
38: int<lower=0> N;
-------------------------------------------------
Could not find include file 'utils/silly.stan' in specified include paths.
Current include paths: NoneSame if I set include_paths to "bin/stan/utils", file.path(getwd(), "bin/stan"), or file.path(getwd(), "bin/stan/utils").
R version 4.5.0 (2025-04-11)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Indiana/Indianapolis
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cmdstanr_0.9.0
loaded via a namespace (and not attached):
[1] tensorA_0.36.2.1 backports_1.5.0 R6_2.6.1 xfun_0.52
[5] magrittr_2.0.3 posterior_1.6.1 glue_1.8.0 abind_1.4-8
[9] tibble_3.2.1 knitr_1.50 pkgconfig_2.0.3 generics_0.1.3
[13] lifecycle_1.0.4 ps_1.9.1 cli_3.6.4 processx_3.8.6
[17] vctrs_0.6.5 withr_3.0.2 compiler_4.5.0 distributional_0.5.0
[21] rstudioapi_0.17.1 tools_4.5.0 checkmate_2.3.2 evaluate_1.0.3
[25] pillar_1.10.2 jsonlite_2.0.0 rlang_1.1.6