stan-dev
expose_stan_functions causes error: "$ operator is invalid for atomic vectors"
I'm working with experimental version 2.26 of RStan on Windows and I'm getting an error, "$ operator is invalid for atomic vectors", from expose_stan_functions.
I researched this a bit and did not find anything the same. Issue #899 mentions expose_stan_functions in passing but that appeared to be about other errors.
I get the error from an existing .stan file for which expose_stan_functions does not cause an error with RStan 2.26 on macOS. Instead of including the .stan file I'm working with, here is a shorter example which I nicked from another discussion. See: https://discourse.mc-stan.org/t/mixture-models/17721/9
functions {
real repulsive_lpdf(vector mu, vector rho) {
int K = num_elements(mu);
matrix[K, K] S = diag_matrix(rep_vector(1, K));
matrix[K, K] L;
int c = 0;
for (k1 in 1:(K - 1))
for (k2 in (k1 + 1):K){
c += 1;
S[k1, k2] = log(1 - exp(- squared_distance(mu[k1], mu[k2]) / rho[c]));
S[k2, k1] = S[k1, k2];
}
L = cholesky_decompose(S);
return 2 * sum(log(diagonal(L)));
}
}
data {
int<lower=1> K;
int<lower=1> N;
real y[N];
}
parameters {
ordered[K] mu;
vector<lower=0>[choose(K, 2)] rho;
real<lower=0> sigma[K];
simplex[K] lambda;
}
model {
// Prior model
mu ~ normal(0, 5);
sigma ~ std_normal();
lambda ~ dirichlet(rep_vector(3, K));
rho ~ gamma(1, 2);
mu ~ repulsive(rho);
// Observational model
for (n in 1:N) {
real comp_lpdf[K];
for (k in 1:K) {
comp_lpdf[k] = log(lambda[k]) + normal_lpdf(y[n] | mu[k], sigma[k]);
}
target += log_sum_exp(comp_lpdf);
}
}
I put that into a file name example.stan and then I get, in my R session:
> expose_stan_functions ("example.stan")
Error: $ operator is invalid for atomic vectors
packageVersion ("RStan") reports 2.26.2.
R.version.string reports "R version 4.1.0 (2021-05-18)".
Operating system is MS Windows 10.
I installed RStan following these instructions. (I was trying the officially released version 2.21, however, it lacks the %/% operator which I want to use.) See: https://discourse.mc-stan.org/t/problems-installing-rstan-2-21-2-with-rtools-4/22492/5
remove.packages(c("StanHeaders", "rstan"))
install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
PS. This page (https://cran.r-project.org/web/checks/check_results_rstanarm.html) which appears to report build info has the same error (https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64-gcc10-UCRT/rstanarm-00check.html). I guess that page gets updated so the error might go away or something different reported; the one I'm looking at has the timestamp 2021-07-23 01:49:38 CEST.
can confirm, I am also getting this issue.
rstan::stan_version()
[1] "2.26.1"
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
other attached packages:
[1] ggplot2_3.3.5 data.table_1.14.2 xts_0.12.1 zoo_1.8-9 dlm_1.1-5 rstan_2.26.6 StanHeaders_2.26.6
loaded via a namespace (and not attached):
[1] RcppEigen_0.3.3.9.1 tidyselect_1.1.1 xfun_0.29 purrr_0.3.4 lattice_0.20-45 V8_4.0.0 colorspace_2.0-2 vctrs_0.3.8
[9] generics_0.1.1 htmltools_0.5.2 stats4_4.1.2 loo_2.4.1 yaml_2.2.1 utf8_1.2.2 rlang_0.4.12 pkgbuild_1.3.1
[17] pillar_1.6.4 glue_1.6.0 withr_2.4.3 matrixStats_0.61.0 lifecycle_1.0.1 munsell_0.5.0 gtable_0.3.0 codetools_0.2-18
[25] evaluate_0.14 inline_0.3.19 knitr_1.37 callr_3.7.0 fastmap_1.1.0 ps_1.6.0 curl_4.3.2 parallel_4.1.2
[33] fansi_1.0.0 Rcpp_1.0.7 scales_1.1.1 RcppParallel_5.1.5 jsonlite_1.7.2 gridExtra_2.3 digest_0.6.29 processx_3.5.2
[41] dplyr_1.0.7 grid_4.1.2 BH_1.78.0-0 cli_3.1.0 tools_4.1.2 magrittr_2.0.1 tibble_3.1.6 crayon_1.4.2
[49] pkgconfig_2.0.3 ellipsis_0.3.2 Matrix_1.3-4 prettyunits_1.1.1 rmarkdown_2.11 R6_2.5.1 compiler_4.1.2
