Hi,
I try to run a stan model in R 4.0.2 and the session crashes if I run the code
interactively (sourcing from an interactive session or from Rstudio) but runs
fine if run with Rscript or R -e 'source("rstan_test.R")' . I
don't really know where to begin to debug this.
I'm not sure if this is due to the setup on my machine or if this is a bug
in either the packaging on Debian, the rstan package or R itself, so I'm
posting it here in the most general mailinglist.
For now just running the model in a non-interactive session is a workaround. R
and stan code and sessionInfo below.
All the best and thanks in advance, Tobias
==== rstan_test.R ===library(rstan)
schools_dat <- list(J = 8,
y = c(28, 8, -3, 7, -1, 1, 18, 12),
sigma = c(15, 10, 16, 11, 9, 11, 10, 18))
fit <- stan(file = 'schools.stan', data = schools_dat)
message("done")
===
==== schools.stan ===
// saved as schools.stan
data {
int<lower=0> J; // number of schools
real y[J]; // estimated treatment effects
real<lower=0> sigma[J]; // standard error of effect estimates
}
parameters {
real mu; // population treatment effect
real<lower=0> tau; // standard deviation in treatment effects
vector[J] eta; // unscaled deviation from mu by school
}
transformed parameters {
vector[J] theta = mu + tau * eta; // school treatment effects
}
model {
target += normal_lpdf(eta | 0, 1); // prior log-density
target += normal_lpdf(y | theta, sigma); // log-likelihood
}
===
==== output of sessionInfo ===
$ R -e 'library(rstan); sessionInfo()'
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(rstan); sessionInfo()
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_DK.UTF-8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_DK.UTF-8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_DK.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_DK.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rstan_2.21.2 ggplot2_3.3.2 StanHeaders_2.21.0-6
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 pillar_1.4.6 compiler_4.0.2 prettyunits_1.1.1
[5] tools_4.0.2 pkgbuild_1.1.0 jsonlite_1.7.0 lifecycle_0.2.0
[9] tibble_3.0.3 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.7
[13] cli_2.0.2 parallel_4.0.2 curl_4.3 loo_2.3.1
[17] gridExtra_2.3 withr_2.2.0 dplyr_1.0.2 generics_0.0.2
[21] vctrs_0.3.4 stats4_4.0.2 grid_4.0.2 tidyselect_1.1.0
[25] glue_1.4.2 inline_0.3.15 R6_2.4.1 processx_3.4.3
[29] fansi_0.4.1 callr_3.4.3 purrr_0.3.4 magrittr_1.5
[33] codetools_0.2-16 scales_1.1.1 ps_1.3.4 ellipsis_0.3.1
[37] matrixStats_0.56.0 assertthat_0.2.1 colorspace_1.4-1 V8_3.2.0
[41] RcppParallel_5.0.2 munsell_0.5.0 crayon_1.3.4
>
>
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