Hi all,
This morning I encountered an odd problem. When trying to run the GP example straight out of the manual (10.3 Fitting a Gaussian process | Stan User’s Guide), I run into trouble with the compiler.
Model:
data {
int<lower=1> N;
array[N] real x;
vector[N] y;
}
transformed data {
vector[N] mu = rep_vector(0, N);
}
parameters {
real<lower=0> rho;
real<lower=0> alpha;
real<lower=0> sigma;
}
model {
matrix[N, N] L_K;
matrix[N, N] K = cov_exp_quad(x, alpha, rho);
real sq_sigma = square(sigma);
// diagonal elements
for (n in 1:N) {
K[n, n] = K[n, n] + sq_sigma;
}
L_K = cholesky_decompose(K);
rho ~ inv_gamma(5, 5);
alpha ~ std_normal();
sigma ~ std_normal();
y ~ multi_normal_cholesky(mu, L_K) T[0, 1];
}
The error:
> stan("models/gp", chains = 1, iter = 100)
SYNTAX ERROR, MESSAGE(S) FROM PARSER:
error in 'modelfd8a6dfc59a6_gp_truncated_normal' at line 4, column 2
-------------------------------------------------
2: int<lower=1> N;
3: vector[N] y;
4: array[N] real x;
^
5: }
-------------------------------------------------
PARSER EXPECTED: <one of the following:
a variable declaration, beginning with type,
(int, real, vector, row_vector, matrix, unit_vector,
simplex, ordered, positive_ordered,
corr_matrix, cov_matrix,
cholesky_corr, cholesky_cov
or '}' to close variable declarations>
In the script editor pane, the word array shows as black text (unlike i.a. vector) suggesting that it’s not recognised:
I just followed the steps in the RStan manual to reinstall RStan and it works (and also clearly the compiler is called):
> sessionInfo("rstan")
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
character(0)
other attached packages:
[1] rstan_2.21.3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8 lubridate_1.8.0 tidyr_1.1.4 prettyunits_1.1.1
[5] ps_1.6.0 assertthat_0.2.1 digest_0.6.29 utf8_1.2.2
[9] R6_2.5.1 cellranger_1.1.0 backports_1.4.1 reprex_2.0.1
[13] stats4_4.1.2 evaluate_0.14 httr_1.4.2 ggplot2_3.3.5
[17] pillar_1.7.0 utils_4.1.2 rlang_1.0.0 readxl_1.3.1
[21] rstudioapi_0.13 callr_3.7.0 rmarkdown_2.11 stringr_1.4.0
[25] readr_2.1.2 loo_2.4.1 munsell_0.5.0 broom_0.7.12
[29] compiler_4.1.2 modelr_0.1.8 xfun_0.29 pkgconfig_2.0.3
[33] stats_4.1.2 pkgbuild_1.3.1 htmltools_0.5.2 tidyselect_1.1.1
[37] tibble_3.1.6 gridExtra_2.3 codetools_0.2-18 matrixStats_0.61.0
[41] grDevices_4.1.2 fansi_1.0.2 crayon_1.4.2 dplyr_1.0.7
[45] tzdb_0.2.0 dbplyr_2.1.1 withr_2.4.3 grid_4.1.2
[49] jsonlite_1.7.3 gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2
[53] magrittr_2.0.2 datasets_4.1.2 StanHeaders_2.21.0-7 scales_1.1.1
[57] RcppParallel_5.1.5 stringi_1.7.6 cli_3.1.1 fs_1.5.2
[61] tidyverse_1.3.1 xml2_1.3.3 ellipsis_0.3.2 graphics_4.1.2
[65] generics_0.1.2 vctrs_0.3.8 base_4.1.2 tools_4.1.2
[69] forcats_0.5.1 glue_1.6.1 purrr_0.3.4 hms_1.1.1
[73] processx_3.5.2 parallel_4.1.2 fastmap_1.1.0 yaml_2.2.2
[77] inline_0.3.19 colorspace_2.0-2 rvest_1.0.2 knitr_1.37
[81] haven_2.4.3 patchwork_1.1.1 methods_4.1.2
Does anyone have a good idea as to why this happens? I have a nasty feeling that I’m missing something obvious.
Best,
Ben