Eight schools example fails after new rstan install

Interfaces RStan
,
1

After a fresh install of rstan with
R version 4.2.1
RTools 4.2
Rstudio version 2022.02.0 Build 443

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")))

I can successfully run the example
example(stan_model, package = "rstan", run.dontrun = TRUE)

and the rats example 

y <- as.matrix(read.table('temp/rats.txt', header = TRUE))
x <- c(8, 15, 22, 29, 36)
xbar <- mean(x)
N <- nrow(y)
T <- ncol(y)
rats_fit <- stan(file='temp/rats.stan', data = list(N=N, T=T, y=y, x=x, xbar=xbar))

But the Eight Schools example fails:

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 <- rstan::stan(file = 'temp/schools.stan', data = schools_dat)

Error in stanc(file = file, model_code = model_code, model_name = model_name,  : 
  parser failed badly

  • Operating System
    Windows 10 Enterprise 
Version 21H2
OS build 19044.2130
  • RStan Version
    rstan_2.26.13
StanHeaders_2.26.13
  • Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
    Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/.../.R/Makevars': No such file or directory
  • Output of devtools::session_info("rstan")
    ─ Session info 
──────────────────────────────────────────────────────────────── ──────────────────────────────────
 setting  value
 version  R version 4.2.1 (2022-06-23 ucrt)
 os       Windows 10 x64 (build 19044)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       America/New_York
 date     2022-11-14
 rstudio  2022.02.0+443 Prairie Trillium (desktop)
 pandoc   NA

─ Packages     ──────────────────────────────────────────────────────────────────────────────────────────────────────
 package      * version   date (UTC) lib source
 backports      1.4.1     2021-12-13 [1] CRAN (R 4.2.0)
 BH             1.78.0-0  2021-12-15 [1] CRAN (R 4.2.0)
 callr          3.7.2     2022-08-22 [1] CRAN (R 4.2.1)
 checkmate      2.1.0     2022-04-21 [1] CRAN (R 4.2.1)
 cli            3.4.1     2022-09-23 [1] CRAN (R 4.2.1)
 colorspace     2.0-3     2022-02-21 [1] CRAN (R 4.2.1)
 crayon         1.5.2     2022-09-29 [1] CRAN (R 4.2.1)
 curl           4.3.3     2022-10-06 [1] CRAN (R 4.2.1)
 desc           1.4.2     2022-09-08 [1] CRAN (R 4.2.2)
 digest         0.6.29    2021-12-01 [1] CRAN (R 4.2.1)
 fansi          1.0.3     2022-03-24 [1] CRAN (R 4.2.1)
 farver         2.1.1     2022-07-06 [1] CRAN (R 4.2.1)
 ggplot2        3.3.6     2022-05-03 [1] CRAN (R 4.2.1)
 glue           1.6.2     2022-02-24 [1] CRAN (R 4.2.1)
 gridExtra      2.3       2017-09-09 [1] CRAN (R 4.2.1)
 gtable         0.3.1     2022-09-01 [1] CRAN (R 4.2.1)
 inline         0.3.19    2021-05-31 [1] CRAN (R 4.2.2)
 isoband        0.2.6     2022-10-06 [1] CRAN (R 4.2.1)
 jsonlite       1.8.2     2022-10-02 [1] CRAN (R 4.2.1)
 labeling       0.4.2     2020-10-20 [1] CRAN (R 4.2.0)
 lattice        0.20-45   2021-09-22 [1] CRAN (R 4.2.1)
 lifecycle      1.0.3     2022-10-07 [1] CRAN (R 4.2.1)
 loo            2.5.1     2022-03-24 [1] CRAN (R 4.2.2)
 magrittr       2.0.3     2022-03-30 [1] CRAN (R 4.2.1)
 MASS           7.3-58.1  2022-08-03 [1] CRAN (R 4.2.1)
 Matrix         1.5-1     2022-09-13 [1] CRAN (R 4.2.1)
 matrixStats    0.62.0    2022-04-19 [1] CRAN (R 4.2.2)
 mgcv           1.8-40    2022-03-29 [1] CRAN (R 4.2.1)
 munsell        0.5.0     2018-06-12 [1] CRAN (R 4.2.1)
 nlme           3.1-160   2022-10-10 [1] CRAN (R 4.2.1)
 pillar         1.8.1     2022-08-19 [1] CRAN (R 4.2.1)
 pkgbuild       1.3.1     2021-12-20 [1] CRAN (R 4.2.2)
 pkgconfig      2.0.3     2019-09-22 [1] CRAN (R 4.2.1)
 prettyunits    1.1.1     2020-01-24 [1] CRAN (R 4.2.1)
 processx       3.7.0     2022-07-07 [1] CRAN (R 4.2.1)
 ps             1.7.1     2022-06-18 [1] CRAN (R 4.2.1)
 R6             2.5.1     2021-08-19 [1] CRAN (R 4.2.1)
 RColorBrewer   1.1-3     2022-04-03 [1] CRAN (R 4.2.0)
 Rcpp           1.0.9     2022-07-08 [1] CRAN (R 4.2.1)
 RcppEigen      0.3.3.9.2 2022-04-08 [1] CRAN (R 4.2.1)
 RcppParallel   5.1.5     2022-01-05 [1] CRAN (R 4.2.1)
 rlang          1.0.6     2022-09-24 [1] CRAN (R 4.2.1)
 rprojroot      2.0.3     2022-04-02 [1] CRAN (R 4.2.2)
 rstan        * 2.26.13   2022-06-25 [1] local
 scales         1.2.1     2022-08-20 [1] CRAN (R 4.2.1)
 StanHeaders  * 2.26.13   2022-06-25 [1] local
 tibble         3.1.8     2022-07-22 [1] CRAN (R 4.2.1)
 utf8           1.2.2     2021-07-24 [1] CRAN (R 4.2.1)
 V8             4.2.2     2022-11-03 [1] CRAN (R 4.2.2)
 vctrs          0.5.0     2022-10-22 [1] CRAN (R 4.2.2)
 viridisLite    0.4.1     2022-08-22 [1] CRAN (R 4.2.1)
 withr          2.5.0     2022-03-03 [1] CRAN (R 4.2.1)

 [1] C:/R-4.2.1/library
2

Can you post the output from:

cat(readLines("temp/schools.stan"), sep="\n")
3

I copied-and-pasted it from the example:

// https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#example-1-eight-schools
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
}
4

Ah, it looks like we still have parsing issues when there’s a # in the file. If you remove the URL at the top of the file, it should compile fine

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