segfault on very simple program

Summary:

fit <- stan(file = 'schools.stan', data = schools_dat)
from the RStan tutorial results in failure

Description:

*** caught segfault ***
address 0x3c580e7ca670, cause 'memory not mapped'

Traceback:
1: context_eval(join(src), private$context, serialize)
2: get_str_output(context_eval(join(src), private$context, serialize))
3: evaluate_js(src, serialize = TRUE)
4: get_json_output(evaluate_js(src, serialize = TRUE))
5: ctx$call("stanc", model_name, paste(model_code, collapse = "\n"))
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
10: try(ctx$call("stanc", model_name, paste(model_code, collapse = "\n")), silent = TRUE)
11: stanc_beta(model_code, model_name, isystem)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
16: try(stanc_beta(model_code, model_name, isystem))
17: stanc(file = file, model_code = model_code, model_name = model_name, verbose = verbose, obfuscate_model_name = obfuscate_model_name, allow_undefined = allow_undefined, isystem = isystem)
18: stan_model(file, model_name = model_name, model_code = model_code, stanc_ret = NULL, boost_lib = boost_lib, eigen_lib = eigen_lib, save_dso = save_dso, verbose = verbose)
19: stan(file = "schools.stan", data = schools_dat)

Reproducible Steps:

fit <- stan(file = 'schools.stan', data = schools_dat)
shools_dat and schools.stan initialised as instructed

Current Output:

Segfault

Expected Output:

as explained in tutorial

RStan Version:

The version of RStan you are running (e.g., from packageVersion("rstan"))
2.21.2

R Version:

The version of R you are running (e.g., from R.version.string)
R version 4.0.2 (2020-06-22)

Operating System:

CentOS-8 on a x86_64 machine
I took libnghttp2-devel-1.41 and nodejs-12.18.3 from Fedora32 and recompiled them using the rpm build system. This way everything is supposed to be coherent (same compiler, ...)

Any idea ?
Thanks
Pascal Dupuis

Start by reproducing the tutorial call stan(file = 'schools.stan', data = schools_dat) with RStan 2.21.2 on R 4.0.2 and CentOS 8. Trace the failure through stanc_beta, context_eval, and evaluate_js, using the reported stack and environment details. Done means the schools example completes without a segmentation fault and produces the tutorial's expected result.