[R-pkg-team] Bug#962794: r-cran-stanheaders: breaks r-cran-rstanarm autopkgtests

[Graham Inggs]

Source: r-cran-stanheaders
Version: 2.21.0-3-1
Severity: serious
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks

Hi Maintainer

The recent upload of r-cran-stanheaders causes the autopkgtests of
r-cran-rstanarm to fail [1].
This prevents the migration of r-cran-stanheaders to testing for 8 days already.

I've copied what I hope is the relevant part of the log below.

Regards
Graham


[1] https://ci.debian.net/packages/r/r-cran-rstanarm/testing/amd64/


 *** caught segfault ***
address 0x9b377c, cause 'memory not mapped'

Traceback:
 1: dyn.load("/tmp/RtmpFHXEap/sourceCpp-x86_64-pc-linux-gnu-1.0.4.6/sourcecpp_15d03ae3f182/sourceCpp_2.so")
 2: eval(ei, envir)
 3: eval(ei, envir)
 4: withVisible(eval(ei, envir))
 5: source(scriptPath, local = env)
 6: Rcpp::sourceCpp(code = paste(code, collapse = "\n"), ...)
 7: withCallingHandlers(expr, warning = function(w) if (inherits(w,
 classes)) tryInvokeRestart("muffleWarning"))
 8: suppressWarnings(Rcpp::sourceCpp(code = paste(code, collapse =
"\n"),     ...))
 9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: 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))})
13: try(suppressWarnings(Rcpp::sourceCpp(code = paste(code, collapse =
"\n"),     ...)), silent = TRUE)
14: pkgbuild::with_build_tools(try(suppressWarnings(Rcpp::sourceCpp(code
= paste(code,     collapse = "\n"), ...)), silent = TRUE), required =
rstan_options("required") &&     identical(Sys.getenv("WINDOWS"),
"TRUE") && !identical(Sys.getenv("R_PACKAGE_SOURCE"),     ""))
15: expose_stan_functions(stanc_ret, rebuild = TRUE)
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({    eval(code, test_env)    if (!handled &&
!is.null(test)) {        skip_empty()    }}, expectation =
handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv,
handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch(withCallingHandlers({    eval(code, test_env)    if
(!handled && !is.null(test)) {        skip_empty()    }}, expectation
= handle_expectation, skip = handle_skip, warning = handle_warning,
 message = handle_message, error = handle_error), error =
handle_fatal,     skip = function(e) {    })
26: test_code(NULL, exprs, env)
27: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
28: force(code)
29: doWithOneRestart(return(expr), restart)
30: withOneRestart(expr, restarts[[1L]])
31: withRestarts(testthat_abort_reporter = function() NULL, force(code))
32: with_reporter(reporter = reporter, start_end_reporter =
start_end_reporter,     {        reporter$start_file(basename(path))
     lister$start_file(basename(path))        source_file(path,
new.env(parent = env), chdir = TRUE,             wrap = wrap)
reporter$.end_context()        reporter$end_file()    })
33: FUN(X[[i]], ...)
34: lapply(paths, test_file, env = env, reporter = current_reporter,
  start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
35: force(code)
36: doWithOneRestart(return(expr), restart)
37: withOneRestart(expr, restarts[[1L]])
38: withRestarts(testthat_abort_reporter = function() NULL, force(code))
39: with_reporter(reporter = current_reporter, results <-
lapply(paths,     test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
40: test_files(paths, reporter = reporter, env = env, stop_on_failure
= stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
41: test_dir(path = test_path, reporter = reporter, env = env, filter
= filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning
= stop_on_warning,     wrap = wrap)
42: test_package_dir(package = package, test_path = test_path, filter
= filter,     reporter = reporter, ..., stop_on_failure =
stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
43: test_check("rstanarm", invert = FALSE, filter = if
(Sys.getenv("NOT_CRAN") !=     "true") "stan_functions")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
autopkgtest [07:12:51]: test run-unit-test: -----------------------]
autopkgtest [07:12:51]: test run-unit-test:  - - - - - - - - - -
results - - - - - - - - - -
run-unit-test        FAIL non-zero exit status 139