[R-pkg-team] Bug#971940: r-cran-shinystan: autopkgtest regression

[Graham Inggs]

Source: r-cran-shinystan
Version: 2.5.0-3
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: regression

Hi Maintainer

Since the removal of r-cran-rstanarm from testing on 2020-07-22,
r-cran-shinystan's autopkgtests have been failing there [1].

However, r-cran-shinystan's tests currently also fail in unstable [2],
where r-cran-rstanarm is still available.

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-shinystan/testing/amd64/
[2] https://ci.debian.net/packages/r/r-cran-shinystan/unstable/amd64/


> library(testthat)
> library(shinystan)
Loading required package: shiny
code for methods in class “Rcpp_model_base” was not checked for
suspicious field assignments (recommended package ‘codetools’ not
available?)
code for methods in class “Rcpp_model_base” was not checked for
suspicious field assignments (recommended package ‘codetools’ not
available?)
code for methods in class “Rcpp_stan_fit” was not checked for
suspicious field assignments (recommended package ‘codetools’ not
available?)
code for methods in class “Rcpp_stan_fit” was not checked for
suspicious field assignments (recommended package ‘codetools’ not
available?)

This is shinystan version 2.5.0

>
> test_check("shinystan")

 *** caught segfault ***
address 0x7f883b78e008, cause 'invalid permissions'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <-
loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos =
pos, deps, exclude, include.only)}, error = function(e) {    P <- if
(!is.null(cc <- conditionCall(e)))         paste(" in",
deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace
load failed for %s%s:\n %s",         sQuote(package), P,
conditionMessage(e))    if (logical.return)
message(paste("Error:", msg), domain = NA)    else stop(msg, call. =
FALSE, domain = NA)})
 8: library(rstanarm)
 9: withCallingHandlers(expr, packageStartupMessage = function(c)
tryInvokeRestart("muffleMessage"))
10: suppressPackageStartupMessages(library(rstanarm))
11: eval(code, test_env)
12: eval(code, test_env)
13: 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)
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(tryCatchList(expr, names[-nh], parentenv,
handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 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) {    })
21: test_code(NULL, exprs, env)
22: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
23: force(code)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestarts(testthat_abort_reporter = function() NULL, force(code))
27: 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()    })
28: FUN(X[[i]], ...)
29: lapply(paths, test_file, env = env, reporter = current_reporter,
  start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
30: force(code)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestarts(testthat_abort_reporter = function() NULL, force(code))
34: with_reporter(reporter = current_reporter, results <-
lapply(paths,     test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
35: test_files(paths, reporter = reporter, env = env, stop_on_failure
= stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
36: 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)
37: 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)
38: test_check("shinystan")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
autopkgtest [16:04:30]: test run-unit-test: -----------------------]
autopkgtest [16:04:30]: test run-unit-test:  - - - -