Last updated on 2024-05-29 08:56:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.2 | 69.20 | 363.28 | 432.48 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1.2 | 41.99 | 66.59 | 108.58 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.2 | 615.19 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.2 | 623.67 | OK | |||
| r-devel-windows-x86_64 | 1.1.2 | 51.00 | 362.00 | 413.00 | OK | |
| r-patched-linux-x86_64 | 1.1.2 | 54.94 | 375.53 | 430.47 | OK | |
| r-release-linux-x86_64 | 1.1.2 | 40.38 | 363.24 | 403.62 | OK | |
| r-release-macos-arm64 | 1.1.2 | 229.00 | OK | |||
| r-release-macos-x86_64 | 1.1.2 | 710.00 | OK | |||
| r-release-windows-x86_64 | 1.1.2 | 53.00 | 357.00 | 410.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.2 | 234.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.1.2 | 571.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.1.2 | 64.00 | 416.00 | 480.00 | OK |
Version: 1.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(o2geosocial)
Registered S3 methods overwritten by 'o2geosocial':
method from
plot.outbreaker_chains outbreaker2
print.custom_likelihoods outbreaker2
print.custom_priors outbreaker2
print.outbreaker_chains outbreaker2
summary.outbreaker_chains outbreaker2
>
> test_check("o2geosocial")
///// outbreaker custom likelihoods ///
class: custom_likelihoods list
number of items: 5
/// custom likelihoods set to NULL (default used) //
$reporting
NULL
$timing_infections
NULL
$timing_sampling
NULL
$space
NULL
$age
NULL
///// outbreaker custom likelihoods ///
class: custom_likelihoods list
number of items: 5
/// custom likelihoods //
$reporting
function(data, param, i) cpp_ll_reporting(data, param, i)
<environment: 0x55c545b479b0>
$timing_infections
function(data, param, i) cpp_ll_timing_infections(data, param, i)
<environment: 0x55c545b479b0>
$timing_sampling
function(data, param, i) cpp_ll_timing_sampling(data, param, i)
<environment: 0x55c545b479b0>
$space
function(data, config, param, i) cpp_ll_space(data, config, param, i)
<environment: 0x55c545b479b0>
$age
function(data, param, i) cpp_ll_age(data, param, i)
<environment: 0x55c545b479b0>
///// outbreaker results ///
class: outbreaker_chains data.frame
dimensions 21 rows, 22 columns
ancestries not shown: alpha_2 - alpha_5
infection dates not shown: t_inf_1 - t_inf_5
intermediate generations not shown: kappa_1 - kappa_5
/// head //
step post like prior a b pi alpha_1
1 1 -32.88389 -33.28774 0.4038415 0.7 0.1 0.9103669 NA
2 50 -39.51264 -38.91464 -0.5980045 0.7 0.1 0.8051902 2
3 100 -34.21771 -35.52312 1.3054073 0.7 0.1 0.9948269 2
...
/// tail //
step post like prior a b pi alpha_1
19 900 -32.02185 -33.24110 1.2192534 0.7 0.1 0.9853492 5
20 950 -33.65435 -34.66317 1.0088272 0.7 0.1 0.9625783 2
21 1000 -35.73840 -36.49890 0.7604945 0.7 0.1 0.9363814 2
///// outbreaker results ///
class: outbreaker_chains data.frame
dimensions 21 rows, 22 columns
ancestries not shown: alpha_2 - alpha_5
infection dates not shown: t_inf_1 - t_inf_5
intermediate generations not shown: kappa_1 - kappa_5
/// head //
step post like prior a b pi alpha_1
1 1 -32.88389 -33.28774 0.4038415 0.7 0.1 0.9103669 NA
2 50 -39.51264 -38.91464 -0.5980045 0.7 0.1 0.8051902 2
...
/// tail //
step post like prior a b pi alpha_1
20 950 -33.65435 -34.66317 1.0088272 0.7 0.1 0.9625783 2
21 1000 -35.73840 -36.49890 0.7604945 0.7 0.1 0.9363814 2
///// outbreaker results ///
class: outbreaker_chains data.frame
dimensions 21 rows, 22 columns
ancestries not shown: alpha_1 - alpha_5
infection dates not shown: t_inf_1 - t_inf_5
intermediate generations not shown: kappa_1 - kappa_5
/// head //
step post like prior
1 1 -32.88389 -33.28774 0.4038415
2 50 -39.51264 -38.91464 -0.5980045
3 100 -34.21771 -35.52312 1.3054073
...
/// tail //
step post like prior
19 900 -32.02185 -33.24110 1.2192534
20 950 -33.65435 -34.66317 1.0088272
21 1000 -35.73840 -36.49890 0.7604945
/// head //
1 2 3 4 5
1 0 0 0 0 1
2 0 0 0 0 1
3 0 0 0 0 1
...
/// tail //
1 2 3 4 5
19 0 0 0 0 1
20 0 0 0 0 1
21 0 0 0 0 1
Biggest cluster: 5
Cluster not shown: 2 to 5
/// head //
1 2
1 0 0
2 0 0
3 0 0
...
/// tail //
1 2
19 0 0
20 0 0
21 0 0
/// head //
1 2 3 4 5
1 0 0 0 0 1
2 0 0 0 0 1
3 0 0 0 0 1
...
/// tail //
1 2 3 4 5
19 0 0 0 0 1
20 0 0 0 0 1
21 0 0 0 0 1
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: .Call(`_o2geosocial_cpp_move_alpha`, param, data, config, list_custom_ll)
2: moves[[j]](param_current)
3: outbreaker_move(moves = moves, data = data, param_current = param_current, param_store = param_store, config = config, likelihoods = loglike, priors = priors)
4: outbreaker(data, config)
5: eval(code, test_env)
6: eval(code, test_env)
7: 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)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: 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) { })
15: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
16: test_that("Results work, all component", { alpha <- c(NA, rep(1, 4)) times <- c(0, 4, 8, 9, 23) f <- c(0.1, 0.2, 0.4, 0.2, 0.05, 0.03, 0.01, 0.005, 0.005) w <- c(0.05, 0.1, 0.25, 0.5, 0.05, 0.03, 0.01, 0.005, 0.005) data(toy_outbreak_short) age_dens <- toy_outbreak_short$age_contact age <- c(1, 3, 3, 5, 1) regions <- c(1, 1, 2, 2, 3) population <- c(10000, 50000, 5000) distance <- matrix(c(0, 15, 10, 15, 0, 60, 10, 60, 0), ncol = 3) names(population) <- colnames(distance) <- rownames(distance) <- 1:3 genotype <- c("Not attributed", "B4", "Not attributed", "Not attributed", "B4") data <- outbreaker_data(dates = times, region = regions, population = population, distance = distance, age_group = age, a_dens = age_dens, w_dens = w, f_dens = f, genotype = genotype) config <- create_config(data = data, init_tree = alpha, n_iter = 1000, n_iter_import = 500, burnin = 200) out <- outbreaker(data, config) out_summary <- summary(out, burnin = config$burnin) expect_true(all(out_summary$post > -50)) expect_true(out_summary$tree[out_summary$tree$to == 2, "support"] > 0.9) expect_true(out_summary$tree[out_summary$tree$to == 2, "from"] == 1) expect_true(out_summary$tree[out_summary$tree$to == 5, "generations"] == 2)})
17: eval(code, test_env)
18: eval(code, test_env)
19: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
27: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
28: source_file(path, env = env(env), desc = desc, error_call = error_call)
29: FUN(X[[i]], ...)
30: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
35: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
36: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
37: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
38: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
39: test_check("o2geosocial")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.2
Check: examples
Result: ERROR
Running examples in ‘o2geosocial-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: custom_likelihoods
> ### Title: Customise likelihood functions for o2geosocial
> ### Aliases: custom_likelihoods print.custom_likelihoods
>
> ### ** Examples
>
>
> ## specify a null model by disabling all likelihood components
> f_null <- function(data, config = NULL, param, i) {
+ return(0.0)
+ }
>
>
> null_model <- custom_likelihoods(timing_sampling = f_null,
+ timing_infections = f_null,
+ reporting = f_null,
+ space = f_null,
+ age = f_null)
>
> null_config <- list(find_import = FALSE,
+ n_iter = 200, gamma = 100, delta = 30,
+ sample_every = 1)
>
> ## load data
> data("toy_outbreak_short")
> dt_cases <- toy_outbreak_short$cases
> dt_cases <- dt_cases[order(dt_cases$Date), ][1:15,]
> dt_regions <- toy_outbreak_short$dt_regions
> all_dist <- geosphere::distGeo(matrix(c(rep(dt_regions$long, nrow(dt_regions)),
+ rep(dt_regions$lat, nrow(dt_regions))),
+ ncol = 2),
+ matrix(c(rep(dt_regions$long, each = nrow(dt_regions)),
+ rep(dt_regions$lat, each = nrow(dt_regions))),
+ ncol = 2))
>
> dist_mat <- matrix(all_dist/1000, nrow = nrow(dt_regions))
> pop_vect <- dt_regions$population
> names(pop_vect) <- rownames(dist_mat) <- colnames(dist_mat) <- dt_regions$region
>
> data <- outbreaker_data(dates = dt_cases$Date, age_group = dt_cases$age_group,
+ region = dt_cases$Cens_tract, population = pop_vect,
+ distance = dist_mat)
>
> res_null <- outbreaker(data = data,
+ config = null_config,
+ likelihoods = null_model)
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: .Call(`_o2geosocial_cpp_move_swap_cases`, param, data, config, list_custom_ll)
2: moves[[j]](param_current)
3: outbreaker_move(moves = moves, data = data, param_current = param_current, param_store = param_store, config = config, likelihoods = loglike, priors = priors)
4: outbreaker(data = data, config = null_config, likelihoods = null_model)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(o2geosocial)
Registered S3 methods overwritten by 'o2geosocial':
method from
plot.outbreaker_chains outbreaker2
print.custom_likelihoods outbreaker2
print.custom_priors outbreaker2
print.outbreaker_chains outbreaker2
summary.outbreaker_chains outbreaker2
>
> test_check("o2geosocial")
///// outbreaker custom likelihoods ///
class: custom_likelihoods list
number of items: 5
/// custom likelihoods set to NULL (default used) //
$reporting
NULL
$timing_infections
NULL
$timing_sampling
NULL
$space
NULL
$age
NULL
///// outbreaker custom likelihoods ///
class: custom_likelihoods list
number of items: 5
/// custom likelihoods //
$reporting
function(data, param, i) cpp_ll_reporting(data, param, i)
<environment: 0x562a8af416c8>
$timing_infections
function(data, param, i) cpp_ll_timing_infections(data, param, i)
<environment: 0x562a8af416c8>
$timing_sampling
function(data, param, i) cpp_ll_timing_sampling(data, param, i)
<environment: 0x562a8af416c8>
$space
function(data, config, param, i) cpp_ll_space(data, config, param, i)
<environment: 0x562a8af416c8>
$age
function(data, param, i) cpp_ll_age(data, param, i)
<environment: 0x562a8af416c8>
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: .Call(`_o2geosocial_cpp_move_swap_cases`, param, data, config, list_custom_ll)
2: moves[[i]](param = param)
3: eval(code, test_env)
4: eval(code, test_env)
5: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
13: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
14: test_that("test: try different default movements", { data(toy_outbreak_short) x <- toy_outbreak_short dt_cases <- x$cases dt_cases <- dt_cases[order(dt_cases$Date), ] dt_regions <- x$dt_regions all_dist <- geosphere::distGeo(matrix(c(rep(dt_regions$long, nrow(dt_regions)), rep(dt_regions$lat, nrow(dt_regions))), ncol = 2), matrix(c(rep(dt_regions$long, each = nrow(dt_regions)), rep(dt_regions$lat, each = nrow(dt_regions))), ncol = 2)) dist_mat <- matrix(all_dist/1000, nrow = nrow(dt_regions)) pop_vect <- dt_regions$population names(pop_vect) <- rownames(dist_mat) <- colnames(dist_mat) <- dt_regions$region w <- dnorm(x = 1:100, mean = 11.7, sd = 2) data <- outbreaker_data(dates = dt_cases$Date, age_group = dt_cases$age_group, region = dt_cases$Cens_tract, population = pop_vect, distance = dist_mat, a_dens = x$age_contact, f_dens = dgamma(x = 1:100, scale = 0.43, shape = 27), w_dens = w) config <- create_config(data = data) config_no_move <- create_config(data = data, move_alpha = FALSE, move_a = FALSE, move_b = FALSE, move_t_inf = FALSE, move_pi = FALSE, move_kappa = FALSE, move_swap_cases = FALSE) pre_clust <- pre_clustering(data = data, config = config) data <- outbreaker_data(data = pre_clust[["data"]]) config <- create_config(config = pre_clust[["config"]], data = data) data <- add_convolutions(data = data, config = config) if (!is.null(data$log_w_dens[config$max_kappa, ])) { config$delta <- max(which(data$log_w_dens[config$max_kappa, ] > -20)) } param <- create_param(data = data, config = config)$current likeli <- custom_likelihoods() priors <- custom_priors() moves <- bind_moves(config = config, data = data, likelihoods = likeli, priors = priors) moves_no <- bind_moves(config = config_no_move, data = data, likelihoods = likeli, priors = priors) expect_true(all(vapply(moves, is.function, logical(1)))) expect_equal(length(moves), 8) expect_equal(length(moves_no), 0) for (i in seq_along(moves)) { set.seed(1) res <- moves[[i]](param = param) expect_equal(length(param), length(res)) expect_equal(length(unlist(param)), length(unlist(res))) expect_equal(names(param), names(res)) }})
15: eval(code, test_env)
16: eval(code, test_env)
17: 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)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: 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) { })
25: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
26: source_file(path, env = env(env), desc = desc, error_call = error_call)
27: FUN(X[[i]], ...)
28: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
33: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
34: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
35: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
36: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
37: test_check("o2geosocial")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘o2geosocial.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/o2geosocial.Rcheck/vign_test/o2geosocial/vignettes/o2geosocial_files/figure-html/plot_ref-1.png
624x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5405 bytes
Input file size = 6263 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4705
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4705
Output IDAT size = 4705 bytes (700 bytes decrease)
Output file size = 4783 bytes (1480 bytes = 23.63% decrease)
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: .Call(`_o2geosocial_cpp_move_swap_cases`, param, data, config, list_custom_ll)
2: moves_imports[[j]](param_current_imports)
3: MCMC_imports(config_imports = config, data_imports = data, moves_imports = moves, likelihoods_imports = likelihoods, J_imports = J, influences_imports = influences, param_current_imports = param_current)
4: outbreaker_find_imports(moves = moves, data = data, param_current = param_current, param_store = param_store, config = config, likelihoods = loglike)
5: outbreaker(data = data1, config = config1, moves = moves, priors = priors, likelihoods = likelihoods)
6: eval(expr, envir, enclos)
7: eval(expr, envir, enclos)
8: eval_with_user_handlers(expr, envir, enclos, user_handlers)
9: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
10: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
11: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
12: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
13: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
14: evaluate::evaluate(...)
15: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
16: in_dir(input_dir(), expr)
17: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
18: eng_r(options)
19: block_exec(params)
20: call_block(x)
21: process_group(group)
22: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
23: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
24: process_file(text, output)
25: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
26: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
27: vweave_rmarkdown(...)
28: engine$weave(file, quiet = quiet, encoding = enc)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
33: tools::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/o2geosocial.Rcheck/vign_test/o2geosocial", skip = TRUE, ser_elibs = "/home/hornik/tmp/scratch/RtmpmFQEGj/file2a6f7330c56cb4.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc