Last updated on 2024-05-28 06:58:57 CEST.
| Package | ERROR | OK |
|---|---|---|
| o2geosocial | 1 | 12 |
Current CRAN status: ERROR: 1, OK: 12
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: 0x5605df7c3bf8>
$timing_infections
function(data, param, i) cpp_ll_timing_infections(data, param, i)
<environment: 0x5605df7c3bf8>
$timing_sampling
function(data, param, i) cpp_ll_timing_sampling(data, param, i)
<environment: 0x5605df7c3bf8>
$space
function(data, config, param, i) cpp_ll_space(data, config, param, i)
<environment: 0x5605df7c3bf8>
$age
function(data, param, i) cpp_ll_age(data, param, i)
<environment: 0x5605df7c3bf8>
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: .Call(`_o2geosocial_cpp_move_swap_cases`, param, data, config, list_custom_ll)
2: moves[[i]](param = param)
3: eval(code, test_env)
4: eval(code, test_env)
5: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
13: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
14: test_that("test: try different default movements", { data(toy_outbreak_short) x <- toy_outbreak_short dt_cases <- x$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/Rtmp4W1ZWC/file209bcd6da2cdd6.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc