CRAN Package Check Results for Package o2geosocial

Last updated on 2024-06-20 00:59:39 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.2 61.00 386.33 447.33 ERROR
r-devel-linux-x86_64-debian-gcc 1.1.2 48.16 66.54 114.70 ERROR
r-devel-linux-x86_64-fedora-clang 1.1.2 601.98 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1.2 619.15 ERROR
r-devel-windows-x86_64 1.1.2 52.00 103.00 155.00 ERROR
r-patched-linux-x86_64 1.1.2 58.21 373.75 431.96 OK
r-release-linux-x86_64 1.1.2 37.72 369.31 407.03 OK
r-release-macos-arm64 1.1.2 229.00 OK
r-release-macos-x86_64 1.1.2 443.00 OK
r-release-windows-x86_64 1.1.2 50.00 370.00 420.00 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 64.00 412.00 476.00 OK

Additional issues

clang-UBSAN gcc-UBSAN valgrind

Check Details

Version: 1.1.2
Check: tests
Result: ERROR Running ‘testthat.R’ [14s/16s] 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: 0x55636a78e718> $timing_infections function(data, param, i) cpp_ll_timing_infections(data, param, i) <environment: 0x55636a78e718> $timing_sampling function(data, param, i) cpp_ll_timing_sampling(data, param, i) <environment: 0x55636a78e718> $space function(data, config, param, i) cpp_ll_space(data, config, param, i) <environment: 0x55636a78e718> $age function(data, param, i) cpp_ll_age(data, param, i) <environment: 0x55636a78e718> ///// 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: 0x56141c478ac8> $timing_infections function(data, param, i) cpp_ll_timing_infections(data, param, i) <environment: 0x56141c478ac8> $timing_sampling function(data, param, i) cpp_ll_timing_sampling(data, param, i) <environment: 0x56141c478ac8> $space function(data, config, param, i) cpp_ll_space(data, config, param, i) <environment: 0x56141c478ac8> $age function(data, param, i) cpp_ll_age(data, param, i) <environment: 0x56141c478ac8> *** caught segfault *** address 0x1, cause 'memory not mapped' Traceback: 1: .Call(`_o2geosocial_cpp_move_swap_cases`, param, data, config, list_custom_ll) 2: moves[[i]](param = param) 3: eval(code, test_env) 4: eval(code, test_env) 5: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 6: doTryCatch(return(expr), name, parentenv, handler) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 9: doTryCatch(return(expr), name, parentenv, handler) 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 11: tryCatchList(expr, classes, parentenv, handlers) 12: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 13: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter()) 14: test_that("test: try different default movements", { data(toy_outbreak_short) x <- toy_outbreak_short dt_cases <- x$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$render, options))) 18: eng_r(options) 19: block_exec(params) 20: call_block(x) 21: process_group(group) 22: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 23: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 24: process_file(text, output) 25: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 26: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 27: vweave_rmarkdown(...) 28: engine$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/RtmpbH34d7/file154cc56a5bda61.rds") 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’ [19s/59s] 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: 0x55f4837403d8> $timing_infections function(data, param, i) cpp_ll_timing_infections(data, param, i) <environment: 0x55f4837403d8> $timing_sampling function(data, param, i) cpp_ll_timing_sampling(data, param, i) <environment: 0x55f4837403d8> $space function(data, config, param, i) cpp_ll_space(data, config, param, i) <environment: 0x55f4837403d8> $age function(data, param, i) cpp_ll_age(data, param, i) <environment: 0x55f4837403d8> ///// 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 ... Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.2
Check: tests
Result: ERROR Running ‘testthat.R’ [17s/24s] 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: 0x58a5808> $timing_infections function(data, param, i) cpp_ll_timing_infections(data, param, i) <environment: 0x58a5808> $timing_sampling function(data, param, i) cpp_ll_timing_sampling(data, param, i) <environment: 0x58a5808> $space function(data, config, param, i) cpp_ll_space(data, config, param, i) <environment: 0x58a5808> $age function(data, param, i) cpp_ll_age(data, param, i) <environment: 0x58a5808> ///// 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 ... Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.1.2
Check: examples
Result: ERROR Running examples in 'o2geosocial-Ex.R' failed The error most likely occurred in: > ### 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) Flavor: r-devel-windows-x86_64

Version: 1.1.2
Check: tests
Result: ERROR Running 'testthat.R' [3s] 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: 0x000001ec7e6027d8> $timing_infections function(data, param, i) cpp_ll_timing_infections(data, param, i) <environment: 0x000001ec7e6027d8> $timing_sampling function(data, param, i) cpp_ll_timing_sampling(data, param, i) <environment: 0x000001ec7e6027d8> $space function(data, config, param, i) cpp_ll_space(data, config, param, i) <environment: 0x000001ec7e6027d8> $age function(data, param, i) cpp_ll_age(data, param, i) <environment: 0x000001ec7e6027d8> Flavor: r-devel-windows-x86_64

Version: 1.1.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'o2geosocial.Rmd' using rmarkdown Flavor: r-devel-windows-x86_64