Last updated on 2026-11-08 18:52:38 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 83.53 | 339.15 | 422.68 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 59.78 | 228.81 | 288.59 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 57.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 239.38 | 303.38 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 417.00 | 508.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | OK | ||||
| r-release-linux-x86_64 | 1.1.0 | 78.58 | 329.18 | 407.76 | OK | |
| r-release-macos-arm64 | 1.1.0 | 17.00 | 92.00 | 109.00 | OK | |
| r-release-macos-x86_64 | 1.1.0 | 59.00 | 456.00 | 515.00 | OK | |
| r-release-windows-x86_64 | 1.1.0 | 101.00 | 348.00 | 449.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 20.00 | 98.00 | 118.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 118.00 | 480.00 | 598.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [34s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missSBM)
>
> test_check("missSBM")
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 3 model(s).
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degreeTested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degree
sampling: dyad new better on connectivity
node
double-standard
block-node new better on mixture
Adjusting Variational EM for Stochastic Block Model
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'node' network-sampling process
Initialization of 1 model(s).
Performing VEM inference
Model with 3 blocks.
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 2 model(s).
Performing VEM inference
Model with 2 blocks.
Model with 1 blocks.
Polishing (node-swap)
Looking for better solutions
Pass 1 Going forward +
Pass 1 Going backward +
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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, nlines = 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))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", { sampler_undirected_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, "bernoulli", FALSE, covarList = covarList_undirected) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85) })
Traceback:
1:
dispatcher(membership_name, membership_init$to_cc(), model_name, 30: .self$network_to_cc(), TRUE)eval(code, test_env)
2: 31: FUN(X[[i]], ...)eval(code, test_env)
3: 32: lapply(X = S, FUN = FUN, ...)withCallingHandlers({
eval(code, test_env) 4: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
skip("On CRAN") 5: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty() 6: }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { 7: skip(paste0("{", e$package, "} is not installed."))tryCatch(expr, error = function(e) { } call <- conditionCall(e)}, snapshot_on_cran = function(cnd) { if (!is.null(call)) { snapshot_skipped <<- TRUE if (identical(call[[1L]], quote(doTryCatch))) invokeRestart("muffle_cran_snapshot") call <- sys.call(-4L)}, skip = handle_skip, warning = handle_warning, message = handle_message, dcall <- deparse(call, nlines = 1L) error = handle_error, interrupt = handle_interrupt) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L33: sm <- strsplit(conditionMessage(e), "\n")[[1L]]doTryCatch(return(expr), name, parentenv, handler) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 34: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatchOne(expr, names, parentenv, handlers[[1L]]) type = "b")
if (w > LONG) 35: prefix <- paste0(prefix, "\n ")tryCatchList(expr, classes, parentenv, handlers) }
else prefix <- "Error : "36: msg <- paste0(prefix, conditionMessage(e), "\n")tryCatch(withCallingHandlers({ .Internal(seterrmessage(msg[1L])) eval(code, test_env) if (!silent && isTRUE(getOption("show.error.messages"))) { new_expectations <- the$test_expectations > starting_expectations cat(msg, file = outFile) if (snapshot_skipped) { .Internal(printDeferredWarnings()) skip("On CRAN") } } invisible(structure(msg, class = "try-error", condition = e)) else if (!new_expectations && skip_on_empty) {}) skip_empty()
} 8: }, expectation = handle_expectation, packageNotFoundError = function(e) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 9: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE10: invokeRestart("muffle_cran_snapshot")FUN(X[[i]], ...)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)11:
lapply(seq_len(cores), inner.do)37:
doWithOneRestart(return(expr), restart)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 38: mc.silent = TRUE)withOneRestart(expr, restarts[[1L]])
13: 39: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, withRestarts(tryCatch(withCallingHandlers({ verbose = (verbosity > 4)) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations14: if (snapshot_skipped) {.self$do_with_inits(inits, Q, reinitialization_effort) skip("On CRAN")
}15: else if (!new_expectations && skip_on_empty) {.self$estim_ascend(reinitialization_effort, changing_effort) skip_empty()
}16: }, expectation = handle_expectation, packageNotFoundError = function(e) {private$BMobject$estimate() if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))17: }mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE18: invokeRestart("muffle_cran_snapshot")eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 19: end_test = function() {eval(code, test_env) })
20: 40: withCallingHandlers({test_code(code = exprs, env = env, reporter = get_reporter() %||% eval(code, test_env) StopReporter$new()) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {41: skip("On CRAN")source_file(path, env = env(env), desc = desc, shuffle = shuffle, } error_call = error_call) else if (!new_expectations && skip_on_empty) {
skip_empty()42: }FUN(X[[i]], ...)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {43: skip(paste0("{", e$package, "} is not installed."))lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } error_call = error_call)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE44: invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])21:
doTryCatch(return(expr), name, parentenv, handler)46:
tryCatchList(expr, classes, parentenv, handlers)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])47:
tryCatch(code, testthat_abort_reporter = function(cnd) {23: cat(conditionMessage(cnd), "\n")tryCatchList(expr, classes, parentenv, handlers) NULL
})24:
tryCatch(withCallingHandlers({48: eval(code, test_env)with_reporter(reporters$multi, lapply(test_paths, test_one_file, new_expectations <- the$test_expectations > starting_expectations env = env, desc = desc, shuffle = shuffle, error_call = error_call)) if (snapshot_skipped) {
skip("On CRAN")49: }test_files_serial(test_dir = test_dir, test_package = test_package, else if (!new_expectations && skip_on_empty) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, skip_empty() env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } desc = desc, load_package = load_package, shuffle = shuffle, }, expectation = handle_expectation, packageNotFoundError = function(e) { error_call = error_call) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
50: }test_files(test_dir = path, test_paths = test_paths, test_package = package, }, snapshot_on_cran = function(cnd) { reporter = reporter, load_helpers = load_helpers, env = env, snapshot_skipped <<- TRUE stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, invokeRestart("muffle_cran_snapshot") load_package = load_package, parallel = parallel, shuffle = shuffle)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)51:
test_dir("testthat", package = package, reporter = reporter, 25: ..., load_package = "installed")doWithOneRestart(return(expr), restart)
52: 26: test_check("missSBM")withOneRestart(expr, restarts[[1L]])
An irrecoverable exception occurred. R is aborting now ...
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", { sampler_undirected_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, "bernoulli", FALSE, covarList = covarList_undirected) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: 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, shuffle = shuffle, error_call = error_call)
50: 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, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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, nlines = 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))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", { sampler_directed_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData,
Traceback:
1: covariates = covarList_directed)dispatcher(membership_name, membership_init$to_cc(), model_name, cls <- net$clustering(1:(2 * Q)) .self$network_to_cc(), TRUE) cl <- cls[[Q]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, 2: clusterInit = cl, covarList = covarList_directed)FUN(X[[i]], ...) mySBM_missSBM$doVEM(trace = TRUE)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) 3: lapply(X = S, FUN = FUN, ...) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.8) 4: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), doTryCatch(return(expr), name, parentenv, handler) 0.05)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 5: 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 0.85)tryCatchOne(expr, names, parentenv, handlers[[1L]]) })
6: tryCatchList(expr, classes, parentenv, handlers)30:
eval(code, test_env) 7: tryCatch(expr, error = function(e) {
call <- conditionCall(e) if (!is.null(call)) {31: eval(code, test_env) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)32: dcall <- deparse(call, nlines = 1L)withCallingHandlers({ eval(code, test_env) prefix <- paste("Error in", dcall, ": ") new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] skip("On CRAN") } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) else if (!new_expectations && skip_on_empty) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") skip_empty() if (w > LONG) } prefix <- paste0(prefix, "\n ")}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) { else prefix <- "Error : " skip(paste0("{", e$package, "} is not installed.")) msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L]))}, snapshot_on_cran = function(cnd) { if (!silent && isTRUE(getOption("show.error.messages"))) { snapshot_skipped <<- TRUE cat(msg, file = outFile) .Internal(printDeferredWarnings()) invokeRestart("muffle_cran_snapshot") } invisible(structure(msg, class = "try-error", condition = e))}, skip = handle_skip, warning = handle_warning, message = handle_message, }) error = handle_error, interrupt = handle_interrupt)
8: 33: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)doTryCatch(return(expr), name, parentenv, handler)
9: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))35:
tryCatchList(expr, classes, parentenv, handlers)10:
FUN(X[[i]], ...)
11: 36: lapply(seq_len(cores), inner.do)tryCatch(withCallingHandlers({ eval(code, test_env)
12: new_expectations <- the$test_expectations > starting_expectationsparallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE) if (snapshot_skipped) {
skip("On CRAN")13: }parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, else if (!new_expectations && skip_on_empty) { verbose = (verbosity > 4)) skip_empty()
}14: .self$do_with_inits(inits, Q, reinitialization_effort)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
15: skip(paste0("{", e$package, "} is not installed.")).self$estim_ascend(reinitialization_effort, changing_effort) }}, snapshot_on_cran = function(cnd) {
16: snapshot_skipped <<- TRUEprivate$BMobject$estimate() invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 17: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: 37: eval(code, test_env)
doWithOneRestart(return(expr), restart)19:
eval(code, test_env)38:
withOneRestart(expr, restarts[[1L]])
20: 39: withCallingHandlers({ eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { else if (!new_expectations && skip_on_empty) { skip_empty() skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, skip = handle_skip, warning = handle_warning, message = handle_message, end_test = function() { error = handle_error, interrupt = handle_interrupt)
})
40: 21: test_code(code = exprs, env = env, reporter = get_reporter() %||% doTryCatch(return(expr), name, parentenv, handler) StopReporter$new())
22: 41: tryCatchOne(expr, names, parentenv, handlers[[1L]])source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)23:
tryCatchList(expr, classes, parentenv, handlers)42:
FUN(X[[i]], ...)
43: 24: tryCatch(withCallingHandlers({lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, eval(code, test_env) error_call = error_call) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {44: skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler) }
else if (!new_expectations && skip_on_empty) {45: skip_empty()tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {46: if (on_cran()) {tryCatchList(expr, classes, parentenv, handlers) skip(paste0("{", e$package, "} is not installed."))
}47: }, snapshot_on_cran = function(cnd) {tryCatch(code, testthat_abort_reporter = function(cnd) { snapshot_skipped <<- TRUE cat(conditionMessage(cnd), "\n") invokeRestart("muffle_cran_snapshot") NULL}, skip = handle_skip, warning = handle_warning, message = handle_message, }) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
48: 25: with_reporter(reporters$multi, lapply(test_paths, test_one_file, doWithOneRestart(return(expr), restart) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
26: 49: withOneRestart(expr, restarts[[1L]])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, 27: desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)50: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {test_files(test_dir = path, test_paths = test_paths, test_package = package, skip("On CRAN") reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } load_package = load_package, parallel = parallel, shuffle = shuffle) else if (!new_expectations && skip_on_empty) {
skip_empty()51: }test_dir("testthat", package = package, reporter = reporter, }, expectation = handle_expectation, packageNotFoundError = function(e) { ..., load_package = "installed") if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
}52: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUEtest_check("missSBM")
invokeRestart("muffle_cran_snapshot")An irrecoverable exception occurred. R is aborting now ...
}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", { sampler_directed_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, covariates = covarList_directed) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_directed) mySBM_missSBM$doVEM(trace = TRUE) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.05) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 0.85) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: 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, shuffle = shuffle, error_call = error_call)
50: 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, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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, nlines = 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))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18:
Traceback:
1: eval(code, test_env)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE)19:
eval(code, test_env) 2: FUN(X[[i]], ...)
3: 20: lapply(X = S, FUN = FUN, ...)withCallingHandlers({
eval(code, test_env) 4: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
skip("On CRAN") 5: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty() 6: }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { 7: skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) {tryCatch(expr, error = function(e) { call <- conditionCall(e) snapshot_skipped <<- TRUE if (!is.null(call)) { invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, if (identical(call[[1L]], quote(doTryCatch))) error = handle_error, interrupt = handle_interrupt) call <- sys.call(-4L)
21: dcall <- deparse(call, nlines = 1L)doTryCatch(return(expr), name, parentenv, handler)
prefix <- paste("Error in", dcall, ": ")22: LONG <- 75LtryCatchOne(expr, names, parentenv, handlers[[1L]]) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")23: if (is.na(w)) tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")24: if (w > LONG) tryCatch(withCallingHandlers({ prefix <- paste0(prefix, "\n ") eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else prefix <- "Error : " skip("On CRAN") msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) else if (!new_expectations && skip_on_empty) { if (!silent && isTRUE(getOption("show.error.messages"))) { skip_empty() cat(msg, file = outFile) } .Internal(printDeferredWarnings())}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) { invisible(structure(msg, class = "try-error", condition = e)) skip(paste0("{", e$package, "} is not installed."))}) }
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE 8: invokeRestart("muffle_cran_snapshot")try(lapply(X = S, FUN = FUN, ...), silent = TRUE)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))25:
doWithOneRestart(return(expr), restart)10:
FUN(X[[i]], ...)26:
withOneRestart(expr, restarts[[1L]])11:
lapply(seq_len(cores), inner.do)27:
withRestarts(tryCatch(withCallingHandlers({12: eval(code, test_env)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, new_expectations <- the$test_expectations > starting_expectations mc.silent = TRUE) if (snapshot_skipped) {
skip("On CRAN")13: }parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, else if (!new_expectations && skip_on_empty) { verbose = (verbosity > 4)) skip_empty()
}14: }, expectation = handle_expectation, packageNotFoundError = function(e) {.self$do_with_inits(inits, Q, reinitialization_effort) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))15: }.self$estim_ascend(reinitialization_effort, changing_effort)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE16: invokeRestart("muffle_cran_snapshot")private$BMobject$estimate()}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 17: end_test = function() {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) })
18: 28: eval(code, test_env)test_code(code, parent.frame())
19: 29: eval(code, test_env)test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate",
{20: sampler_undirected_nocov$rNetwork(store = TRUE)withCallingHandlers({ mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, eval(code, test_env) "bernoulli", FALSE) new_expectations <- the$test_expectations > starting_expectations mySBM_sbm$optimize(estimOptions = list(verbosity = 0, if (snapshot_skipped) { plot = FALSE)) skip("On CRAN") mySBM_sbm$setModel(3) } net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) else if (!new_expectations && skip_on_empty) { cl <- net$clustering(3)[[1]] skip_empty() mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, } clusterInit = cl)}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_missSBM$doVEM() if (on_cran()) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), skip(paste0("{", e$package, "} is not installed.")) 0.05) } expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }, snapshot_on_cran = function(cnd) { 0.95) snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), invokeRestart("muffle_cran_snapshot") 0.01)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), error = handle_error, interrupt = handle_interrupt) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 21: 0.95)doTryCatch(return(expr), name, parentenv, handler) })
22: 30: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(code, test_env)
23: 31: tryCatchList(expr, classes, parentenv, handlers)eval(code, test_env)
24: 32: tryCatch(withCallingHandlers({withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { }}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")25: }, skip = handle_skip, warning = handle_warning, message = handle_message, doWithOneRestart(return(expr), restart) error = handle_error, interrupt = handle_interrupt)
26: 33: withOneRestart(expr, restarts[[1L]])doTryCatch(return(expr), name, parentenv, handler)
27: 34: withRestarts(tryCatch(withCallingHandlers({tryCatchOne(expr, names, parentenv, handlers[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {35: skip("On CRAN")tryCatchList(expr, classes, parentenv, handlers) }
36: else if (!new_expectations && skip_on_empty) {tryCatch(withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip(paste0("{", e$package, "} is not installed.")) end_test = function() { } })}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 28: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)test_code(code, parent.frame())
37: 29: doWithOneRestart(return(expr), restart)test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate",
{38: sampler_undirected_nocov$rNetwork(store = TRUE)withOneRestart(expr, restarts[[1L]]) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData,
"bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 39: plot = FALSE))withRestarts(tryCatch(withCallingHandlers({ mySBM_sbm$setModel(3) eval(code, test_env) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) new_expectations <- the$test_expectations > starting_expectations cl <- net$clustering(3)[[1]] if (snapshot_skipped) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, skip("On CRAN") clusterInit = cl) } mySBM_missSBM$doVEM() else if (!new_expectations && skip_on_empty) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), skip_empty() 0.05) } expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.95) if (on_cran()) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), skip(paste0("{", e$package, "} is not installed.")) 0.01) } expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), }, snapshot_on_cran = function(cnd) { 0.05) snapshot_skipped <<- TRUE expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), invokeRestart("muffle_cran_snapshot") 0.95)}, skip = handle_skip, warning = handle_warning, message = handle_message, }) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {30: })eval(code, test_env)
40: 31: test_code(code = exprs, env = env, reporter = get_reporter() %||% eval(code, test_env) StopReporter$new())
32: 41: withCallingHandlers({source_file(path, env = env(env), desc = desc, shuffle = shuffle, eval(code, test_env) error_call = error_call) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {42: skip("On CRAN")FUN(X[[i]], ...) }
else if (!new_expectations && skip_on_empty) {43: skip_empty()lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } error_call = error_call)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {44: skip(paste0("{", e$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) {45: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 46: error = handle_error, interrupt = handle_interrupt)tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n")33: NULLdoTryCatch(return(expr), name, parentenv, handler)})
34: 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))tryCatchOne(expr, names, parentenv, handlers[[1L]])
49:
35: test_files_serial(test_dir = test_dir, test_package = test_package, tryCatchList(expr, classes, parentenv, handlers) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 36: desc = desc, load_package = load_package, shuffle = shuffle, tryCatch(withCallingHandlers({ error_call = error_call) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations50: if (snapshot_skipped) {test_files(test_dir = path, test_paths = test_paths, test_package = package, skip("On CRAN") reporter = reporter, load_helpers = load_helpers, env = env, } stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, else if (!new_expectations && skip_on_empty) { load_package = load_package, parallel = parallel, shuffle = shuffle) skip_empty()
}}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {51: skip(paste0("{", e$package, "} is not installed."))test_dir("testthat", package = package, reporter = reporter, } ..., load_package = "installed")}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE52: invokeRestart("muffle_cran_snapshot")test_check("missSBM")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
An irrecoverable exception occurred. R is aborting now ...
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: 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, shuffle = shuffle, error_call = error_call)
50: 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, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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, nlines = 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))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", { sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
Traceback:
0.1) 1: dispatcher(membership_name, membership_init$to_cc(), model_name, expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), .self$network_to_cc(), TRUE) 0.95)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 2: 0.01)FUN(X[[i]], ...) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean),
3: 0.1)lapply(X = S, FUN = FUN, ...) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam),
0.2) 4: expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), doTryCatch(return(expr), name, parentenv, handler) 0.95)
}) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 30: tryCatchList(expr, classes, parentenv, handlers)eval(code, test_env)
7: 31: tryCatch(expr, error = function(e) { call <- conditionCall(e)eval(code, test_env) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 32: call <- sys.call(-4L)withCallingHandlers({ eval(code, test_env) dcall <- deparse(call, nlines = 1L) new_expectations <- the$test_expectations > starting_expectations prefix <- paste("Error in", dcall, ": ") if (snapshot_skipped) { LONG <- 75L skip("On CRAN") sm <- strsplit(conditionMessage(e), "\n")[[1L]] } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") else if (!new_expectations && skip_on_empty) { if (is.na(w)) skip_empty() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b")}, expectation = handle_expectation, packageNotFoundError = function(e) { if (w > LONG) if (on_cran()) { prefix <- paste0(prefix, "\n ") skip(paste0("{", e$package, "} is not installed.")) } } else prefix <- "Error : "}, snapshot_on_cran = function(cnd) { msg <- paste0(prefix, conditionMessage(e), "\n") snapshot_skipped <<- TRUE .Internal(seterrmessage(msg[1L])) invokeRestart("muffle_cran_snapshot") if (!silent && isTRUE(getOption("show.error.messages"))) {}, skip = handle_skip, warning = handle_warning, message = handle_message, cat(msg, file = outFile) .Internal(printDeferredWarnings()) error = handle_error, interrupt = handle_interrupt) } invisible(structure(msg, class = "try-error", condition = e))
})33:
doTryCatch(return(expr), name, parentenv, handler) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
34: 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
35: 10: tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)
36: 11: tryCatch(withCallingHandlers({ eval(code, test_env)lapply(seq_len(cores), inner.do) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN")12: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, else if (!new_expectations && skip_on_empty) { mc.silent = TRUE) skip_empty() }
}, expectation = handle_expectation, packageNotFoundError = function(e) {13: if (on_cran()) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, skip(paste0("{", e$package, "} is not installed.")) verbose = (verbosity > 4)) }
}, snapshot_on_cran = function(cnd) {14: snapshot_skipped <<- TRUE.self$do_with_inits(inits, Q, reinitialization_effort)
invokeRestart("muffle_cran_snapshot")15: }, skip = handle_skip, warning = handle_warning, message = handle_message, .self$estim_ascend(reinitialization_effort, changing_effort) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
16: 37: private$BMobject$estimate()doWithOneRestart(return(expr), restart)
17: 38: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))withOneRestart(expr, restarts[[1L]])
18: 39: eval(code, test_env)
withRestarts(tryCatch(withCallingHandlers({19: eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {20: skip("On CRAN")withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$test_expectations > starting_expectations skip_empty() } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, snapshot_on_cran = function(cnd) { end_test = function() { snapshot_skipped <<- TRUE }) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 40: test_code(code = exprs, env = env, reporter = get_reporter() %||% error = handle_error, interrupt = handle_interrupt) StopReporter$new())
21: 41: doTryCatch(return(expr), name, parentenv, handler)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
22: error_call = error_call)tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: 23: FUN(X[[i]], ...)tryCatchList(expr, classes, parentenv, handlers)
43: 24: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, tryCatch(withCallingHandlers({ error_call = error_call) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations44: if (snapshot_skipped) {doTryCatch(return(expr), name, parentenv, handler) skip("On CRAN")
}45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) { skip_empty()
}46: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
}47: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUEtryCatch(code, testthat_abort_reporter = function(cnd) { invokeRestart("muffle_cran_snapshot") cat(conditionMessage(cnd), "\n") NULL}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)})
25: 48: doWithOneRestart(return(expr), restart)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))26:
withOneRestart(expr, restarts[[1L]])49:
test_files_serial(test_dir = test_dir, test_package = test_package, 27: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, withRestarts(tryCatch(withCallingHandlers({ env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, eval(code, test_env) desc = desc, load_package = load_package, shuffle = shuffle, new_expectations <- the$test_expectations > starting_expectations error_call = error_call) if (snapshot_skipped) {
skip("On CRAN")50: }test_files(test_dir = path, test_paths = test_paths, test_package = package, else if (!new_expectations && skip_on_empty) { reporter = reporter, load_helpers = load_helpers, env = env, skip_empty() stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } load_package = load_package, parallel = parallel, shuffle = shuffle)
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {51: skip(paste0("{", e$package, "} is not installed."))test_dir("testthat", package = package, reporter = reporter, } ..., load_package = "installed")}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE52: invokeRestart("muffle_cran_snapshot")test_check("missSBM")
}, skip = handle_skip, warning = handle_warning, message = handle_message, An irrecoverable exception occurred. R is aborting now ...
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", { sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.2) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: 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, shuffle = shuffle, error_call = error_call)
50: 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, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-44.R
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-explore-block-count.R:4:3',
'test-missSBM_collection-degenerate.R:80:3',
'test-missSBM_collection-estimate_chain.R:64:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-sbm-bernoulli-with-covariates.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-with-covariates.R:46:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:46:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:44:3'): SimpleSBM_fit 'Bernoulli' model, directed, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:44:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64