Last updated on 2026-10-17 06:51:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 88.36 | 352.66 | 441.02 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 58.03 | 240.79 | 298.82 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 57.00 | 247.35 | 304.35 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 63.00 | 247.59 | 310.59 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 95.00 | 449.00 | 544.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 85.58 | 342.08 | 427.66 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 74.39 | 345.64 | 420.03 | 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 | 98.00 | 358.00 | 456.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 23.00 | 87.00 | 110.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 119.00 | 528.00 | 647.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [37s/31s]
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)
Traceback:
1: new_expectations <- the$test_expectations > starting_expectationsdispatcher(membership_name, membership_init$to_cc(), model_name, if (snapshot_skipped) { .self$network_to_cc(), TRUE) skip("On CRAN")
2: }FUN(X[[i]], ...)
else if (!new_expectations && skip_on_empty) { skip_empty() 3: }lapply(X = S, FUN = FUN, ...)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 4: }doTryCatch(return(expr), name, parentenv, handler)
}, snapshot_on_cran = function(cnd) { 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 6: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt)
7: 21: tryCatch(expr, error = function(e) {doTryCatch(return(expr), name, parentenv, handler) call <- conditionCall(e)
22: if (!is.null(call)) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (identical(call[[1L]], quote(doTryCatch)))
23: call <- sys.call(-4L)tryCatchList(expr, classes, parentenv, handlers) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") LONG <- 75L24: sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatch(withCallingHandlers({ w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (is.na(w)) if (snapshot_skipped) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } skip("On CRAN") } else prefix <- "Error : " else if (!new_expectations && skip_on_empty) { msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) skip_empty() if (!silent && isTRUE(getOption("show.error.messages"))) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { cat(msg, file = outFile) if (on_cran()) { .Internal(printDeferredWarnings()) skip(paste0("{", e$package, "} is not installed.")) } } invisible(structure(msg, class = "try-error", condition = e))})}, 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,
9: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
25: 10: doWithOneRestart(return(expr), restart)FUN(X[[i]], ...)
26: 11: withOneRestart(expr, restarts[[1L]])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$test_expectations > starting_expectations mc.silent = TRUE) if (snapshot_skipped) {
13: skip("On CRAN")parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, } verbose = (verbosity > 4)) else if (!new_expectations && skip_on_empty) {
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)) end_test = function() {
})18:
eval(code, test_env)28:
test_code(code, parent.frame())19:
eval(code, test_env)29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", {20: sampler_undirected_cov$rNetwork(store = TRUE)withCallingHandlers({ mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, eval(code, test_env) "bernoulli", FALSE, covarList = covarList_undirected) new_expectations <- the$test_expectations > starting_expectations mySBM_sbm$optimize(estimOptions = list(verbosity = 0, if (snapshot_skipped) { plot = FALSE)) skip("On CRAN") } mySBM_sbm$setModel(Q) else if (!new_expectations && skip_on_empty) { net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, skip_empty() covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) } cl <- cls[[Q]]}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, if (on_cran()) { clusterInit = cl, covarList = covarList_undirected) skip(paste0("{", e$package, "} is not installed.")) mySBM_missSBM$doVEM() } expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, snapshot_on_cran = function(cnd) { 0.05) snapshot_skipped <<- TRUE expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), invokeRestart("muffle_cran_snapshot") 0.8)}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)21: doTryCatch(return(expr), name, parentenv, handler) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean),
0.1)22: expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 23: 0.85)tryCatchList(expr, classes, parentenv, handlers) })
24: 30: tryCatch(withCallingHandlers({eval(code, test_env) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations31: if (snapshot_skipped) {eval(code, test_env) skip("On CRAN") }
else if (!new_expectations && skip_on_empty) {32: skip_empty()withCallingHandlers({ } eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))25: }doWithOneRestart(return(expr), restart)
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE26: invokeRestart("muffle_cran_snapshot")withOneRestart(expr, restarts[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)27:
withRestarts(tryCatch(withCallingHandlers({33: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler)
new_expectations <- the$test_expectations > starting_expectations34: if (snapshot_skipped) { skip("On CRAN")tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
else if (!new_expectations && skip_on_empty) {35: skip_empty()tryCatchList(expr, classes, parentenv, handlers) }}, expectation = handle_expectation, packageNotFoundError = function(e) {
36: tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } else if (!new_expectations && skip_on_empty) { skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip(paste0("{", e$package, "} is not installed.")) end_test = function() { } })}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE28: invokeRestart("muffle_cran_snapshot")test_code(code, parent.frame())}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", 37: { sampler_undirected_cov$rNetwork(store = TRUE)doWithOneRestart(return(expr), restart) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData,
"bernoulli", FALSE, covarList = covarList_undirected)38: withOneRestart(expr, restarts[[1L]]) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))39: mySBM_sbm$setModel(Q)withRestarts(tryCatch(withCallingHandlers({ net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, eval(code, test_env) covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) new_expectations <- the$test_expectations > starting_expectations cl <- cls[[Q]] if (snapshot_skipped) { skip("On CRAN") mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, } else if (!new_expectations && skip_on_empty) { clusterInit = cl, covarList = covarList_undirected) skip_empty() mySBM_missSBM$doVEM() } expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { 0.05) skip(paste0("{", e$package, "} is not installed.")) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) } expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE 0.01) invokeRestart("muffle_cran_snapshot") expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.1) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), end_test = function() { 0.1) }) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85)
})40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 30: StopReporter$new())
eval(code, test_env)41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 31: error_call = error_call)eval(code, test_env)
42: 32: FUN(X[[i]], ...)withCallingHandlers({
eval(code, test_env)43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, new_expectations <- the$test_expectations > starting_expectations error_call = error_call) if (snapshot_skipped) {
skip("On CRAN") }44: else if (!new_expectations && skip_on_empty) { skip_empty()doTryCatch(return(expr), name, parentenv, handler)
}45: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))46: }tryCatchList(expr, classes, parentenv, handlers)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE47: tryCatch(code, testthat_abort_reporter = function(cnd) { invokeRestart("muffle_cran_snapshot") cat(conditionMessage(cnd), "\n") NULL}, skip = handle_skip, warning = handle_warning, message = handle_message, }) error = handle_error, interrupt = handle_interrupt)
48: 33: with_reporter(reporters$multi, lapply(test_paths, test_one_file, doTryCatch(return(expr), name, parentenv, handler) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
34: 49: tryCatchOne(expr, names, parentenv, handlers[[1L]])test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 35: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, tryCatchList(expr, classes, parentenv, handlers) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)36:
tryCatch(withCallingHandlers({50: eval(code, test_env)test_files(test_dir = path, test_paths = test_paths, test_package = package, new_expectations <- the$test_expectations > starting_expectations reporter = reporter, load_helpers = load_helpers, env = env, if (snapshot_skipped) { stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, skip("On CRAN") } load_package = load_package, parallel = parallel, shuffle = shuffle) else if (!new_expectations && skip_on_empty) {
skip_empty()51: }test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {52: skip(paste0("{", e$package, "} is not installed."))test_check("missSBM") }
}, snapshot_on_cran = function(cnd) {An irrecoverable exception occurred. R is aborting now ...
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))
Traceback:
1: })dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 2:
FUN(X[[i]], ...) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 3:
lapply(X = S, FUN = FUN, ...)
10: 4: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)
5: 11: lapply(seq_len(cores), inner.do)tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: 6: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, tryCatchList(expr, classes, parentenv, handlers) mc.silent = TRUE)
7:
tryCatch(expr, error = function(e) {13: call <- conditionCall(e) if (!is.null(call)) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, if (identical(call[[1L]], quote(doTryCatch))) verbose = (verbosity > 4)) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)14: prefix <- paste("Error in", dcall, ": ").self$do_with_inits(inits, Q, reinitialization_effort) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]15: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w").self$estim_ascend(reinitialization_effort, changing_effort) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 16: type = "b")private$BMobject$estimate() if (w > LONG)
prefix <- paste0(prefix, "\n ")17: }mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")18: .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {eval(code, test_env) cat(msg, file = outFile)
.Internal(printDeferredWarnings())19: }eval(code, test_env) invisible(structure(msg, class = "try-error", condition = e))
})20:
withCallingHandlers({ 8: eval(code, test_env)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { 9: skip("On CRAN")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
else if (!new_expectations && skip_on_empty) {10: skip_empty()FUN(X[[i]], ...) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {11: if (on_cran()) {lapply(seq_len(cores), inner.do) skip(paste0("{", e$package, "} is not installed."))
}12: }, snapshot_on_cran = function(cnd) {parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, snapshot_skipped <<- TRUE mc.silent = TRUE) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 13: error = handle_error, interrupt = handle_interrupt)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))21:
doTryCatch(return(expr), name, parentenv, handler)
14: 22: .self$do_with_inits(inits, Q, reinitialization_effort)tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: 23: .self$estim_ascend(reinitialization_effort, changing_effort)tryCatchList(expr, classes, parentenv, handlers)
16: 24: private$BMobject$estimate()tryCatch(withCallingHandlers({
eval(code, test_env)17: new_expectations <- the$test_expectations > starting_expectationsmySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) if (snapshot_skipped) {
skip("On CRAN")18: }eval(code, test_env) else if (!new_expectations && skip_on_empty) { skip_empty()
}19: }, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))20: }withCallingHandlers({}, snapshot_on_cran = function(cnd) { eval(code, test_env) snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
else if (!new_expectations && skip_on_empty) {25: skip_empty()doWithOneRestart(return(expr), restart) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {26: if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))withOneRestart(expr, restarts[[1L]]) }
}, snapshot_on_cran = function(cnd) {27: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")withRestarts(tryCatch(withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {21: skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler)
}22: tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()23: tryCatchList(expr, classes, parentenv, handlers) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {24: if (on_cran()) {tryCatch(withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") } else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }}, expectation = handle_expectation, packageNotFoundError = function(e) { end_test = function() { if (on_cran()) { }) skip(paste0("{", e$package, "} is not installed."))
}28: }, snapshot_on_cran = function(cnd) {test_code(code, parent.frame()) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")29: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", error = handle_error, interrupt = handle_interrupt), error = handle_fatal) {
sampler_directed_cov$rNetwork(store = TRUE)25: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, doWithOneRestart(return(expr), restart) "bernoulli", TRUE, covarList = covarList_directed)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 26: plot = FALSE))withOneRestart(expr, restarts[[1L]]) mySBM_sbm$setModel(Q)
net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, 27: covariates = covarList_directed)withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) cls <- net$clustering(1:(2 * Q)) new_expectations <- the$test_expectations > starting_expectations cl <- cls[[Q]] if (snapshot_skipped) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, skip("On CRAN") clusterInit = cl, covarList = covarList_directed) } mySBM_missSBM$doVEM(trace = TRUE) else if (!new_expectations && skip_on_empty) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), skip_empty() 0.1) } expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.8) if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), }}, snapshot_on_cran = function(cnd) { 0.05) snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), invokeRestart("muffle_cran_snapshot") 0.1)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 0.85) end_test = function() { }) })
30: 28: test_code(code, parent.frame())eval(code, test_env)
29: 31: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", eval(code, test_env) {
sampler_directed_cov$rNetwork(store = TRUE)32: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, withCallingHandlers({ "bernoulli", TRUE, covarList = covarList_directed) eval(code, test_env) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, new_expectations <- the$test_expectations > starting_expectations plot = FALSE)) if (snapshot_skipped) { mySBM_sbm$setModel(Q) skip("On CRAN") net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, } covariates = covarList_directed) else if (!new_expectations && skip_on_empty) { cls <- net$clustering(1:(2 * Q)) skip_empty() cl <- cls[[Q]] } mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, }, expectation = handle_expectation, packageNotFoundError = function(e) { clusterInit = cl, covarList = covarList_directed) if (on_cran()) { mySBM_missSBM$doVEM(trace = TRUE) skip(paste0("{", e$package, "} is not installed.")) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), } 0.1)}, snapshot_on_cran = function(cnd) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), snapshot_skipped <<- TRUE 0.8) invokeRestart("muffle_cran_snapshot") expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.05) error = handle_error, interrupt = handle_interrupt) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 33: 0.85)doTryCatch(return(expr), name, parentenv, handler) })
34: 30: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(code, test_env)
35: 31: tryCatchList(expr, classes, parentenv, handlers)eval(code, test_env)
36: 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() 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 snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) error = handle_error, interrupt = handle_interrupt)
37: 33: doWithOneRestart(return(expr), restart)doTryCatch(return(expr), name, parentenv, handler)
38: 34: withOneRestart(expr, restarts[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: 35: withRestarts(tryCatch(withCallingHandlers({tryCatchList(expr, classes, parentenv, handlers) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations36: if (snapshot_skipped) {tryCatch(withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() 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 end_test = function() { invokeRestart("muffle_cran_snapshot") })}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 37: StopReporter$new())doWithOneRestart(return(expr), restart)
41: 38: source_file(path, env = env(env), desc = desc, shuffle = shuffle, withOneRestart(expr, restarts[[1L]]) error_call = error_call)
39: 42: withRestarts(tryCatch(withCallingHandlers({FUN(X[[i]], ...) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations43: if (snapshot_skipped) {lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, skip("On CRAN") error_call = error_call) }
else if (!new_expectations && skip_on_empty) {44: skip_empty()doTryCatch(return(expr), name, parentenv, handler) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {45: if (on_cran()) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}46: }, snapshot_on_cran = function(cnd) {tryCatchList(expr, classes, parentenv, handlers) snapshot_skipped <<- TRUE
47: invokeRestart("muffle_cran_snapshot")tryCatch(code, testthat_abort_reporter = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, cat(conditionMessage(cnd), "\n") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), NULL end_test = function() {}) })
48: 40: with_reporter(reporters$multi, lapply(test_paths, test_one_file, test_code(code = exprs, env = env, reporter = get_reporter() %||% env = env, desc = desc, shuffle = shuffle, error_call = error_call)) StopReporter$new())
49:
test_files_serial(test_dir = test_dir, test_package = test_package, 41: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, source_file(path, env = env(env), desc = desc, shuffle = shuffle, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, error_call = error_call) desc = desc, load_package = load_package, shuffle = shuffle,
42: error_call = error_call)FUN(X[[i]], ...)
50: 43: test_files(test_dir = path, test_paths = test_paths, test_package = package, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, reporter = reporter, load_helpers = load_helpers, env = env, error_call = error_call) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)44:
doTryCatch(return(expr), name, parentenv, handler)51:
test_dir("testthat", package = package, reporter = reporter, 45: ..., load_package = "installed")tryCatchOne(expr, names, parentenv, handlers[[1L]])
52: 46: tryCatchList(expr, classes, parentenv, handlers)test_check("missSBM")
47: An irrecoverable exception occurred. R is aborting now ...
tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$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: 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:
Traceback:
doTryCatch(return(expr), name, parentenv, handler) 1:
dispatcher(membership_name, membership_init$to_cc(), model_name, 22: .self$network_to_cc(), TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: 2: tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)
3: 24: lapply(X = S, FUN = FUN, ...)tryCatch(withCallingHandlers({ eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations 4: if (snapshot_skipped) {doTryCatch(return(expr), name, parentenv, handler) skip("On CRAN") }
else if (!new_expectations && skip_on_empty) { 5: skip_empty()tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { 6: if (on_cran()) {tryCatchList(expr, classes, parentenv, handlers) skip(paste0("{", e$package, "} is not installed."))
} 7: }, snapshot_on_cran = function(cnd) {tryCatch(expr, error = function(e) { snapshot_skipped <<- TRUE call <- conditionCall(e) invokeRestart("muffle_cran_snapshot") if (!is.null(call)) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (identical(call[[1L]], quote(doTryCatch))) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)25: prefix <- paste("Error in", dcall, ": ")doWithOneRestart(return(expr), restart) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]26: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")withOneRestart(expr, restarts[[1L]]) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 27: type = "b")withRestarts(tryCatch(withCallingHandlers({ if (w > LONG) eval(code, test_env) prefix <- paste0(prefix, "\n ") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else prefix <- "Error : " skip("On CRAN") msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) else if (!new_expectations && skip_on_empty) { if (!silent && isTRUE(getOption("show.error.messages"))) { skip_empty() cat(msg, file = outFile) } .Internal(printDeferredWarnings())}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) invisible(structure(msg, class = "try-error", condition = e)) }})}, 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: end_test = function() {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) })
10: 28: FUN(X[[i]], ...)test_code(code, parent.frame())
11: 29: lapply(seq_len(cores), inner.do)test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate",
{12: sampler_undirected_nocov$rNetwork(store = TRUE)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, mc.silent = TRUE) "bernoulli", FALSE)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 13: plot = FALSE))parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) verbose = (verbosity > 4)) cl <- net$clustering(3)[[1]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, 14: clusterInit = cl).self$do_with_inits(inits, Q, reinitialization_effort) mySBM_missSBM$doVEM()
15: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), .self$estim_ascend(reinitialization_effort, changing_effort) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 16: 0.95)private$BMobject$estimate() expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)17: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.95)18: })eval(code, test_env)
30: eval(code, test_env)19:
eval(code, test_env)31:
eval(code, test_env)20:
withCallingHandlers({32: eval(code, test_env)withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty()}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip(paste0("{", e$package, "} is not installed.")) if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, snapshot_on_cran = function(cnd) { 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)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)21:
doTryCatch(return(expr), name, parentenv, handler)33:
doTryCatch(return(expr), name, parentenv, handler)22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
tryCatchList(expr, classes, parentenv, handlers)35:
tryCatchList(expr, classes, parentenv, handlers)24: tryCatch(withCallingHandlers({
eval(code, test_env)36: new_expectations <- the$test_expectations > starting_expectationstryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, snapshot_on_cran = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, snapshot_skipped <<- TRUE error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 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)37:
doWithOneRestart(return(expr), restart)26:
withOneRestart(expr, restarts[[1L]])38:
withOneRestart(expr, restarts[[1L]])27:
withRestarts(tryCatch(withCallingHandlers({39: eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_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 snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { end_test = function() { }) })
28: 40: test_code(code, parent.frame())test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", 41: { sampler_undirected_nocov$rNetwork(store = TRUE)source_file(path, env = env(env), desc = desc, shuffle = shuffle, mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, error_call = error_call) "bernoulli", FALSE)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 42: plot = FALSE))FUN(X[[i]], ...) mySBM_sbm$setModel(3)
net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData)43: cl <- net$clustering(3)[[1]]lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, error_call = error_call) clusterInit = cl)
mySBM_missSBM$doVEM()44: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), doTryCatch(return(expr), name, parentenv, handler) 0.05)
45: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0.95)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 46: 0.01)tryCatchList(expr, classes, parentenv, handlers) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean),
0.05)47: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), tryCatch(code, testthat_abort_reporter = function(cnd) { 0.95) cat(conditionMessage(cnd), "\n") }) NULL})
30: 48: eval(code, test_env)
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 31: env = env, desc = desc, shuffle = shuffle, error_call = error_call))eval(code, test_env)
49: 32: test_files_serial(test_dir = test_dir, test_package = test_package, withCallingHandlers({ test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, eval(code, test_env) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, new_expectations <- the$test_expectations > starting_expectations desc = desc, load_package = load_package, shuffle = shuffle, if (snapshot_skipped) { error_call = error_call) skip("On CRAN")
}50: else if (!new_expectations && skip_on_empty) {test_files(test_dir = path, test_paths = test_paths, test_package = package, skip_empty() reporter = reporter, load_helpers = load_helpers, env = env, } stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }, expectation = handle_expectation, packageNotFoundError = function(e) { load_package = load_package, parallel = parallel, shuffle = shuffle) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))51: }test_dir("testthat", package = package, reporter = reporter, }, snapshot_on_cran = function(cnd) { ..., load_package = "installed") snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")52: test_check("missSBM")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)An irrecoverable exception occurred. R is aborting now ...
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-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, ...)
Traceback:
4: 1: doTryCatch(return(expr), name, parentenv, handler)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 2: FUN(X[[i]], ...)tryCatchList(expr, classes, parentenv, handlers)
3:
lapply(X = S, FUN = FUN, ...) 7:
tryCatch(expr, error = function(e) { 4: call <- conditionCall(e)doTryCatch(return(expr), name, parentenv, handler) if (!is.null(call)) {
5: if (identical(call[[1L]], quote(doTryCatch))) tryCatchOne(expr, names, parentenv, handlers[[1L]]) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") 6: LONG <- 75LtryCatchList(expr, classes, parentenv, handlers) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 7: if (is.na(w)) tryCatch(expr, error = function(e) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], call <- conditionCall(e) type = "b") if (w > LONG) if (!is.null(call)) { prefix <- paste0(prefix, "\n ") if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) else prefix <- "Error : " dcall <- deparse(call, nlines = 1L) msg <- paste0(prefix, conditionMessage(e), "\n") prefix <- paste("Error in", dcall, ": ") .Internal(seterrmessage(msg[1L])) LONG <- 75L if (!silent && isTRUE(getOption("show.error.messages"))) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] cat(msg, file = outFile) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") .Internal(printDeferredWarnings()) if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], invisible(structure(msg, class = "try-error", condition = e))}) type = "b")
if (w > LONG) 8: prefix <- paste0(prefix, "\n ")try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }
else prefix <- "Error : " 9: msg <- paste0(prefix, conditionMessage(e), "\n")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {10: cat(msg, file = outFile)FUN(X[[i]], ...) .Internal(printDeferredWarnings()) }
invisible(structure(msg, class = "try-error", condition = e))11: })lapply(seq_len(cores), inner.do)
8: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE,
mc.silent = TRUE) 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: 10: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, FUN(X[[i]], ...) verbose = (verbosity > 4))
11: 14: lapply(seq_len(cores), inner.do).self$do_with_inits(inits, Q, reinitialization_effort)
12: 15: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, .self$estim_ascend(reinitialization_effort, changing_effort) mc.silent = TRUE)
13: 16: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, private$BMobject$estimate() verbose = (verbosity > 4))
17: 14: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)).self$do_with_inits(inits, Q, reinitialization_effort)
18: 15: eval(code, test_env).self$estim_ascend(reinitialization_effort, changing_effort)
19: 16: eval(code, test_env)private$BMobject$estimate()
20:
withCallingHandlers({17: eval(code, test_env)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {18: skip("On CRAN") }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()19: }eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {20: skip(paste0("{", e$package, "} is not installed."))withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) { skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt) skip_empty()
}21: }, expectation = handle_expectation, packageNotFoundError = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))22: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")23: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt)
24: 21: tryCatch(withCallingHandlers({doTryCatch(return(expr), name, parentenv, handler) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations22: if (snapshot_skipped) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip("On CRAN")
}23: else if (!new_expectations && skip_on_empty) {tryCatchList(expr, classes, parentenv, handlers) skip_empty()
}24: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip_empty()
25: }doWithOneRestart(return(expr), restart)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {26: skip(paste0("{", e$package, "} is not installed."))withOneRestart(expr, restarts[[1L]]) }}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE27: invokeRestart("muffle_cran_snapshot")withRestarts(tryCatch(withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {25: skip("On CRAN") }doWithOneRestart(return(expr), restart) else if (!new_expectations && skip_on_empty) {
skip_empty()26: }withOneRestart(expr, restarts[[1L]])}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {27: skip(paste0("{", e$package, "} is not installed."))withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { invokeRestart("muffle_cran_snapshot") skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), else if (!new_expectations && skip_on_empty) { end_test = function() { skip_empty() }) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {28: if (on_cran()) {test_code(code, parent.frame()) skip(paste0("{", e$package, "} is not installed."))
}29: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUEtest_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", invokeRestart("muffle_cran_snapshot") {}, skip = handle_skip, warning = handle_warning, message = handle_message, sampler_directed_nocov$rNetwork(store = TRUE) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) end_test = function() { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, })
plot = FALSE))28: mySBM_sbm$setModel(3)test_code(code, parent.frame()) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)
cl <- net$clustering(3)[[1]]29: mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", clusterInit = cl) { sampler_directed_nocov$rNetwork(store = TRUE) mySBM_missSBM$doVEM() mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), "bernoulli", TRUE) 0.1) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), plot = FALSE)) 0.95) mySBM_sbm$setModel(3) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) 0.01) cl <- net$clustering(3)[[1]] expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, 0.1) clusterInit = cl) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), mySBM_missSBM$doVEM() 0.2) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.1) 0.95) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }) 0.95)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 30: 0.01)eval(code, test_env) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean),
0.1)31: expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), eval(code, test_env) 0.2)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 32: 0.95)withCallingHandlers({ }) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {30: skip("On CRAN")eval(code, test_env) }
else if (!new_expectations && skip_on_empty) {31: skip_empty()eval(code, test_env) }
32: withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) } new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { skip_empty() } error = handle_error, interrupt = handle_interrupt)
}, expectation = handle_expectation, packageNotFoundError = function(e) {33: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
}34: tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE35: invokeRestart("muffle_cran_snapshot")tryCatchList(expr, classes, parentenv, handlers)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)36:
33: tryCatch(withCallingHandlers({doTryCatch(return(expr), name, parentenv, handler) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations34: if (snapshot_skipped) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip("On CRAN") }
else if (!new_expectations && skip_on_empty) {35: skip_empty()tryCatchList(expr, classes, parentenv, handlers) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {36: if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))tryCatch(withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { invokeRestart("muffle_cran_snapshot") skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal) else if (!new_expectations && skip_on_empty) {
skip_empty()37: }doWithOneRestart(return(expr), restart)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {38: withOneRestart(expr, restarts[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}39: }, snapshot_on_cran = function(cnd) {withRestarts(tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) { skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal) else if (!new_expectations && skip_on_empty) {
skip_empty()37: }doWithOneRestart(return(expr), restart)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {38: skip(paste0("{", e$package, "} is not installed."))withOneRestart(expr, restarts[[1L]]) }
}, snapshot_on_cran = function(cnd) {39: snapshot_skipped <<- TRUEwithRestarts(tryCatch(withCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt), error = handle_fatal), if (snapshot_skipped) { end_test = function() { }) skip("On CRAN")
} else if (!new_expectations && skip_on_empty) {40: skip_empty() }test_code(code = exprs, env = env, reporter = get_reporter() %||% }, expectation = handle_expectation, packageNotFoundError = function(e) { StopReporter$new()) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) }41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, }, snapshot_on_cran = function(cnd) { error_call = error_call) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")42: }, skip = handle_skip, warning = handle_warning, message = handle_message, FUN(X[[i]], ...) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {43: })lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: 40: doTryCatch(return(expr), name, parentenv, handler)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 46: error_call = error_call)tryCatchList(expr, classes, parentenv, handlers)
42: 47: FUN(X[[i]], ...)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")43: NULLlapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, }) error_call = error_call)
44: 48: doTryCatch(return(expr), name, parentenv, handler)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])49:
test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 46: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, tryCatchList(expr, classes, parentenv, handlers) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)47:
tryCatch(code, testthat_abort_reporter = function(cnd) {50: cat(conditionMessage(cnd), "\n")test_files(test_dir = path, test_paths = test_paths, test_package = package, NULL reporter = reporter, load_helpers = load_helpers, env = env, }) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 51: env = env, desc = desc, shuffle = shuffle, error_call = error_call))test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")49:
test_files_serial(test_dir = test_dir, test_package = test_package, 52: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, test_check("missSBM") 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)An irrecoverable exception occurred. R is aborting now ...
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