Last updated on 2026-10-26 13:53:12 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 82.72 | 340.58 | 423.30 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 58.23 | 230.24 | 288.47 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 59.00 | 271.80 | 330.80 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 62.00 | 241.02 | 303.02 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 417.00 | 508.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 87.75 | 330.28 | 418.03 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 81.31 | 327.81 | 409.12 | 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 | 96.00 | 347.00 | 443.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | ERROR | ||||
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 117.00 | 477.00 | 594.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [38s/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$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
Traceback:
14: 1: .self$do_with_inits(inits, Q, reinitialization_effort)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE)15:
.self$estim_ascend(reinitialization_effort, changing_effort) 2:
FUN(X[[i]], ...)16:
private$BMobject$estimate() 3:
lapply(X = S, FUN = FUN, ...)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) 4:
doTryCatch(return(expr), name, parentenv, handler)18:
eval(code, test_env) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])19:
eval(code, test_env) 6:
tryCatchList(expr, classes, parentenv, handlers)20:
withCallingHandlers({ 7: eval(code, test_env)tryCatch(expr, error = function(e) { new_expectations <- the$test_expectations > starting_expectations call <- conditionCall(e) if (snapshot_skipped) { if (!is.null(call)) { skip("On CRAN") if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) else if (!new_expectations && skip_on_empty) { dcall <- deparse(call, nlines = 1L) skip_empty() prefix <- paste("Error in", dcall, ": ") } LONG <- 75L}, expectation = handle_expectation, packageNotFoundError = function(e) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (on_cran()) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") skip(paste0("{", e$package, "} is not installed.")) if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }, snapshot_on_cran = function(cnd) { type = "b") snapshot_skipped <<- TRUE if (w > LONG) invokeRestart("muffle_cran_snapshot") prefix <- paste0(prefix, "\n ")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")21: .Internal(seterrmessage(msg[1L]))doTryCatch(return(expr), name, parentenv, handler) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)22: .Internal(printDeferredWarnings())tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
invisible(structure(msg, class = "try-error", condition = e))23: })tryCatchList(expr, classes, parentenv, handlers)
8: 24: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatch(withCallingHandlers({
eval(code, test_env) 9: new_expectations <- the$test_expectations > starting_expectationssendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (snapshot_skipped) {
skip("On CRAN")10: }FUN(X[[i]], ...) else if (!new_expectations && skip_on_empty) {
skip_empty()11: }lapply(seq_len(cores), inner.do)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {12: skip(paste0("{", e$package, "} is not installed."))parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, } mc.silent = TRUE)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE13: invokeRestart("muffle_cran_snapshot")parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, }, skip = handle_skip, warning = handle_warning, message = handle_message, verbose = (verbosity > 4)) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
14: 25: .self$do_with_inits(inits, Q, reinitialization_effort)doWithOneRestart(return(expr), restart)
15: 26: .self$estim_ascend(reinitialization_effort, changing_effort)withOneRestart(expr, restarts[[1L]])
16: 27: private$BMobject$estimate()withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)17: new_expectations <- the$test_expectations > starting_expectationsmySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) if (snapshot_skipped) {
skip("On CRAN")18: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()19: }eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {20: skip(paste0("{", e$package, "} is not installed."))withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { 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) {test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", snapshot_skipped <<- TRUE { invokeRestart("muffle_cran_snapshot") sampler_undirected_cov$rNetwork(store = TRUE)}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, error = handle_error, interrupt = handle_interrupt) "bernoulli", FALSE, covarList = covarList_undirected)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 21: plot = FALSE))doTryCatch(return(expr), name, parentenv, handler) mySBM_sbm$setModel(Q)
net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, 22: covariates = covarList_undirected)tryCatchOne(expr, names, parentenv, handlers[[1L]]) cls <- net$clustering(1:(2 * Q))
cl <- cls[[Q]]23: mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, tryCatchList(expr, classes, parentenv, handlers) clusterInit = cl, covarList = covarList_undirected)
mySBM_missSBM$doVEM()24: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), tryCatch(withCallingHandlers({ 0.05) eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { 0.8) skip("On CRAN") expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), } 0.01) else if (!new_expectations && skip_on_empty) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), skip_empty() 0.1) } expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.1) if (on_cran()) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), skip(paste0("{", e$package, "} is not installed.")) 0.85) } })}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE30: 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)31:
eval(code, test_env)25:
doWithOneRestart(return(expr), restart)32:
withCallingHandlers({26: eval(code, test_env)withOneRestart(expr, restarts[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {27: skip("On CRAN")withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$test_expectations > starting_expectations skip_empty() if (snapshot_skipped) { } skip("On CRAN")}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) { else if (!new_expectations && skip_on_empty) { skip(paste0("{", e$package, "} is not installed.")) skip_empty() } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE33: 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), error = handle_fatal), 34: end_test = function() {tryCatchOne(expr, names, parentenv, handlers[[1L]]) })
35: 28: tryCatchList(expr, classes, parentenv, handlers)test_code(code, parent.frame())
36: 29: tryCatch(withCallingHandlers({test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", eval(code, test_env) { new_expectations <- the$test_expectations > starting_expectations sampler_undirected_cov$rNetwork(store = TRUE) if (snapshot_skipped) { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, skip("On CRAN") "bernoulli", FALSE, covarList = covarList_undirected) } mySBM_sbm$optimize(estimOptions = list(verbosity = 0, else if (!new_expectations && skip_on_empty) { plot = FALSE)) skip_empty() mySBM_sbm$setModel(Q) } net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, }, expectation = handle_expectation, packageNotFoundError = function(e) { covariates = covarList_undirected) if (on_cran()) { cls <- net$clustering(1:(2 * Q)) skip(paste0("{", e$package, "} is not installed.")) cl <- cls[[Q]] } mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, }, snapshot_on_cran = function(cnd) { clusterInit = cl, covarList = covarList_undirected) snapshot_skipped <<- TRUE mySBM_missSBM$doVEM() invokeRestart("muffle_cran_snapshot") expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.05) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.8)37: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), doWithOneRestart(return(expr), restart) 0.01)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 38: 0.1)withOneRestart(expr, restarts[[1L]]) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam),
0.1)39: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), withRestarts(tryCatch(withCallingHandlers({ 0.85) eval(code, test_env) }) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {30: skip("On CRAN")eval(code, test_env) }
else if (!new_expectations && skip_on_empty) {31: skip_empty()eval(code, test_env) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {32: if (on_cran()) {withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip_empty() end_test = function() { } })}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {40: skip(paste0("{", e$package, "} is not installed."))test_code(code = exprs, env = env, reporter = get_reporter() %||% } StopReporter$new())}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE41: invokeRestart("muffle_cran_snapshot")source_file(path, env = env(env), desc = desc, shuffle = shuffle, }, skip = handle_skip, warning = handle_warning, message = handle_message, error_call = error_call) error = handle_error, interrupt = handle_interrupt)
42: 33: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)
43: 34: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, tryCatchOne(expr, names, parentenv, handlers[[1L]]) error_call = error_call)
35: 44: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
36: 45: tryCatch(withCallingHandlers({tryCatchOne(expr, names, parentenv, handlers[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations46: if (snapshot_skipped) {tryCatchList(expr, classes, parentenv, handlers) skip("On CRAN")
}47: else if (!new_expectations && skip_on_empty) {tryCatch(code, testthat_abort_reporter = function(cnd) { skip_empty() cat(conditionMessage(cnd), "\n") } NULL}, expectation = handle_expectation, packageNotFoundError = function(e) {}) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))48: }with_reporter(reporters$multi, lapply(test_paths, test_one_file, }, snapshot_on_cran = function(cnd) { env = env, desc = desc, shuffle = shuffle, error_call = error_call)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")49: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_files_serial(test_dir = test_dir, test_package = test_package, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 37: desc = desc, load_package = load_package, shuffle = shuffle, doWithOneRestart(return(expr), restart) error_call = error_call)
50: 38: test_files(test_dir = path, test_paths = test_paths, test_package = package, withOneRestart(expr, restarts[[1L]]) reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 39: load_package = load_package, parallel = parallel, shuffle = shuffle)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)51: new_expectations <- the$test_expectations > starting_expectationstest_dir("testthat", package = package, reporter = reporter, if (snapshot_skipped) { ..., load_package = "installed") skip("On CRAN")
}52: else if (!new_expectations && skip_on_empty) {test_check("missSBM") skip_empty()
}An irrecoverable exception occurred. R is aborting now ...
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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$networkData, covariates = covarList_directed) cls <- net$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)
Traceback:
new_expectations <- the$test_expectations > starting_expectations 1: if (snapshot_skipped) {dispatcher(membership_name, membership_init$to_cc(), model_name, skip("On CRAN") .self$network_to_cc(), TRUE) }
else if (!new_expectations && skip_on_empty) { skip_empty() 2: }FUN(X[[i]], ...)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { 3: skip(paste0("{", e$package, "} is not installed."))lapply(X = S, FUN = FUN, ...) }
}, snapshot_on_cran = function(cnd) { 4: snapshot_skipped <<- TRUEdoTryCatch(return(expr), name, parentenv, handler) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 5: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)tryCatchOne(expr, names, parentenv, handlers[[1L]])
37: 6: doWithOneRestart(return(expr), restart)
tryCatchList(expr, classes, parentenv, handlers)38:
withOneRestart(expr, restarts[[1L]]) 7:
39: tryCatch(expr, error = function(e) {withRestarts(tryCatch(withCallingHandlers({ call <- conditionCall(e) eval(code, test_env) if (!is.null(call)) { new_expectations <- the$test_expectations > starting_expectations if (identical(call[[1L]], quote(doTryCatch))) if (snapshot_skipped) { call <- sys.call(-4L) skip("On CRAN") } dcall <- deparse(call, nlines = 1L) else if (!new_expectations && skip_on_empty) { prefix <- paste("Error in", dcall, ": ") skip_empty() LONG <- 75L } sm <- strsplit(conditionMessage(e), "\n")[[1L]]}, expectation = handle_expectation, packageNotFoundError = function(e) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (on_cran()) { if (is.na(w)) skip(paste0("{", e$package, "} is not installed.")) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b")}, snapshot_on_cran = function(cnd) { if (w > LONG) snapshot_skipped <<- TRUE prefix <- paste0(prefix, "\n ") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else prefix <- "Error : " error = handle_error, interrupt = handle_interrupt), error = handle_fatal), msg <- paste0(prefix, conditionMessage(e), "\n") end_test = function() { .Internal(seterrmessage(msg[1L])) })
if (!silent && isTRUE(getOption("show.error.messages"))) {40: cat(msg, file = outFile)test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) .Internal(printDeferredWarnings())
41: }source_file(path, env = env(env), desc = desc, shuffle = shuffle, invisible(structure(msg, class = "try-error", condition = e)) error_call = error_call)})
42: 8: FUN(X[[i]], ...)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
43: 9: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) error_call = error_call)
10: 44: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)
11: 45: lapply(seq_len(cores), inner.do)tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: 46: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, tryCatchList(expr, classes, parentenv, handlers) mc.silent = TRUE)
47:
tryCatch(code, testthat_abort_reporter = function(cnd) {13: cat(conditionMessage(cnd), "\n")parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, NULL verbose = (verbosity > 4))})
14: 48: .self$do_with_inits(inits, Q, reinitialization_effort)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))15:
.self$estim_ascend(reinitialization_effort, changing_effort)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 16: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, private$BMobject$estimate() env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 18: reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, eval(code, test_env) load_package = load_package, parallel = parallel, shuffle = shuffle)
51: 19: test_dir("testthat", package = package, reporter = reporter, eval(code, test_env) ..., load_package = "installed")
20: 52: withCallingHandlers({test_check("missSBM") eval(code, test_env)
An irrecoverable exception occurred. R is aborting now ...
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$networkData, covariates = covarList_directed) cls <- net$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: 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."))
Traceback:
1: }dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)}, 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), 2: end_test = function() {FUN(X[[i]], ...) })
3: 28: lapply(X = S, FUN = FUN, ...)test_code(code, parent.frame())
29: 4: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", doTryCatch(return(expr), name, parentenv, handler) {
sampler_undirected_nocov$rNetwork(store = TRUE) 5: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) 6: mySBM_sbm$setModel(3)tryCatchList(expr, classes, parentenv, handlers)
net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) 7: tryCatch(expr, error = function(e) { cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, call <- conditionCall(e) clusterInit = cl) mySBM_missSBM$doVEM() if (!is.null(call)) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) 0.05) dcall <- deparse(call, nlines = 1L) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), prefix <- paste("Error in", dcall, ": ") LONG <- 75L 0.95) sm <- strsplit(conditionMessage(e), "\n")[[1L]] expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), if (is.na(w)) 0.05) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), type = "b") if (w > LONG) 0.95) prefix <- paste0(prefix, "\n ") })
}30: else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")eval(code, test_env) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)31: .Internal(printDeferredWarnings())eval(code, test_env) } invisible(structure(msg, class = "try-error", condition = e))
})32:
8: withCallingHandlers({try(lapply(X = S, FUN = FUN, ...), silent = TRUE) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN") 9: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) else if (!new_expectations && skip_on_empty) {
skip_empty()10: FUN(X[[i]], ...) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {11: if (on_cran()) {lapply(seq_len(cores), inner.do)
skip(paste0("{", e$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")13: }, skip = handle_skip, warning = handle_warning, message = handle_message, parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4)) error = handle_error, interrupt = handle_interrupt)
33: 14: doTryCatch(return(expr), name, parentenv, handler)
.self$do_with_inits(inits, Q, reinitialization_effort)34:
15: tryCatchOne(expr, names, parentenv, handlers[[1L]]).self$estim_ascend(reinitialization_effort, changing_effort)
35:
tryCatchList(expr, classes, parentenv, handlers)16:
36: private$BMobject$estimate()tryCatch(withCallingHandlers({
17: eval(code, test_env)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN")18: eval(code, test_env) }
19: else if (!new_expectations && skip_on_empty) { skip_empty()eval(code, test_env) }
20: withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { }}, snapshot_on_cran = function(cnd) { skip("On CRAN") } snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) { skip_empty() }}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {37: doWithOneRestart(return(expr), restart) skip(paste0("{", e$package, "} is not installed.")) }
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE38: invokeRestart("muffle_cran_snapshot")withOneRestart(expr, restarts[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)
39: withRestarts(tryCatch(withCallingHandlers({21: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler)
22: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {tryCatchOne(expr, names, parentenv, handlers[[1L]])
skip("On CRAN")23: tryCatchList(expr, classes, parentenv, handlers) } else if (!new_expectations && skip_on_empty) {
24: skip_empty() }tryCatch(withCallingHandlers({ eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) } skip("On CRAN")}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) { skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }}, expectation = handle_expectation, packageNotFoundError = function(e) { end_test = function() { }) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))40: }test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
42: 25: doWithOneRestart(return(expr), restart)FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 26: error_call = error_call)withOneRestart(expr, restarts[[1L]])
44: doTryCatch(return(expr), name, parentenv, handler)
27: withRestarts(tryCatch(withCallingHandlers({45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) eval(code, test_env)
46: new_expectations <- the$test_expectations > starting_expectationstryCatchList(expr, classes, parentenv, handlers)
if (snapshot_skipped) { skip("On CRAN")47: tryCatch(code, testthat_abort_reporter = function(cnd) { } else if (!new_expectations && skip_on_empty) { cat(conditionMessage(cnd), "\n") NULL skip_empty() }})
}, expectation = handle_expectation, packageNotFoundError = function(e) {48: if (on_cran()) {with_reporter(reporters$multi, lapply(test_paths, test_one_file, skip(paste0("{", e$package, "} is not installed.")) env = env, desc = desc, shuffle = shuffle, error_call = error_call)) }
}, snapshot_on_cran = function(cnd) {49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, snapshot_skipped <<- TRUE env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error_call = error_call)
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, end_test = function() { reporter = reporter, load_helpers = load_helpers, env = env, }) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
28: load_package = load_package, parallel = parallel, shuffle = shuffle)
test_code(code, parent.frame())
51: test_dir("testthat", package = package, reporter = reporter, 29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", ..., load_package = "installed") { sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData,
52: "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))test_check("missSBM") mySBM_sbm$setModel(3)
An irrecoverable exception occurred. R is aborting now ...
net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$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-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)
Traceback:
1:
dispatcher(membership_name, membership_init$to_cc(), model_name, 25: .self$network_to_cc(), TRUE)doWithOneRestart(return(expr), restart)
2: 26: FUN(X[[i]], ...)withOneRestart(expr, restarts[[1L]])
3: 27: lapply(X = S, FUN = FUN, ...)withRestarts(tryCatch(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)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) snapshot_skipped <<- TRUE dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") invokeRestart("muffle_cran_snapshot") LONG <- 75L}, skip = handle_skip, warning = handle_warning, message = handle_message, sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), if (is.na(w)) end_test = function() { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }) type = "b")
if (w > LONG) 28: prefix <- paste0(prefix, "\n ")test_code(code, parent.frame()) }
else prefix <- "Error : "29: msg <- paste0(prefix, conditionMessage(e), "\n")test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", .Internal(seterrmessage(msg[1L])) { if (!silent && isTRUE(getOption("show.error.messages"))) { sampler_directed_nocov$rNetwork(store = TRUE) cat(msg, file = outFile) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, .Internal(printDeferredWarnings()) "bernoulli", TRUE) } mySBM_sbm$optimize(estimOptions = list(verbosity = 0, invisible(structure(msg, class = "try-error", condition = e)) plot = FALSE))}) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)
cl <- net$clustering(3)[[1]] 8: mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) clusterInit = cl)
mySBM_missSBM$doVEM() 9: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 10: 0.95)FUN(X[[i]], ...) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)11: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), lapply(seq_len(cores), inner.do) 0.1)
expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 12: 0.2)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), mc.silent = TRUE) 0.95)
})13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 30: verbose = (verbosity > 4))eval(code, test_env)
31: 14: eval(code, test_env).self$do_with_inits(inits, Q, reinitialization_effort)
32: withCallingHandlers({15: eval(code, test_env).self$estim_ascend(reinitialization_effort, changing_effort) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {16: skip("On CRAN") }private$BMobject$estimate() else if (!new_expectations && skip_on_empty) {
skip_empty()17: }mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {18: skip(paste0("{", e$package, "} is not installed."))eval(code, test_env) }
}, snapshot_on_cran = function(cnd) {19: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 20: error = handle_error, interrupt = handle_interrupt)withCallingHandlers({
eval(code, test_env)33: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
skip("On CRAN")34: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()35: }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {36: 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) else if (!new_expectations && skip_on_empty) {
skip_empty()21: }doTryCatch(return(expr), name, parentenv, handler)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {22: skip(paste0("{", e$package, "} is not installed."))tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, snapshot_on_cran = function(cnd) {23: snapshot_skipped <<- TRUEtryCatchList(expr, classes, parentenv, handlers)
invokeRestart("muffle_cran_snapshot")24: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatch(withCallingHandlers({ error = handle_error, interrupt = handle_interrupt), error = handle_fatal) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {37: skip("On CRAN")doWithOneRestart(return(expr), restart) }
else if (!new_expectations && skip_on_empty) {38: skip_empty()withOneRestart(expr, restarts[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {39: if (on_cran()) {withRestarts(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") }}, 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: }, expectation = handle_expectation, packageNotFoundError = function(e) {doWithOneRestart(return(expr), restart) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))26: }withOneRestart(expr, restarts[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE27: invokeRestart("muffle_cran_snapshot")withRestarts(tryCatch(withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), new_expectations <- the$test_expectations > starting_expectations end_test = function() { if (snapshot_skipped) { }) skip("On CRAN")
}40: else if (!new_expectations && skip_on_empty) {test_code(code = exprs, env = env, reporter = get_reporter() %||% skip_empty() StopReporter$new()) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {41: if (on_cran()) {source_file(path, env = env(env), desc = desc, shuffle = shuffle, skip(paste0("{", e$package, "} is not installed.")) error_call = error_call) }
}, snapshot_on_cran = function(cnd) {42: snapshot_skipped <<- TRUEFUN(X[[i]], ...) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 43: end_test = function() {lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, }) error_call = error_call)
28: 44: test_code(code, parent.frame())doTryCatch(return(expr), name, parentenv, handler)
29:
test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", 45: {tryCatchOne(expr, names, parentenv, handlers[[1L]]) sampler_directed_nocov$rNetwork(store = TRUE)
mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, 46: "bernoulli", TRUE)tryCatchList(expr, classes, parentenv, handlers) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))47: mySBM_sbm$setModel(3)tryCatch(code, testthat_abort_reporter = function(cnd) { net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cat(conditionMessage(cnd), "\n") cl <- net$clustering(3)[[1]] NULL 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$mean), 48: 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), with_reporter(reporters$multi, lapply(test_paths, test_one_file, 0.95) env = env, desc = desc, shuffle = shuffle, error_call = error_call)) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)49: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), test_files_serial(test_dir = test_dir, test_package = test_package, 0.1) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 0.2) desc = desc, load_package = load_package, shuffle = shuffle, expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), error_call = error_call) 0.95)
})50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 30: reporter = reporter, load_helpers = load_helpers, env = env, eval(code, test_env) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)31:
eval(code, test_env)51:
test_dir("testthat", package = package, reporter = reporter, 32: ..., load_package = "installed")withCallingHandlers({
eval(code, test_env)52: new_expectations <- the$test_expectations > starting_expectationstest_check("missSBM") if (snapshot_skipped) {
skip("On CRAN")An irrecoverable exception occurred. R is aborting now ...
} else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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