Last updated on 2026-10-29 15:54:51 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 89.17 | 339.94 | 429.11 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 60.82 | 232.18 | 293.00 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 60.00 | 235.13 | 295.13 | 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 | 85.14 | 334.40 | 419.54 | 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 | 101.00 | 348.00 | 449.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 19.00 | 87.00 | 106.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 117.00 | 477.00 | 594.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [36s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missSBM)
>
> test_check("missSBM")
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 3 model(s).
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degreeTested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degree
sampling: dyad new better on connectivity
node
double-standard
block-node new better on mixture
Adjusting Variational EM for Stochastic Block Model
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'node' network-sampling process
Initialization of 1 model(s).
Performing VEM inference
Model with 3 blocks.
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 2 model(s).
Performing VEM inference
Model with 2 blocks.
Model with 1 blocks.
Polishing (node-swap)
Looking for better solutions
Pass 1 Going forward +
Pass 1 Going backward +
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
Traceback:
3: lapply(X = S, FUN = FUN, ...) 1:
dispatcher(membership_name, membership_init$to_cc(), model_name, 4: .self$network_to_cc(), TRUE)doTryCatch(return(expr), name, parentenv, handler)
2: 5: FUN(X[[i]], ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 3: tryCatchList(expr, classes, parentenv, handlers)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)) {
if (identical(call[[1L]], quote(doTryCatch))) 5: call <- sys.call(-4L)tryCatchOne(expr, names, parentenv, handlers[[1L]]) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") 6: LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 7: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatch(expr, error = function(e) { type = "b") call <- conditionCall(e) if (w > LONG) prefix <- paste0(prefix, "\n ") if (!is.null(call)) { } if (identical(call[[1L]], quote(doTryCatch))) else prefix <- "Error : " call <- sys.call(-4L) msg <- paste0(prefix, conditionMessage(e), "\n") dcall <- deparse(call, nlines = 1L) .Internal(seterrmessage(msg[1L])) prefix <- paste("Error in", dcall, ": ") if (!silent && isTRUE(getOption("show.error.messages"))) { LONG <- 75L cat(msg, file = outFile) sm <- strsplit(conditionMessage(e), "\n")[[1L]] .Internal(printDeferredWarnings()) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } if (is.na(w)) invisible(structure(msg, class = "try-error", condition = e)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }) 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())
}11: invisible(structure(msg, class = "try-error", condition = e))lapply(seq_len(cores), inner.do)})
12: 8: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) mc.silent = TRUE)
9: 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))10:
FUN(X[[i]], ...)
14: 11: .self$do_with_inits(inits, Q, reinitialization_effort)lapply(seq_len(cores), inner.do)
15: 12: .self$estim_ascend(reinitialization_effort, changing_effort)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE,
mc.silent = TRUE)16:
private$BMobject$estimate()13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 17: verbose = (verbosity > 4))mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
14: .self$do_with_inits(inits, Q, reinitialization_effort)18:
eval(code, test_env)
15: 19: .self$estim_ascend(reinitialization_effort, changing_effort)
eval(code, test_env)16:
private$BMobject$estimate()20:
withCallingHandlers({17: eval(code, test_env) new_expectations <- the$test_expectations > starting_expectationsmySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) if (snapshot_skipped) {
18: skip("On CRAN")eval(code, test_env) }
else if (!new_expectations && skip_on_empty) {19: skip_empty()eval(code, test_env) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {20: if (on_cran()) {withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt) skip_empty()
}21: }, expectation = handle_expectation, packageNotFoundError = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))22: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE23: invokeRestart("muffle_cran_snapshot")tryCatchList(expr, classes, parentenv, handlers)
}, skip = handle_skip, warning = handle_warning, message = handle_message, 24: error = handle_error, interrupt = handle_interrupt)tryCatch(withCallingHandlers({
eval(code, test_env)21: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
skip("On CRAN")22: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()23: }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {24: skip(paste0("{", e$package, "} is not installed."))tryCatch(withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
else if (!new_expectations && skip_on_empty) {25: skip_empty()doWithOneRestart(return(expr), restart) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {26: withOneRestart(expr, restarts[[1L]]) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))27: }withRestarts(tryCatch(withCallingHandlers({}, snapshot_on_cran = function(cnd) { eval(code, test_env) snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
else if (!new_expectations && skip_on_empty) {25: skip_empty()doWithOneRestart(return(expr), restart) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {26: if (on_cran()) {withOneRestart(expr, restarts[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}27: }, snapshot_on_cran = function(cnd) {withRestarts(tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip("On CRAN") end_test = function() { } }) else if (!new_expectations && skip_on_empty) {
skip_empty()28: }test_code(code, parent.frame())}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {29: skip(paste0("{", e$package, "} is not installed."))test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", } {}, snapshot_on_cran = function(cnd) { sampler_undirected_cov$rNetwork(store = TRUE) snapshot_skipped <<- TRUE mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, invokeRestart("muffle_cran_snapshot") "bernoulli", FALSE, covarList = covarList_undirected)}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), plot = FALSE)) end_test = function() { mySBM_sbm$setModel(Q) }) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected)
cls <- net$clustering(1:(2 * Q))28: cl <- cls[[Q]]test_code(code, parent.frame()) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net,
clusterInit = cl, covarList = covarList_undirected)29: mySBM_missSBM$doVEM()test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), { 0.05) sampler_undirected_cov$rNetwork(store = TRUE) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, 0.8) "bernoulli", FALSE, covarList = covarList_undirected) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 0.01) plot = FALSE)) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, 0.1) covariates = covarList_undirected) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), cls <- net$clustering(1:(2 * Q)) 0.1) cl <- cls[[Q]] expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, 0.85) clusterInit = cl, covarList = covarList_undirected) }) mySBM_missSBM$doVEM()
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 30: 0.05)eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.8)31: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), eval(code, test_env)
0.01)32: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), withCallingHandlers({ 0.1) eval(code, test_env) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), new_expectations <- the$test_expectations > starting_expectations 0.1) if (snapshot_skipped) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), skip("On CRAN") 0.85) } }) else if (!new_expectations && skip_on_empty) {
skip_empty()30: }eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {31: skip(paste0("{", e$package, "} is not installed."))eval(code, test_env) }
}, snapshot_on_cran = function(cnd) {32: snapshot_skipped <<- TRUEwithCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt) if (snapshot_skipped) {
skip("On CRAN")33: }doTryCatch(return(expr), name, parentenv, handler) else if (!new_expectations && skip_on_empty) {
skip_empty()34: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {35: skip(paste0("{", e$package, "} is not installed."))tryCatchList(expr, classes, parentenv, handlers) }
36: }, snapshot_on_cran = function(cnd) {tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt) skip("On CRAN")
}33: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler) skip_empty()
34: }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}35: }, snapshot_on_cran = function(cnd) {tryCatchList(expr, classes, parentenv, handlers) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")36: }, 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$test_expectations > starting_expectations37: if (snapshot_skipped) {doWithOneRestart(return(expr), restart) skip("On CRAN")
}38: else if (!new_expectations && skip_on_empty) {withOneRestart(expr, restarts[[1L]]) skip_empty()
}39: }, expectation = handle_expectation, packageNotFoundError = function(e) {withRestarts(tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") } else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))37: }doWithOneRestart(return(expr), restart)}, 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), error = handle_fatal), end_test = function() {39: })withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)40: new_expectations <- the$test_expectations > starting_expectationstest_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) if (snapshot_skipped) {
skip("On CRAN")41: }source_file(path, env = env(env), desc = desc, shuffle = shuffle, else if (!new_expectations && skip_on_empty) { skip_empty() error_call = error_call) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {42: if (on_cran()) {FUN(X[[i]], ...) skip(paste0("{", e$package, "} is not installed."))
}43: }, snapshot_on_cran = function(cnd) {lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") error_call = error_call)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 44: end_test = function() { })doTryCatch(return(expr), name, parentenv, handler)
40: 45: test_code(code = exprs, env = env, reporter = get_reporter() %||% tryCatchOne(expr, names, parentenv, handlers[[1L]]) StopReporter$new())
41: 46: source_file(path, env = env(env), desc = desc, shuffle = shuffle, tryCatchList(expr, classes, parentenv, handlers) error_call = error_call)
47: 42: tryCatch(code, testthat_abort_reporter = function(cnd) {FUN(X[[i]], ...) cat(conditionMessage(cnd), "\n")
NULL43: })lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 44: env = env, desc = desc, shuffle = shuffle, error_call = error_call))doTryCatch(return(expr), name, parentenv, handler)
49: test_files_serial(test_dir = test_dir, test_package = test_package, 45: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, tryCatchOne(expr, names, parentenv, handlers[[1L]]) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 46: error_call = error_call)tryCatchList(expr, classes, parentenv, handlers)
47: 50: tryCatch(code, testthat_abort_reporter = function(cnd) {test_files(test_dir = path, test_paths = test_paths, test_package = package, cat(conditionMessage(cnd), "\n") reporter = reporter, load_helpers = load_helpers, env = env, NULL stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }) load_package = load_package, parallel = parallel, shuffle = shuffle)
48: 51: with_reporter(reporters$multi, lapply(test_paths, test_one_file, test_dir("testthat", package = package, reporter = reporter, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) ..., load_package = "installed")
49: 52: test_files_serial(test_dir = test_dir, test_package = test_package, 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, An irrecoverable exception occurred. R is aborting now ...
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:
Traceback:
1: 1: dispatcher(membership_name, membership_init$to_cc(), model_name, dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) .self$network_to_cc(), TRUE)
2: 2: FUN(X[[i]], ...)FUN(X[[i]], ...)
3: 3: lapply(X = S, FUN = FUN, ...)lapply(X = S, FUN = FUN, ...)
4: 4: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
5: 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 6: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
7: 7: tryCatch(expr, error = function(e) {tryCatch(expr, error = function(e) { call <- conditionCall(e) call <- conditionCall(e) if (!is.null(call)) { if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") prefix <- paste("Error in", dcall, ": ") LONG <- 75L LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") type = "b") if (w > LONG) if (w > LONG) prefix <- paste0(prefix, "\n ") prefix <- paste0(prefix, "\n ") } } else prefix <- "Error : " else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) cat(msg, file = outFile) .Internal(printDeferredWarnings()) .Internal(printDeferredWarnings()) } } invisible(structure(msg, class = "try-error", condition = e)) invisible(structure(msg, class = "try-error", condition = e))})})
8: 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: 10: FUN(X[[i]], ...)FUN(X[[i]], ...)
11: 11: lapply(seq_len(cores), inner.do)lapply(seq_len(cores), inner.do)
12: 12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE) mc.silent = TRUE)
13: 13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4)) verbose = (verbosity > 4))
14: 14: .self$do_with_inits(inits, Q, reinitialization_effort).self$do_with_inits(inits, Q, reinitialization_effort)
15: 15: .self$estim_ascend(reinitialization_effort, changing_effort).self$estim_ascend(reinitialization_effort, changing_effort)
16: 16: private$BMobject$estimate()private$BMobject$estimate()
17: 17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: 18: eval(code, test_env)eval(code, test_env)
19: 19: eval(code, test_env)eval(code, test_env)
20: 20: 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_error, interrupt = handle_interrupt)
21: 21: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
22: 22: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: 23: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
24: 24: tryCatch(withCallingHandlers({ eval(code, test_env)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) { } 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), error = handle_fatal)}, skip = handle_skip, warning = handle_warning, message = handle_message,
25: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)doWithOneRestart(return(expr), restart)
25: 26: doWithOneRestart(return(expr), restart)withOneRestart(expr, restarts[[1L]])
26: 27: withOneRestart(expr, restarts[[1L]])withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)27: new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$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") end_test = function() {}, 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())
28: 29: test_code(code, parent.frame())test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate",
{29: sampler_directed_cov$rNetwork(store = TRUE)test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, { "bernoulli", TRUE, covarList = covarList_directed) sampler_directed_cov$rNetwork(store = TRUE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, plot = FALSE)) "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$setModel(Q) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, mySBM_sbm$setModel(Q) covariates = covarList_directed) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, cls <- net$clustering(1:(2 * Q)) covariates = covarList_directed) cl <- cls[[Q]] cls <- net$clustering(1:(2 * Q)) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, cl <- cls[[Q]] clusterInit = cl, covarList = covarList_directed) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, mySBM_missSBM$doVEM(trace = TRUE) clusterInit = cl, covarList = covarList_directed) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), mySBM_missSBM$doVEM(trace = TRUE) 0.1) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.1) 0.8) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.8) 0.05) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 0.05) 0.1) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 0.1) 0.85) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), }) 0.85)
})30:
eval(code, test_env)30:
eval(code, test_env)31:
eval(code, test_env)31:
eval(code, test_env)32:
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) { } 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_error, interrupt = handle_interrupt)33:
doTryCatch(return(expr), name, parentenv, handler)33:
doTryCatch(return(expr), name, parentenv, handler)34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])35:
tryCatchList(expr, classes, parentenv, handlers)35:
tryCatchList(expr, classes, parentenv, handlers)36: 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, 37: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)doWithOneRestart(return(expr), restart)
37: 38: doWithOneRestart(return(expr), restart)withOneRestart(expr, restarts[[1L]])
38: 39: withOneRestart(expr, restarts[[1L]])withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)39: new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$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") end_test = function() {}, 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$new())40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 41: StopReporter$new())source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 42: error_call = error_call)FUN(X[[i]], ...)
42: 43: FUN(X[[i]], ...)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 44: error_call = error_call)doTryCatch(return(expr), name, parentenv, handler)
44: 45: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: 46: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
46: 47: tryCatchList(expr, classes, parentenv, handlers)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")47: NULLtryCatch(code, testthat_abort_reporter = function(cnd) {}) cat(conditionMessage(cnd), "\n")
NULL48: })with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 49: env = env, desc = desc, shuffle = shuffle, error_call = error_call))test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 49: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_files_serial(test_dir = test_dir, test_package = test_package, desc = desc, load_package = load_package, shuffle = shuffle, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, error_call = error_call) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 50: error_call = error_call)test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 50: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_files(test_dir = path, test_paths = test_paths, test_package = package, load_package = load_package, parallel = parallel, shuffle = shuffle) reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 51: load_package = load_package, parallel = parallel, shuffle = shuffle)test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")51:
test_dir("testthat", package = package, reporter = reporter, 52: ..., load_package = "installed")test_check("missSBM")
52: An irrecoverable exception occurred. R is aborting now ...
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:
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) .self$network_to_cc(), TRUE)
2: 2: FUN(X[[i]], ...)FUN(X[[i]], ...)
3: 3: lapply(X = S, FUN = FUN, ...)lapply(X = S, FUN = FUN, ...)
4: 4: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
5: 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 6: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
7: 7: tryCatch(expr, error = function(e) {tryCatch(expr, error = function(e) { call <- conditionCall(e) call <- conditionCall(e) if (!is.null(call)) { if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") prefix <- paste("Error in", dcall, ": ") LONG <- 75L LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") type = "b") if (is.na(w)) if (w > LONG) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], prefix <- paste0(prefix, "\n ") type = "b") } if (w > LONG) else prefix <- "Error : " prefix <- paste0(prefix, "\n ") msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) else prefix <- "Error : " if (!silent && isTRUE(getOption("show.error.messages"))) { msg <- paste0(prefix, conditionMessage(e), "\n") cat(msg, file = outFile) .Internal(seterrmessage(msg[1L])) .Internal(printDeferredWarnings()) if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile) invisible(structure(msg, class = "try-error", condition = e)) .Internal(printDeferredWarnings())}) }
invisible(structure(msg, class = "try-error", condition = e)) 8: })try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
8: 9: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: 10: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...)
10: 11: FUN(X[[i]], ...)lapply(seq_len(cores), inner.do)
11: 12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, lapply(seq_len(cores), inner.do) mc.silent = TRUE)
12: 13: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, mc.silent = TRUE) verbose = (verbosity > 4))
13: 14: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, .self$do_with_inits(inits, Q, reinitialization_effort) verbose = (verbosity > 4))
15: 14: .self$estim_ascend(reinitialization_effort, changing_effort).self$do_with_inits(inits, Q, reinitialization_effort)
16: 15: private$BMobject$estimate().self$estim_ascend(reinitialization_effort, changing_effort)
17: 16: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))private$BMobject$estimate()
18: 17: eval(code, test_env)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
19: 18: eval(code, test_env)eval(code, test_env)
19: 20: eval(code, test_env)withCallingHandlers({
eval(code, test_env)20: new_expectations <- the$test_expectations > starting_expectationswithCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$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}, 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)21:
doTryCatch(return(expr), name, parentenv, handler)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])23:
tryCatchList(expr, classes, parentenv, handlers)23:
tryCatchList(expr, classes, parentenv, handlers)24:
tryCatch(withCallingHandlers({24: eval(code, test_env)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) { } 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, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 25: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
doWithOneRestart(return(expr), restart)25:
doWithOneRestart(return(expr), restart)26:
withOneRestart(expr, restarts[[1L]])26:
withOneRestart(expr, restarts[[1L]])27:
withRestarts(tryCatch(withCallingHandlers({27: eval(code, test_env) new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } 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$package, "} is not installed.")) if (on_cran()) { }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE skip(paste0("{", e$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, 28: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_code(code, parent.frame()) end_test = function() {
})29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", 28: {test_code(code, parent.frame()) sampler_undirected_nocov$rNetwork(store = TRUE)
mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, 29: "bernoulli", FALSE)test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", mySBM_sbm$optimize(estimOptions = list(verbosity = 0, { plot = FALSE)) sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm$setModel(3) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) "bernoulli", FALSE) cl <- net$clustering(3)[[1]] mySBM_sbm$optimize(estimOptions = list(verbosity = 0, mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, plot = FALSE)) clusterInit = cl) mySBM_sbm$setModel(3) mySBM_missSBM$doVEM() net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), cl <- net$clustering(3)[[1]] 0.05) mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), clusterInit = cl) 0.95) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.01) 0.05) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.05) 0.95) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.95) 0.01) }) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean),
0.05)30: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), eval(code, test_env) 0.95)
})31:
eval(code, test_env)30:
eval(code, test_env)32:
withCallingHandlers({31: eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {32: skip("On CRAN")withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() 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_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_error, interrupt = handle_interrupt)
33: 33: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
34: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: 35: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
36: 36: tryCatch(withCallingHandlers({tryCatch(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), error = handle_fatal)
37: 37: doWithOneRestart(return(expr), restart)doWithOneRestart(return(expr), restart)
38: 38: withOneRestart(expr, restarts[[1L]])withOneRestart(expr, restarts[[1L]])
39:
39: withRestarts(tryCatch(withCallingHandlers({withRestarts(tryCatch(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), error = handle_fatal), end_test = function() { end_test = function() { }) })
40: 40: test_code(code = exprs, env = env, reporter = get_reporter() %||% test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) StopReporter$new())
41: 41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) error_call = error_call)
42: 42: FUN(X[[i]], ...)FUN(X[[i]], ...)
43: 43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) error_call = error_call)
44: 44: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
45: 45: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
46:
tryCatchList(expr, classes, parentenv, handlers)
46: 47: tryCatchList(expr, classes, parentenv, handlers)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")47: NULLtryCatch(code, testthat_abort_reporter = function(cnd) {}) cat(conditionMessage(cnd), "\n")
NULL48: })with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 49: env = env, desc = desc, shuffle = shuffle, error_call = error_call))
test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 49: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, test_files_serial(test_dir = test_dir, test_package = test_package, error_call = error_call) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 50: desc = desc, load_package = load_package, shuffle = shuffle, test_files(test_dir = path, test_paths = test_paths, test_package = package, error_call = error_call) 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)50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 51: reporter = reporter, load_helpers = load_helpers, env = env, test_dir("testthat", package = package, reporter = reporter, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle) ..., load_package = "installed")
51: 52: test_dir("testthat", package = package, reporter = reporter, test_check("missSBM") ..., load_package = "installed")
An irrecoverable exception occurred. R is aborting now ...
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]], ...)
Traceback:
11: 1: lapply(seq_len(cores), inner.do)dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 2: mc.silent = TRUE)FUN(X[[i]], ...)
13: 3: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))lapply(X = S, FUN = FUN, ...)
14:
.self$do_with_inits(inits, Q, reinitialization_effort) 4:
doTryCatch(return(expr), name, parentenv, handler)
15: .self$estim_ascend(reinitialization_effort, changing_effort) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])16: private$BMobject$estimate()
6:
tryCatchList(expr, classes, parentenv, handlers)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) 7:
tryCatch(expr, error = function(e) {18: eval(code, test_env) call <- conditionCall(e)
if (!is.null(call)) {19: if (identical(call[[1L]], quote(doTryCatch))) eval(code, test_env)
call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)20: withCallingHandlers({ prefix <- paste("Error in", dcall, ": ") eval(code, test_env) LONG <- 75L new_expectations <- the$test_expectations > starting_expectations sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (snapshot_skipped) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") skip("On CRAN") if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], else if (!new_expectations && skip_on_empty) { type = "b") skip_empty() } if (w > LONG) }, expectation = handle_expectation, packageNotFoundError = function(e) { prefix <- paste0(prefix, "\n ") if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) { else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") .Internal(seterrmessage(msg[1L]))}, skip = handle_skip, warning = handle_warning, message = handle_message, if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) error = handle_error, interrupt = handle_interrupt) .Internal(printDeferredWarnings()) }
invisible(structure(msg, class = "try-error", condition = e))21: })doTryCatch(return(expr), name, parentenv, handler)
8:
22: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: 23: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchList(expr, classes, parentenv, handlers)
10:
FUN(X[[i]], ...)24:
tryCatch(withCallingHandlers({11: eval(code, test_env)lapply(seq_len(cores), inner.do) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {12: skip("On CRAN")parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, } else if (!new_expectations && skip_on_empty) { skip_empty() mc.silent = TRUE) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {13: if (on_cran()) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, skip(paste0("{", e$package, "} is not installed.")) } verbose = (verbosity > 4))
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE14: invokeRestart("muffle_cran_snapshot").self$do_with_inits(inits, Q, reinitialization_effort)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)15:
.self$estim_ascend(reinitialization_effort, changing_effort)25:
doWithOneRestart(return(expr), restart)
16: 26: private$BMobject$estimate()withOneRestart(expr, restarts[[1L]])
17: 27: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)18: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env)
if (snapshot_skipped) { skip("On CRAN")19: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()20: withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { new_expectations <- the$test_expectations > starting_expectations if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN") }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty() }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { if (on_cran()) { }) skip(paste0("{", e$package, "} is not installed."))
}}, snapshot_on_cran = function(cnd) {28: snapshot_skipped <<- TRUEtest_code(code, parent.frame()) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 29: error = handle_error, interrupt = handle_interrupt)test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate",
{ sampler_directed_nocov$rNetwork(store = TRUE)21: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, doTryCatch(return(expr), name, parentenv, handler) "bernoulli", TRUE)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 22: plot = FALSE))tryCatchOne(expr, names, parentenv, handlers[[1L]]) mySBM_sbm$setModel(3)
23: tryCatchList(expr, classes, parentenv, handlers) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)
cl <- net$clustering(3)[[1]]24: mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, tryCatch(withCallingHandlers({ clusterInit = cl) eval(code, test_env) mySBM_missSBM$doVEM() new_expectations <- the$test_expectations > starting_expectations expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), if (snapshot_skipped) { 0.1) skip("On CRAN") expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), } 0.95) else if (!new_expectations && skip_on_empty) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), skip_empty() 0.01) } expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.1) if (on_cran()) { expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), skip(paste0("{", e$package, "} is not installed.")) 0.2) } expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), }, snapshot_on_cran = function(cnd) { 0.95) snapshot_skipped <<- TRUE })
invokeRestart("muffle_cran_snapshot")30: }, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
31: 25: eval(code, test_env)doWithOneRestart(return(expr), restart)
32:
withCallingHandlers({26: eval(code, test_env)withOneRestart(expr, restarts[[1L]]) new_expectations <- the$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$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE33: invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 34: end_test = function() {tryCatchOne(expr, names, parentenv, handlers[[1L]]) })
35: 28: tryCatchList(expr, classes, parentenv, handlers)test_code(code, parent.frame())
36: 29: tryCatch(withCallingHandlers({test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", eval(code, test_env) { new_expectations <- the$test_expectations > starting_expectations sampler_directed_nocov$rNetwork(store = TRUE) if (snapshot_skipped) { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, skip("On CRAN") "bernoulli", TRUE) } mySBM_sbm$optimize(estimOptions = list(verbosity = 0, else if (!new_expectations && skip_on_empty) { plot = FALSE)) skip_empty() mySBM_sbm$setModel(3) } net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)}, expectation = handle_expectation, packageNotFoundError = function(e) { cl <- net$clustering(3)[[1]] if (on_cran()) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, skip(paste0("{", e$package, "} is not installed.")) clusterInit = cl) } mySBM_missSBM$doVEM()}, snapshot_on_cran = function(cnd) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), snapshot_skipped <<- TRUE 0.1) invokeRestart("muffle_cran_snapshot") expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.95) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)37: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), doWithOneRestart(return(expr), restart) 0.1)
expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 38: 0.2)withOneRestart(expr, restarts[[1L]]) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships),
0.95)39: })withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)30: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
skip("On CRAN")31: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()32: }withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, expectation = handle_expectation, packageNotFoundError = function(e) { end_test = function() { if (on_cran()) { }) skip(paste0("{", e$package, "} is not installed."))
}40: }, snapshot_on_cran = function(cnd) {test_code(code = exprs, env = env, reporter = get_reporter() %||% snapshot_skipped <<- TRUE StopReporter$new()) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 41: error = handle_error, interrupt = handle_interrupt)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)33:
doTryCatch(return(expr), name, parentenv, handler)42:
FUN(X[[i]], ...)34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 35: error_call = error_call)tryCatchList(expr, classes, parentenv, handlers)
44: 36: doTryCatch(return(expr), name, parentenv, handler)tryCatch(withCallingHandlers({
eval(code, test_env)45: new_expectations <- the$test_expectations > starting_expectationstryCatchOne(expr, names, parentenv, handlers[[1L]]) if (snapshot_skipped) {
skip("On CRAN")46: }tryCatchList(expr, classes, parentenv, handlers) else if (!new_expectations && skip_on_empty) {
skip_empty()47: }tryCatch(code, testthat_abort_reporter = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { cat(conditionMessage(cnd), "\n") if (on_cran()) { NULL skip(paste0("{", e$package, "} is not installed."))}) }
}, snapshot_on_cran = function(cnd) {48: snapshot_skipped <<- TRUEwith_reporter(reporters$multi, lapply(test_paths, test_one_file, invokeRestart("muffle_cran_snapshot") 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)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 37: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, doWithOneRestart(return(expr), restart) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 38: error_call = error_call)withOneRestart(expr, restarts[[1L]])
50: 39: test_files(test_dir = path, test_paths = test_paths, test_package = package, withRestarts(tryCatch(withCallingHandlers({ reporter = reporter, load_helpers = load_helpers, env = env, eval(code, test_env) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, new_expectations <- the$test_expectations > starting_expectations load_package = load_package, parallel = parallel, shuffle = shuffle) if (snapshot_skipped) {
skip("On CRAN")51: }test_dir("testthat", package = package, reporter = reporter, else if (!new_expectations && skip_on_empty) { ..., load_package = "installed") skip_empty()
}52: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_check("missSBM") if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))An irrecoverable exception occurred. R is aborting now ...
}}, 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