Last updated on 2026-11-08 01:51:29 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 83.53 | 339.15 | 422.68 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 59.78 | 228.81 | 288.59 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 57.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 239.38 | 303.38 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 417.00 | 508.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | OK | ||||
| r-release-linux-x86_64 | 1.1.0 | 78.27 | 331.21 | 409.48 | 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 | ERROR | ||||
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 118.00 | 480.00 | 598.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [34s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missSBM)
>
> test_check("missSBM")
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 3 model(s).
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degreeTested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degree
sampling: dyad new better on connectivity
node
double-standard
block-node new better on mixture
Adjusting Variational EM for Stochastic Block Model
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'node' network-sampling process
Initialization of 1 model(s).
Performing VEM inference
Model with 3 blocks.
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 2 model(s).
Performing VEM inference
Model with 2 blocks.
Model with 1 blocks.
Polishing (node-swap)
Looking for better solutions
Pass 1 Going forward +
Pass 1 Going backward +
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", { sampler_undirected_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, "bernoulli", FALSE, covarList = covarList_undirected) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85) })
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$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") }
Traceback:
else if (!new_expectations && skip_on_empty) { 1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
skip_empty() 2: }FUN(X[[i]], ...)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { 3: skip(paste0("{", e$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, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])37:
doWithOneRestart(return(expr), restart) 6:
tryCatchList(expr, classes, parentenv, handlers)38:
withOneRestart(expr, restarts[[1L]])
7: 39: withRestarts(tryCatch(withCallingHandlers({tryCatch(expr, error = function(e) { eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { call <- conditionCall(e) skip("On CRAN") } if (!is.null(call)) { else if (!new_expectations && skip_on_empty) { if (identical(call[[1L]], quote(doTryCatch))) skip_empty() call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) } prefix <- paste("Error in", dcall, ": ")}, expectation = handle_expectation, packageNotFoundError = function(e) { LONG <- 75L if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, snapshot_on_cran = function(cnd) { if (is.na(w)) snapshot_skipped <<- TRUE w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], invokeRestart("muffle_cran_snapshot") type = "b")}, skip = handle_skip, warning = handle_warning, message = handle_message, if (w > LONG) prefix <- paste0(prefix, "\n ") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() { else prefix <- "Error : " }) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))40: if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) .Internal(printDeferredWarnings())
}41: invisible(structure(msg, class = "try-error", condition = e))source_file(path, env = env(env), desc = desc, shuffle = shuffle, }) error_call = error_call)
8: 42: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
FUN(X[[i]], ...) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))43:
10: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, FUN(X[[i]], ...) error_call = error_call)
11: 44: lapply(seq_len(cores), inner.do)doTryCatch(return(expr), name, parentenv, handler)
12: 45: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, tryCatchOne(expr, names, parentenv, handlers[[1L]]) mc.silent = TRUE)
13: 46: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, tryCatchList(expr, classes, parentenv, handlers) verbose = (verbosity > 4))
14: 47: .self$do_with_inits(inits, Q, reinitialization_effort)tryCatch(code, testthat_abort_reporter = function(cnd) {
15: .self$estim_ascend(reinitialization_effort, changing_effort) cat(conditionMessage(cnd), "\n")
NULL16: })private$BMobject$estimate()
17: 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
env = env, desc = desc, shuffle = shuffle, error_call = error_call))18: eval(code, test_env)
49: 19: eval(code, test_env)test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 20: withCallingHandlers({ env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, eval(code, test_env) error_call = error_call)
new_expectations <- the$test_expectations > starting_expectations50: test_files(test_dir = path, test_paths = test_paths, test_package = package, if (snapshot_skipped) { reporter = reporter, load_helpers = load_helpers, env = env, skip("On CRAN") } stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, else if (!new_expectations && skip_on_empty) { load_package = load_package, parallel = parallel, shuffle = shuffle) skip_empty()
51: }test_dir("testthat", package = package, reporter = reporter, }, expectation = handle_expectation, packageNotFoundError = function(e) { ..., load_package = "installed")
if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))52: test_check("missSBM") }}, snapshot_on_cran = function(cnd) {
An irrecoverable exception occurred. R is aborting now ...
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", { sampler_undirected_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, "bernoulli", FALSE, covarList = covarList_undirected) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") }
Traceback:
1: else prefix <- "Error : "dispatcher(membership_name, membership_init$to_cc(), model_name, msg <- paste0(prefix, conditionMessage(e), "\n") .self$network_to_cc(), TRUE)
.Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { 2: cat(msg, file = outFile)FUN(X[[i]], ...) .Internal(printDeferredWarnings())
} 3: invisible(structure(msg, class = "try-error", condition = e))lapply(X = S, FUN = FUN, ...)})
4: 8: doTryCatch(return(expr), name, parentenv, handler)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
5:
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
6:
tryCatchList(expr, classes, parentenv, handlers)
10: 7: FUN(X[[i]], ...)
tryCatch(expr, error = function(e) {11: call <- conditionCall(e)lapply(seq_len(cores), inner.do) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L13: sm <- strsplit(conditionMessage(e), "\n")[[1L]]parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) verbose = (verbosity > 4)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")
if (w > LONG) 14: prefix <- paste0(prefix, "\n ").self$do_with_inits(inits, Q, reinitialization_effort) }
else prefix <- "Error : "15: msg <- paste0(prefix, conditionMessage(e), "\n").self$estim_ascend(reinitialization_effort, changing_effort) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)16: private$BMobject$estimate() .Internal(printDeferredWarnings()) }
invisible(structure(msg, class = "try-error", condition = e))17: })mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
18: 9: eval(code, test_env)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
19: 10: eval(code, test_env)FUN(X[[i]], ...)
20: 11: withCallingHandlers({ eval(code, test_env)lapply(seq_len(cores), inner.do) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {12: skip("On CRAN")parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, } else if (!new_expectations && skip_on_empty) { mc.silent = TRUE) skip_empty()
}13: }, expectation = handle_expectation, packageNotFoundError = function(e) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4)) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) }14: }, snapshot_on_cran = function(cnd) {.self$do_with_inits(inits, Q, reinitialization_effort) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")15: }, skip = handle_skip, warning = handle_warning, message = handle_message, .self$estim_ascend(reinitialization_effort, changing_effort)
error = handle_error, interrupt = handle_interrupt)16:
private$BMobject$estimate()21:
doTryCatch(return(expr), name, parentenv, handler)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])18:
eval(code, test_env)23:
tryCatchList(expr, classes, parentenv, handlers)19:
eval(code, test_env)24:
tryCatch(withCallingHandlers({20: eval(code, test_env)withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip(paste0("{", e$package, "} is not installed.")) if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, snapshot_on_cran = function(cnd) { invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)25:
doWithOneRestart(return(expr), restart)21: doTryCatch(return(expr), name, parentenv, handler)
26: 22: withOneRestart(expr, restarts[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: 23: withRestarts(tryCatch(withCallingHandlers({tryCatchList(expr, classes, parentenv, handlers) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations24: if (snapshot_skipped) {tryCatch(withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() skip(paste0("{", e$package, "} is not installed.")) } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { skip(paste0("{", e$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)
28: 25: test_code(code, parent.frame())
doWithOneRestart(return(expr), restart)29:
test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", 26: {withOneRestart(expr, restarts[[1L]])
sampler_directed_cov$rNetwork(store = TRUE)27: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, withRestarts(tryCatch(withCallingHandlers({ "bernoulli", TRUE, covarList = covarList_directed) eval(code, test_env) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, new_expectations <- the$test_expectations > starting_expectations plot = FALSE)) if (snapshot_skipped) { mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, skip("On CRAN") covariates = covarList_directed) } else if (!new_expectations && skip_on_empty) { cls <- net$clustering(1:(2 * Q)) skip_empty() cl <- cls[[Q]] } mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, }, expectation = handle_expectation, packageNotFoundError = function(e) { clusterInit = cl, covarList = covarList_directed) if (on_cran()) { mySBM_missSBM$doVEM(trace = TRUE) skip(paste0("{", e$package, "} is not installed.")) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }}, snapshot_on_cran = function(cnd) { 0.1) snapshot_skipped <<- TRUE expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), invokeRestart("muffle_cran_snapshot") 0.8)}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.05) end_test = function() { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), }) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 28: 0.85)test_code(code, parent.frame()) })
29: 30: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", eval(code, test_env) {
sampler_directed_cov$rNetwork(store = TRUE)31: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, eval(code, test_env) "bernoulli", TRUE, covarList = covarList_directed)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 32: plot = FALSE))withCallingHandlers({ mySBM_sbm$setModel(Q) eval(code, test_env) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { covariates = covarList_directed) skip("On CRAN") cls <- net$clustering(1:(2 * Q)) } cl <- cls[[Q]] else if (!new_expectations && skip_on_empty) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, skip_empty() clusterInit = cl, covarList = covarList_directed) } mySBM_missSBM$doVEM(trace = TRUE) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.1) if (on_cran()) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), skip(paste0("{", e$package, "} is not installed.")) 0.8) } expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), }, snapshot_on_cran = function(cnd) { 0.05) snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), invokeRestart("muffle_cran_snapshot") 0.1)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), error = handle_error, interrupt = handle_interrupt) 0.85)
})33:
doTryCatch(return(expr), name, parentenv, handler)30:
eval(code, test_env)34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])31:
eval(code, test_env)35: tryCatchList(expr, classes, parentenv, handlers)
32: 36: 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_error, interrupt = handle_interrupt), error = handle_fatal)
33: 37: doTryCatch(return(expr), name, parentenv, handler)doWithOneRestart(return(expr), restart)
34: 38: tryCatchOne(expr, names, parentenv, handlers[[1L]])withOneRestart(expr, restarts[[1L]])
35: 39: tryCatchList(expr, classes, parentenv, handlers)withRestarts(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 invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, skip = handle_skip, warning = handle_warning, message = handle_message, end_test = function() { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) })
37: 40: doWithOneRestart(return(expr), restart)
test_code(code = exprs, env = env, reporter = get_reporter() %||% 38: StopReporter$new())withOneRestart(expr, restarts[[1L]])
41: 39: source_file(path, env = env(env), desc = desc, shuffle = shuffle, withRestarts(tryCatch(withCallingHandlers({ error_call = error_call) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {42: skip("On CRAN")FUN(X[[i]], ...) }
else if (!new_expectations && skip_on_empty) {43: skip_empty()lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } error_call = error_call)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {44: skip(paste0("{", e$package, "} is not installed.")) }doTryCatch(return(expr), name, parentenv, handler)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE45: invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 46: end_test = function() {tryCatchList(expr, classes, parentenv, handlers) })
47: 40: tryCatch(code, testthat_abort_reporter = function(cnd) {test_code(code = exprs, env = env, reporter = get_reporter() %||% cat(conditionMessage(cnd), "\n") StopReporter$new()) NULL
41: })source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 42: FUN(X[[i]], ...) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
43: 49: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, test_files_serial(test_dir = test_dir, test_package = test_package, error_call = error_call) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 44: doTryCatch(return(expr), name, parentenv, handler) error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, 45: reporter = reporter, load_helpers = load_helpers, env = env, tryCatchOne(expr, names, parentenv, handlers[[1L]]) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)46: tryCatchList(expr, classes, parentenv, handlers)
51: 47: test_dir("testthat", package = package, reporter = reporter, tryCatch(code, testthat_abort_reporter = function(cnd) { ..., load_package = "installed") cat(conditionMessage(cnd), "\n")
NULL52: })test_check("missSBM")
48: An irrecoverable exception occurred. R is aborting now ...
with_reporter(reporters$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:
Traceback:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 1:
dispatcher(membership_name, membership_init$to_cc(), model_name, 9: .self$network_to_cc(), TRUE)
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 2: FUN(X[[i]], ...)
10: 3: FUN(X[[i]], ...)lapply(X = S, FUN = FUN, ...)
4: 11: lapply(seq_len(cores), inner.do)doTryCatch(return(expr), name, parentenv, handler)
12: 5: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, tryCatchOne(expr, names, parentenv, handlers[[1L]]) mc.silent = TRUE)
6: 13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, tryCatchList(expr, classes, parentenv, handlers) verbose = (verbosity > 4))
7: 14: tryCatch(expr, error = function(e) {.self$do_with_inits(inits, Q, reinitialization_effort) call <- conditionCall(e)
if (!is.null(call)) {15: if (identical(call[[1L]], quote(doTryCatch))) .self$estim_ascend(reinitialization_effort, changing_effort) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)16: prefix <- paste("Error in", dcall, ": ")private$BMobject$estimate() LONG <- 75L
17: sm <- strsplit(conditionMessage(e), "\n")[[1L]]mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 18: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], eval(code, test_env) type = "b")
if (w > LONG) 19: prefix <- paste0(prefix, "\n ")eval(code, test_env) }
else prefix <- "Error : "20: msg <- paste0(prefix, conditionMessage(e), "\n")withCallingHandlers({ .Internal(seterrmessage(msg[1L])) eval(code, test_env) if (!silent && isTRUE(getOption("show.error.messages"))) { new_expectations <- the$test_expectations > starting_expectations cat(msg, file = outFile) if (snapshot_skipped) { .Internal(printDeferredWarnings()) skip("On CRAN") } } invisible(structure(msg, class = "try-error", condition = e)) else if (!new_expectations && skip_on_empty) {}) skip_empty()
} 8: }, expectation = handle_expectation, packageNotFoundError = function(e) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (on_cran()) {
9: skip(paste0("{", e$package, "} is not installed."))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
}, snapshot_on_cran = function(cnd) {10: snapshot_skipped <<- TRUEFUN(X[[i]], ...)
invokeRestart("muffle_cran_snapshot")11: }, skip = handle_skip, warning = handle_warning, message = handle_message, lapply(seq_len(cores), inner.do) error = handle_error, interrupt = handle_interrupt)
12: 21: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, doTryCatch(return(expr), name, parentenv, handler) mc.silent = TRUE)
13: 22: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: 23: .self$do_with_inits(inits, Q, reinitialization_effort)tryCatchList(expr, classes, parentenv, handlers)
15: .self$estim_ascend(reinitialization_effort, changing_effort)24:
tryCatch(withCallingHandlers({16: private$BMobject$estimate() eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations17: mySBM_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$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { invokeRestart("muffle_cran_snapshot") skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal) else if (!new_expectations && skip_on_empty) {
skip_empty()25: }doWithOneRestart(return(expr), restart)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {26: skip(paste0("{", e$package, "} is not installed."))withOneRestart(expr, restarts[[1L]]) }
}, snapshot_on_cran = function(cnd) {27: snapshot_skipped <<- TRUEwithRestarts(tryCatch(withCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt) skip("On CRAN")
}21: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler) skip_empty()
}22: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
}23: }, snapshot_on_cran = function(cnd) {tryCatchList(expr, classes, parentenv, handlers) snapshot_skipped <<- TRUE
24: tryCatch(withCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { if (snapshot_skipped) { }) skip("On CRAN")
}28: test_code(code, parent.frame()) else if (!new_expectations && skip_on_empty) {
skip_empty()29: }test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", }, expectation = handle_expectation, packageNotFoundError = function(e) { { if (on_cran()) { sampler_undirected_nocov$rNetwork(store = TRUE) skip(paste0("{", e$package, "} is not installed.")) } mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, }, snapshot_on_cran = function(cnd) { "bernoulli", FALSE) snapshot_skipped <<- TRUE mySBM_sbm$optimize(estimOptions = list(verbosity = 0, invokeRestart("muffle_cran_snapshot") plot = FALSE))}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) cl <- net$clustering(3)[[1]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, 25: doWithOneRestart(return(expr), restart) clusterInit = cl)
mySBM_missSBM$doVEM()26: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), withOneRestart(expr, restarts[[1L]]) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 27: 0.95)withRestarts(tryCatch(withCallingHandlers({ expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), eval(code, test_env) 0.01) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), skip("On CRAN") 0.05) } expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), else if (!new_expectations && skip_on_empty) { 0.95) skip_empty() }) }}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))30: eval(code, test_env) }
}, snapshot_on_cran = function(cnd) {31: snapshot_skipped <<- TRUE 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), 32: withCallingHandlers({ end_test = function() { eval(code, test_env) }) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {28: skip("On CRAN")test_code(code, parent.frame()) }
29: else if (!new_expectations && skip_on_empty) {test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", skip_empty() { } sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, }, expectation = handle_expectation, packageNotFoundError = function(e) { "bernoulli", FALSE) if (on_cran()) { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) skip(paste0("{", e$package, "} is not installed.")) mySBM_sbm$setModel(3) } net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData)}, snapshot_on_cran = function(cnd) { cl <- net$clustering(3)[[1]] snapshot_skipped <<- TRUE mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, invokeRestart("muffle_cran_snapshot") clusterInit = cl) mySBM_missSBM$doVEM()}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) error = handle_error, interrupt = handle_interrupt)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 33: 0.95)doTryCatch(return(expr), name, parentenv, handler) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)34: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 35: 0.95)tryCatchList(expr, classes, parentenv, handlers) })
36: 30: tryCatch(withCallingHandlers({eval(code, test_env) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations31: if (snapshot_skipped) {eval(code, test_env)
skip("On CRAN")32: }withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty() }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE37: invokeRestart("muffle_cran_snapshot")doWithOneRestart(return(expr), restart)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)38:
withOneRestart(expr, restarts[[1L]])33:
doTryCatch(return(expr), name, parentenv, handler)39:
withRestarts(tryCatch(withCallingHandlers({34: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {35: skip("On CRAN")tryCatchList(expr, classes, parentenv, handlers) }
else if (!new_expectations && skip_on_empty) {36: skip_empty()tryCatch(withCallingHandlers({ eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip(paste0("{", e$package, "} is not installed.")) end_test = function() { } })}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE40: invokeRestart("muffle_cran_snapshot")test_code(code = exprs, env = env, reporter = get_reporter() %||% }, skip = handle_skip, warning = handle_warning, message = handle_message, StopReporter$new()) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
41: 37: source_file(path, env = env(env), desc = desc, shuffle = shuffle, doWithOneRestart(return(expr), restart) error_call = error_call)
38: 42: withOneRestart(expr, restarts[[1L]])FUN(X[[i]], ...)
43: 39: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN") }44: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler) skip_empty()
}45: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))46: }tryCatchList(expr, classes, parentenv, handlers)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE47: invokeRestart("muffle_cran_snapshot")tryCatch(code, testthat_abort_reporter = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, cat(conditionMessage(cnd), "\n") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), NULL}) end_test = function() {
})48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 40: test_code(code = exprs, env = env, reporter = get_reporter() %||% env = env, desc = desc, shuffle = shuffle, error_call = error_call)) StopReporter$new())
49: 41: test_files_serial(test_dir = test_dir, test_package = test_package, source_file(path, env = env(env), desc = desc, shuffle = shuffle, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, error_call = error_call) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 42: error_call = error_call)FUN(X[[i]], ...)
43: 50: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, test_files(test_dir = path, test_paths = test_paths, test_package = package, error_call = error_call) reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 44: doTryCatch(return(expr), name, parentenv, handler)
45: load_package = load_package, parallel = parallel, shuffle = shuffle)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: 51: tryCatchList(expr, classes, parentenv, handlers)
test_dir("testthat", package = package, reporter = reporter, 47: ..., load_package = "installed")tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL
})52: test_check("missSBM")
48: An irrecoverable exception occurred. R is aborting now ...
with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", { sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.2) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.95) })
Traceback:
30: 1: eval(code, test_env)
dispatcher(membership_name, membership_init$to_cc(), model_name, 31: .self$network_to_cc(), TRUE)
eval(code, test_env) 2:
FUN(X[[i]], ...)32:
withCallingHandlers({ 3: eval(code, test_env)lapply(X = S, FUN = FUN, ...) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { 4: skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler) }
else if (!new_expectations && skip_on_empty) { 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip_empty()
} 6: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 7: }tryCatch(expr, error = function(e) {}, snapshot_on_cran = function(cnd) { call <- conditionCall(e) snapshot_skipped <<- TRUE if (!is.null(call)) { invokeRestart("muffle_cran_snapshot") if (identical(call[[1L]], quote(doTryCatch))) }, skip = handle_skip, warning = handle_warning, message = handle_message, call <- sys.call(-4L) error = handle_error, interrupt = handle_interrupt) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")33: doTryCatch(return(expr), name, parentenv, handler) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]34: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 35: tryCatchList(expr, classes, parentenv, handlers) type = "b")
if (w > LONG) 36: prefix <- paste0(prefix, "\n ")tryCatch(withCallingHandlers({ eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else prefix <- "Error : " if (snapshot_skipped) { msg <- paste0(prefix, conditionMessage(e), "\n") skip("On CRAN") .Internal(seterrmessage(msg[1L])) } if (!silent && isTRUE(getOption("show.error.messages"))) { else if (!new_expectations && skip_on_empty) { cat(msg, file = outFile) skip_empty() .Internal(printDeferredWarnings()) } } invisible(structure(msg, class = "try-error", condition = e))}, expectation = handle_expectation, packageNotFoundError = function(e) {}) if (on_cran()) {
8: skip(paste0("{", e$package, "} is not installed."))try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }
}, snapshot_on_cran = function(cnd) { 9: snapshot_skipped <<- TRUEsendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 10: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)FUN(X[[i]], ...)
37: 11: doWithOneRestart(return(expr), restart)lapply(seq_len(cores), inner.do)
38: 12: withOneRestart(expr, restarts[[1L]])parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
39: 13: withRestarts(tryCatch(withCallingHandlers({parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, eval(code, test_env) verbose = (verbosity > 4)) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {14: skip("On CRAN").self$do_with_inits(inits, Q, reinitialization_effort) }
else if (!new_expectations && skip_on_empty) {15: skip_empty().self$estim_ascend(reinitialization_effort, changing_effort) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {16: if (on_cran()) {private$BMobject$estimate() skip(paste0("{", e$package, "} is not installed."))
}17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")18: }, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {19: })eval(code, test_env)
40: 20: test_code(code = exprs, env = env, reporter = get_reporter() %||% withCallingHandlers({ StopReporter$new()) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, if (snapshot_skipped) { error_call = error_call) skip("On CRAN")
}42: else if (!new_expectations && skip_on_empty) {FUN(X[[i]], ...)
skip_empty()43: }lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {44: skip(paste0("{", e$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) {45: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 46: error = handle_error, interrupt = handle_interrupt)tryCatchList(expr, classes, parentenv, handlers)
21:
doTryCatch(return(expr), name, parentenv, handler)47:
tryCatch(code, testthat_abort_reporter = function(cnd) {22: cat(conditionMessage(cnd), "\n")tryCatchOne(expr, names, parentenv, handlers[[1L]]) NULL
})23:
48: tryCatchList(expr, classes, parentenv, handlers)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))24:
tryCatch(withCallingHandlers({49: eval(code, test_env) new_expectations <- the$test_expectations > starting_expectationstest_files_serial(test_dir = test_dir, test_package = test_package, if (snapshot_skipped) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, skip("On CRAN") desc = desc, load_package = load_package, shuffle = shuffle, } error_call = error_call) else if (!new_expectations && skip_on_empty) {
skip_empty()50: }test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, }, expectation = handle_expectation, packageNotFoundError = function(e) { stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, if (on_cran()) { load_package = load_package, parallel = parallel, shuffle = shuffle) skip(paste0("{", e$package, "} is not installed.")) }
51: }, snapshot_on_cran = function(cnd) {test_dir("testthat", package = package, reporter = reporter, snapshot_skipped <<- TRUE ..., load_package = "installed") invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 52: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)test_check("missSBM")
25:
doWithOneRestart(return(expr), restart)An irrecoverable exception occurred. R is aborting now ...
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", { sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.2) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-44.R
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-explore-block-count.R:4:3',
'test-missSBM_collection-degenerate.R:80:3',
'test-missSBM_collection-estimate_chain.R:64:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-sbm-bernoulli-with-covariates.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-with-covariates.R:46:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:46:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:44:3'): SimpleSBM_fit 'Bernoulli' model, directed, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:44:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64