Last updated on 2026-11-09 01:52:22 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 | 57.60 | 229.27 | 286.87 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 57.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 239.38 | 303.38 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 417.00 | 508.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | OK | ||||
| r-release-linux-x86_64 | 1.1.0 | 78.58 | 329.18 | 407.76 | OK | |
| r-release-macos-arm64 | 1.1.0 | 17.00 | 92.00 | 109.00 | OK | |
| r-release-macos-x86_64 | 1.1.0 | 59.00 | 456.00 | 515.00 | OK | |
| r-release-windows-x86_64 | 1.1.0 | 101.00 | 348.00 | 449.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 18.00 | 90.00 | 108.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 118.00 | 480.00 | 598.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [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:
Traceback:
dispatcher(membership_name, membership_init$to_cc(), model_name, 1: .self$network_to_cc(), TRUE)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE) 2:
FUN(X[[i]], ...) 2:
FUN(X[[i]], ...) 3:
lapply(X = S, FUN = FUN, ...) 3:
lapply(X = S, FUN = FUN, ...) 4:
doTryCatch(return(expr), name, parentenv, handler) 4:
doTryCatch(return(expr), name, parentenv, handler) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6:
tryCatchList(expr, classes, parentenv, handlers) 6:
tryCatchList(expr, classes, parentenv, handlers) 7:
tryCatch(expr, error = function(e) { 7: call <- conditionCall(e)tryCatch(expr, error = function(e) { if (!is.null(call)) { call <- conditionCall(e) if (identical(call[[1L]], quote(doTryCatch))) if (!is.null(call)) { call <- sys.call(-4L) if (identical(call[[1L]], quote(doTryCatch))) dcall <- deparse(call, nlines = 1L) call <- sys.call(-4L) prefix <- paste("Error in", dcall, ": ") dcall <- deparse(call, nlines = 1L) LONG <- 75L prefix <- paste("Error in", dcall, ": ") sm <- strsplit(conditionMessage(e), "\n")[[1L]] LONG <- 75L 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 = "w") + nchar(sm[1L], type = "w") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (is.na(w)) type = "b") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (w > LONG) type = "b") prefix <- paste0(prefix, "\n ") if (w > LONG) 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$test_expectations > starting_expectations if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty()}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip(paste0("{", e$package, "} is not installed.")) if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, snapshot_on_cran = function(cnd) { invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)21:
doTryCatch(return(expr), name, parentenv, handler)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, 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), error = handle_fatal)25:
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)withRestarts(tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty()}, expectation = handle_expectation, packageNotFoundError = function(e) { } 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 invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { end_test = function() { }) })
28: 28: test_code(code, parent.frame())test_code(code, parent.frame())
29: 29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", { { sampler_undirected_cov$rNetwork(store = TRUE) sampler_undirected_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, "bernoulli", FALSE, covarList = covarList_undirected) "bernoulli", FALSE, covarList = covarList_undirected) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) plot = FALSE)) mySBM_sbm$setModel(Q) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected) covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM() mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 0.1) 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85) 0.85) }) })
30: 30: eval(code, test_env)eval(code, test_env)
31: 31: eval(code, test_env)eval(code, test_env)
32: 32: 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)
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: 46: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
47: 47: tryCatch(code, testthat_abort_reporter = function(cnd) {tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") cat(conditionMessage(cnd), "\n") NULL NULL})})
48: 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: 49: test_files_serial(test_dir = test_dir, test_package = test_package, test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) error_call = error_call)
50: 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle) load_package = load_package, parallel = parallel, shuffle = shuffle)
51: 51: test_dir("testthat", package = package, reporter = reporter, test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") ..., load_package = "installed")
52: 52: test_check("missSBM")test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) {
Traceback:
1: skip_empty()dispatcher(membership_name, membership_init$to_cc(), model_name, } .self$network_to_cc(), TRUE)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
} 2: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUEFUN(X[[i]], ...) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt) 3:
lapply(X = S, FUN = FUN, ...)21:
doTryCatch(return(expr), name, parentenv, handler) 4:
doTryCatch(return(expr), name, parentenv, handler)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
24: 6: tryCatchList(expr, classes, parentenv, handlers)tryCatch(withCallingHandlers({ eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations 7: if (snapshot_skipped) { skip("On CRAN")tryCatch(expr, error = function(e) { call <- conditionCall(e) } else if (!new_expectations && skip_on_empty) { skip_empty() if (!is.null(call)) { } if (identical(call[[1L]], quote(doTryCatch))) }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { call <- sys.call(-4L) skip(paste0("{", e$package, "} is not installed.")) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") } LONG <- 75L}, snapshot_on_cran = function(cnd) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] snapshot_skipped <<- TRUE w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") invokeRestart("muffle_cran_snapshot") if (is.na(w)) }, skip = handle_skip, warning = handle_warning, message = handle_message, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], error = handle_error, interrupt = handle_interrupt), error = handle_fatal) type = "b")
if (w > LONG) prefix <- paste0(prefix, "\n ")25: }doWithOneRestart(return(expr), restart) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")26: .Internal(seterrmessage(msg[1L]))withOneRestart(expr, restarts[[1L]]) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile) .Internal(printDeferredWarnings())27: }withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) invisible(structure(msg, class = "try-error", condition = e)) new_expectations <- the$test_expectations > starting_expectations})
if (snapshot_skipped) { 8: skip("On CRAN")try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }
else if (!new_expectations && skip_on_empty) { 9: skip_empty()sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
}10: }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {FUN(X[[i]], ...)
11: skip(paste0("{", e$package, "} is not installed.")) }lapply(seq_len(cores), inner.do)}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, }, skip = handle_skip, warning = handle_warning, message = handle_message, mc.silent = TRUE) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {13: })parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
28: 14: test_code(code, parent.frame()).self$do_with_inits(inits, Q, reinitialization_effort)
29:
test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", 15: .self$estim_ascend(reinitialization_effort, changing_effort) {
sampler_directed_cov$rNetwork(store = TRUE)16: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, private$BMobject$estimate() "bernoulli", TRUE, covarList = covarList_directed)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 17: plot = FALSE))mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q)
net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, 18: covariates = covarList_directed)eval(code, test_env) cls <- net$clustering(1:(2 * Q))
cl <- cls[[Q]]19: mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_directed)eval(code, test_env) mySBM_missSBM$doVEM(trace = TRUE)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 20: 0.1)withCallingHandlers({ expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), eval(code, test_env) 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), new_expectations <- the$test_expectations > starting_expectations 0.05) if (snapshot_skipped) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), skip("On CRAN") 0.1) } expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), else if (!new_expectations && skip_on_empty) { 0.85) skip_empty() } })}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {30: skip(paste0("{", e$package, "} is not installed."))eval(code, test_env)
}31: }, snapshot_on_cran = function(cnd) {eval(code, test_env) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")32: }, skip = handle_skip, warning = handle_warning, message = handle_message, withCallingHandlers({ error = handle_error, interrupt = handle_interrupt)
eval(code, test_env)21: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
skip("On CRAN")22: tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
else if (!new_expectations && skip_on_empty) {23: skip_empty() }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {24: skip(paste0("{", e$package, "} is not installed."))tryCatch(withCallingHandlers({ } eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt)
skip_empty() }33: }, expectation = handle_expectation, packageNotFoundError = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) }34: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")35: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)tryCatchList(expr, classes, parentenv, handlers)
25: 36: doWithOneRestart(return(expr), restart)
tryCatch(withCallingHandlers({26: eval(code, test_env)withOneRestart(expr, restarts[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {27: skip("On CRAN") }withRestarts(tryCatch(withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { skip("On CRAN") if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip(paste0("{", e$package, "} is not installed."))
}37: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUEdoWithOneRestart(return(expr), restart) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 38: withOneRestart(expr, restarts[[1L]]) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {39: })withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)28: new_expectations <- the$test_expectations > starting_expectationstest_code(code, parent.frame()) if (snapshot_skipped) {
skip("On CRAN")29: } else if (!new_expectations && skip_on_empty) {test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", skip_empty() { } sampler_directed_cov$rNetwork(store = TRUE)}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, if (on_cran()) { "bernoulli", TRUE, covarList = covarList_directed) skip(paste0("{", e$package, "} is not installed.")) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, } plot = FALSE)) mySBM_sbm$setModel(Q)}, snapshot_on_cran = function(cnd) { net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, covariates = covarList_directed) snapshot_skipped <<- TRUE cls <- net$clustering(1:(2 * Q)) invokeRestart("muffle_cran_snapshot") cl <- cls[[Q]]}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), clusterInit = cl, covarList = covarList_directed) end_test = function() { mySBM_missSBM$doVEM(trace = TRUE) }) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
0.1)40: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), test_code(code = exprs, env = env, reporter = get_reporter() %||% 0.8) StopReporter$new()) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.05) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 41: 0.1)source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 0.85)
42: })FUN(X[[i]], ...)
30:
43: eval(code, test_env)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
31: 44: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler)
32: 45: withCallingHandlers({tryCatchOne(expr, names, parentenv, handlers[[1L]])
eval(code, test_env)46: tryCatchList(expr, classes, parentenv, handlers) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {47: skip("On CRAN")tryCatch(code, testthat_abort_reporter = function(cnd) { } cat(conditionMessage(cnd), "\n") else if (!new_expectations && skip_on_empty) { NULL skip_empty()}) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {48: if (on_cran()) {with_reporter(reporters$multi, lapply(test_paths, test_one_file, skip(paste0("{", e$package, "} is not installed.")) } env = env, desc = desc, shuffle = shuffle, error_call = error_call))}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE
49: invokeRestart("muffle_cran_snapshot")test_files_serial(test_dir = test_dir, test_package = test_package, }, skip = handle_skip, warning = handle_warning, message = handle_message, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, error = handle_error, interrupt = handle_interrupt) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)33:
50: doTryCatch(return(expr), name, parentenv, handler)
test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, 34: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, tryCatchOne(expr, names, parentenv, handlers[[1L]]) load_package = load_package, parallel = parallel, shuffle = shuffle)
35: 51: tryCatchList(expr, classes, parentenv, handlers)test_dir("testthat", package = package, reporter = reporter,
36: ..., load_package = "installed")
tryCatch(withCallingHandlers({52: test_check("missSBM") eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectationsAn irrecoverable exception occurred. R is aborting now ...
if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
Traceback:
1: 12: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
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$do_one_estim, mc.cores = ncores, lapply(X = S, FUN = FUN, ...) verbose = (verbosity > 4))
4: 14: doTryCatch(return(expr), name, parentenv, handler).self$do_with_inits(inits, Q, reinitialization_effort)
5: 15: tryCatchOne(expr, names, parentenv, handlers[[1L]]).self$estim_ascend(reinitialization_effort, changing_effort)
6: 16: tryCatchList(expr, classes, parentenv, handlers)private$BMobject$estimate()
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) {17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) if (identical(call[[1L]], quote(doTryCatch)))
18: call <- sys.call(-4L)eval(code, test_env) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")19: LONG <- 75Leval(code, test_env)
20: sm <- strsplit(conditionMessage(e), "\n")[[1L]]withCallingHandlers({ w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") eval(code, test_env) if (is.na(w)) new_expectations <- the$test_expectations > starting_expectations w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (snapshot_skipped) { type = "b") skip("On CRAN") if (w > LONG) } prefix <- paste0(prefix, "\n ") else if (!new_expectations && skip_on_empty) { } skip_empty() else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n")}, expectation = handle_expectation, packageNotFoundError = function(e) { .Internal(seterrmessage(msg[1L])) if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile)}, snapshot_on_cran = function(cnd) { .Internal(printDeferredWarnings()) snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") invisible(structure(msg, class = "try-error", condition = e))}, skip = handle_skip, warning = handle_warning, message = handle_message, }) error = handle_error, interrupt = handle_interrupt)
8: 21: doTryCatch(return(expr), name, parentenv, handler)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchList(expr, classes, parentenv, handlers)
10: FUN(X[[i]], ...)24:
tryCatch(withCallingHandlers({ eval(code, test_env)11: new_expectations <- the$test_expectations > starting_expectationslapply(seq_len(cores), inner.do) if (snapshot_skipped) {
skip("On CRAN")12: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, else if (!new_expectations && skip_on_empty) { mc.silent = TRUE) skip_empty()
}13: }, expectation = handle_expectation, packageNotFoundError = function(e) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
if (on_cran()) {14: skip(paste0("{", e$package, "} is not installed.")).self$do_with_inits(inits, Q, reinitialization_effort) }
}, snapshot_on_cran = function(cnd) {15: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot").self$estim_ascend(reinitialization_effort, changing_effort)
}, skip = handle_skip, warning = handle_warning, message = handle_message, 16: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)private$BMobject$estimate()
25: doWithOneRestart(return(expr), restart)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: 26: eval(code, test_env)withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({19: eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN")20: }withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() } new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip(paste0("{", e$package, "} is not installed.")) end_test = function() { } })
}, snapshot_on_cran = function(cnd) {28: test_code(code, parent.frame())
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")29: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", error = handle_error, interrupt = handle_interrupt) {
sampler_undirected_nocov$rNetwork(store = TRUE)21: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, doTryCatch(return(expr), name, parentenv, handler) "bernoulli", FALSE)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 22: plot = FALSE))tryCatchOne(expr, names, parentenv, handlers[[1L]]) mySBM_sbm$setModel(3)
net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData)23: cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl)tryCatchList(expr, classes, parentenv, handlers) mySBM_missSBM$doVEM()
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 24: 0.05)tryCatch(withCallingHandlers({ expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), eval(code, test_env) 0.95) new_expectations <- the$test_expectations > starting_expectations expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), if (snapshot_skipped) { 0.01) skip("On CRAN") expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), } 0.05) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), else if (!new_expectations && skip_on_empty) { 0.95) skip_empty() }) }
30: eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))31: }eval(code, test_env)}, snapshot_on_cran = function(cnd) {
32: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {doWithOneRestart(return(expr), restart) skip("On CRAN")
26: }withOneRestart(expr, restarts[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty() }27: }, expectation = handle_expectation, packageNotFoundError = function(e) {withRestarts(tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") } else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) skip_empty() }
}, expectation = handle_expectation, packageNotFoundError = function(e) {33: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler)
skip(paste0("{", e$package, "} is not installed.")) }34: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: snapshot_skipped <<- TRUEtryCatchList(expr, classes, parentenv, handlers)
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) end_test = function() { new_expectations <- the$test_expectations > starting_expectations }) if (snapshot_skipped) {
skip("On CRAN")28: } else if (!new_expectations && skip_on_empty) {test_code(code, parent.frame()) skip_empty()
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", } {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { sampler_undirected_nocov$rNetwork(store = TRUE) skip(paste0("{", e$package, "} is not installed.")) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, } "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, }, snapshot_on_cran = function(cnd) { plot = FALSE)) mySBM_sbm$setModel(3) snapshot_skipped <<- TRUE net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, clusterInit = cl) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
mySBM_missSBM$doVEM()37: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), doWithOneRestart(return(expr), restart) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 38: 0.95)withOneRestart(expr, restarts[[1L]]) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)39: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), withRestarts(tryCatch(withCallingHandlers({ 0.05) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), skip("On CRAN") 0.95) } }) else if (!new_expectations && skip_on_empty) {
skip_empty()30: eval(code, test_env) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {31: skip(paste0("{", e$package, "} is not installed.")) }eval(code, test_env)
}, snapshot_on_cran = function(cnd) {32: withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() { else if (!new_expectations && skip_on_empty) { }) skip_empty()
}40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())}, expectation = handle_expectation, packageNotFoundError = function(e) {
41: if (on_cran()) {source_file(path, env = env(env), desc = desc, shuffle = shuffle, skip(paste0("{", e$package, "} is not installed.")) error_call = error_call) }
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")42: FUN(X[[i]], ...)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 33: error_call = error_call)doTryCatch(return(expr), name, parentenv, handler)
44: 34: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])36:
tryCatch(withCallingHandlers({46: tryCatchList(expr, classes, parentenv, handlers)
47: eval(code, test_env)tryCatch(code, testthat_abort_reporter = function(cnd) { new_expectations <- the$test_expectations > starting_expectations cat(conditionMessage(cnd), "\n") if (snapshot_skipped) { NULL skip("On CRAN")}) }
else if (!new_expectations && skip_on_empty) {48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, skip_empty() env = env, desc = desc, shuffle = shuffle, error_call = error_call)) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {49: test_files_serial(test_dir = test_dir, test_package = test_package, skip(paste0("{", e$package, "} is not installed.")) 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)}, snapshot_on_cran = function(cnd) {
50: snapshot_skipped <<- TRUEtest_files(test_dir = path, test_paths = test_paths, test_package = package, invokeRestart("muffle_cran_snapshot") reporter = reporter, load_helpers = load_helpers, env = env, }, skip = handle_skip, warning = handle_warning, message = handle_message, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
51: 37: test_dir("testthat", package = package, reporter = reporter, doWithOneRestart(return(expr), restart) ..., load_package = "installed")
52: test_check("missSBM")
38: An irrecoverable exception occurred. R is aborting now ...
withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1:
Traceback:
dispatcher(membership_name, membership_init$to_cc(), model_name, 1: .self$network_to_cc(), TRUE)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE) 2:
FUN(X[[i]], ...) 2:
FUN(X[[i]], ...) 3:
lapply(X = S, FUN = FUN, ...) 3:
lapply(X = S, FUN = FUN, ...) 4:
doTryCatch(return(expr), name, parentenv, handler)
4: 5: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
6: 7: tryCatchList(expr, classes, parentenv, handlers)tryCatch(expr, error = function(e) {
call <- conditionCall(e) 7: if (!is.null(call)) {tryCatch(expr, error = function(e) { if (identical(call[[1L]], quote(doTryCatch))) call <- conditionCall(e) call <- sys.call(-4L) if (!is.null(call)) { dcall <- deparse(call, nlines = 1L) if (identical(call[[1L]], quote(doTryCatch))) prefix <- paste("Error in", dcall, ": ") call <- sys.call(-4L) LONG <- 75L dcall <- deparse(call, nlines = 1L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] prefix <- paste("Error in", dcall, ": ") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") LONG <- 75L if (is.na(w)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] 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)
9: 8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
10: 9: FUN(X[[i]], ...)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
11: 10: lapply(seq_len(cores), inner.do)FUN(X[[i]], ...)
12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 11: mc.silent = TRUE)lapply(seq_len(cores), inner.do)
13: 12: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, verbose = (verbosity > 4)) mc.silent = TRUE)
14: 13: .self$do_with_inits(inits, Q, reinitialization_effort)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))15:
.self$estim_ascend(reinitialization_effort, changing_effort)14:
.self$do_with_inits(inits, Q, reinitialization_effort)16:
private$BMobject$estimate()15:
.self$estim_ascend(reinitialization_effort, changing_effort)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))16:
private$BMobject$estimate()18:
eval(code, test_env)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))19:
eval(code, test_env)18:
eval(code, test_env)20:
withCallingHandlers({19: eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
20: if (snapshot_skipped) {withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$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$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$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 <<- TRUE21: 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)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])21: doTryCatch(return(expr), name, parentenv, handler)
23: 22: tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: 23: tryCatch(withCallingHandlers({tryCatchList(expr, classes, parentenv, handlers) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations24: if (snapshot_skipped) { skip("On CRAN")tryCatch(withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$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$package, "} is not installed.")) skip_empty() }}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, snapshot_on_cran = function(cnd) {25: snapshot_skipped <<- TRUEdoWithOneRestart(return(expr), restart) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 26: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)withOneRestart(expr, restarts[[1L]])
25: 27: doWithOneRestart(return(expr), restart)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)26: new_expectations <- the$test_expectations > starting_expectationswithOneRestart(expr, restarts[[1L]]) if (snapshot_skipped) {
skip("On CRAN")27: }withRestarts(tryCatch(withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() {}, snapshot_on_cran = function(cnd) { })
snapshot_skipped <<- TRUE28: invokeRestart("muffle_cran_snapshot")test_code(code, parent.frame())}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 29: end_test = function() {test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", }) {
sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, 28: "bernoulli", TRUE)test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) { mySBM_sbm$setModel(3) sampler_directed_nocov$rNetwork(store = TRUE) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, clusterInit = cl) plot = FALSE)) mySBM_missSBM$doVEM() mySBM_sbm$setModel(3) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) 0.1) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) clusterInit = cl) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), mySBM_missSBM$doVEM() 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 0.1) 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.95) 0.2) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.01) 0.95) 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)
30: 31: eval(code, test_env)eval(code, test_env)
31: 32: eval(code, test_env)withCallingHandlers({
eval(code, test_env)32: 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 } 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)
}, skip = handle_skip, warning = handle_warning, message = handle_message, 33: error = handle_error, interrupt = handle_interrupt)doTryCatch(return(expr), name, parentenv, handler)
33:
doTryCatch(return(expr), name, parentenv, handler)34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
35: tryCatchList(expr, classes, parentenv, handlers)36:
tryCatch(withCallingHandlers({36: eval(code, test_env)tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { 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()) { 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_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) { skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty()}, expectation = handle_expectation, packageNotFoundError = function(e) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) { snapshot_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), end_test = function() { invokeRestart("muffle_cran_snapshot") })}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 40: end_test = function() {test_code(code = exprs, env = env, reporter = get_reporter() %||% }) StopReporter$new())
40: 41: test_code(code = exprs, env = env, reporter = get_reporter() %||% source_file(path, env = env(env), desc = desc, shuffle = shuffle, StopReporter$new()) error_call = error_call)
41: 42: source_file(path, env = env(env), desc = desc, shuffle = shuffle, FUN(X[[i]], ...) error_call = error_call)
43: 42: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, FUN(X[[i]], ...) error_call = error_call)
44: 43: doTryCatch(return(expr), name, parentenv, handler)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])44:
doTryCatch(return(expr), name, parentenv, handler)46:
tryCatchList(expr, classes, parentenv, handlers)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])47:
tryCatch(code, testthat_abort_reporter = function(cnd) {46: tryCatchList(expr, classes, parentenv, handlers) cat(conditionMessage(cnd), "\n")
NULL47: })tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, NULL env = env, desc = desc, shuffle = shuffle, error_call = error_call))})
49: 48: test_files_serial(test_dir = test_dir, test_package = test_package, with_reporter(reporters$multi, lapply(test_paths, test_one_file, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, desc = desc, shuffle = shuffle, 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, 49: 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, 50: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_files(test_dir = path, test_paths = test_paths, test_package = package, desc = desc, load_package = load_package, shuffle = shuffle, reporter = reporter, load_helpers = load_helpers, env = env, error_call = error_call) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)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 = "installed")
load_package = load_package, parallel = parallel, shuffle = shuffle)52:
test_check("missSBM")51: test_dir("testthat", package = package, reporter = reporter,
..., 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-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