Last updated on 2026-11-13 12:51:15 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 86.01 | 338.45 | 424.46 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 58.86 | 260.29 | 319.15 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 60.00 | 254.27 | 314.27 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 257.44 | 321.44 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 422.00 | 513.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 80.59 | 359.22 | 439.81 | 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 | 99.00 | 414.00 | 513.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 20.00 | 87.00 | 107.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 117.00 | 542.00 | 659.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [38s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missSBM)
>
> test_check("missSBM")
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 3 model(s).
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degreeTested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degree
sampling: dyad new better on connectivity
node
double-standard
block-node new better on mixture
Adjusting Variational EM for Stochastic Block Model
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'node' network-sampling process
Initialization of 1 model(s).
Performing VEM inference
Model with 3 blocks.
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 2 model(s).
Performing VEM inference
Model with 2 blocks.
Model with 1 blocks.
Polishing (node-swap)
Looking for better solutions
Pass 1 Going forward +
Pass 1 Going backward +
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$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$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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 ...
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$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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 ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
Traceback:
11: 1: lapply(seq_len(cores), inner.do)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 2: mc.silent = TRUE)FUN(X[[i]], ...)
13: 3: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, lapply(X = S, FUN = FUN, ...) verbose = (verbosity > 4))
4: doTryCatch(return(expr), name, parentenv, handler)14:
.self$do_with_inits(inits, Q, reinitialization_effort) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 15: tryCatchList(expr, classes, parentenv, handlers).self$estim_ascend(reinitialization_effort, changing_effort)
7:
tryCatch(expr, error = function(e) {16: call <- conditionCall(e)private$BMobject$estimate() if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 17: call <- sys.call(-4L)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")18: LONG <- 75Leval(code, test_env) 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")19: if (w > LONG) 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$test_expectations > starting_expectations cat(msg, file = outFile) if (snapshot_skipped) { .Internal(printDeferredWarnings()) skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { invisible(structure(msg, class = "try-error", condition = e)) skip_empty()}) }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 8: }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)FUN(X[[i]], ...)
21: doTryCatch(return(expr), name, parentenv, handler)11:
lapply(seq_len(cores), inner.do)22:
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
23: 13: tryCatchList(expr, classes, parentenv, handlers)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))24:
tryCatch(withCallingHandlers({14: eval(code, test_env).self$do_with_inits(inits, Q, reinitialization_effort) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {15: skip("On CRAN").self$estim_ascend(reinitialization_effort, changing_effort) }
else if (!new_expectations && skip_on_empty) {16: skip_empty()private$BMobject$estimate() }}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {17: skip(paste0("{", e$package, "} is not installed."))mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) }
}, snapshot_on_cran = function(cnd) {18: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)19:
eval(code, test_env)25:
doWithOneRestart(return(expr), restart)20:
withCallingHandlers({26: eval(code, test_env) 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$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { }}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt) skip(paste0("{", e$package, "} is not installed."))
}21: }, snapshot_on_cran = function(cnd) {doTryCatch(return(expr), name, parentenv, handler) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")22: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {23: })tryCatchList(expr, classes, parentenv, handlers)
28: 24: test_code(code, parent.frame())tryCatch(withCallingHandlers({
eval(code, test_env)29: new_expectations <- the$test_expectations > starting_expectationstest_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", if (snapshot_skipped) { { skip("On CRAN") sampler_directed_cov$rNetwork(store = TRUE) } mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, else if (!new_expectations && skip_on_empty) { "bernoulli", TRUE, covarList = covarList_directed) skip_empty() mySBM_sbm$optimize(estimOptions = list(verbosity = 0, }}, expectation = handle_expectation, packageNotFoundError = function(e) { plot = FALSE)) mySBM_sbm$setModel(Q) if (on_cran()) { net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, skip(paste0("{", e$package, "} is not installed.")) covariates = covarList_directed) } cls <- net$clustering(1:(2 * Q))}, snapshot_on_cran = function(cnd) { cl <- cls[[Q]] snapshot_skipped <<- TRUE mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, invokeRestart("muffle_cran_snapshot") clusterInit = cl, covarList = covarList_directed)}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_missSBM$doVEM(trace = TRUE) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
0.1)25: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), doWithOneRestart(return(expr), restart) 0.8)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 26: 0.05)withOneRestart(expr, restarts[[1L]]) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean),
0.1)27: expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), withRestarts(tryCatch(withCallingHandlers({ 0.85) eval(code, test_env) }) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {30: skip("On CRAN")eval(code, test_env) }
else if (!new_expectations && skip_on_empty) {31: skip_empty()eval(code, test_env) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {32: skip(paste0("{", e$package, "} is not installed."))withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { invokeRestart("muffle_cran_snapshot") skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), else if (!new_expectations && skip_on_empty) { end_test = function() { skip_empty() })
}28: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_code(code, parent.frame()) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))29: }test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", }, snapshot_on_cran = function(cnd) { { snapshot_skipped <<- TRUE sampler_directed_cov$rNetwork(store = TRUE) invokeRestart("muffle_cran_snapshot") mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, }, skip = handle_skip, warning = handle_warning, message = handle_message, "bernoulli", TRUE, covarList = covarList_directed) error = handle_error, interrupt = handle_interrupt) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))33: mySBM_sbm$setModel(Q)doTryCatch(return(expr), name, parentenv, handler) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData,
covariates = covarList_directed)34: cls <- net$clustering(1:(2 * Q))tryCatchOne(expr, names, parentenv, handlers[[1L]]) cl <- cls[[Q]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, 35: clusterInit = cl, covarList = covarList_directed)tryCatchList(expr, classes, parentenv, handlers) mySBM_missSBM$doVEM(trace = TRUE)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 36: 0.1)tryCatch(withCallingHandlers({ expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), eval(code, test_env) 0.8) new_expectations <- the$test_expectations > starting_expectations expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), if (snapshot_skipped) { 0.05) skip("On CRAN") expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), } 0.1) else if (!new_expectations && skip_on_empty) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), skip_empty() 0.85) } })}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {30: skip(paste0("{", e$package, "} is not installed."))eval(code, test_env) }
}, snapshot_on_cran = function(cnd) {31: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 32: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)withCallingHandlers({
eval(code, test_env)37: new_expectations <- the$test_expectations > starting_expectationsdoWithOneRestart(return(expr), restart) if (snapshot_skipped) {
skip("On CRAN")38: }withOneRestart(expr, restarts[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()39: }withRestarts(tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {33: skip(paste0("{", e$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) {34: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 35: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), tryCatchList(expr, classes, parentenv, handlers) end_test = function() {
})36:
tryCatch(withCallingHandlers({40: eval(code, test_env)test_code(code = exprs, env = env, reporter = get_reporter() %||% new_expectations <- the$test_expectations > starting_expectations StopReporter$new()) if (snapshot_skipped) {
skip("On CRAN")41: }source_file(path, env = env(env), desc = desc, shuffle = shuffle, else if (!new_expectations && skip_on_empty) { error_call = error_call) skip_empty()
}42: }, expectation = handle_expectation, packageNotFoundError = function(e) {FUN(X[[i]], ...) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))43: }lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, }, snapshot_on_cran = function(cnd) { error_call = error_call) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")44: }, skip = handle_skip, warning = handle_warning, message = handle_message, doTryCatch(return(expr), name, parentenv, handler) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
45: 37: tryCatchOne(expr, names, parentenv, handlers[[1L]])doWithOneRestart(return(expr), restart)
46: 38: tryCatchList(expr, classes, parentenv, handlers)withOneRestart(expr, restarts[[1L]])
47: 39: tryCatch(code, testthat_abort_reporter = function(cnd) {withRestarts(tryCatch(withCallingHandlers({ cat(conditionMessage(cnd), "\n") eval(code, test_env) NULL new_expectations <- the$test_expectations > starting_expectations}) if (snapshot_skipped) {
skip("On CRAN")48: }with_reporter(reporters$multi, lapply(test_paths, test_one_file, else if (!new_expectations && skip_on_empty) { env = env, desc = desc, shuffle = shuffle, error_call = error_call)) skip_empty()
}49: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_files_serial(test_dir = test_dir, test_package = test_package, if (on_cran()) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, skip(paste0("{", e$package, "} is not installed.")) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } desc = desc, load_package = load_package, shuffle = shuffle, }, snapshot_on_cran = function(cnd) { error_call = error_call) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")50: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_files(test_dir = path, test_paths = test_paths, test_package = package, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), reporter = reporter, load_helpers = load_helpers, env = env, end_test = function() { stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }) load_package = load_package, parallel = parallel, shuffle = shuffle)
40: 51: test_code(code = exprs, env = env, reporter = get_reporter() %||% test_dir("testthat", package = package, reporter = reporter, StopReporter$new()) ..., load_package = "installed")
41: 52: source_file(path, env = env(env), desc = desc, shuffle = shuffle, test_check("missSBM") error_call = error_call)
An irrecoverable exception occurred. R is aborting now ...
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
Traceback:
1: 16: dispatcher(membership_name, membership_init$to_cc(), model_name, private$BMobject$estimate() .self$network_to_cc(), TRUE)
17: 2: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))FUN(X[[i]], ...)
18: 3: eval(code, test_env)lapply(X = S, FUN = FUN, ...)
19: 4: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler)
20: 5: withCallingHandlers({tryCatchOne(expr, names, parentenv, handlers[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations 6: if (snapshot_skipped) {tryCatchList(expr, classes, parentenv, handlers) skip("On CRAN")
} 7: else if (!new_expectations && skip_on_empty) {tryCatch(expr, error = function(e) { skip_empty() call <- conditionCall(e) } if (!is.null(call)) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (identical(call[[1L]], quote(doTryCatch))) if (on_cran()) { call <- sys.call(-4L) skip(paste0("{", e$package, "} is not installed.")) dcall <- deparse(call, nlines = 1L) } prefix <- paste("Error in", dcall, ": ")}, snapshot_on_cran = function(cnd) { LONG <- 75L snapshot_skipped <<- TRUE sm <- strsplit(conditionMessage(e), "\n")[[1L]] invokeRestart("muffle_cran_snapshot") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, skip = handle_skip, warning = handle_warning, message = handle_message, if (is.na(w)) error = handle_error, interrupt = handle_interrupt) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")21: if (w > LONG) doTryCatch(return(expr), name, parentenv, handler) prefix <- paste0(prefix, "\n ")
}22: else prefix <- "Error : "tryCatchOne(expr, names, parentenv, handlers[[1L]]) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))23: if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatchList(expr, classes, parentenv, handlers) cat(msg, file = outFile)
.Internal(printDeferredWarnings())24: }tryCatch(withCallingHandlers({ invisible(structure(msg, class = "try-error", condition = e)) eval(code, test_env)}) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty()
} 8: }, expectation = handle_expectation, packageNotFoundError = function(e) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) } 9: }, snapshot_on_cran = function(cnd) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")10: }, skip = handle_skip, warning = handle_warning, message = handle_message, FUN(X[[i]], ...)
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)11:
lapply(seq_len(cores), inner.do)
25: 12: doWithOneRestart(return(expr), restart)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE,
mc.silent = TRUE)26:
withOneRestart(expr, restarts[[1L]])13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 27: verbose = (verbosity > 4))
withRestarts(tryCatch(withCallingHandlers({14: eval(code, test_env).self$do_with_inits(inits, Q, reinitialization_effort) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {15: skip("On CRAN").self$estim_ascend(reinitialization_effort, changing_effort)
}16: else if (!new_expectations && skip_on_empty) { skip_empty() }private$BMobject$estimate()}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
}17: }, snapshot_on_cran = function(cnd) {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) 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)
28: 20: test_code(code, parent.frame())withCallingHandlers({
eval(code, test_env)29: new_expectations <- the$test_expectations > starting_expectationstest_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", if (snapshot_skipped) { { skip("On CRAN") sampler_undirected_nocov$rNetwork(store = TRUE) } mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, else if (!new_expectations && skip_on_empty) { "bernoulli", FALSE) skip_empty() mySBM_sbm$optimize(estimOptions = list(verbosity = 0, } plot = FALSE))}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_sbm$setModel(3) if (on_cran()) { net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) skip(paste0("{", e$package, "} is not installed.")) cl <- net$clustering(3)[[1]] } mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, }, snapshot_on_cran = function(cnd) { clusterInit = cl) snapshot_skipped <<- TRUE mySBM_missSBM$doVEM() invokeRestart("muffle_cran_snapshot") expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.05) error = handle_error, interrupt = handle_interrupt) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.95)21: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), doTryCatch(return(expr), name, parentenv, handler) 0.01)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 22: 0.05)tryCatchOne(expr, names, parentenv, handlers[[1L]]) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships),
0.95)23: })tryCatchList(expr, classes, parentenv, handlers)
30: 24: eval(code, test_env)tryCatch(withCallingHandlers({
eval(code, test_env)31: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
skip("On CRAN")32: }withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$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)withOneRestart(expr, restarts[[1L]])
33: 27: doTryCatch(return(expr), name, parentenv, handler)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)34: new_expectations <- the$test_expectations > starting_expectationstryCatchOne(expr, names, parentenv, handlers[[1L]]) if (snapshot_skipped) {
skip("On CRAN")35: }tryCatchList(expr, classes, parentenv, handlers) else if (!new_expectations && skip_on_empty) {
skip_empty()36: }tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, expectation = handle_expectation, packageNotFoundError = function(e) { end_test = function() { if (on_cran()) { }) skip(paste0("{", e$package, "} is not installed."))
}28: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUEtest_code(code, parent.frame()) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", 37: {doWithOneRestart(return(expr), restart) sampler_undirected_nocov$rNetwork(store = TRUE)
mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, 38: "bernoulli", FALSE)withOneRestart(expr, restarts[[1L]]) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))39: mySBM_sbm$setModel(3)withRestarts(tryCatch(withCallingHandlers({ net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) eval(code, test_env) cl <- net$clustering(3)[[1]] new_expectations <- the$test_expectations > starting_expectations mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, if (snapshot_skipped) { clusterInit = cl) skip("On CRAN") mySBM_missSBM$doVEM() } expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), else if (!new_expectations && skip_on_empty) { 0.05) skip_empty() } expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.95) if (on_cran()) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), skip(paste0("{", e$package, "} is not installed.")) 0.01) } expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), }, snapshot_on_cran = function(cnd) { 0.05) snapshot_skipped <<- TRUE expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), invokeRestart("muffle_cran_snapshot") 0.95)}, skip = handle_skip, warning = handle_warning, message = handle_message, }) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {30: })eval(code, test_env)
40: 31: test_code(code = exprs, env = env, reporter = get_reporter() %||% eval(code, test_env) StopReporter$new())
32: 41: withCallingHandlers({source_file(path, env = env(env), desc = desc, shuffle = shuffle, eval(code, test_env) error_call = error_call) new_expectations <- the$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$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE45: invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)46:
tryCatchList(expr, classes, parentenv, handlers)33:
doTryCatch(return(expr), name, parentenv, handler)
47: 34: tryCatch(code, testthat_abort_reporter = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) cat(conditionMessage(cnd), "\n") NULL
})35:
tryCatchList(expr, classes, parentenv, handlers)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 36: env = env, desc = desc, shuffle = shuffle, error_call = error_call))tryCatch(withCallingHandlers({
eval(code, test_env)49: new_expectations <- the$test_expectations > starting_expectationstest_files_serial(test_dir = test_dir, test_package = test_package, if (snapshot_skipped) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, skip("On CRAN") env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } desc = desc, load_package = load_package, shuffle = shuffle, else if (!new_expectations && skip_on_empty) { error_call = error_call) skip_empty()
}50: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_files(test_dir = path, test_paths = test_paths, test_package = package, if (on_cran()) { reporter = reporter, load_helpers = load_helpers, env = env, skip(paste0("{", e$package, "} is not installed.")) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } load_package = load_package, parallel = parallel, shuffle = shuffle)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE51: invokeRestart("muffle_cran_snapshot")test_dir("testthat", package = package, reporter = reporter, }, skip = handle_skip, warning = handle_warning, message = handle_message, ..., load_package = "installed") error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
52: 37: test_check("missSBM")doWithOneRestart(return(expr), restart)
An irrecoverable exception occurred. R is aborting now ...
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
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$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37:
Traceback:
doWithOneRestart(return(expr), restart)
1: 38: withOneRestart(expr, restarts[[1L]])
dispatcher(membership_name, membership_init$to_cc(), model_name, 39: .self$network_to_cc(), TRUE)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { 2: skip("On CRAN")FUN(X[[i]], ...)
} 3: lapply(X = S, FUN = FUN, ...) else if (!new_expectations && skip_on_empty) {
skip_empty() } 4: }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
} 5: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 6: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() { 7: })tryCatch(expr, error = function(e) {
call <- conditionCall(e)40: if (!is.null(call)) {test_code(code = exprs, env = env, reporter = get_reporter() %||% if (identical(call[[1L]], quote(doTryCatch))) StopReporter$new()) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)41: prefix <- paste("Error in", dcall, ": ")source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]42: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")FUN(X[[i]], ...) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 43: type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ")lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } else prefix <- "Error : " error_call = error_call) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))44: if (!silent && isTRUE(getOption("show.error.messages"))) {doTryCatch(return(expr), name, parentenv, handler) cat(msg, file = outFile)
.Internal(printDeferredWarnings())45: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) invisible(structure(msg, class = "try-error", condition = e))
})46:
tryCatchList(expr, classes, parentenv, handlers) 8:
47: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n") 9: NULL})sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, FUN(X[[i]], ...) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
11:
49: lapply(seq_len(cores), inner.do)test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 12: desc = desc, load_package = load_package, shuffle = shuffle, parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE) error_call = error_call)
13: 50: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, test_files(test_dir = path, test_paths = test_paths, test_package = package, verbose = (verbosity > 4)) 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)
14: 51: .self$do_with_inits(inits, Q, reinitialization_effort)test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")15:
.self$estim_ascend(reinitialization_effort, changing_effort)An irrecoverable exception occurred. R is aborting now ...
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) })
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