Last updated on 2026-09-30 07:50:50 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 86.89 | 357.64 | 444.53 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 56.32 | 242.68 | 299.00 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 59.00 | 243.15 | 302.15 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 63.00 | 247.50 | 310.50 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 450.00 | 541.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 83.11 | 346.95 | 430.06 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 80.87 | 341.38 | 422.25 | 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 | 98.00 | 361.00 | 459.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 19.00 | 106.00 | 125.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 119.00 | 513.00 | 632.00 | 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)
Traceback:
expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) 1: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), dispatcher(membership_name, membership_init$to_cc(), model_name, 0.85) .self$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)) 30: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], eval(code, test_env) type = "b")
if (w > LONG) 31: prefix <- paste0(prefix, "\n ")eval(code, test_env) }
else prefix <- "Error : "32: 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$test_expectations > starting_expectations if (snapshot_skipped) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } skip("On CRAN") invisible(structure(msg, class = "try-error", condition = e)) }}) else if (!new_expectations && skip_on_empty) {
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: skip_empty()sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
}10: }, expectation = handle_expectation, packageNotFoundError = function(e) {FUN(X[[i]], ...) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))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$do_one_estim, mc.cores = ncores, }, snapshot_on_cran = function(cnd) { verbose = (verbosity > 4)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env)14: .self$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) { skip_empty()
}16: }, expectation = handle_expectation, packageNotFoundError = function(e) {private$BMobject$estimate()
if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))17: }mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE19: invokeRestart("muffle_cran_snapshot")eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: 20: withRestarts(tryCatch(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) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$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 <<- 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() %||% 21: StopReporter$new())doTryCatch(return(expr), name, parentenv, handler)
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])44:
doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchList(expr, classes, parentenv, handlers)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {46: tryCatchList(expr, classes, parentenv, handlers) skip("On CRAN") }
else if (!new_expectations && skip_on_empty) {47: skip_empty()tryCatch(code, testthat_abort_reporter = function(cnd) { } cat(conditionMessage(cnd), "\n")}, expectation = handle_expectation, packageNotFoundError = function(e) { NULL}) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))48: }with_reporter(reporters$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, }, snapshot_on_cran = function(cnd) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, snapshot_skipped <<- TRUE env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, invokeRestart("muffle_cran_snapshot") desc = desc, load_package = load_package, shuffle = shuffle, }, skip = handle_skip, warning = handle_warning, message = handle_message, error_call = error_call) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: 50: doWithOneRestart(return(expr), restart)test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 26: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, withOneRestart(expr, restarts[[1L]]) load_package = load_package, parallel = parallel, shuffle = shuffle)
27:
withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN")51: }test_dir("testthat", package = package, reporter = reporter, else if (!new_expectations && skip_on_empty) { ..., load_package = "installed") skip_empty()
}}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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: 52: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", test_check("missSBM") { 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), An irrecoverable exception occurred. R is aborting now ...
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)
Traceback:
2: 1: FUN(X[[i]], ...)
dispatcher(membership_name, membership_init$to_cc(), model_name, 3: .self$network_to_cc(), TRUE)lapply(X = S, FUN = FUN, ...)
4: 2: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)
5: 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])lapply(X = S, FUN = FUN, ...)
6: 4: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
7: 5: tryCatch(expr, error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]])
call <- conditionCall(e) 6: tryCatchList(expr, classes, parentenv, handlers) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 7: tryCatch(expr, error = function(e) { call <- sys.call(-4L) call <- conditionCall(e) dcall <- deparse(call, nlines = 1L) if (!is.null(call)) { prefix <- paste("Error in", dcall, ": ") if (identical(call[[1L]], quote(doTryCatch))) LONG <- 75L call <- sys.call(-4L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] dcall <- deparse(call, nlines = 1L) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") prefix <- paste("Error in", dcall, ": ") if (is.na(w)) LONG <- 75L w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], sm <- strsplit(conditionMessage(e), "\n")[[1L]] type = "b") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (w > LONG) if (is.na(w)) prefix <- paste0(prefix, "\n ") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b") else prefix <- "Error : " if (w > LONG) msg <- paste0(prefix, conditionMessage(e), "\n") prefix <- paste0(prefix, "\n ") .Internal(seterrmessage(msg[1L])) } if (!silent && isTRUE(getOption("show.error.messages"))) { else prefix <- "Error : " cat(msg, file = outFile) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(printDeferredWarnings()) .Internal(seterrmessage(msg[1L])) } if (!silent && isTRUE(getOption("show.error.messages"))) { invisible(structure(msg, class = "try-error", condition = e)) cat(msg, file = outFile)}) .Internal(printDeferredWarnings())
} 8: invisible(structure(msg, class = "try-error", condition = e))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)
9: 10: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...)
10: 11: FUN(X[[i]], ...)lapply(seq_len(cores), inner.do)
12: 11: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, lapply(seq_len(cores), inner.do)
mc.silent = TRUE)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 13: mc.silent = TRUE)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 14: .self$do_with_inits(inits, Q, reinitialization_effort) verbose = (verbosity > 4))
15: 14: .self$estim_ascend(reinitialization_effort, changing_effort).self$do_with_inits(inits, Q, reinitialization_effort)
16: 15: private$BMobject$estimate()
.self$estim_ascend(reinitialization_effort, changing_effort)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))16:
private$BMobject$estimate()18:
eval(code, test_env)
17: 19: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))eval(code, test_env)
20: 18: withCallingHandlers({eval(code, test_env) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations19: if (snapshot_skipped) {eval(code, test_env) skip("On CRAN")
}20: else if (!new_expectations && skip_on_empty) {withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))21: }doTryCatch(return(expr), name, parentenv, handler)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE22: 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)23:
tryCatchList(expr, classes, parentenv, handlers)21:
doTryCatch(return(expr), name, parentenv, handler)24:
tryCatch(withCallingHandlers({22: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {23: skip("On CRAN")tryCatchList(expr, classes, parentenv, handlers) }
else if (!new_expectations && skip_on_empty) {24: skip_empty()tryCatch(withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {25: if (on_cran()) {doWithOneRestart(return(expr), restart) skip(paste0("{", e$package, "} is not installed."))
26: }}, snapshot_on_cran = function(cnd) {withOneRestart(expr, restarts[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")27: }, skip = handle_skip, warning = handle_warning, message = handle_message, withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {25: skip("On CRAN")doWithOneRestart(return(expr), restart) }
else if (!new_expectations && skip_on_empty) {26: skip_empty() }withOneRestart(expr, restarts[[1L]])}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {27: skip(paste0("{", e$package, "} is not installed."))withRestarts(tryCatch(withCallingHandlers({ }}, snapshot_on_cran = function(cnd) { eval(code, test_env) snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip("On CRAN") end_test = function() { } }) else if (!new_expectations && skip_on_empty) {
skip_empty()28: }test_code(code, parent.frame())}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {29: skip(paste0("{", e$package, "} is not installed."))test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", } {}, snapshot_on_cran = function(cnd) { sampler_directed_cov$rNetwork(store = TRUE) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, }, skip = handle_skip, warning = handle_warning, message = handle_message, "bernoulli", TRUE, covarList = covarList_directed) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, }) plot = FALSE))
mySBM_sbm$setModel(Q)28: net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, test_code(code, parent.frame()) covariates = covarList_directed)
cls <- net$clustering(1:(2 * Q))29: cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", clusterInit = cl, covarList = covarList_directed) { mySBM_missSBM$doVEM(trace = TRUE) sampler_directed_cov$rNetwork(store = TRUE) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) "bernoulli", TRUE, covarList = covarList_directed) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 0.05) plot = FALSE)) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), mySBM_sbm$setModel(Q) 0.1) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), covariates = covarList_directed) cls <- net$clustering(1:(2 * Q)) 0.85) cl <- cls[[Q]] }) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net,
clusterInit = cl, covarList = covarList_directed)30: mySBM_missSBM$doVEM(trace = TRUE)eval(code, test_env) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
0.1)31: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), eval(code, test_env)
0.8)32: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.05)withCallingHandlers({ expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 0.1) eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), new_expectations <- the$test_expectations > starting_expectations 0.85) if (snapshot_skipped) { }) skip("On CRAN")
}30: else if (!new_expectations && skip_on_empty) {eval(code, test_env) skip_empty() }
}, expectation = handle_expectation, packageNotFoundError = function(e) {31: if (on_cran()) {eval(code, test_env)
skip(paste0("{", e$package, "} is not installed."))32: }withCallingHandlers({}, snapshot_on_cran = function(cnd) { eval(code, test_env) snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") error = handle_error, interrupt = handle_interrupt)
}33: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler) skip_empty()
}34: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))35: }tryCatchList(expr, classes, parentenv, handlers)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE36: invokeRestart("muffle_cran_snapshot")tryCatch(withCallingHandlers({ eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt) if (snapshot_skipped) {
skip("On CRAN") }33: doTryCatch(return(expr), name, parentenv, handler) else if (!new_expectations && skip_on_empty) {
skip_empty()34: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {35: skip(paste0("{", e$package, "} is not installed.")) }tryCatchList(expr, classes, parentenv, handlers)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE36: invokeRestart("muffle_cran_snapshot")tryCatch(withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
new_expectations <- the$test_expectations > starting_expectations37: if (snapshot_skipped) {doWithOneRestart(return(expr), restart) skip("On CRAN")
}38: else if (!new_expectations && skip_on_empty) {withOneRestart(expr, restarts[[1L]]) skip_empty()
}39: }, expectation = handle_expectation, packageNotFoundError = function(e) {withRestarts(tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {37: if (on_cran()) {doWithOneRestart(return(expr), restart)
skip(paste0("{", e$package, "} is not installed."))38: }withOneRestart(expr, restarts[[1L]])
}, snapshot_on_cran = function(cnd) {39: snapshot_skipped <<- TRUEwithRestarts(tryCatch(withCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt), error = handle_fatal), if (snapshot_skipped) { skip("On CRAN") end_test = function() { } }) else if (!new_expectations && skip_on_empty) {
skip_empty()40: }test_code(code = exprs, env = env, reporter = get_reporter() %||% }, expectation = handle_expectation, packageNotFoundError = function(e) { StopReporter$new()) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))41: }source_file(path, env = env(env), desc = desc, shuffle = shuffle, }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE error_call = error_call) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 42: end_test = function() {FUN(X[[i]], ...) })
43: 40: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, test_code(code = exprs, env = env, reporter = get_reporter() %||% error_call = error_call) StopReporter$new())
44: 41: doTryCatch(return(expr), name, parentenv, handler)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: 46: FUN(X[[i]], ...)tryCatchList(expr, classes, parentenv, handlers)
47: 43: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n")lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) NULL})
48: 44: with_reporter(reporters$multi, lapply(test_paths, test_one_file, doTryCatch(return(expr), name, parentenv, handler) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
45: 49: tryCatchOne(expr, names, parentenv, handlers[[1L]])test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 46: tryCatchList(expr, classes, parentenv, handlers) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 47: error_call = error_call)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")50: NULL})test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 51: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, test_dir("testthat", package = package, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, ..., load_package = "installed") desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)52: test_check("missSBM")
50: An irrecoverable exception occurred. R is aborting now ...
test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, 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, no covariate", { sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net,
Traceback:
1: clusterInit = cl)dispatcher(membership_name, membership_init$to_cc(), model_name, mySBM_missSBM$doVEM() .self$network_to_cc(), TRUE) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
0.05) 2: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), FUN(X[[i]], ...) 0.95)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 3: 0.01)lapply(X = S, FUN = FUN, ...) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean),
0.05) 4: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), doTryCatch(return(expr), name, parentenv, handler) 0.95)
}) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])30:
eval(code, test_env) 6:
tryCatchList(expr, classes, parentenv, handlers)31:
eval(code, test_env) 7:
tryCatch(expr, error = function(e) {32: call <- conditionCall(e)withCallingHandlers({ eval(code, test_env) if (!is.null(call)) { new_expectations <- the$test_expectations > starting_expectations if (identical(call[[1L]], quote(doTryCatch))) if (snapshot_skipped) { call <- sys.call(-4L) skip("On CRAN") dcall <- deparse(call, nlines = 1L) } prefix <- paste("Error in", dcall, ": ") else if (!new_expectations && skip_on_empty) { LONG <- 75L skip_empty() sm <- strsplit(conditionMessage(e), "\n")[[1L]] } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, expectation = handle_expectation, packageNotFoundError = function(e) { if (is.na(w)) if (on_cran()) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], skip(paste0("{", e$package, "} is not installed.")) type = "b") } if (w > LONG) }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " invokeRestart("muffle_cran_snapshot") msg <- paste0(prefix, conditionMessage(e), "\n")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
.Internal(seterrmessage(msg[1L]))33: if (!silent && isTRUE(getOption("show.error.messages"))) {doTryCatch(return(expr), name, parentenv, handler) cat(msg, file = outFile)
34: .Internal(printDeferredWarnings())tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
35: invisible(structure(msg, class = "try-error", condition = e))tryCatchList(expr, classes, parentenv, handlers)})
36: tryCatch(withCallingHandlers({ 8: eval(code, test_env)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { skip("On CRAN") 9: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) else if (!new_expectations && skip_on_empty) {
skip_empty()10: FUN(X[[i]], ...) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {11: if (on_cran()) {lapply(seq_len(cores), inner.do) skip(paste0("{", e$package, "} is not installed."))
}12: }, snapshot_on_cran = function(cnd) {parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, snapshot_skipped <<- TRUE mc.silent = TRUE) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 13: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))37:
doWithOneRestart(return(expr), restart)14:
.self$do_with_inits(inits, Q, reinitialization_effort)38:
withOneRestart(expr, restarts[[1L]])15:
.self$estim_ascend(reinitialization_effort, changing_effort)39:
withRestarts(tryCatch(withCallingHandlers({16: private$BMobject$estimate() eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations17: if (snapshot_skipped) {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) skip("On CRAN")
}18: eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()19: }eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {20: skip(paste0("{", e$package, "} is not installed."))withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() { else if (!new_expectations && skip_on_empty) { })
skip_empty()40: test_code(code = exprs, env = env, reporter = get_reporter() %||% } StopReporter$new())}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {41: skip(paste0("{", e$package, "} is not installed."))source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) }
42: FUN(X[[i]], ...)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")43: }, skip = handle_skip, warning = handle_warning, message = handle_message, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) error = handle_error, interrupt = handle_interrupt)
44: 21: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
45: 22: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)23:
tryCatchList(expr, classes, parentenv, handlers)47:
24: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n")tryCatch(withCallingHandlers({ NULL eval(code, test_env)}) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {48: skip("On CRAN")with_reporter(reporters$multi, lapply(test_paths, test_one_file, } env = env, desc = desc, shuffle = shuffle, error_call = error_call)) else if (!new_expectations && skip_on_empty) {
skip_empty()49: }test_files_serial(test_dir = test_dir, test_package = test_package, }, expectation = handle_expectation, packageNotFoundError = function(e) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, if (on_cran()) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, skip(paste0("{", e$package, "} is not installed.")) }}, 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)
25: reporter = reporter, load_helpers = load_helpers, env = env, doWithOneRestart(return(expr), restart) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)26:
withOneRestart(expr, restarts[[1L]])51: test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")27:
withRestarts(tryCatch(withCallingHandlers({52: eval(code, test_env)test_check("missSBM") new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {An irrecoverable exception occurred. R is aborting now ...
skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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, no covariate", { sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name,
Traceback:
1: .self$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: 4: lapply(X = S, FUN = FUN, ...)doTryCatch(return(expr), name, parentenv, handler)
4: 5: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 5: tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatch(expr, error = function(e) { 6: call <- conditionCall(e)tryCatchList(expr, classes, parentenv, handlers) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) 7: dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")tryCatch(expr, error = function(e) { LONG <- 75L call <- conditionCall(e) sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (!is.null(call)) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (identical(call[[1L]], quote(doTryCatch))) if (is.na(w)) call <- sys.call(-4L) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") dcall <- deparse(call, nlines = 1L) if (w > LONG) prefix <- paste0(prefix, "\n ") prefix <- paste("Error in", dcall, ": ") } LONG <- 75L else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") sm <- strsplit(conditionMessage(e), "\n")[[1L]] .Internal(seterrmessage(msg[1L])) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (!silent && isTRUE(getOption("show.error.messages"))) { if (is.na(w)) cat(msg, file = outFile) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], .Internal(printDeferredWarnings()) type = "b") } if (w > LONG) invisible(structure(msg, class = "try-error", condition = e)) prefix <- paste0(prefix, "\n ")}) }
else prefix <- "Error : " 8: msg <- paste0(prefix, conditionMessage(e), "\n")try(lapply(X = S, FUN = FUN, ...), silent = TRUE) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) { 9: cat(msg, file = outFile)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) .Internal(printDeferredWarnings())
}10: invisible(structure(msg, class = "try-error", condition = e))FUN(X[[i]], ...)})
11: 8: lapply(seq_len(cores), inner.do)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: 9: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) mc.silent = TRUE)
10: 13: FUN(X[[i]], ...)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))11:
lapply(seq_len(cores), inner.do)14:
.self$do_with_inits(inits, Q, reinitialization_effort)
12: 15: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, .self$estim_ascend(reinitialization_effort, changing_effort) mc.silent = TRUE)
16: private$BMobject$estimate()13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) verbose = (verbosity > 4))
18: 14: eval(code, test_env).self$do_with_inits(inits, Q, reinitialization_effort)
19: 15: eval(code, test_env).self$estim_ascend(reinitialization_effort, changing_effort)
20: 16: withCallingHandlers({private$BMobject$estimate() eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations17: if (snapshot_skipped) {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) skip("On CRAN")
}18: else if (!new_expectations && skip_on_empty) {eval(code, test_env) skip_empty()
}19: }, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))20: }withCallingHandlers({}, snapshot_on_cran = function(cnd) { eval(code, test_env) snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") error = handle_error, interrupt = handle_interrupt) }
else if (!new_expectations && skip_on_empty) {21: skip_empty()doTryCatch(return(expr), name, parentenv, handler) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {22: if (on_cran()) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}23: }, snapshot_on_cran = function(cnd) {tryCatchList(expr, classes, parentenv, handlers) snapshot_skipped <<- TRUE
24: invokeRestart("muffle_cran_snapshot")tryCatch(withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN")21: }doTryCatch(return(expr), name, parentenv, handler) else if (!new_expectations && skip_on_empty) { skip_empty()
}22: }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}23: }, snapshot_on_cran = function(cnd) {tryCatchList(expr, classes, parentenv, handlers) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, 24: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)tryCatch(withCallingHandlers({
eval(code, test_env)25: new_expectations <- the$test_expectations > starting_expectationsdoWithOneRestart(return(expr), restart) if (snapshot_skipped) {
skip("On CRAN")26: }withOneRestart(expr, restarts[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()27: }withRestarts(tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {25: skip(paste0("{", e$package, "} is not installed."))doWithOneRestart(return(expr), restart) }
}, snapshot_on_cran = function(cnd) {26: snapshot_skipped <<- TRUEwithOneRestart(expr, restarts[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 27: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), withRestarts(tryCatch(withCallingHandlers({ end_test = function() { eval(code, test_env) }) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {28: skip("On CRAN")test_code(code, parent.frame())
}29: else if (!new_expectations && skip_on_empty) {test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", skip_empty() { } sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, }, expectation = handle_expectation, packageNotFoundError = function(e) { "bernoulli", TRUE) if (on_cran()) { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, skip(paste0("{", e$package, "} is not installed.")) plot = FALSE)) } mySBM_sbm$setModel(3)}, snapshot_on_cran = function(cnd) { net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) snapshot_skipped <<- TRUE cl <- net$clustering(3)[[1]] invokeRestart("muffle_cran_snapshot") mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl)}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_missSBM$doVEM() error = handle_error, interrupt = handle_interrupt), error = handle_fatal), expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), end_test = function() { 0.1) }) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.95)28: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), test_code(code, parent.frame()) 0.01)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 29: 0.1)test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), { 0.2) sampler_directed_nocov$rNetwork(store = TRUE) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, 0.95) "bernoulli", TRUE) }) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))30: mySBM_sbm$setModel(3)eval(code, test_env) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)
cl <- net$clustering(3)[[1]]31: mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, eval(code, test_env) clusterInit = cl)
mySBM_missSBM$doVEM()32: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), withCallingHandlers({ 0.1) eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), new_expectations <- the$test_expectations > starting_expectations 0.95) if (snapshot_skipped) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), skip("On CRAN") 0.01) } expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), else if (!new_expectations && skip_on_empty) { 0.1) skip_empty() expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), } 0.2)}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), if (on_cran()) { 0.95) skip(paste0("{", e$package, "} is not installed.")) } })}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE30: invokeRestart("muffle_cran_snapshot")eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)31:
eval(code, test_env)33:
doTryCatch(return(expr), name, parentenv, handler)32:
withCallingHandlers({34: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]])
new_expectations <- the$test_expectations > starting_expectations35: if (snapshot_skipped) {tryCatchList(expr, classes, parentenv, handlers) skip("On CRAN")
}36: else if (!new_expectations && skip_on_empty) {tryCatch(withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt) skip(paste0("{", e$package, "} is not installed."))
}33: }, snapshot_on_cran = function(cnd) {doTryCatch(return(expr), name, parentenv, handler) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")34: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)tryCatchOne(expr, names, parentenv, handlers[[1L]])
37: 35: doWithOneRestart(return(expr), restart)tryCatchList(expr, classes, parentenv, handlers)
38: 36: withOneRestart(expr, restarts[[1L]])tryCatch(withCallingHandlers({
eval(code, test_env)39: new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { }}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 37: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), doWithOneRestart(return(expr), restart) end_test = function() {
38: })withOneRestart(expr, restarts[[1L]])
40: 39: test_code(code = exprs, env = env, reporter = get_reporter() %||% withRestarts(tryCatch(withCallingHandlers({ StopReporter$new()) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations41: if (snapshot_skipped) {source_file(path, env = env(env), desc = desc, shuffle = shuffle, skip("On CRAN") error_call = error_call) }
else if (!new_expectations && skip_on_empty) {42: skip_empty()FUN(X[[i]], ...) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {43: if (on_cran()) {lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, skip(paste0("{", e$package, "} is not installed.")) error_call = error_call) }
}, snapshot_on_cran = function(cnd) {44: snapshot_skipped <<- TRUEdoTryCatch(return(expr), name, parentenv, handler)
invokeRestart("muffle_cran_snapshot")45: tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 46: end_test = function() {tryCatchList(expr, classes, parentenv, handlers) })
47: 40: tryCatch(code, testthat_abort_reporter = function(cnd) {test_code(code = exprs, env = env, reporter = get_reporter() %||% cat(conditionMessage(cnd), "\n") StopReporter$new()) NULL
})41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 48: error_call = error_call)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))42:
FUN(X[[i]], ...)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 43: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, error_call = error_call)
desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)44:
doTryCatch(return(expr), name, parentenv, handler)50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 45: reporter = reporter, load_helpers = load_helpers, env = env, tryCatchOne(expr, names, parentenv, handlers[[1L]])
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 46: load_package = load_package, parallel = parallel, shuffle = shuffle)tryCatchList(expr, classes, parentenv, handlers)
51: 47: tryCatch(code, testthat_abort_reporter = function(cnd) {test_dir("testthat", package = package, reporter = reporter, cat(conditionMessage(cnd), "\n") ..., load_package = "installed") NULL
})52:
test_check("missSBM")48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, An irrecoverable exception occurred. R is aborting now ...
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