Last updated on 2026-10-17 20:50:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 88.36 | 352.66 | 441.02 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 58.03 | 240.79 | 298.82 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 57.00 | 247.35 | 304.35 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 63.00 | 247.59 | 310.59 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 95.00 | 449.00 | 544.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 85.58 | 342.08 | 427.66 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 74.39 | 345.64 | 420.03 | 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 | 358.00 | 456.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | ERROR | ||||
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 119.00 | 528.00 | 647.00 | 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)
Traceback:
1: 38: withOneRestart(expr, restarts[[1L]])dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE)39:
withRestarts(tryCatch(withCallingHandlers({ 2: eval(code, test_env)FUN(X[[i]], ...) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { 3: lapply(X = S, FUN = FUN, ...) skip("On CRAN")
} else if (!new_expectations && skip_on_empty) { 4: skip_empty()doTryCatch(return(expr), name, parentenv, handler) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) } 6: }, snapshot_on_cran = function(cnd) {tryCatchList(expr, classes, parentenv, handlers) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 7: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatch(expr, error = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), call <- conditionCall(e) end_test = function() { if (!is.null(call)) { }) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)40: test_code(code = exprs, env = env, reporter = get_reporter() %||% dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") StopReporter$new()) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]41: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")source_file(path, env = env(env), desc = desc, shuffle = shuffle, if (is.na(w)) error_call = error_call) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")42: if (w > LONG) FUN(X[[i]], ...) prefix <- paste0(prefix, "\n ")
}43: else prefix <- "Error : "lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, msg <- paste0(prefix, conditionMessage(e), "\n") error_call = error_call)
.Internal(seterrmessage(msg[1L]))44: if (!silent && isTRUE(getOption("show.error.messages"))) {doTryCatch(return(expr), name, parentenv, handler) cat(msg, file = outFile)
.Internal(printDeferredWarnings())45: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) invisible(structure(msg, class = "try-error", condition = e))
})46:
tryCatchList(expr, classes, parentenv, handlers) 8:
47: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n") 9: NULLsendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
})10:
FUN(X[[i]], ...)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 11: lapply(seq_len(cores), inner.do) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
12: 49: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, test_files_serial(test_dir = test_dir, test_package = test_package, mc.silent = TRUE)
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, verbose = (verbosity > 4)) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)14: .self$do_with_inits(inits, Q, reinitialization_effort)
50: 15: .self$estim_ascend(reinitialization_effort, changing_effort)test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 16: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)private$BMobject$estimate()
51: 17: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: 52: eval(code, test_env)test_check("missSBM")
19:
eval(code, test_env)
An irrecoverable exception occurred. R is aborting now ...
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)
Traceback:
prefix <- paste0(prefix, "\n ") 1: }dispatcher(membership_name, membership_init$to_cc(), model_name, else prefix <- "Error : " .self$network_to_cc(), TRUE) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) 2: if (!silent && isTRUE(getOption("show.error.messages"))) {FUN(X[[i]], ...) cat(msg, file = outFile)
.Internal(printDeferredWarnings()) 3: } invisible(structure(msg, class = "try-error", condition = e))lapply(X = S, FUN = FUN, ...)})
4:
doTryCatch(return(expr), name, parentenv, handler) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
5: 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
6: 10: tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)
7: 11: tryCatch(expr, error = function(e) {lapply(seq_len(cores), inner.do) call <- conditionCall(e)
12: if (!is.null(call)) {parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, if (identical(call[[1L]], quote(doTryCatch))) mc.silent = TRUE) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)13: prefix <- paste("Error in", dcall, ": ")parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, LONG <- 75L verbose = (verbosity > 4))
sm <- strsplit(conditionMessage(e), "\n")[[1L]]14: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w").self$do_with_inits(inits, Q, reinitialization_effort) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")15: .self$estim_ascend(reinitialization_effort, changing_effort) if (w > LONG)
16: prefix <- paste0(prefix, "\n ")private$BMobject$estimate() }
17: else prefix <- "Error : "mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {18: cat(msg, file = outFile)eval(code, test_env) .Internal(printDeferredWarnings())
}19: invisible(structure(msg, class = "try-error", condition = e))eval(code, test_env)})
20: withCallingHandlers({ 8: eval(code, test_env)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN") 9: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) else if (!new_expectations && skip_on_empty) { skip_empty()
}10: FUN(X[[i]], ...)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {11: skip(paste0("{", e$package, "} is not installed.")) }lapply(seq_len(cores), inner.do)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE12: invokeRestart("muffle_cran_snapshot")parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, }, skip = handle_skip, warning = handle_warning, message = handle_message, mc.silent = TRUE) error = handle_error, interrupt = handle_interrupt)
21: 13: doTryCatch(return(expr), name, parentenv, handler)
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 22: verbose = (verbosity > 4))tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: 23: .self$do_with_inits(inits, Q, reinitialization_effort)
tryCatchList(expr, classes, parentenv, handlers)
15: 24: .self$estim_ascend(reinitialization_effort, changing_effort)
tryCatch(withCallingHandlers({ eval(code, test_env)16: new_expectations <- the$test_expectations > starting_expectationsprivate$BMobject$estimate() if (snapshot_skipped) {
skip("On CRAN")17: }mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) else if (!new_expectations && skip_on_empty) {
skip_empty()18: }eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {19: skip(paste0("{", e$package, "} is not installed."))eval(code, test_env) }
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE20: invokeRestart("muffle_cran_snapshot")withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { skip("On CRAN")25: }doWithOneRestart(return(expr), restart)
else if (!new_expectations && skip_on_empty) {26: skip_empty()withOneRestart(expr, restarts[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {27: if (on_cran()) {withRestarts(tryCatch(withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt) else if (!new_expectations && skip_on_empty) { skip_empty()
}21: }, expectation = handle_expectation, packageNotFoundError = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))22: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE23: invokeRestart("muffle_cran_snapshot")}, 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() {24: })tryCatch(withCallingHandlers({
eval(code, test_env)28: new_expectations <- the$test_expectations > starting_expectationstest_code(code, parent.frame()) if (snapshot_skipped) {
skip("On CRAN")29: }test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", { else if (!new_expectations && skip_on_empty) { sampler_directed_cov$rNetwork(store = TRUE) skip_empty() mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, } "bernoulli", TRUE, covarList = covarList_directed)}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, if (on_cran()) { plot = FALSE)) skip(paste0("{", e$package, "} is not installed.")) } mySBM_sbm$setModel(Q)}, snapshot_on_cran = function(cnd) { net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, snapshot_skipped <<- TRUE covariates = covarList_directed) invokeRestart("muffle_cran_snapshot") cls <- net$clustering(1:(2 * Q))}, skip = handle_skip, warning = handle_warning, message = handle_message, cl <- cls[[Q]] error = handle_error, interrupt = handle_interrupt), error = handle_fatal) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net,
clusterInit = cl, covarList = covarList_directed)25: mySBM_missSBM$doVEM(trace = TRUE)doWithOneRestart(return(expr), restart) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
0.1)26: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), withOneRestart(expr, restarts[[1L]]) 0.8)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 27: 0.05)withRestarts(tryCatch(withCallingHandlers({ expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations 0.1) if (snapshot_skipped) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), skip("On CRAN") 0.85) } })
else if (!new_expectations && skip_on_empty) {30: skip_empty()eval(code, test_env)
}31: }, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))32: }withCallingHandlers({}, snapshot_on_cran = function(cnd) { eval(code, test_env) snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip("On CRAN") end_test = function() { } }) else if (!new_expectations && skip_on_empty) {
skip_empty() }28: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_code(code, parent.frame()) if (on_cran()) {
skip(paste0("{", e$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), 0.1)36: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), tryCatch(withCallingHandlers({ 0.8) eval(code, test_env) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), new_expectations <- the$test_expectations > starting_expectations 0.05) if (snapshot_skipped) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), skip("On CRAN") 0.1) } expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), else if (!new_expectations && skip_on_empty) { 0.85) skip_empty() }) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {30: if (on_cran()) {eval(code, test_env) skip(paste0("{", e$package, "} is not installed."))
}}, 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({37: eval(code, test_env)doWithOneRestart(return(expr), restart) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { skip("On CRAN")38: }withOneRestart(expr, restarts[[1L]]) else if (!new_expectations && skip_on_empty) { skip_empty()
}39: withRestarts(tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {33: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
}34: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")35: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
36: end_test = function() {tryCatch(withCallingHandlers({ }) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations40: if (snapshot_skipped) {test_code(code = exprs, env = env, reporter = get_reporter() %||% skip("On CRAN") } StopReporter$new()) else if (!new_expectations && skip_on_empty) {
skip_empty()41: }}, expectation = handle_expectation, packageNotFoundError = function(e) {source_file(path, env = env(env), desc = desc, shuffle = shuffle, if (on_cran()) { error_call = error_call)
skip(paste0("{", e$package, "} is not installed.")) }42: }, snapshot_on_cran = function(cnd) {FUN(X[[i]], ...) snapshot_skipped <<- TRUE
43: invokeRestart("muffle_cran_snapshot")lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) error_call = error_call)
37: 44: doWithOneRestart(return(expr), restart)doTryCatch(return(expr), name, parentenv, handler)
38: 45: withOneRestart(expr, restarts[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: 46: withRestarts(tryCatch(withCallingHandlers({tryCatchList(expr, classes, parentenv, handlers) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {47: tryCatch(code, testthat_abort_reporter = function(cnd) { skip("On CRAN") cat(conditionMessage(cnd), "\n") } NULL else if (!new_expectations && skip_on_empty) {}) skip_empty()
}48: }, expectation = handle_expectation, packageNotFoundError = function(e) {with_reporter(reporters$multi, lapply(test_paths, test_one_file, if (on_cran()) { env = env, desc = desc, shuffle = shuffle, error_call = error_call)) skip(paste0("{", e$package, "} is not installed."))
}49: }, snapshot_on_cran = function(cnd) {test_files_serial(test_dir = test_dir, test_package = test_package, snapshot_skipped <<- TRUE test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 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),
end_test = function() {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, 40: load_package = load_package, parallel = parallel, shuffle = shuffle)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())51:
test_dir("testthat", package = package, reporter = reporter, 41: ..., load_package = "installed")source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)
52: 42: test_check("missSBM")FUN(X[[i]], ...)
An irrecoverable exception occurred. R is aborting now ...
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$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:
Traceback:
lapply(X = S, FUN = FUN, ...) 1:
dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) 4:
doTryCatch(return(expr), name, parentenv, handler) 2:
FUN(X[[i]], ...) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3:
lapply(X = S, FUN = FUN, ...) 6: tryCatchList(expr, classes, parentenv, handlers)
4: 7: doTryCatch(return(expr), name, parentenv, handler)tryCatch(expr, error = function(e) {
call <- conditionCall(e) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!is.null(call)) {
6: if (identical(call[[1L]], quote(doTryCatch))) tryCatchList(expr, classes, parentenv, handlers) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) 7: prefix <- paste("Error in", dcall, ": ")tryCatch(expr, error = function(e) { LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] call <- conditionCall(e) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (!is.null(call)) { if (is.na(w)) if (identical(call[[1L]], quote(doTryCatch))) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], call <- sys.call(-4L) type = "b") dcall <- deparse(call, nlines = 1L) if (w > LONG) prefix <- paste("Error in", dcall, ": ") prefix <- paste0(prefix, "\n ") LONG <- 75L } sm <- strsplit(conditionMessage(e), "\n")[[1L]] else prefix <- "Error : " w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") msg <- paste0(prefix, conditionMessage(e), "\n") if (is.na(w)) .Internal(seterrmessage(msg[1L])) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (!silent && isTRUE(getOption("show.error.messages"))) { type = "b") cat(msg, file = outFile) if (w > LONG) prefix <- paste0(prefix, "\n ") .Internal(printDeferredWarnings()) } } else prefix <- "Error : " invisible(structure(msg, class = "try-error", condition = e)) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))}) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)
.Internal(printDeferredWarnings()) 8: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) invisible(structure(msg, class = "try-error", condition = e))
}) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)10:
FUN(X[[i]], ...) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))11:
lapply(seq_len(cores), inner.do)
10: 12: FUN(X[[i]], ...)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE,
mc.silent = TRUE)11:
lapply(seq_len(cores), inner.do)13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 12: verbose = (verbosity > 4))
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 14: mc.silent = TRUE).self$do_with_inits(inits, Q, reinitialization_effort)
13: 15: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, .self$estim_ascend(reinitialization_effort, changing_effort) verbose = (verbosity > 4))
16: 14: private$BMobject$estimate().self$do_with_inits(inits, Q, reinitialization_effort)
17: 15: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)).self$estim_ascend(reinitialization_effort, changing_effort)
18: 16: eval(code, test_env)private$BMobject$estimate()
19: 17: eval(code, test_env)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
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 (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."))
}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, error = handle_error, interrupt = handle_interrupt)tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: 23: doTryCatch(return(expr), name, parentenv, handler)tryCatchList(expr, classes, parentenv, handlers)
22: 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch(withCallingHandlers({
eval(code, test_env)23: new_expectations <- the$test_expectations > starting_expectationstryCatchList(expr, classes, parentenv, handlers) if (snapshot_skipped) {
skip("On CRAN")24: }tryCatch(withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, 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: withOneRestart(expr, restarts[[1L]]) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
27: withRestarts(tryCatch(withCallingHandlers({25: eval(code, test_env)doWithOneRestart(return(expr), restart) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {26: skip("On CRAN")withOneRestart(expr, restarts[[1L]]) }
else if (!new_expectations && skip_on_empty) {27: skip_empty()withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { new_expectations <- the$test_expectations > starting_expectations if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), if (on_cran()) { end_test = function() { skip(paste0("{", e$package, "} is not installed.")) }) }
28: test_code(code, parent.frame())}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE29: invokeRestart("muffle_cran_snapshot")test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", }, skip = handle_skip, warning = handle_warning, message = handle_message, { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), sampler_undirected_nocov$rNetwork(store = TRUE) end_test = function() { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, }) "bernoulli", FALSE)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 28: plot = FALSE))test_code(code, parent.frame()) mySBM_sbm$setModel(3)
net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData)29: cl <- net$clustering(3)[[1]]test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, { clusterInit = cl) sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_missSBM$doVEM() mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), "bernoulli", FALSE) 0.05) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), plot = FALSE)) 0.95) mySBM_sbm$setModel(3) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) 0.01) cl <- net$clustering(3)[[1]] expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl) 0.05) mySBM_missSBM$doVEM() expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.95) }) 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.95)30: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), eval(code, test_env) 0.01)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 31: 0.05)eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships),
0.95)32: })withCallingHandlers({
eval(code, test_env)30: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
skip("On CRAN")31: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()32: }withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {33: skip(paste0("{", e$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)tryCatchList(expr, classes, parentenv, handlers)
33: 36: doTryCatch(return(expr), name, parentenv, handler)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$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {37: skip(paste0("{", e$package, "} is not installed."))doWithOneRestart(return(expr), restart) }
}, snapshot_on_cran = function(cnd) {38: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")withOneRestart(expr, restarts[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)39:
withRestarts(tryCatch(withCallingHandlers({37: eval(code, test_env)doWithOneRestart(return(expr), restart) new_expectations <- the$test_expectations > starting_expectations
38: withOneRestart(expr, restarts[[1L]]) if (snapshot_skipped) {
39: skip("On CRAN")withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { else if (!new_expectations && skip_on_empty) { skip(paste0("{", e$package, "} is not installed.")) skip_empty() } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, snapshot_on_cran = function(cnd) { end_test = function() { snapshot_skipped <<- TRUE }) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 40: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_code(code = exprs, env = env, reporter = get_reporter() %||% end_test = function() { StopReporter$new()) })
41: 40: source_file(path, env = env(env), desc = desc, shuffle = shuffle, test_code(code = exprs, env = env, reporter = get_reporter() %||% error_call = error_call) StopReporter$new())
42: 41: FUN(X[[i]], ...)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 42: error_call = error_call)FUN(X[[i]], ...)
44: 43: doTryCatch(return(expr), name, parentenv, handler)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])44: doTryCatch(return(expr), name, parentenv, handler)
46:
tryCatchList(expr, classes, parentenv, handlers)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])47:
tryCatch(code, testthat_abort_reporter = function(cnd) {46: cat(conditionMessage(cnd), "\n")tryCatchList(expr, classes, parentenv, handlers) NULL
})47:
tryCatch(code, testthat_abort_reporter = function(cnd) {48: cat(conditionMessage(cnd), "\n")with_reporter(reporters$multi, lapply(test_paths, test_one_file, NULL env = env, desc = desc, shuffle = shuffle, error_call = error_call))})
49: 48: test_files_serial(test_dir = test_dir, test_package = test_package, with_reporter(reporters$multi, lapply(test_paths, test_one_file, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 49: error_call = error_call)test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 50: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_files(test_dir = path, test_paths = test_paths, test_package = package, desc = desc, load_package = load_package, shuffle = shuffle, reporter = reporter, load_helpers = load_helpers, env = env, error_call = error_call) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 51: reporter = reporter, load_helpers = load_helpers, env = env, test_dir("testthat", package = package, reporter = reporter, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, ..., load_package = "installed") load_package = load_package, parallel = parallel, shuffle = shuffle)
52: 51: test_check("missSBM")test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")An irrecoverable exception occurred. R is aborting now ...
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name,
Traceback:
.self$network_to_cc(), TRUE) 1:
dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) 2:
FUN(X[[i]], ...)
2: 3: FUN(X[[i]], ...)lapply(X = S, FUN = FUN, ...)
3: 4: lapply(X = S, FUN = FUN, ...)doTryCatch(return(expr), name, parentenv, handler)
4: doTryCatch(return(expr), name, parentenv, handler) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6:
tryCatchList(expr, classes, parentenv, handlers) 6:
tryCatchList(expr, classes, parentenv, handlers) 7:
tryCatch(expr, error = function(e) { 7: call <- conditionCall(e)tryCatch(expr, error = function(e) { if (!is.null(call)) { call <- conditionCall(e) if (identical(call[[1L]], quote(doTryCatch))) if (!is.null(call)) { call <- sys.call(-4L) if (identical(call[[1L]], quote(doTryCatch))) dcall <- deparse(call, nlines = 1L) call <- sys.call(-4L) prefix <- paste("Error in", dcall, ": ") dcall <- deparse(call, nlines = 1L) LONG <- 75L prefix <- paste("Error in", dcall, ": ") sm <- strsplit(conditionMessage(e), "\n")[[1L]] LONG <- 75L w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (is.na(w)) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (is.na(w)) type = "b") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (w > LONG) prefix <- paste0(prefix, "\n ") type = "b") } if (w > LONG) else prefix <- "Error : " prefix <- paste0(prefix, "\n ") msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) else prefix <- "Error : " if (!silent && isTRUE(getOption("show.error.messages"))) { msg <- paste0(prefix, conditionMessage(e), "\n") cat(msg, file = outFile) .Internal(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: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) invisible(structure(msg, class = "try-error", condition = e))
9: })sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
8: 10: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
FUN(X[[i]], ...) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))11:
lapply(seq_len(cores), inner.do)10:
FUN(X[[i]], ...)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 11: mc.silent = TRUE)lapply(seq_len(cores), inner.do)
12: 13: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, mc.silent = TRUE)
verbose = (verbosity > 4))13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 14: verbose = (verbosity > 4)).self$do_with_inits(inits, Q, reinitialization_effort)
14: 15: .self$do_with_inits(inits, Q, reinitialization_effort).self$estim_ascend(reinitialization_effort, changing_effort)
15: 16: .self$estim_ascend(reinitialization_effort, changing_effort)private$BMobject$estimate()
17: 16: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))private$BMobject$estimate()
18: 17: eval(code, test_env)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
19: 18: eval(code, test_env)eval(code, test_env)
20: 19: withCallingHandlers({eval(code, test_env) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations20: if (snapshot_skipped) {withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, snapshot_on_cran = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, snapshot_skipped <<- TRUE error = handle_error, interrupt = handle_interrupt) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 21: error = handle_error, interrupt = handle_interrupt)doTryCatch(return(expr), name, parentenv, handler)
21: 22: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
23: tryCatchList(expr, classes, parentenv, handlers)24:
tryCatch(withCallingHandlers({24: eval(code, test_env)tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, snapshot_on_cran = function(cnd) { invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)25:
doWithOneRestart(return(expr), restart)25:
26: doWithOneRestart(return(expr), restart)withOneRestart(expr, restarts[[1L]])
26: 27: withOneRestart(expr, restarts[[1L]])withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)27: new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), snapshot_skipped <<- TRUE end_test = function() { invokeRestart("muffle_cran_snapshot") })}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 28: end_test = function() {test_code(code, parent.frame()) })
29: 28: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", test_code(code, parent.frame()) {
sampler_directed_nocov$rNetwork(store = TRUE)29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, { sampler_directed_nocov$rNetwork(store = TRUE) "bernoulli", TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, "bernoulli", TRUE) plot = FALSE)) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]] cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl) clusterInit = cl) mySBM_missSBM$doVEM() mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.1) 0.2) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.2) 0.95) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), }) 0.95)
})30:
eval(code, test_env)30:
eval(code, test_env)31:
eval(code, test_env)31:
eval(code, test_env)32:
32: withCallingHandlers({ eval(code, test_env)withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) error = handle_error, interrupt = handle_interrupt)
33: 33: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
34: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: 35: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
36: 36: tryCatch(withCallingHandlers({tryCatch(withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { else if (!new_expectations && skip_on_empty) { skip_empty() skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)37:
doWithOneRestart(return(expr), restart)38:
withOneRestart(expr, restarts[[1L]])38:
withOneRestart(expr, restarts[[1L]])39:
withRestarts(tryCatch(withCallingHandlers({39: eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") } else if (!new_expectations && skip_on_empty) { else if (!new_expectations && skip_on_empty) { skip_empty() skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, skip = handle_skip, warning = handle_warning, message = handle_message, end_test = function() { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }) end_test = function() {
})40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 40: StopReporter$new())test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())41: source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)41: source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)42:
FUN(X[[i]], ...)42:
43: FUN(X[[i]], ...)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)
43: 44: doTryCatch(return(expr), name, parentenv, handler)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
45: error_call = error_call)tryCatchOne(expr, names, parentenv, handlers[[1L]])
44: 46: doTryCatch(return(expr), name, parentenv, handler)tryCatchList(expr, classes, parentenv, handlers)
45: 47: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")46: NULLtryCatchList(expr, classes, parentenv, handlers)})
48: 47: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")49: NULLtest_files_serial(test_dir = test_dir, test_package = test_package, })
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 48: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, with_reporter(reporters$multi, lapply(test_paths, test_one_file, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
50: 49: test_files(test_dir = path, test_paths = test_paths, test_package = package, test_files_serial(test_dir = test_dir, test_package = test_package, reporter = reporter, load_helpers = load_helpers, env = env, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, load_package = load_package, parallel = parallel, shuffle = shuffle) error_call = error_call)
51: 50: test_dir("testthat", package = package, reporter = reporter, test_files(test_dir = path, test_paths = test_paths, test_package = package, ..., load_package = "installed") reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 52: load_package = load_package, parallel = parallel, shuffle = shuffle)test_check("missSBM")
51: An irrecoverable exception occurred. R is aborting now ...
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