Last updated on 2026-10-14 17:54:09 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 80.54 | 363.82 | 444.36 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 59.89 | 238.24 | 298.13 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 58.00 | 243.36 | 301.36 | 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 | 91.00 | 450.00 | 541.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 82.95 | 348.35 | 431.30 | 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 | 95.00 | 361.00 | 456.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 21.00 | 100.00 | 121.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 117.00 | 498.00 | 615.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [35s/32s]
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",
Traceback:
1: {dispatcher(membership_name, membership_init$to_cc(), model_name, sampler_undirected_cov$rNetwork(store = TRUE) .self$network_to_cc(), TRUE)
mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, "bernoulli", FALSE, covarList = covarList_undirected) 2: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, FUN(X[[i]], ...)
plot = FALSE)) 3: mySBM_sbm$setModel(Q)lapply(X = S, FUN = FUN, ...)
net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, 4: covariates = covarList_undirected)doTryCatch(return(expr), name, parentenv, handler) cls <- net$clustering(1:(2 * Q))
cl <- cls[[Q]] 5: mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, tryCatchOne(expr, names, parentenv, handlers[[1L]]) clusterInit = cl, covarList = covarList_undirected)
6: mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), tryCatchList(expr, classes, parentenv, handlers) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 7: 0.8)tryCatch(expr, error = function(e) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), call <- conditionCall(e) 0.01) if (!is.null(call)) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), if (identical(call[[1L]], quote(doTryCatch))) 0.1) call <- sys.call(-4L) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) dcall <- deparse(call, nlines = 1L) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), prefix <- paste("Error in", dcall, ": ") 0.85) LONG <- 75L })
sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")30: if (is.na(w)) eval(code, test_env)
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 31: type = "b")eval(code, test_env) if (w > LONG)
32: prefix <- paste0(prefix, "\n ")withCallingHandlers({ eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else prefix <- "Error : " if (snapshot_skipped) { msg <- paste0(prefix, conditionMessage(e), "\n") skip("On CRAN") } .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { else if (!new_expectations && skip_on_empty) { skip_empty() cat(msg, file = outFile) } .Internal(printDeferredWarnings())}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { } invisible(structure(msg, class = "try-error", condition = e)) skip(paste0("{", e$package, "} is not installed.")) }})}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE 8: invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: error = handle_error, interrupt = handle_interrupt)
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))33:
doTryCatch(return(expr), name, parentenv, handler)10:
FUN(X[[i]], ...)34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11:
35: lapply(seq_len(cores), inner.do)tryCatchList(expr, classes, parentenv, handlers)
12: 36: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)tryCatch(withCallingHandlers({ eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {13: skip("On CRAN")parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, } verbose = (verbosity > 4)) else if (!new_expectations && skip_on_empty) {
skip_empty()14: }.self$do_with_inits(inits, Q, reinitialization_effort)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))15: }.self$estim_ascend(reinitialization_effort, changing_effort)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE16: invokeRestart("muffle_cran_snapshot")private$BMobject$estimate()}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))37:
doWithOneRestart(return(expr), restart)18:
eval(code, test_env)38: withOneRestart(expr, restarts[[1L]])
19:
39: eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)20: new_expectations <- the$test_expectations > starting_expectationswithCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { skip(paste0("{", e$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,
40: error = handle_error, interrupt = handle_interrupt)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())21:
doTryCatch(return(expr), name, parentenv, handler)41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 22: error_call = error_call)
tryCatchOne(expr, names, parentenv, handlers[[1L]])42:
FUN(X[[i]], ...)23: tryCatchList(expr, classes, parentenv, handlers)
43: 24: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, tryCatch(withCallingHandlers({ error_call = error_call) eval(code, test_env)
44: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) { skip("On CRAN")
}45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) { skip_empty() }
46: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (on_cran()) {
47: skip(paste0("{", e$package, "} is not installed."))tryCatch(code, testthat_abort_reporter = function(cnd) { } cat(conditionMessage(cnd), "\n")}, snapshot_on_cran = function(cnd) { NULL snapshot_skipped <<- TRUE}) invokeRestart("muffle_cran_snapshot")
48: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))
25: 49: doWithOneRestart(return(expr), restart)test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 26: withOneRestart(expr, restarts[[1L]])
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 27: desc = desc, load_package = load_package, shuffle = shuffle, withRestarts(tryCatch(withCallingHandlers({ error_call = error_call) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations50: if (snapshot_skipped) {test_files(test_dir = path, test_paths = test_paths, test_package = package, skip("On CRAN") reporter = reporter, load_helpers = load_helpers, env = env, } stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, else if (!new_expectations && skip_on_empty) { load_package = load_package, parallel = parallel, shuffle = shuffle) skip_empty()
}51: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_dir("testthat", package = package, reporter = reporter, if (on_cran()) { ..., load_package = "installed") skip(paste0("{", e$package, "} is not installed.")) }
}, snapshot_on_cran = function(cnd) {52: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")test_check("missSBM")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() {An irrecoverable exception occurred. R is aborting now ...
})
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", { sampler_undirected_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, "bernoulli", FALSE, covarList = covarList_undirected) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", { sampler_directed_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, "bernoulli", TRUE, covarList = covarList_directed)
Traceback:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 1: plot = FALSE))dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) mySBM_sbm$setModel(Q)
net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, covariates = covarList_directed) 2: cls <- net$clustering(1:(2 * Q))FUN(X[[i]], ...) cl <- cls[[Q]]
3: mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, lapply(X = S, FUN = FUN, ...) clusterInit = cl, covarList = covarList_directed)
mySBM_missSBM$doVEM(trace = TRUE) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) 4: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), doTryCatch(return(expr), name, parentenv, handler)
0.8) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
6: 0.05)tryCatchList(expr, classes, parentenv, handlers) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean),
0.1) 7: expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), tryCatch(expr, error = function(e) { 0.85) call <- conditionCall(e) }) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 30: call <- sys.call(-4L)eval(code, test_env) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")31: LONG <- 75Leval(code, test_env) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")32: if (is.na(w)) withCallingHandlers({ w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], eval(code, test_env) type = "b") new_expectations <- the$test_expectations > starting_expectations if (w > LONG) if (snapshot_skipped) { prefix <- paste0(prefix, "\n ") skip("On CRAN") } } else prefix <- "Error : " else if (!new_expectations && skip_on_empty) { msg <- paste0(prefix, conditionMessage(e), "\n") skip_empty() .Internal(seterrmessage(msg[1L])) } if (!silent && isTRUE(getOption("show.error.messages"))) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { cat(msg, file = outFile) skip(paste0("{", e$package, "} is not installed.")) .Internal(printDeferredWarnings()) }}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE invisible(structure(msg, class = "try-error", condition = e)) invokeRestart("muffle_cran_snapshot")})}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
8: 33: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)doTryCatch(return(expr), name, parentenv, handler)
9: 34: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: 10: tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)
36: 11: tryCatch(withCallingHandlers({ eval(code, test_env)lapply(seq_len(cores), inner.do) new_expectations <- the$test_expectations > starting_expectations
12: if (snapshot_skipped) {parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, skip("On CRAN") mc.silent = TRUE) } else if (!new_expectations && skip_on_empty) {
skip_empty()13: }parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, }, expectation = handle_expectation, packageNotFoundError = function(e) { verbose = (verbosity > 4))
if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))14: .self$do_with_inits(inits, Q, reinitialization_effort) }
15: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE.self$estim_ascend(reinitialization_effort, changing_effort) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 16: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)private$BMobject$estimate()
37: 17: doWithOneRestart(return(expr), restart)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))38:
withOneRestart(expr, restarts[[1L]])
18: 39: eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)19: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env)
if (snapshot_skipped) {20: skip("On CRAN")withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$test_expectations > starting_expectations skip_empty() if (snapshot_skipped) { } skip("On CRAN")}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) { else if (!new_expectations && skip_on_empty) { skip(paste0("{", e$package, "} is not installed.")) skip_empty() } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$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), end_test = function() { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") })}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)40: test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())
21: 41: doTryCatch(return(expr), name, parentenv, handler)
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 22: tryCatchOne(expr, names, parentenv, handlers[[1L]]) error_call = error_call)
23: 42: tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)
24: tryCatch(withCallingHandlers({43: eval(code, test_env)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, new_expectations <- the$test_expectations > starting_expectations error_call = error_call) if (snapshot_skipped) {
skip("On CRAN") }44: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler) skip_empty()
}45: }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}46: }, snapshot_on_cran = function(cnd) {tryCatchList(expr, classes, parentenv, handlers) snapshot_skipped <<- TRUE
47: invokeRestart("muffle_cran_snapshot")tryCatch(code, testthat_abort_reporter = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) cat(conditionMessage(cnd), "\n")
NULL25: })
doWithOneRestart(return(expr), restart)48: with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))26: withOneRestart(expr, restarts[[1L]])
49: 27: test_files_serial(test_dir = test_dir, test_package = test_package, withRestarts(tryCatch(withCallingHandlers({ test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, eval(code, test_env) desc = desc, load_package = load_package, shuffle = shuffle, new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { error_call = error_call)
skip("On CRAN")50: }test_files(test_dir = path, test_paths = test_paths, test_package = package, else if (!new_expectations && skip_on_empty) { reporter = reporter, load_helpers = load_helpers, env = env, skip_empty() stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } load_package = load_package, parallel = parallel, shuffle = shuffle)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))51: test_dir("testthat", package = package, reporter = reporter, }}, snapshot_on_cran = function(cnd) { ..., load_package = "installed")
snapshot_skipped <<- TRUE52: invokeRestart("muffle_cran_snapshot")test_check("missSBM")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), An irrecoverable exception occurred. R is aborting now ...
end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", { sampler_directed_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, covariates = covarList_directed) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_directed) mySBM_missSBM$doVEM(trace = TRUE) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.05) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$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-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name,
Traceback:
.self$network_to_cc(), TRUE)
2: 1: dispatcher(membership_name, membership_init$to_cc(), model_name, FUN(X[[i]], ...)
.self$network_to_cc(), TRUE) 3:
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)lapply(X = S, FUN = FUN, ...)
4: 4: doTryCatch(return(expr), name, parentenv, handler)
5: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
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) { call <- conditionCall(e) if (!is.null(call)) { if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") 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], LONG <- 75L type = "b") sm <- strsplit(conditionMessage(e), "\n")[[1L]] 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()) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } invisible(structure(msg, class = "try-error", condition = e))}) if (is.na(w))
8: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], try(lapply(X = S, FUN = FUN, ...), silent = TRUE) type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ")
} 9: else prefix <- "Error : "sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
msg <- paste0(prefix, conditionMessage(e), "\n")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$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4)) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)14: .self$do_with_inits(inits, Q, reinitialization_effort) .Internal(printDeferredWarnings()) }
15: invisible(structure(msg, class = "try-error", condition = e))}).self$estim_ascend(reinitialization_effort, changing_effort)
8: 16: private$BMobject$estimate()try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
eval(code, test_env)
19: eval(code, test_env)
10: FUN(X[[i]], ...)20: withCallingHandlers({
eval(code, test_env)11: new_expectations <- the$test_expectations > starting_expectationslapply(seq_len(cores), inner.do) if (snapshot_skipped) {
skip("On CRAN")12: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, else if (!new_expectations && skip_on_empty) { skip_empty() mc.silent = TRUE) }}, expectation = handle_expectation, packageNotFoundError = function(e) {
13: if (on_cran()) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, skip(paste0("{", e$package, "} is not installed.")) } verbose = (verbosity > 4))
}, snapshot_on_cran = function(cnd) {14: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot").self$do_with_inits(inits, Q, reinitialization_effort)
}, skip = handle_skip, warning = handle_warning, message = handle_message, 15: error = handle_error, interrupt = handle_interrupt)
.self$estim_ascend(reinitialization_effort, changing_effort)21: doTryCatch(return(expr), name, parentenv, handler)
22: 16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)private$BMobject$estimate()
24:
17: tryCatch(withCallingHandlers({ eval(code, test_env)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { skip("On CRAN")18: eval(code, test_env) } else if (!new_expectations && skip_on_empty) {
skip_empty()19: }}, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
}20: }, snapshot_on_cran = function(cnd) {withCallingHandlers({ snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) if (snapshot_skipped) {
25: skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty()doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]]) }
27: withRestarts(tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { }}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
}21: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)}, skip = handle_skip, warning = handle_warning, message = handle_message,
22: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), tryCatchOne(expr, names, parentenv, handlers[[1L]])
end_test = function() {23: })tryCatchList(expr, classes, parentenv, handlers)
24: 28: test_code(code, parent.frame())tryCatch(withCallingHandlers({
eval(code, test_env)29: new_expectations <- the$test_expectations > starting_expectationstest_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", { sampler_undirected_nocov$rNetwork(store = TRUE) if (snapshot_skipped) { skip("On CRAN") } mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, else if (!new_expectations && skip_on_empty) { plot = FALSE)) skip_empty() mySBM_sbm$setModel(3) }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) skip(paste0("{", e$package, "} is not installed.")) } cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, }, snapshot_on_cran = function(cnd) { clusterInit = cl) mySBM_missSBM$doVEM() snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, 0.05) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95)25: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), doWithOneRestart(return(expr), restart) 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), 26: 0.95) })
30: eval(code, test_env)withOneRestart(expr, restarts[[1L]])
31: 27: eval(code, test_env)
withRestarts(tryCatch(withCallingHandlers({32: 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) { 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_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE33: invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)
}, skip = handle_skip, warning = handle_warning, message = handle_message, 34: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), tryCatchOne(expr, names, parentenv, handlers[[1L]])
end_test = function() {35: })tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({28: test_code(code, parent.frame()) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", if (snapshot_skipped) { { skip("On CRAN") sampler_undirected_nocov$rNetwork(store = TRUE) } else if (!new_expectations && skip_on_empty) { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) skip_empty() mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) } mySBM_sbm$setModel(3)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) }}, snapshot_on_cran = function(cnd) { cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, snapshot_skipped <<- TRUE clusterInit = cl) invokeRestart("muffle_cran_snapshot") mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.05) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.95)37: doWithOneRestart(return(expr), restart)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 38: 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), withOneRestart(expr, restarts[[1L]]) 0.05) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships),
39: withRestarts(tryCatch(withCallingHandlers({ 0.95) eval(code, test_env) })
30: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
31: skip("On CRAN")eval(code, test_env) } else if (!new_expectations && skip_on_empty) { skip_empty() }
32: withCallingHandlers({ eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { skip_empty() }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), if (on_cran()) { end_test = function() { }) skip(paste0("{", e$package, "} is not installed.")) }
}, snapshot_on_cran = function(cnd) {40: test_code(code = exprs, env = env, reporter = get_reporter() %||% snapshot_skipped <<- TRUE StopReporter$new()) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
41: error = handle_error, interrupt = handle_interrupt)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)
33: 42: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)
34: 44: tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])35:
tryCatchList(expr, classes, parentenv, handlers)
46: tryCatchList(expr, classes, parentenv, handlers)36:
47: tryCatch(withCallingHandlers({tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") eval(code, test_env) NULL})
48: new_expectations <- the$test_expectations > starting_expectationswith_reporter(reporters$multi, lapply(test_paths, test_one_file, if (snapshot_skipped) { env = env, desc = desc, shuffle = shuffle, error_call = error_call)) skip("On CRAN")
}49: else if (!new_expectations && skip_on_empty) {test_files_serial(test_dir = test_dir, test_package = test_package, skip_empty() test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, } env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { error_call = error_call)
skip(paste0("{", e$package, "} is not installed."))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, }, snapshot_on_cran = function(cnd) { load_package = load_package, parallel = parallel, shuffle = shuffle)
51: snapshot_skipped <<- TRUEtest_dir("testthat", package = package, reporter = reporter, invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, ..., load_package = "installed") error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
52:
test_check("missSBM")37:
An irrecoverable exception occurred. R is aborting now ...
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$to_cc(), model_name, .self$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))})
Traceback:
8: 1: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 2:
FUN(X[[i]], ...)10:
FUN(X[[i]], ...) 3:
lapply(X = S, FUN = FUN, ...)11:
lapply(seq_len(cores), inner.do) 4:
doTryCatch(return(expr), name, parentenv, handler)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 5: mc.silent = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: 6: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, tryCatchList(expr, classes, parentenv, handlers) verbose = (verbosity > 4))
7: 14: tryCatch(expr, error = function(e) {.self$do_with_inits(inits, Q, reinitialization_effort) call <- conditionCall(e)
if (!is.null(call)) {15: if (identical(call[[1L]], quote(doTryCatch))) .self$estim_ascend(reinitialization_effort, changing_effort) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)16: prefix <- paste("Error in", dcall, ": ")private$BMobject$estimate() LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]17: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 18: type = "b")eval(code, test_env) if (w > LONG)
prefix <- paste0(prefix, "\n ")19: }eval(code, test_env) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")20: .Internal(seterrmessage(msg[1L]))withCallingHandlers({ if (!silent && isTRUE(getOption("show.error.messages"))) { eval(code, test_env) cat(msg, file = outFile) new_expectations <- the$test_expectations > starting_expectations .Internal(printDeferredWarnings()) if (snapshot_skipped) { } skip("On CRAN") invisible(structure(msg, class = "try-error", condition = e)) }}) else if (!new_expectations && skip_on_empty) {
skip_empty() 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { 9: if (on_cran()) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) skip(paste0("{", e$package, "} is not installed."))
}10: }, snapshot_on_cran = function(cnd) {FUN(X[[i]], ...) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")11: }, skip = handle_skip, warning = handle_warning, message = handle_message, lapply(seq_len(cores), inner.do) error = handle_error, interrupt = handle_interrupt)
12: 21: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, doTryCatch(return(expr), name, parentenv, handler) mc.silent = TRUE)
22: 13: tryCatchOne(expr, names, parentenv, handlers[[1L]])parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))23:
14: tryCatchList(expr, classes, parentenv, handlers).self$do_with_inits(inits, Q, reinitialization_effort)
24: 15: tryCatch(withCallingHandlers({.self$estim_ascend(reinitialization_effort, changing_effort) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations16: if (snapshot_skipped) {private$BMobject$estimate() skip("On CRAN")
}17: else if (!new_expectations && skip_on_empty) {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) skip_empty()
}18: }, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))19: }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$test_expectations > starting_expectations
if (snapshot_skipped) {25: skip("On CRAN")doWithOneRestart(return(expr), restart) }
else if (!new_expectations && skip_on_empty) {26: skip_empty()withOneRestart(expr, restarts[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {27: if (on_cran()) {withRestarts(tryCatch(withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt) skip_empty()
}21: }, expectation = handle_expectation, packageNotFoundError = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))22: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE23: invokeRestart("muffle_cran_snapshot")tryCatchList(expr, classes, parentenv, handlers)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 24: end_test = function() {tryCatch(withCallingHandlers({ }) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations28: if (snapshot_skipped) {test_code(code, parent.frame()) skip("On CRAN")
}29: else if (!new_expectations && skip_on_empty) {test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", skip_empty() { } sampler_directed_nocov$rNetwork(store = TRUE)}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, if (on_cran()) { "bernoulli", TRUE) skip(paste0("{", e$package, "} is not installed.")) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, } plot = FALSE))}, snapshot_on_cran = function(cnd) { mySBM_sbm$setModel(3) snapshot_skipped <<- TRUE net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) invokeRestart("muffle_cran_snapshot") cl <- net$clustering(3)[[1]]}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) clusterInit = cl)
mySBM_missSBM$doVEM()25: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), doWithOneRestart(return(expr), restart) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 26: 0.95)withOneRestart(expr, restarts[[1L]])
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 27: 0.01)withRestarts(tryCatch(withCallingHandlers({ expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), eval(code, test_env) 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), new_expectations <- the$test_expectations > starting_expectations 0.2) if (snapshot_skipped) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), skip("On CRAN") 0.95) } }) else if (!new_expectations && skip_on_empty) {
skip_empty()30: }eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {31: skip(paste0("{", e$package, "} is not installed."))eval(code, test_env) }
}, snapshot_on_cran = function(cnd) {32: snapshot_skipped <<- TRUEwithCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations 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$package, "} is not installed."))test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", } {}, snapshot_on_cran = function(cnd) { sampler_directed_nocov$rNetwork(store = TRUE) snapshot_skipped <<- TRUE mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, invokeRestart("muffle_cran_snapshot") "bernoulli", TRUE)}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, error = handle_error, interrupt = handle_interrupt) plot = FALSE))
mySBM_sbm$setModel(3)33: net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)doTryCatch(return(expr), name, parentenv, handler) cl <- net$clustering(3)[[1]]
34: mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, tryCatchOne(expr, names, parentenv, handlers[[1L]]) clusterInit = cl)
mySBM_missSBM$doVEM()35: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), tryCatchList(expr, classes, parentenv, handlers) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 36: 0.95)tryCatch(withCallingHandlers({ expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), eval(code, test_env) 0.01) new_expectations <- the$test_expectations > starting_expectations expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), if (snapshot_skipped) { 0.1) skip("On CRAN") expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), } 0.2) else if (!new_expectations && skip_on_empty) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), skip_empty() 0.95) } })}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {30: skip(paste0("{", e$package, "} is not installed."))eval(code, test_env) }
}, snapshot_on_cran = function(cnd) {31: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 32: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)withCallingHandlers({
eval(code, test_env)37: new_expectations <- the$test_expectations > starting_expectationsdoWithOneRestart(return(expr), restart) if (snapshot_skipped) {
skip("On CRAN")38: }withOneRestart(expr, restarts[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()39: }withRestarts(tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {33: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$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),
end_test = function() {36: })tryCatch(withCallingHandlers({
eval(code, test_env)40: new_expectations <- the$test_expectations > starting_expectationstest_code(code = exprs, env = env, reporter = get_reporter() %||% if (snapshot_skipped) { StopReporter$new()) skip("On CRAN")
}41: else if (!new_expectations && skip_on_empty) {source_file(path, env = env(env), desc = desc, shuffle = shuffle, skip_empty() error_call = error_call) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {42: if (on_cran()) {FUN(X[[i]], ...) skip(paste0("{", e$package, "} is not installed."))
}43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, }, snapshot_on_cran = function(cnd) { error_call = error_call) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")44: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)doTryCatch(return(expr), name, parentenv, handler)
37: 45: doWithOneRestart(return(expr), restart)tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: 46: withOneRestart(expr, restarts[[1L]])
tryCatchList(expr, classes, parentenv, handlers)39:
withRestarts(tryCatch(withCallingHandlers({47: eval(code, test_env)tryCatch(code, testthat_abort_reporter = function(cnd) { new_expectations <- the$test_expectations > starting_expectations cat(conditionMessage(cnd), "\n") if (snapshot_skipped) { NULL skip("On CRAN")}) }
else if (!new_expectations && skip_on_empty) {48: skip_empty()with_reporter(reporters$multi, lapply(test_paths, test_one_file, } env = env, desc = desc, shuffle = shuffle, error_call = error_call))}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {49: skip(paste0("{", e$package, "} is not installed."))test_files_serial(test_dir = test_dir, test_package = test_package, } test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, }, snapshot_on_cran = function(cnd) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, snapshot_skipped <<- TRUE desc = desc, load_package = load_package, shuffle = shuffle, invokeRestart("muffle_cran_snapshot") error_call = error_call)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 50: end_test = function() {test_files(test_dir = path, test_paths = test_paths, test_package = package, })
reporter = reporter, load_helpers = load_helpers, env = env, 40: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_code(code = exprs, env = env, reporter = get_reporter() %||% load_package = load_package, parallel = parallel, shuffle = shuffle) StopReporter$new())
51: 41: test_dir("testthat", package = package, reporter = reporter, source_file(path, env = env(env), desc = desc, shuffle = shuffle, ..., load_package = "installed") error_call = error_call)
52: 42: test_check("missSBM")FUN(X[[i]], ...)
43: An irrecoverable exception occurred. R is aborting now ...
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-44.R
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-explore-block-count.R:4:3',
'test-missSBM_collection-degenerate.R:80:3',
'test-missSBM_collection-estimate_chain.R:64:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-sbm-bernoulli-with-covariates.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-with-covariates.R:46:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:46:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:44:3'): SimpleSBM_fit 'Bernoulli' model, directed, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:44:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64