Last updated on 2026-11-15 00:50:14 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 74.27 | 371.31 | 445.58 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 57.20 | 257.14 | 314.34 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 60.00 | 254.27 | 314.27 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 257.44 | 321.44 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 422.00 | 513.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 80.59 | 359.22 | 439.81 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 78.58 | 329.18 | 407.76 | OK | |
| r-release-macos-arm64 | 1.1.0 | 17.00 | 92.00 | 109.00 | OK | |
| r-release-macos-x86_64 | 1.1.0 | 59.00 | 456.00 | 515.00 | OK | |
| r-release-windows-x86_64 | 1.1.0 | 99.00 | 414.00 | 513.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 23.00 | 94.00 | 117.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 117.00 | 542.00 | 659.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [36s/34s]
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$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
Traceback:
1: skip(paste0("{", e$package, "} is not installed."))dispatcher(membership_name, membership_init$to_cc(), model_name, }}, snapshot_on_cran = function(cnd) { .self$network_to_cc(), TRUE) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 2: FUN(X[[i]], ...)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 3:
lapply(X = S, FUN = FUN, ...)25:
doWithOneRestart(return(expr), restart) 4:
doTryCatch(return(expr), name, parentenv, handler)26:
withOneRestart(expr, restarts[[1L]]) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])27:
withRestarts(tryCatch(withCallingHandlers({ 6: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers)
new_expectations <- the$test_expectations > starting_expectations 7: if (snapshot_skipped) {tryCatch(expr, error = function(e) { skip("On CRAN") call <- conditionCall(e) } if (!is.null(call)) { else if (!new_expectations && skip_on_empty) { if (identical(call[[1L]], quote(doTryCatch))) skip_empty() call <- sys.call(-4L) } dcall <- deparse(call, nlines = 1L)}, expectation = handle_expectation, packageNotFoundError = function(e) { prefix <- paste("Error in", dcall, ": ") if (on_cran()) { LONG <- 75L skip(paste0("{", e$package, "} is not installed.")) sm <- strsplit(conditionMessage(e), "\n")[[1L]] } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, snapshot_on_cran = function(cnd) { if (is.na(w)) snapshot_skipped <<- TRUE w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], invokeRestart("muffle_cran_snapshot") type = "b")}, skip = handle_skip, warning = handle_warning, message = handle_message, if (w > LONG) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), prefix <- paste0(prefix, "\n ") end_test = function() { } }) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")28: .Internal(seterrmessage(msg[1L]))test_code(code, parent.frame()) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)29: .Internal(printDeferredWarnings())test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", } { invisible(structure(msg, class = "try-error", condition = e)) sampler_undirected_cov$rNetwork(store = TRUE)}) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData,
"bernoulli", FALSE, covarList = covarList_undirected) 8: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) plot = FALSE))
mySBM_sbm$setModel(Q) 9: net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) covariates = covarList_undirected)
cls <- net$clustering(1:(2 * Q))10: cl <- cls[[Q]]FUN(X[[i]], ...) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net,
clusterInit = cl, covarList = covarList_undirected)11: mySBM_missSBM$doVEM()lapply(seq_len(cores), inner.do) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
12: 0.05)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), mc.silent = TRUE) 0.8)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 13: 0.01)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), verbose = (verbosity > 4)) 0.1)
expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 14: 0.1).self$do_with_inits(inits, Q, reinitialization_effort) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships),
0.85)15: }).self$estim_ascend(reinitialization_effort, changing_effort)
30: 16: eval(code, test_env)private$BMobject$estimate()
31: 17: eval(code, test_env)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
32: 18: withCallingHandlers({eval(code, test_env) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations19: if (snapshot_skipped) {eval(code, test_env) skip("On CRAN")
}20: else if (!new_expectations && skip_on_empty) { skip_empty()withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt) skip(paste0("{", e$package, "} is not installed."))
}33: }, snapshot_on_cran = function(cnd) {doTryCatch(return(expr), name, parentenv, handler) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")34: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = handle_error, interrupt = handle_interrupt)
35: 21: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
36: 22: tryCatch(withCallingHandlers({tryCatchOne(expr, names, parentenv, handlers[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations23: if (snapshot_skipped) {tryCatchList(expr, classes, parentenv, handlers) skip("On CRAN")
}24: else if (!new_expectations && skip_on_empty) {tryCatch(withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip(paste0("{", e$package, "} is not installed."))
}37: }, snapshot_on_cran = function(cnd) {doWithOneRestart(return(expr), restart) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")38: }, skip = handle_skip, warning = handle_warning, message = handle_message, withOneRestart(expr, restarts[[1L]]) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
39: 25: withRestarts(tryCatch(withCallingHandlers({doWithOneRestart(return(expr), restart) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations26: if (snapshot_skipped) {withOneRestart(expr, restarts[[1L]]) skip("On CRAN")
}27: else if (!new_expectations && skip_on_empty) {withRestarts(tryCatch(withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip(paste0("{", e$package, "} is not installed.")) end_test = function() { } })}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE40: invokeRestart("muffle_cran_snapshot")test_code(code = exprs, env = env, reporter = get_reporter() %||% }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), StopReporter$new()) end_test = function() {
})41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 28: error_call = error_call)test_code(code, parent.frame())
42: 29: FUN(X[[i]], ...)test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate",
{43: sampler_undirected_cov$rNetwork(store = TRUE)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, error_call = error_call) "bernoulli", FALSE, covarList = covarList_undirected)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 44: plot = FALSE))doTryCatch(return(expr), name, parentenv, handler) mySBM_sbm$setModel(Q)
net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, 45: covariates = covarList_undirected)tryCatchOne(expr, names, parentenv, handlers[[1L]]) cls <- net$clustering(1:(2 * Q))
cl <- cls[[Q]]46: mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, tryCatchList(expr, classes, parentenv, handlers) clusterInit = cl, covarList = covarList_undirected)
mySBM_missSBM$doVEM()47: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), tryCatch(code, testthat_abort_reporter = function(cnd) { 0.05) cat(conditionMessage(cnd), "\n") expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), NULL 0.8)}) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)48: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), with_reporter(reporters$multi, lapply(test_paths, test_one_file, 0.1) env = env, desc = desc, shuffle = shuffle, error_call = error_call)) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam),
0.1)49: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), test_files_serial(test_dir = test_dir, test_package = test_package, 0.85) 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, 30: error_call = error_call)eval(code, test_env)
50: 31: test_files(test_dir = path, test_paths = test_paths, test_package = package, eval(code, test_env) reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 32: load_package = load_package, parallel = parallel, shuffle = shuffle)withCallingHandlers({
eval(code, test_env)51: new_expectations <- the$test_expectations > starting_expectationstest_dir("testthat", package = package, reporter = reporter, if (snapshot_skipped) { ..., load_package = "installed") skip("On CRAN")
52: }test_check("missSBM") else if (!new_expectations && skip_on_empty) {
skip_empty()An irrecoverable exception occurred. R is aborting now ...
}}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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]])
Traceback:
1: 6: dispatcher(membership_name, membership_init$to_cc(), model_name, tryCatchList(expr, classes, parentenv, handlers) .self$network_to_cc(), TRUE)
7: 2: tryCatch(expr, error = function(e) { call <- conditionCall(e)FUN(X[[i]], ...) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 3: call <- sys.call(-4L)lapply(X = S, FUN = FUN, ...) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") 4: LONG <- 75LdoTryCatch(return(expr), name, parentenv, handler) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) 5: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatchOne(expr, names, parentenv, handlers[[1L]])
type = "b") 6: if (w > LONG) tryCatchList(expr, classes, parentenv, handlers) prefix <- paste0(prefix, "\n ")
} 7: else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")tryCatch(expr, error = function(e) { .Internal(seterrmessage(msg[1L])) call <- conditionCall(e) if (!silent && isTRUE(getOption("show.error.messages"))) { if (!is.null(call)) { cat(msg, file = outFile) if (identical(call[[1L]], quote(doTryCatch))) .Internal(printDeferredWarnings()) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") } invisible(structure(msg, class = "try-error", condition = e))}) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 8: if (is.na(w)) try(lapply(X = S, FUN = FUN, ...), silent = TRUE) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") 9: if (w > LONG) sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) prefix <- paste0(prefix, "\n ")
}10: else prefix <- "Error : "FUN(X[[i]], ...) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))11: if (!silent && isTRUE(getOption("show.error.messages"))) {lapply(seq_len(cores), inner.do) cat(msg, file = outFile)
.Internal(printDeferredWarnings()) }12: invisible(structure(msg, class = "try-error", condition = e))parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, }) mc.silent = TRUE)
8: 13: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 9: verbose = (verbosity > 4))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: 10: .self$do_with_inits(inits, Q, reinitialization_effort)FUN(X[[i]], ...)
15: 11: .self$estim_ascend(reinitialization_effort, changing_effort)lapply(seq_len(cores), inner.do)
12: 16: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, private$BMobject$estimate() mc.silent = TRUE)
17: 13: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))18:
eval(code, test_env)14:
.self$do_with_inits(inits, Q, reinitialization_effort)19:
eval(code, test_env)15:
.self$estim_ascend(reinitialization_effort, changing_effort)20:
withCallingHandlers({16: eval(code, test_env)private$BMobject$estimate() new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {17: skip("On CRAN")mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) }
else if (!new_expectations && skip_on_empty) {18: skip_empty()eval(code, test_env) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {19: skip(paste0("{", e$package, "} is not installed."))eval(code, test_env) }}, snapshot_on_cran = function(cnd) {
20: snapshot_skipped <<- TRUEwithCallingHandlers({ eval(code, test_env) 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$test_expectations > starting_expectations new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") } 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()) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { skip(paste0("{", e$package, "} is not installed.")) if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, snapshot_on_cran = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, snapshot_skipped <<- TRUE error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
invokeRestart("muffle_cran_snapshot")25: }, skip = handle_skip, warning = handle_warning, message = handle_message, doWithOneRestart(return(expr), restart)
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)26:
withOneRestart(expr, restarts[[1L]])25:
doWithOneRestart(return(expr), restart)27:
withRestarts(tryCatch(withCallingHandlers({26: eval(code, test_env)withOneRestart(expr, restarts[[1L]])
new_expectations <- the$test_expectations > starting_expectations27: if (snapshot_skipped) {withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() } if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { }}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) } snapshot_skipped <<- TRUE}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() {}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }) end_test = function() { })
28: 28: test_code(code, parent.frame())test_code(code, parent.frame())
29: 29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", { { sampler_directed_cov$rNetwork(store = TRUE) sampler_directed_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) plot = FALSE)) mySBM_sbm$setModel(Q) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, covariates = covarList_directed) cls <- net$clustering(1:(2 * Q)) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, covariates = covarList_directed) cl <- cls[[Q]] cls <- net$clustering(1:(2 * Q)) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, cl <- cls[[Q]] clusterInit = cl, covarList = covarList_directed) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_directed) mySBM_missSBM$doVEM(trace = TRUE) mySBM_missSBM$doVEM(trace = TRUE) 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), 0.8) 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.05) 0.05) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 0.1) 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 0.85) }) 0.85)
30: })eval(code, test_env)
30: 31: eval(code, test_env)eval(code, test_env)
31: 32: withCallingHandlers({eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {32: skip("On CRAN")withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$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_empty() skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) {
33: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, doTryCatch(return(expr), name, parentenv, handler) error = handle_error, interrupt = handle_interrupt)
34: 33: tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
35: 34: tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: 35: tryCatch(withCallingHandlers({tryCatchList(expr, classes, parentenv, handlers) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations36: if (snapshot_skipped) {tryCatch(withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$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) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip_empty() }}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, snapshot_on_cran = function(cnd) {37: snapshot_skipped <<- TRUEdoWithOneRestart(return(expr), restart) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 38: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)withOneRestart(expr, restarts[[1L]])
37: 39: doWithOneRestart(return(expr), restart)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)38: new_expectations <- the$test_expectations > starting_expectationswithOneRestart(expr, restarts[[1L]]) if (snapshot_skipped) {
skip("On CRAN")39: }withRestarts(tryCatch(withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }}, 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: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {41: })source_file(path, env = env(env), desc = desc, shuffle = shuffle,
40: error_call = error_call)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())
42: FUN(X[[i]], ...)41:
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,
error_call = error_call)
42: 44: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 46: error_call = error_call)tryCatchList(expr, classes, parentenv, handlers)
44: 47: doTryCatch(return(expr), name, parentenv, handler)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")45: NULLtryCatchOne(expr, names, parentenv, handlers[[1L]])})
46: 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, tryCatchList(expr, classes, parentenv, handlers) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
47: 49: tryCatch(code, testthat_abort_reporter = function(cnd) {test_files_serial(test_dir = test_dir, test_package = test_package, cat(conditionMessage(cnd), "\n") test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, NULL desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)})
50: 48: test_files(test_dir = path, test_paths = test_paths, test_package = package, with_reporter(reporters$multi, lapply(test_paths, test_one_file, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) load_package = load_package, parallel = parallel, shuffle = shuffle)
49: 51: test_files_serial(test_dir = test_dir, test_package = test_package, test_dir("testthat", package = package, reporter = reporter, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, ..., load_package = "installed") env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 52: error_call = error_call)test_check("missSBM")
50: An irrecoverable exception occurred. R is aborting now ...
test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
Traceback:
1:
dispatcher(membership_name, membership_init$to_cc(), model_name, 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) .self$network_to_cc(), TRUE)
6: 2: tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)
7:
tryCatch(expr, error = function(e) { 3: call <- conditionCall(e) if (!is.null(call)) {lapply(X = S, FUN = FUN, ...) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) 4: dcall <- deparse(call, nlines = 1L)doTryCatch(return(expr), name, parentenv, handler) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L 5: sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatchOne(expr, names, parentenv, handlers[[1L]])
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 6: if (is.na(w)) tryCatchList(expr, classes, parentenv, handlers)
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 7: type = "b")tryCatch(expr, error = function(e) { call <- conditionCall(e) if (w > LONG) if (!is.null(call)) { prefix <- paste0(prefix, "\n ") if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) else prefix <- "Error : " dcall <- deparse(call, nlines = 1L) msg <- paste0(prefix, conditionMessage(e), "\n") prefix <- paste("Error in", dcall, ": ") .Internal(seterrmessage(msg[1L])) LONG <- 75L if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) sm <- strsplit(conditionMessage(e), "\n")[[1L]] .Internal(printDeferredWarnings()) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } if (is.na(w)) invisible(structure(msg, class = "try-error", condition = e)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }) type = "b")
8: if (w > LONG) try(lapply(X = S, FUN = FUN, ...), silent = TRUE) prefix <- paste0(prefix, "\n ")
} 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")10: .Internal(seterrmessage(msg[1L]))FUN(X[[i]], ...) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)11: .Internal(printDeferredWarnings())lapply(seq_len(cores), inner.do)
}12: invisible(structure(msg, class = "try-error", condition = e))parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, }) mc.silent = TRUE)
8: 13: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4)) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))14:
.self$do_with_inits(inits, Q, reinitialization_effort)10:
FUN(X[[i]], ...)15:
.self$estim_ascend(reinitialization_effort, changing_effort)11:
lapply(seq_len(cores), inner.do)16:
private$BMobject$estimate()12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 17: mc.silent = TRUE)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
13: 18: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, eval(code, test_env) verbose = (verbosity > 4))
19: 14: eval(code, test_env).self$do_with_inits(inits, Q, reinitialization_effort)
20: 15: 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) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {21: skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler) }
else if (!new_expectations && skip_on_empty) {22: skip_empty()tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {23: if (on_cran()) {tryCatchList(expr, classes, parentenv, handlers) skip(paste0("{", e$package, "} is not installed."))
}24: }, snapshot_on_cran = function(cnd) {tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt) skip("On CRAN")
}21: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler) skip_empty()
}22: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))23: }tryCatchList(expr, classes, parentenv, handlers)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE24: invokeRestart("muffle_cran_snapshot")tryCatch(withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
new_expectations <- the$test_expectations > starting_expectations25: if (snapshot_skipped) {doWithOneRestart(return(expr), restart) skip("On CRAN")
}26: else if (!new_expectations && skip_on_empty) {withOneRestart(expr, restarts[[1L]]) skip_empty()
}27: }, expectation = handle_expectation, packageNotFoundError = function(e) {withRestarts(tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {25: skip(paste0("{", e$package, "} is not installed."))doWithOneRestart(return(expr), restart) }
}, snapshot_on_cran = function(cnd) {26: snapshot_skipped <<- TRUEwithOneRestart(expr, restarts[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 27: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), withRestarts(tryCatch(withCallingHandlers({ end_test = function() { eval(code, test_env) }) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {28: skip("On CRAN")test_code(code, parent.frame()) }
else if (!new_expectations && skip_on_empty) {29: skip_empty()test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", } {}, expectation = handle_expectation, packageNotFoundError = function(e) { sampler_undirected_nocov$rNetwork(store = TRUE) if (on_cran()) { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, skip(paste0("{", e$package, "} is not installed.")) "bernoulli", FALSE) } mySBM_sbm$optimize(estimOptions = list(verbosity = 0, }, snapshot_on_cran = function(cnd) { plot = FALSE)) snapshot_skipped <<- TRUE mySBM_sbm$setModel(3) invokeRestart("muffle_cran_snapshot") net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData)}, skip = handle_skip, warning = handle_warning, message = handle_message, cl <- net$clustering(3)[[1]] error = handle_error, interrupt = handle_interrupt), error = handle_fatal), mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, end_test = function() { clusterInit = cl) }) mySBM_missSBM$doVEM()
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 28: 0.05)test_code(code, parent.frame()) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.95)29: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", 0.01) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), sampler_undirected_nocov$rNetwork(store = TRUE) 0.05) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), "bernoulli", FALSE) 0.95) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, }) plot = FALSE))
mySBM_sbm$setModel(3)30: net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData)eval(code, test_env) cl <- net$clustering(3)[[1]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, 31: clusterInit = cl) mySBM_missSBM$doVEM()eval(code, test_env) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
0.05)32: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), withCallingHandlers({ 0.95) eval(code, test_env) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), new_expectations <- the$test_expectations > starting_expectations 0.05) if (snapshot_skipped) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.95) }) skip("On CRAN")
}30: else if (!new_expectations && skip_on_empty) {eval(code, test_env)
skip_empty() }31: }, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env)
if (on_cran()) {32: skip(paste0("{", e$package, "} is not installed."))withCallingHandlers({ eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {33: if (on_cran()) { skip(paste0("{", e$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: doTryCatch(return(expr), name, parentenv, handler)
36:
34: tryCatch(withCallingHandlers({tryCatchOne(expr, names, parentenv, handlers[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations35: if (snapshot_skipped) { skip("On CRAN") }tryCatchList(expr, classes, parentenv, handlers)
else if (!new_expectations && skip_on_empty) {36: tryCatch(withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
if (on_cran()) {37: skip(paste0("{", e$package, "} is not installed."))doWithOneRestart(return(expr), restart) }
}, snapshot_on_cran = function(cnd) {38: snapshot_skipped <<- TRUEwithOneRestart(expr, restarts[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 39: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)37: new_expectations <- the$test_expectations > starting_expectationsdoWithOneRestart(return(expr), restart) if (snapshot_skipped) {
skip("On CRAN")38: }withOneRestart(expr, restarts[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()39: }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {withRestarts(tryCatch(withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) }}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip_empty() } end_test = function() { })}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {40: skip(paste0("{", e$package, "} is not installed."))test_code(code = exprs, env = env, reporter = get_reporter() %||% }}, snapshot_on_cran = function(cnd) { StopReporter$new()) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")41: }, skip = handle_skip, warning = handle_warning, message = handle_message, source_file(path, env = env(env), desc = desc, shuffle = shuffle, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), error_call = error_call) end_test = function() {
})42:
FUN(X[[i]], ...)40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 43: StopReporter$new())lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 44: error_call = error_call)doTryCatch(return(expr), name, parentenv, handler)
42: 45: FUN(X[[i]], ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
43: 46: tryCatchList(expr, classes, parentenv, handlers)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)47:
tryCatch(code, testthat_abort_reporter = function(cnd) {44: cat(conditionMessage(cnd), "\n")doTryCatch(return(expr), name, parentenv, handler)
NULL45: })tryCatchOne(expr, names, parentenv, handlers[[1L]])
48: 46: with_reporter(reporters$multi, lapply(test_paths, test_one_file, tryCatchList(expr, classes, parentenv, handlers) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
47: 49: tryCatch(code, testthat_abort_reporter = function(cnd) {test_files_serial(test_dir = test_dir, test_package = test_package, cat(conditionMessage(cnd), "\n") test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, NULL env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 50: env = env, desc = desc, shuffle = shuffle, error_call = error_call))test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 49: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_files_serial(test_dir = test_dir, test_package = test_package, load_package = load_package, parallel = parallel, shuffle = shuffle) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 51: desc = desc, load_package = load_package, shuffle = shuffle, test_dir("testthat", package = package, reporter = reporter, error_call = error_call) ..., load_package = "installed")
50: 52: test_files(test_dir = path, test_paths = test_paths, test_package = package, test_check("missSBM") reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, An irrecoverable exception occurred. R is aborting now ...
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, ...)
Traceback:
4: 1: doTryCatch(return(expr), name, parentenv, handler)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
2: 6: FUN(X[[i]], ...)
tryCatchList(expr, classes, parentenv, handlers) 3:
lapply(X = S, FUN = FUN, ...) 7:
tryCatch(expr, error = function(e) { 4: call <- conditionCall(e)doTryCatch(return(expr), name, parentenv, handler) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 5: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)tryCatchOne(expr, names, parentenv, handlers[[1L]])
prefix <- paste("Error in", dcall, ": ") LONG <- 75L 6: sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 7: tryCatch(expr, error = function(e) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], call <- conditionCall(e) type = "b") if (!is.null(call)) { if (w > LONG) if (identical(call[[1L]], quote(doTryCatch))) prefix <- paste0(prefix, "\n ") call <- sys.call(-4L) } dcall <- deparse(call, nlines = 1L) else prefix <- "Error : " prefix <- paste("Error in", dcall, ": ") msg <- paste0(prefix, conditionMessage(e), "\n") LONG <- 75L .Internal(seterrmessage(msg[1L])) sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (!silent && isTRUE(getOption("show.error.messages"))) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") cat(msg, file = outFile) if (is.na(w)) .Internal(printDeferredWarnings()) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b") invisible(structure(msg, class = "try-error", condition = e))}) if (w > LONG)
prefix <- paste0(prefix, "\n ") 8: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n") 9: .Internal(seterrmessage(msg[1L]))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)10: .Internal(printDeferredWarnings()) }FUN(X[[i]], ...) invisible(structure(msg, class = "try-error", condition = e))
})11: lapply(seq_len(cores), inner.do)
8: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE,
mc.silent = TRUE) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 10: verbose = (verbosity > 4))FUN(X[[i]], ...)
14: 11: .self$do_with_inits(inits, Q, reinitialization_effort)
lapply(seq_len(cores), inner.do)15:
.self$estim_ascend(reinitialization_effort, changing_effort)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 16: mc.silent = TRUE)private$BMobject$estimate()
13: 17: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) verbose = (verbosity > 4))
18: 14: eval(code, test_env).self$do_with_inits(inits, Q, reinitialization_effort)
19: 15: eval(code, test_env).self$estim_ascend(reinitialization_effort, changing_effort)
20: 16: withCallingHandlers({private$BMobject$estimate() eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations17: if (snapshot_skipped) {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
skip("On CRAN")18: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()19: }eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {20: skip(paste0("{", e$package, "} is not installed."))withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { invokeRestart("muffle_cran_snapshot") skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt) else if (!new_expectations && skip_on_empty) {
skip_empty()21: }doTryCatch(return(expr), name, parentenv, handler)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {22: skip(paste0("{", e$package, "} is not installed."))tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, snapshot_on_cran = function(cnd) {23: tryCatchList(expr, classes, parentenv, handlers)
24: 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$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) { skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE25: invokeRestart("muffle_cran_snapshot")doWithOneRestart(return(expr), restart)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)26:
withOneRestart(expr, restarts[[1L]])25:
doWithOneRestart(return(expr), restart)27:
26: withRestarts(tryCatch(withCallingHandlers({withOneRestart(expr, restarts[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations27: if (snapshot_skipped) {withRestarts(tryCatch(withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() skip(paste0("{", e$package, "} is not installed.")) } }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, snapshot_on_cran = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), 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() {
})28:
test_code(code, parent.frame())28:
test_code(code, parent.frame())29:
test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", 29: {test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", sampler_directed_nocov$rNetwork(store = TRUE) { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, sampler_directed_nocov$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, mySBM_sbm$setModel(3) plot = FALSE)) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) mySBM_sbm$setModel(3) cl <- net$clustering(3)[[1]] net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, cl <- net$clustering(3)[[1]] clusterInit = cl) mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, mySBM_missSBM$doVEM() clusterInit = cl) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), mySBM_missSBM$doVEM() 0.1) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.1) 0.95) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.95) 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) 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.2) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: 0.2)eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships),
0.95)32: })
withCallingHandlers({30: eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN")
}31: else if (!new_expectations && skip_on_empty) {eval(code, test_env) skip_empty()
}32: }, expectation = handle_expectation, packageNotFoundError = function(e) {withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {33: if (on_cran()) { skip(paste0("{", e$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) new_expectations <- the$test_expectations > starting_expectations34: if (snapshot_skipped) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip("On CRAN")
}35: else if (!new_expectations && skip_on_empty) {tryCatchList(expr, classes, parentenv, handlers) skip_empty()
}36: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {37: if (on_cran()) {doWithOneRestart(return(expr), restart) skip(paste0("{", e$package, "} is not installed."))
}38: }, snapshot_on_cran = function(cnd) {withOneRestart(expr, restarts[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")39: }, skip = handle_skip, warning = handle_warning, message = handle_message, withRestarts(tryCatch(withCallingHandlers({ error = handle_error, interrupt = handle_interrupt), error = handle_fatal) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations37: if (snapshot_skipped) {doWithOneRestart(return(expr), restart) skip("On CRAN")
}38: else if (!new_expectations && skip_on_empty) {withOneRestart(expr, restarts[[1L]]) skip_empty()
}39: withRestarts(tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { } })}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))40: test_code(code = exprs, env = env, reporter = get_reporter() %||% } StopReporter$new())}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE41: invokeRestart("muffle_cran_snapshot")source_file(path, env = env(env), desc = desc, shuffle = shuffle, }, skip = handle_skip, warning = handle_warning, message = handle_message, error_call = error_call) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {42: })FUN(X[[i]], ...)
40: 43: test_code(code = exprs, env = env, reporter = get_reporter() %||% lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, StopReporter$new()) error_call = error_call)
44: 41: doTryCatch(return(expr), name, parentenv, handler)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])42:
FUN(X[[i]], ...)46:
tryCatchList(expr, classes, parentenv, handlers)43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 47: error_call = error_call)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")44: NULLdoTryCatch(return(expr), name, parentenv, handler)})
45: 48: tryCatchOne(expr, names, parentenv, handlers[[1L]])with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))46:
tryCatchList(expr, classes, parentenv, handlers)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 47: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, tryCatch(code, testthat_abort_reporter = function(cnd) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, cat(conditionMessage(cnd), "\n") desc = desc, load_package = load_package, shuffle = shuffle, NULL error_call = error_call)})
50: 48: test_files(test_dir = path, test_paths = test_paths, test_package = package, with_reporter(reporters$multi, lapply(test_paths, test_one_file, reporter = reporter, load_helpers = load_helpers, env = env, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 51: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, test_dir("testthat", package = package, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, ..., load_package = "installed") desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)52:
test_check("missSBM")50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, An irrecoverable exception occurred. R is aborting now ...
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