Last updated on 2026-10-22 18:55:26 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 80.98 | 341.84 | 422.82 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 59.86 | 235.73 | 295.59 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 59.00 | 271.80 | 330.80 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 237.71 | 301.71 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 420.00 | 511.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 87.75 | 330.28 | 418.03 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 86.79 | 329.37 | 416.16 | 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 | 93.00 | 345.00 | 438.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 19.00 | 87.00 | 106.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 121.00 | 474.00 | 595.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [37s/30s]
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$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) {
Traceback:
1: skip_empty() }dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { 2: FUN(X[[i]], ...) skip(paste0("{", e$package, "} is not installed.")) }
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE 3: invokeRestart("muffle_cran_snapshot")lapply(X = S, FUN = FUN, ...)}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
4:
21: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5:
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
tryCatchList(expr, classes, parentenv, handlers)
6: 24: tryCatch(withCallingHandlers({tryCatchList(expr, classes, parentenv, handlers)
eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations 7: if (snapshot_skipped) { skip("On CRAN")tryCatch(expr, error = function(e) { call <- conditionCall(e) } if (!is.null(call)) { else if (!new_expectations && skip_on_empty) { skip_empty() if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) } dcall <- deparse(call, nlines = 1L)}, expectation = handle_expectation, packageNotFoundError = function(e) { prefix <- paste("Error in", dcall, ": ") LONG <- 75L if (on_cran()) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] skip(paste0("{", e$package, "} is not installed.")) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }, snapshot_on_cran = function(cnd) { type = "b") snapshot_skipped <<- TRUE if (w > LONG) prefix <- paste0(prefix, "\n ") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else prefix <- "Error : " error = handle_error, interrupt = handle_interrupt), error = handle_fatal) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {25: cat(msg, file = outFile)doWithOneRestart(return(expr), restart) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error", condition = e))26: withOneRestart(expr, restarts[[1L]])})
27:
withRestarts(tryCatch(withCallingHandlers({ 8: eval(code, test_env)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN") 9: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) else if (!new_expectations && skip_on_empty) {
skip_empty()10: }FUN(X[[i]], ...)}, expectation = handle_expectation, packageNotFoundError = function(e) {
11: if (on_cran()) {lapply(seq_len(cores), inner.do) skip(paste0("{", e$package, "} is not installed."))
}12: }, snapshot_on_cran = function(cnd) {parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, snapshot_skipped <<- TRUE mc.silent = TRUE) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 13: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, end_test = function() { verbose = (verbosity > 4))
})14:
.self$do_with_inits(inits, Q, reinitialization_effort)28:
test_code(code, parent.frame())15:
.self$estim_ascend(reinitialization_effort, changing_effort)29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", 16: {private$BMobject$estimate() sampler_undirected_cov$rNetwork(store = TRUE)
mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, 17: "bernoulli", FALSE, covarList = covarList_undirected)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))18: mySBM_sbm$setModel(Q)eval(code, test_env) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData,
covariates = covarList_undirected)19: cls <- net$clustering(1:(2 * Q))eval(code, test_env) cl <- cls[[Q]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, 20: clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM()withCallingHandlers({ expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), eval(code, test_env) 0.05) new_expectations <- the$test_expectations > starting_expectations expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), if (snapshot_skipped) { 0.8) skip("On CRAN") expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), } 0.01) else if (!new_expectations && skip_on_empty) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), skip_empty() 0.1) } expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.1) if (on_cran()) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), skip(paste0("{", e$package, "} is not installed.")) 0.85) } })}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE30: invokeRestart("muffle_cran_snapshot")eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)31:
eval(code, test_env)21:
doTryCatch(return(expr), name, parentenv, handler)32:
withCallingHandlers({22: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {23: skip("On CRAN")tryCatchList(expr, classes, parentenv, handlers) }
else if (!new_expectations && skip_on_empty) {24: skip_empty()tryCatch(withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { new_expectations <- the$test_expectations > starting_expectations if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))33: }doTryCatch(return(expr), name, parentenv, handler)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE34: invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)35:
tryCatchList(expr, classes, parentenv, handlers)25:
doWithOneRestart(return(expr), restart)36:
tryCatch(withCallingHandlers({26: eval(code, test_env)withOneRestart(expr, restarts[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {27: skip("On CRAN")withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$test_expectations > starting_expectations skip_empty() if (snapshot_skipped) { } skip("On CRAN")}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { } 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) {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]]) end_test = function() {
})39:
28: withRestarts(tryCatch(withCallingHandlers({test_code(code, parent.frame()) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations29: if (snapshot_skipped) {test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", skip("On CRAN") { } sampler_undirected_cov$rNetwork(store = TRUE) else if (!new_expectations && skip_on_empty) { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, skip_empty() "bernoulli", FALSE, covarList = covarList_undirected) } mySBM_sbm$optimize(estimOptions = list(verbosity = 0, }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { plot = FALSE)) skip(paste0("{", e$package, "} is not installed.")) mySBM_sbm$setModel(Q) } net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, }, snapshot_on_cran = function(cnd) { covariates = covarList_undirected) snapshot_skipped <<- TRUE cls <- net$clustering(1:(2 * Q)) invokeRestart("muffle_cran_snapshot") cl <- cls[[Q]]}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), clusterInit = cl, covarList = covarList_undirected) end_test = function() { mySBM_missSBM$doVEM() }) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
0.05)40: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), test_code(code = exprs, env = env, reporter = get_reporter() %||% 0.8) StopReporter$new()) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)41: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), source_file(path, env = env(env), desc = desc, shuffle = shuffle, 0.1) error_call = error_call) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam),
0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 42: 0.85)FUN(X[[i]], ...) })
43: 30: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, eval(code, test_env) error_call = error_call)
31: 44: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler)
32: 45: withCallingHandlers({tryCatchOne(expr, names, parentenv, handlers[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations46: if (snapshot_skipped) {tryCatchList(expr, classes, parentenv, handlers) skip("On CRAN")
}47: else if (!new_expectations && skip_on_empty) {tryCatch(code, testthat_abort_reporter = function(cnd) { skip_empty() cat(conditionMessage(cnd), "\n") } NULL}, expectation = handle_expectation, packageNotFoundError = function(e) {}) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))48: }with_reporter(reporters$multi, lapply(test_paths, test_one_file, }, snapshot_on_cran = function(cnd) { env = env, desc = desc, shuffle = shuffle, error_call = error_call)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")49: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_files_serial(test_dir = test_dir, test_package = test_package, error = handle_error, interrupt = handle_interrupt) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 33: desc = desc, load_package = load_package, shuffle = shuffle, doTryCatch(return(expr), name, parentenv, handler) error_call = error_call)
34: 50: tryCatchOne(expr, names, parentenv, handlers[[1L]])test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 35: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, tryCatchList(expr, classes, parentenv, handlers) load_package = load_package, parallel = parallel, shuffle = shuffle)
36: 51: tryCatch(withCallingHandlers({test_dir("testthat", package = package, reporter = reporter, eval(code, test_env) ..., load_package = "installed") new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {52: skip("On CRAN")test_check("missSBM") }
else if (!new_expectations && skip_on_empty) {An irrecoverable exception occurred. R is aborting now ...
skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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$networkData, "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$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]])
Traceback:
1:
dispatcher(membership_name, membership_init$to_cc(), model_name, 35: .self$network_to_cc(), TRUE)
tryCatchList(expr, classes, parentenv, handlers) 2:
FUN(X[[i]], ...)36:
tryCatch(withCallingHandlers({ 3: eval(code, test_env)lapply(X = S, FUN = FUN, ...)
new_expectations <- the$test_expectations > starting_expectations 4: if (snapshot_skipped) {doTryCatch(return(expr), name, parentenv, handler) skip("On CRAN")
} 5: else if (!new_expectations && skip_on_empty) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip_empty()
} 6: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 7: }tryCatch(expr, error = function(e) {}, snapshot_on_cran = function(cnd) { call <- conditionCall(e) snapshot_skipped <<- TRUE if (!is.null(call)) { invokeRestart("muffle_cran_snapshot") if (identical(call[[1L]], quote(doTryCatch))) }, skip = handle_skip, warning = handle_warning, message = handle_message, call <- sys.call(-4L) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")37: LONG <- 75LdoWithOneRestart(return(expr), restart) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")38: if (is.na(w)) withOneRestart(expr, restarts[[1L]]) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")39: if (w > LONG) withRestarts(tryCatch(withCallingHandlers({ prefix <- paste0(prefix, "\n ") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else prefix <- "Error : " if (snapshot_skipped) { msg <- paste0(prefix, conditionMessage(e), "\n") skip("On CRAN") .Internal(seterrmessage(msg[1L])) } if (!silent && isTRUE(getOption("show.error.messages"))) { else if (!new_expectations && skip_on_empty) { cat(msg, file = outFile) skip_empty() .Internal(printDeferredWarnings()) } }}, expectation = handle_expectation, packageNotFoundError = function(e) { invisible(structure(msg, class = "try-error", condition = e)) if (on_cran()) {}) skip(paste0("{", e$package, "} is not installed."))
} 8: }, snapshot_on_cran = function(cnd) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 9: }, skip = handle_skip, warning = handle_warning, message = handle_message, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {10: })FUN(X[[i]], ...)
40: 11: test_code(code = exprs, env = env, reporter = get_reporter() %||% lapply(seq_len(cores), inner.do) StopReporter$new())
12: 41: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, source_file(path, env = env(env), desc = desc, shuffle = shuffle, mc.silent = TRUE) error_call = error_call)
13: 42: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))FUN(X[[i]], ...)
14: 43: .self$do_with_inits(inits, Q, reinitialization_effort)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)15:
.self$estim_ascend(reinitialization_effort, changing_effort)44:
doTryCatch(return(expr), name, parentenv, handler)16:
private$BMobject$estimate()45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))46:
tryCatchList(expr, classes, parentenv, handlers)18:
eval(code, test_env)47:
tryCatch(code, testthat_abort_reporter = function(cnd) {19: eval(code, test_env) cat(conditionMessage(cnd), "\n")
NULL20: })withCallingHandlers({ eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations48: if (snapshot_skipped) { skip("On CRAN")with_reporter(reporters$multi, lapply(test_paths, test_one_file, } env = env, desc = desc, shuffle = shuffle, error_call = error_call)) else if (!new_expectations && skip_on_empty) {
skip_empty()49: }test_files_serial(test_dir = test_dir, test_package = test_package, }, expectation = handle_expectation, packageNotFoundError = function(e) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, if (on_cran()) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, skip(paste0("{", e$package, "} is not installed.")) desc = desc, load_package = load_package, shuffle = shuffle, } error_call = error_call)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")50: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_files(test_dir = path, test_paths = test_paths, test_package = package, error = handle_error, interrupt = handle_interrupt) reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 21: load_package = load_package, parallel = parallel, shuffle = shuffle)doTryCatch(return(expr), name, parentenv, handler)
51: 22: test_dir("testthat", package = package, reporter = reporter, tryCatchOne(expr, names, parentenv, handlers[[1L]]) ..., load_package = "installed")
23: 52: tryCatchList(expr, classes, parentenv, handlers)test_check("missSBM")
24: An irrecoverable exception occurred. R is aborting now ...
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$networkData, "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$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$to_cc(), model_name, .self$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]))
Traceback:
if (!silent && isTRUE(getOption("show.error.messages"))) { 1: cat(msg, file = outFile)dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) .Internal(printDeferredWarnings())
} 2: invisible(structure(msg, class = "try-error", condition = e))FUN(X[[i]], ...)})
8: 3: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
lapply(X = S, FUN = FUN, ...) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
4: 10: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)
5: 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
lapply(seq_len(cores), inner.do) 6:
tryCatchList(expr, classes, parentenv, handlers)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 7: mc.silent = TRUE)tryCatch(expr, error = function(e) {
call <- conditionCall(e)13: if (!is.null(call)) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, if (identical(call[[1L]], quote(doTryCatch))) verbose = (verbosity > 4))
call <- sys.call(-4L)14: .self$do_with_inits(inits, Q, reinitialization_effort) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")15: LONG <- 75L.self$estim_ascend(reinitialization_effort, changing_effort) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")16: if (is.na(w)) private$BMobject$estimate() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")17: if (w > LONG) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) prefix <- paste0(prefix, "\n ") }
else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")18: .Internal(seterrmessage(msg[1L]))eval(code, test_env) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)19: .Internal(printDeferredWarnings())eval(code, test_env) }
invisible(structure(msg, class = "try-error", condition = e))20: })withCallingHandlers({
eval(code, test_env) 8: new_expectations <- the$test_expectations > starting_expectationstry(lapply(X = S, FUN = FUN, ...), silent = TRUE)
if (snapshot_skipped) { 9: skip("On CRAN")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
}10: else if (!new_expectations && skip_on_empty) {FUN(X[[i]], ...) skip_empty()
}}, expectation = handle_expectation, packageNotFoundError = function(e) {11: if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) {lapply(seq_len(cores), inner.do) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")12: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE,
mc.silent = TRUE)21:
doTryCatch(return(expr), name, parentenv, handler)13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
verbose = (verbosity > 4))23:
tryCatchList(expr, classes, parentenv, handlers)14:
.self$do_with_inits(inits, Q, reinitialization_effort)
24: tryCatch(withCallingHandlers({15: eval(code, test_env).self$estim_ascend(reinitialization_effort, changing_effort)
new_expectations <- the$test_expectations > starting_expectations16: if (snapshot_skipped) {private$BMobject$estimate() skip("On CRAN") }
else if (!new_expectations && skip_on_empty) { skip_empty()17: }}, expectation = handle_expectation, packageNotFoundError = function(e) {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))18: }eval(code, test_env)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE19: invokeRestart("muffle_cran_snapshot")eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)20:
withCallingHandlers({25: eval(code, test_env)doWithOneRestart(return(expr), restart)
new_expectations <- the$test_expectations > starting_expectations26: if (snapshot_skipped) {withOneRestart(expr, restarts[[1L]])
skip("On CRAN")27: }withRestarts(tryCatch(withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt) skip(paste0("{", e$package, "} is not installed."))
}21: }, snapshot_on_cran = function(cnd) {doTryCatch(return(expr), name, parentenv, handler) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")22: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchOne(expr, names, parentenv, handlers[[1L]])
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 23: tryCatchList(expr, classes, parentenv, handlers)
end_test = function() {24: tryCatch(withCallingHandlers({ }) eval(code, test_env)
28: test_code(code, parent.frame()) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { sampler_undirected_nocov$rNetwork(store = TRUE) skip_empty() mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { "bernoulli", FALSE) 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_undirected_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$new(net, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) clusterInit = cl)
mySBM_missSBM$doVEM()25: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), doWithOneRestart(return(expr), restart) 0.05)
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),
0.01)27: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), withRestarts(tryCatch(withCallingHandlers({ 0.05) eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), new_expectations <- the$test_expectations > starting_expectations 0.95) if (snapshot_skipped) { }) skip("On CRAN") }
else if (!new_expectations && skip_on_empty) {30: skip_empty()eval(code, test_env) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {31: if (on_cran()) {eval(code, test_env) skip(paste0("{", e$package, "} is not installed."))
}32: }, snapshot_on_cran = function(cnd) {withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { end_test = function() { skip("On CRAN") }) }
else if (!new_expectations && skip_on_empty) {28: skip_empty()test_code(code, parent.frame()) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {29: if (on_cran()) {test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", { sampler_undirected_nocov$rNetwork(store = TRUE) skip(paste0("{", e$package, "} is not installed.")) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) } mySBM_sbm$optimize(estimOptions = list(verbosity = 0, }, snapshot_on_cran = function(cnd) { plot = FALSE)) snapshot_skipped <<- TRUE mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_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$new(net, error = handle_error, interrupt = handle_interrupt)
clusterInit = cl) mySBM_missSBM$doVEM()33: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), doTryCatch(return(expr), name, parentenv, handler) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 34: 0.95)tryCatchOne(expr, names, parentenv, handlers[[1L]]) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)35: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), tryCatchList(expr, classes, parentenv, handlers) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 36: 0.95) })tryCatch(withCallingHandlers({
eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations30: if (snapshot_skipped) {eval(code, test_env) skip("On CRAN")
}31: else if (!new_expectations && skip_on_empty) {eval(code, test_env) skip_empty()
}32: }, expectation = handle_expectation, packageNotFoundError = function(e) {withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {37: if (on_cran()) {doWithOneRestart(return(expr), restart) skip(paste0("{", e$package, "} is not installed."))
}}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE38: invokeRestart("muffle_cran_snapshot")withOneRestart(expr, restarts[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)39:
withRestarts(tryCatch(withCallingHandlers({33: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {34: skip("On CRAN")tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
else if (!new_expectations && skip_on_empty) {35: skip_empty() }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {36: skip(paste0("{", e$package, "} is not installed."))tryCatch(withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { invokeRestart("muffle_cran_snapshot") skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), else if (!new_expectations && skip_on_empty) { end_test = function() { skip_empty() }) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {40: if (on_cran()) {test_code(code = exprs, env = env, reporter = get_reporter() %||% skip(paste0("{", e$package, "} is not installed.")) StopReporter$new()) }
}, snapshot_on_cran = function(cnd) {41: snapshot_skipped <<- TRUEsource_file(path, env = env(env), desc = desc, shuffle = shuffle, invokeRestart("muffle_cran_snapshot") error_call = error_call)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)42:
FUN(X[[i]], ...)37:
doWithOneRestart(return(expr), restart)43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 38: error_call = error_call)withOneRestart(expr, restarts[[1L]])
44: 39: doTryCatch(return(expr), name, parentenv, handler)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)45: new_expectations <- the$test_expectations > starting_expectationstryCatchOne(expr, names, parentenv, handlers[[1L]]) if (snapshot_skipped) {
skip("On CRAN")46: }tryCatchList(expr, classes, parentenv, handlers) else if (!new_expectations && skip_on_empty) {
skip_empty()47: }tryCatch(code, testthat_abort_reporter = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { cat(conditionMessage(cnd), "\n") if (on_cran()) { NULL skip(paste0("{", e$package, "} is not installed."))}) }
}, snapshot_on_cran = function(cnd) {48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, snapshot_skipped <<- TRUE env = env, desc = desc, shuffle = shuffle, error_call = error_call)) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 49: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_files_serial(test_dir = test_dir, test_package = test_package, end_test = function() { 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, 40: error_call = error_call)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 41: reporter = reporter, load_helpers = load_helpers, env = env, source_file(path, env = env(env), desc = desc, shuffle = shuffle, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, error_call = error_call) load_package = load_package, parallel = parallel, shuffle = shuffle)
42: 51: FUN(X[[i]], ...)test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 52: error_call = error_call)test_check("missSBM")
44: An irrecoverable exception occurred. R is aborting now ...
doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$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]], ...)
Traceback:
3: 1: dispatcher(membership_name, membership_init$to_cc(), model_name, lapply(X = S, FUN = FUN, ...) .self$network_to_cc(), TRUE)
4: 2: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)
3: 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])lapply(X = S, FUN = FUN, ...)
6: 4: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
7: 5: tryCatch(expr, error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) call <- conditionCall(e) if (!is.null(call)) {
6: if (identical(call[[1L]], quote(doTryCatch))) tryCatchList(expr, classes, parentenv, handlers) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) 7: prefix <- paste("Error in", dcall, ": ")tryCatch(expr, error = function(e) { LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] call <- conditionCall(e) if (!is.null(call)) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (identical(call[[1L]], quote(doTryCatch))) if (is.na(w)) call <- sys.call(-4L) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], dcall <- deparse(call, nlines = 1L) type = "b") prefix <- paste("Error in", dcall, ": ") if (w > LONG) LONG <- 75L prefix <- paste0(prefix, "\n ") sm <- strsplit(conditionMessage(e), "\n")[[1L]] } else prefix <- "Error : " w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") msg <- paste0(prefix, conditionMessage(e), "\n") if (is.na(w)) .Internal(seterrmessage(msg[1L])) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (!silent && isTRUE(getOption("show.error.messages"))) { type = "b") cat(msg, file = outFile) if (w > LONG) .Internal(printDeferredWarnings()) prefix <- paste0(prefix, "\n ") } } invisible(structure(msg, class = "try-error", condition = e)) else prefix <- "Error : "}) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) { 8: cat(msg, file = outFile)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) .Internal(printDeferredWarnings())
} 9: invisible(structure(msg, class = "try-error", condition = e))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))})
10: 8: FUN(X[[i]], ...)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
11:
lapply(seq_len(cores), inner.do) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))12:
10: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)FUN(X[[i]], ...)
13: 11: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))lapply(seq_len(cores), inner.do)
14: 12: .self$do_with_inits(inits, Q, reinitialization_effort)
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 15: mc.silent = TRUE)
.self$estim_ascend(reinitialization_effort, changing_effort)13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 16: verbose = (verbosity > 4))private$BMobject$estimate()
14: .self$do_with_inits(inits, Q, reinitialization_effort)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))15:
.self$estim_ascend(reinitialization_effort, changing_effort)18:
eval(code, test_env)16:
private$BMobject$estimate()19:
eval(code, test_env)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))20:
18: withCallingHandlers({ eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
19: if (snapshot_skipped) {eval(code, test_env) skip("On CRAN")
}20: else if (!new_expectations && skip_on_empty) {withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt) skip(paste0("{", e$package, "} is not installed."))
}21: }, snapshot_on_cran = function(cnd) {doTryCatch(return(expr), name, parentenv, handler)
snapshot_skipped <<- TRUE22: invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)23:
tryCatchList(expr, classes, parentenv, handlers)
21: 24: doTryCatch(return(expr), name, parentenv, handler)
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$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))25: }doWithOneRestart(return(expr), restart)
}, snapshot_on_cran = function(cnd) {26: snapshot_skipped <<- TRUEwithOneRestart(expr, restarts[[1L]])
invokeRestart("muffle_cran_snapshot")27: }, skip = handle_skip, warning = handle_warning, message = handle_message, withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt), error = handle_fatal) if (snapshot_skipped) {
skip("On CRAN")25: }doWithOneRestart(return(expr), restart)
else if (!new_expectations && skip_on_empty) {26: skip_empty()withOneRestart(expr, restarts[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {27: if (on_cran()) {withRestarts(tryCatch(withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() {}, expectation = handle_expectation, packageNotFoundError = function(e) { }) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))28: }test_code(code, parent.frame())}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", invokeRestart("muffle_cran_snapshot") {}, skip = handle_skip, warning = handle_warning, message = handle_message, sampler_directed_nocov$rNetwork(store = TRUE) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, end_test = function() { "bernoulli", TRUE) }) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))28: mySBM_sbm$setModel(3)test_code(code, parent.frame()) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)
cl <- net$clustering(3)[[1]]29: mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl)test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", mySBM_missSBM$doVEM() { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) sampler_directed_nocov$rNetwork(store = TRUE) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, 0.95) "bernoulli", TRUE) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 0.01) plot = FALSE)) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), mySBM_sbm$setModel(3) 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) 0.2) cl <- net$clustering(3)[[1]] expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, 0.95) }) clusterInit = cl)
mySBM_missSBM$doVEM()30: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), eval(code, test_env) 0.1)
31: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), eval(code, test_env) 0.95)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 32: 0.01)withCallingHandlers({ expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), eval(code, test_env) 0.1) new_expectations <- the$test_expectations > starting_expectations expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), if (snapshot_skipped) { 0.2) skip("On CRAN") expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), } else if (!new_expectations && skip_on_empty) { 0.95) skip_empty() }) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {30: if (on_cran()) {eval(code, test_env) skip(paste0("{", e$package, "} is not installed."))
}31: }, snapshot_on_cran = function(cnd) {eval(code, test_env) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")32: }, skip = handle_skip, warning = handle_warning, message = handle_message, withCallingHandlers({ error = handle_error, interrupt = handle_interrupt)
eval(code, test_env)33: doTryCatch(return(expr), name, parentenv, handler) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {34: skip("On CRAN")tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
else if (!new_expectations && skip_on_empty) {35: skip_empty()tryCatchList(expr, classes, parentenv, handlers) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {36: if (on_cran()) {tryCatch(withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {33: skip(paste0("{", e$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) {34: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)35:
tryCatchList(expr, classes, parentenv, handlers)37: doWithOneRestart(return(expr), restart)
36: 38: tryCatch(withCallingHandlers({withOneRestart(expr, restarts[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations39: if (snapshot_skipped) {withRestarts(tryCatch(withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$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 error = handle_error, interrupt = handle_interrupt), error = handle_fatal) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 37: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), doWithOneRestart(return(expr), restart) end_test = function() {
})38:
40: withOneRestart(expr, restarts[[1L]])test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())39:
withRestarts(tryCatch(withCallingHandlers({41: eval(code, test_env)source_file(path, env = env(env), desc = desc, shuffle = shuffle, new_expectations <- the$test_expectations > starting_expectations error_call = error_call) if (snapshot_skipped) {
skip("On CRAN")42: }FUN(X[[i]], ...) else if (!new_expectations && skip_on_empty) {
skip_empty()43: }lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, }, expectation = handle_expectation, packageNotFoundError = function(e) { error_call = error_call) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))44: }doTryCatch(return(expr), name, parentenv, handler)
}, snapshot_on_cran = function(cnd) {45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")46: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers)
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 47: end_test = function() {tryCatch(code, testthat_abort_reporter = function(cnd) { }) cat(conditionMessage(cnd), "\n")
NULL40: })test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 41: env = env, desc = desc, shuffle = shuffle, error_call = error_call))source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
49: 42: test_files_serial(test_dir = test_dir, test_package = test_package, FUN(X[[i]], ...) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 43: desc = desc, load_package = load_package, shuffle = shuffle, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) error_call = error_call)
50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 44: reporter = reporter, load_helpers = load_helpers, env = env, doTryCatch(return(expr), name, parentenv, handler) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
45: 51: tryCatchOne(expr, names, parentenv, handlers[[1L]])test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")46:
tryCatchList(expr, classes, parentenv, handlers)52:
test_check("missSBM")47:
tryCatch(code, testthat_abort_reporter = function(cnd) {An irrecoverable exception occurred. R is aborting now ...
cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$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