Last updated on 2026-09-26 09:51:29 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 89.36 | 356.78 | 446.14 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 58.53 | 247.84 | 306.37 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 59.00 | 243.15 | 302.15 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 248.05 | 312.05 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 450.00 | 541.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 83.11 | 346.95 | 430.06 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 90.56 | 343.79 | 434.35 | OK | |
| r-release-macos-arm64 | 1.1.0 | 17.00 | 92.00 | 109.00 | OK | |
| r-release-macos-x86_64 | 1.1.0 | 59.00 | 456.00 | 515.00 | OK | |
| r-release-windows-x86_64 | 1.1.0 | 98.00 | 361.00 | 459.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 19.00 | 239.00 | 258.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 115.00 | 501.00 | 616.00 | 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$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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() { })
Traceback:
1: 28: dispatcher(membership_name, membership_init$to_cc(), model_name, test_code(code, parent.frame())
.self$network_to_cc(), TRUE)29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", 2: {FUN(X[[i]], ...) sampler_undirected_cov$rNetwork(store = TRUE)
mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, 3: "bernoulli", FALSE, covarList = covarList_undirected)lapply(X = S, FUN = FUN, ...) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE)) 4: mySBM_sbm$setModel(Q)doTryCatch(return(expr), name, parentenv, handler) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData,
covariates = covarList_undirected) 5: cls <- net$clustering(1:(2 * Q))tryCatchOne(expr, names, parentenv, handlers[[1L]]) cl <- cls[[Q]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, 6: clusterInit = cl, covarList = covarList_undirected)tryCatchList(expr, classes, parentenv, handlers) mySBM_missSBM$doVEM()
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 7: 0.05)tryCatch(expr, error = function(e) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), call <- conditionCall(e) 0.8) if (!is.null(call)) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), if (identical(call[[1L]], quote(doTryCatch))) 0.01) call <- sys.call(-4L) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), dcall <- deparse(call, nlines = 1L) 0.1) prefix <- paste("Error in", dcall, ": ") expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), LONG <- 75L 0.1) sm <- strsplit(conditionMessage(e), "\n")[[1L]] expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 0.85) }) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
30: type = "b")eval(code, test_env) if (w > LONG)
prefix <- paste0(prefix, "\n ")31: }eval(code, test_env) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))32: withCallingHandlers({ eval(code, test_env) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { .Internal(printDeferredWarnings()) skip("On CRAN") } } invisible(structure(msg, class = "try-error", condition = e)) else if (!new_expectations && skip_on_empty) {}) skip_empty() }
}, expectation = handle_expectation, packageNotFoundError = function(e) { 8: if (on_cran()) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) skip(paste0("{", e$package, "} is not installed."))
} 9: }, snapshot_on_cran = function(cnd) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, 10: error = handle_error, interrupt = handle_interrupt)
FUN(X[[i]], ...)33:
doTryCatch(return(expr), name, parentenv, handler)11:
34: lapply(seq_len(cores), inner.do)tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: 35: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, tryCatchList(expr, classes, parentenv, handlers)
mc.silent = TRUE)36:
13: tryCatch(withCallingHandlers({parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, eval(code, test_env) verbose = (verbosity > 4)) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {14: skip("On CRAN").self$do_with_inits(inits, Q, reinitialization_effort) }
else if (!new_expectations && skip_on_empty) {15: skip_empty().self$estim_ascend(reinitialization_effort, changing_effort) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {16: if (on_cran()) {private$BMobject$estimate() skip(paste0("{", e$package, "} is not installed."))
}17: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUEmySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) invokeRestart("muffle_cran_snapshot")
18: }, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
19: 37: eval(code, test_env)doWithOneRestart(return(expr), restart)
20: 38: withCallingHandlers({withOneRestart(expr, restarts[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {39: skip("On CRAN")withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")21: }, skip = handle_skip, warning = handle_warning, message = handle_message, doTryCatch(return(expr), name, parentenv, handler)
22: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), tryCatchOne(expr, names, parentenv, handlers[[1L]]) end_test = function() {
})23:
tryCatchList(expr, classes, parentenv, handlers)40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 24: StopReporter$new())tryCatch(withCallingHandlers({
eval(code, test_env)41: new_expectations <- the$test_expectations > starting_expectationssource_file(path, env = env(env), desc = desc, shuffle = shuffle, if (snapshot_skipped) { skip("On CRAN") error_call = error_call) }
else if (!new_expectations && skip_on_empty) {42: skip_empty()FUN(X[[i]], ...) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {43: skip(paste0("{", e$package, "} is not installed.")) }lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, }, snapshot_on_cran = function(cnd) { error_call = error_call) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, 44: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)doTryCatch(return(expr), name, parentenv, handler)
25: 45: doWithOneRestart(return(expr), restart)
tryCatchOne(expr, names, parentenv, handlers[[1L]])26:
withOneRestart(expr, restarts[[1L]])46:
tryCatchList(expr, classes, parentenv, handlers)27:
47: withRestarts(tryCatch(withCallingHandlers({tryCatch(code, testthat_abort_reporter = function(cnd) { eval(code, test_env) cat(conditionMessage(cnd), "\n") new_expectations <- the$test_expectations > starting_expectations NULL if (snapshot_skipped) {}) skip("On CRAN")
}48: else if (!new_expectations && skip_on_empty) {with_reporter(reporters$multi, lapply(test_paths, test_one_file, skip_empty() env = env, desc = desc, shuffle = shuffle, error_call = error_call)) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {49: if (on_cran()) {test_files_serial(test_dir = test_dir, test_package = test_package, skip(paste0("{", e$package, "} is not installed.")) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, } env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }, snapshot_on_cran = function(cnd) { desc = desc, load_package = load_package, shuffle = shuffle, snapshot_skipped <<- TRUE error_call = error_call) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 50: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_files(test_dir = path, test_paths = test_paths, test_package = package, end_test = function() { 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)
28: 51: test_code(code, parent.frame())test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", 52: {test_check("missSBM") sampler_undirected_cov$rNetwork(store = TRUE)
mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, An irrecoverable exception occurred. R is aborting now ...
"bernoulli", FALSE, covarList = covarList_undirected) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4:
Traceback:
doTryCatch(return(expr), name, parentenv, handler) 1:
dispatcher(membership_name, membership_init$to_cc(), model_name, 5: .self$network_to_cc(), TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
2: 6: FUN(X[[i]], ...)tryCatchList(expr, classes, parentenv, handlers)
3: 7: lapply(X = S, FUN = FUN, ...)tryCatch(expr, error = function(e) {
call <- conditionCall(e) if (!is.null(call)) { 4: if (identical(call[[1L]], quote(doTryCatch))) doTryCatch(return(expr), name, parentenv, handler) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) 5: prefix <- paste("Error in", dcall, ": ")tryCatchOne(expr, names, parentenv, handlers[[1L]]) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]] 6: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchList(expr, classes, parentenv, handlers) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 7: type = "b")tryCatch(expr, error = function(e) { if (w > LONG) call <- conditionCall(e) prefix <- paste0(prefix, "\n ") if (!is.null(call)) { } if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) else prefix <- "Error : " dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") msg <- paste0(prefix, conditionMessage(e), "\n") LONG <- 75L .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] cat(msg, file = outFile) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") .Internal(printDeferredWarnings()) if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], invisible(structure(msg, class = "try-error", condition = e)) type = "b")}) 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"))) {
10: cat(msg, file = outFile) .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))
10: 13: FUN(X[[i]], ...)
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 11: verbose = (verbosity > 4))lapply(seq_len(cores), inner.do)
14: 12: .self$do_with_inits(inits, Q, reinitialization_effort)
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 15: mc.silent = TRUE).self$estim_ascend(reinitialization_effort, changing_effort)
13:
16: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, private$BMobject$estimate() verbose = (verbosity > 4))
17: 14: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)).self$do_with_inits(inits, Q, reinitialization_effort)
18: 15: eval(code, test_env).self$estim_ascend(reinitialization_effort, changing_effort)
19: 16: eval(code, test_env)private$BMobject$estimate()
20: 17: withCallingHandlers({mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations18: if (snapshot_skipped) {eval(code, test_env) skip("On CRAN")
} else if (!new_expectations && skip_on_empty) {19: skip_empty()eval(code, test_env) }}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {20: skip(paste0("{", e$package, "} is not installed."))withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt) skip_empty()
21: }}, expectation = handle_expectation, packageNotFoundError = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (on_cran()) {
22: skip(paste0("{", e$package, "} is not installed.")) }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE23: tryCatchList(expr, classes, parentenv, handlers)
24: invokeRestart("muffle_cran_snapshot")tryCatch(withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
eval(code, test_env)21: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
skip("On CRAN") }22: else if (!new_expectations && skip_on_empty) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip_empty()
}23: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))24: }tryCatch(withCallingHandlers({ eval(code, test_env)}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
else if (!new_expectations && skip_on_empty) {25: skip_empty()doWithOneRestart(return(expr), restart) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {26: withOneRestart(expr, restarts[[1L]]) skip(paste0("{", e$package, "} is not installed.")) }
}, snapshot_on_cran = function(cnd) {27: snapshot_skipped <<- TRUEwithRestarts(tryCatch(withCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt), error = handle_fatal) if (snapshot_skipped) {
25: skip("On CRAN")doWithOneRestart(return(expr), restart) }
else if (!new_expectations && skip_on_empty) {26: skip_empty()withOneRestart(expr, restarts[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {27: if (on_cran()) {withRestarts(tryCatch(withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip_empty() end_test = function() { } })}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {28: skip(paste0("{", e$package, "} is not installed."))test_code(code, parent.frame()) }
}, snapshot_on_cran = function(cnd) {29: snapshot_skipped <<- TRUEtest_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", invokeRestart("muffle_cran_snapshot") {}, skip = handle_skip, warning = handle_warning, message = handle_message, sampler_directed_cov$rNetwork(store = TRUE) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, end_test = function() { "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, }) plot = FALSE))
mySBM_sbm$setModel(Q)28: net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, test_code(code, parent.frame())
covariates = covarList_directed)29: cls <- net$clustering(1:(2 * Q))test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", cl <- cls[[Q]] { mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, sampler_directed_cov$rNetwork(store = TRUE) clusterInit = cl, covarList = covarList_directed) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, mySBM_missSBM$doVEM(trace = TRUE) "bernoulli", TRUE, covarList = covarList_directed) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 0.1) plot = FALSE)) mySBM_sbm$setModel(Q) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, 0.8) covariates = covarList_directed) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), cls <- net$clustering(1:(2 * Q)) 0.05) cl <- cls[[Q]] expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_directed) 0.1) mySBM_missSBM$doVEM(trace = TRUE) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.85) 0.1) }) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.8)30: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), eval(code, test_env) 0.05)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 31: 0.1)eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships),
0.85)32: })withCallingHandlers({
eval(code, test_env)30: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
skip("On CRAN")31: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) {32: if (on_cran()) {withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {33: doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
}34: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")35: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt)
36: 33: tryCatch(withCallingHandlers({doTryCatch(return(expr), name, parentenv, handler) 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$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {37: doWithOneRestart(return(expr), restart) if (on_cran()) {
38: skip(paste0("{", e$package, "} is not installed."))withOneRestart(expr, restarts[[1L]]) }
}, snapshot_on_cran = function(cnd) {39: snapshot_skipped <<- TRUEwithRestarts(tryCatch(withCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {37: skip("On CRAN")doWithOneRestart(return(expr), restart) }
else if (!new_expectations && skip_on_empty) {38: skip_empty()withOneRestart(expr, restarts[[1L]]) }
39: }, expectation = handle_expectation, packageNotFoundError = function(e) {withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), if (on_cran()) { end_test = function() { skip(paste0("{", e$package, "} is not installed.")) }) }
}, snapshot_on_cran = function(cnd) {40: snapshot_skipped <<- TRUEtest_code(code = exprs, env = env, reporter = get_reporter() %||% invokeRestart("muffle_cran_snapshot") StopReporter$new())}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 41: end_test = function() {source_file(path, env = env(env), desc = desc, shuffle = shuffle, }) error_call = error_call)
40: 42: test_code(code = exprs, env = env, reporter = get_reporter() %||% FUN(X[[i]], ...)
StopReporter$new())43:
41: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) error_call = error_call)
44: 42: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)
43: 45: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, tryCatchOne(expr, names, parentenv, handlers[[1L]]) error_call = error_call)
46: 44: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
47: 45: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")46: NULL})tryCatchList(expr, classes, parentenv, handlers)
48: 47: with_reporter(reporters$multi, lapply(test_paths, test_one_file, tryCatch(code, testthat_abort_reporter = function(cnd) { env = env, desc = desc, shuffle = shuffle, error_call = error_call)) cat(conditionMessage(cnd), "\n")
NULL49: })test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 48: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, with_reporter(reporters$multi, lapply(test_paths, test_one_file, desc = desc, load_package = load_package, shuffle = shuffle, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) error_call = error_call)
49:
50: test_files_serial(test_dir = test_dir, test_package = test_package, test_files(test_dir = path, test_paths = test_paths, test_package = package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, reporter = reporter, load_helpers = load_helpers, env = env, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, load_package = load_package, parallel = parallel, shuffle = shuffle) error_call = error_call)
51: 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, test_dir("testthat", package = package, reporter = reporter, reporter = reporter, load_helpers = load_helpers, env = env, ..., load_package = "installed") stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)52:
test_check("missSBM")51:
test_dir("testthat", package = package, reporter = reporter, An irrecoverable exception occurred. R is aborting now ...
..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
Traceback:
1: end_test = function() {dispatcher(membership_name, membership_init$to_cc(), model_name, }) .self$network_to_cc(), TRUE)
28: 2: test_code(code, parent.frame())FUN(X[[i]], ...)
29: 3: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", lapply(X = S, FUN = FUN, ...) {
sampler_undirected_nocov$rNetwork(store = TRUE) 4: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE)doTryCatch(return(expr), name, parentenv, handler) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE)) 5: mySBM_sbm$setModel(3)tryCatchOne(expr, names, parentenv, handlers[[1L]]) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData)
cl <- net$clustering(3)[[1]] 6: mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, tryCatchList(expr, classes, parentenv, handlers) clusterInit = cl)
mySBM_missSBM$doVEM() 7: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), tryCatch(expr, error = function(e) { 0.05) call <- conditionCall(e) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), if (!is.null(call)) { 0.95) if (identical(call[[1L]], quote(doTryCatch))) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), call <- sys.call(-4L) 0.01) dcall <- deparse(call, nlines = 1L) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), prefix <- paste("Error in", dcall, ": ") 0.05) LONG <- 75L expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), sm <- strsplit(conditionMessage(e), "\n")[[1L]] 0.95) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") }) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 30: type = "b")eval(code, test_env) if (w > LONG)
prefix <- paste0(prefix, "\n ")31: }eval(code, test_env) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")32: .Internal(seterrmessage(msg[1L]))withCallingHandlers({ if (!silent && isTRUE(getOption("show.error.messages"))) { eval(code, test_env) cat(msg, file = outFile) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { .Internal(printDeferredWarnings()) skip("On CRAN") } } invisible(structure(msg, class = "try-error", condition = e)) else if (!new_expectations && skip_on_empty) {}) skip_empty()
} 8: }, expectation = handle_expectation, packageNotFoundError = function(e) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 9: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE10: invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, FUN(X[[i]], ...) error = handle_error, interrupt = handle_interrupt)
11: 33: lapply(seq_len(cores), inner.do)doTryCatch(return(expr), name, parentenv, handler)
12: 34: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, tryCatchOne(expr, names, parentenv, handlers[[1L]]) mc.silent = TRUE)
35: 13: tryCatchList(expr, classes, parentenv, handlers)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))36:
tryCatch(withCallingHandlers({14: eval(code, test_env).self$do_with_inits(inits, Q, reinitialization_effort) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {15: skip("On CRAN").self$estim_ascend(reinitialization_effort, changing_effort) } else if (!new_expectations && skip_on_empty) {
skip_empty()16: }private$BMobject$estimate()}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {17: skip(paste0("{", e$package, "} is not installed."))mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) }
}, snapshot_on_cran = function(cnd) {18: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 19: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)eval(code, test_env)
37: 20: doWithOneRestart(return(expr), restart)
withCallingHandlers({38: eval(code, test_env)withOneRestart(expr, restarts[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {39: skip("On CRAN")withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$test_expectations > starting_expectations 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$package, "} is not installed.")) } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")21: }, skip = handle_skip, warning = handle_warning, message = handle_message, doTryCatch(return(expr), name, parentenv, handler) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {22: })tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: 23: test_code(code = exprs, env = env, reporter = get_reporter() %||% tryCatchList(expr, classes, parentenv, handlers) StopReporter$new())
24: 41: tryCatch(withCallingHandlers({source_file(path, env = env(env), desc = desc, shuffle = shuffle, eval(code, test_env) error_call = error_call) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {42: skip("On CRAN")FUN(X[[i]], ...) }
else if (!new_expectations && skip_on_empty) {43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, skip_empty() error_call = error_call) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {44: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
}45: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")46: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
47: 25: tryCatch(code, testthat_abort_reporter = function(cnd) {doWithOneRestart(return(expr), restart) cat(conditionMessage(cnd), "\n")
NULL26: })withOneRestart(expr, restarts[[1L]])
48: 27: with_reporter(reporters$multi, lapply(test_paths, test_one_file, withRestarts(tryCatch(withCallingHandlers({ env = env, desc = desc, shuffle = shuffle, error_call = error_call)) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations49: if (snapshot_skipped) {test_files_serial(test_dir = test_dir, test_package = test_package, skip("On CRAN") test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, } env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, else if (!new_expectations && skip_on_empty) { desc = desc, load_package = load_package, shuffle = shuffle, skip_empty() error_call = error_call) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {50: if (on_cran()) {test_files(test_dir = path, test_paths = test_paths, test_package = package, skip(paste0("{", e$package, "} is not installed.")) reporter = reporter, load_helpers = load_helpers, env = env, }}, snapshot_on_cran = function(cnd) { stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, snapshot_skipped <<- TRUE load_package = load_package, parallel = parallel, shuffle = shuffle) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 51: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_dir("testthat", package = package, reporter = reporter, end_test = function() { ..., load_package = "installed") })
52: 28: test_check("missSBM")test_code(code, parent.frame())
An irrecoverable exception occurred. R is aborting now ...
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", { sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
Traceback:
1: 5: dispatcher(membership_name, membership_init$to_cc(), model_name, tryCatchOne(expr, names, parentenv, handlers[[1L]])
.self$network_to_cc(), TRUE) 6: tryCatchList(expr, classes, parentenv, handlers)
7: 2: tryCatch(expr, error = function(e) {FUN(X[[i]], ...) call <- conditionCall(e)
if (!is.null(call)) { 3: if (identical(call[[1L]], quote(doTryCatch))) lapply(X = S, FUN = FUN, ...) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) 4: prefix <- paste("Error in", dcall, ": ")doTryCatch(return(expr), name, parentenv, handler) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]] 5: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 6: type = "b")tryCatchList(expr, classes, parentenv, handlers) if (w > LONG)
prefix <- paste0(prefix, "\n ") 7: }tryCatch(expr, error = function(e) { else prefix <- "Error : " call <- conditionCall(e) msg <- paste0(prefix, conditionMessage(e), "\n") if (!is.null(call)) { .Internal(seterrmessage(msg[1L])) if (identical(call[[1L]], quote(doTryCatch))) if (!silent && isTRUE(getOption("show.error.messages"))) { call <- sys.call(-4L) cat(msg, file = outFile) dcall <- deparse(call, nlines = 1L) .Internal(printDeferredWarnings()) prefix <- paste("Error in", dcall, ": ") } LONG <- 75L invisible(structure(msg, class = "try-error", condition = e)) sm <- strsplit(conditionMessage(e), "\n")[[1L]]}) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 8: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], try(lapply(X = S, FUN = FUN, ...), silent = TRUE) type = "b")
if (w > LONG) 9: prefix <- paste0(prefix, "\n ")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
else prefix <- "Error : "10: 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: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, invisible(structure(msg, class = "try-error", condition = e)) mc.silent = TRUE)})
13: 8: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) verbose = (verbosity > 4))
9: 14: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)).self$do_with_inits(inits, Q, reinitialization_effort)
10: 15: .self$estim_ascend(reinitialization_effort, changing_effort)FUN(X[[i]], ...)
16: private$BMobject$estimate()11:
lapply(seq_len(cores), inner.do)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 18: mc.silent = TRUE)eval(code, test_env)
13: 19: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, eval(code, test_env) verbose = (verbosity > 4))
20: withCallingHandlers({14: eval(code, test_env).self$do_with_inits(inits, Q, reinitialization_effort) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {15: skip("On CRAN").self$estim_ascend(reinitialization_effort, changing_effort) }
else if (!new_expectations && skip_on_empty) {16: skip_empty()private$BMobject$estimate() }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {17: skip(paste0("{", e$package, "} is not installed."))mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) }
}, snapshot_on_cran = function(cnd) {18: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 19: error = handle_error, interrupt = handle_interrupt)eval(code, test_env)
21: 20: doTryCatch(return(expr), name, parentenv, handler)withCallingHandlers({
eval(code, test_env)22: new_expectations <- the$test_expectations > starting_expectationstryCatchOne(expr, names, parentenv, handlers[[1L]]) if (snapshot_skipped) {
skip("On CRAN")23: }tryCatchList(expr, classes, parentenv, handlers) else if (!new_expectations && skip_on_empty) {
skip_empty()24: }tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {21: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
}22: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")23: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
24: 25: 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."))
}25: }, snapshot_on_cran = function(cnd) {doWithOneRestart(return(expr), restart) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")26: }, skip = handle_skip, warning = handle_warning, message = handle_message, withOneRestart(expr, restarts[[1L]]) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {27: })withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)28: new_expectations <- the$test_expectations > starting_expectationstest_code(code, parent.frame()) if (snapshot_skipped) {
skip("On CRAN")29: }test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", else if (!new_expectations && skip_on_empty) { { skip_empty() sampler_directed_nocov$rNetwork(store = TRUE) } mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, }, expectation = handle_expectation, packageNotFoundError = function(e) { "bernoulli", TRUE) if (on_cran()) { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, skip(paste0("{", e$package, "} is not installed.")) plot = FALSE)) } mySBM_sbm$setModel(3)}, snapshot_on_cran = function(cnd) { net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) snapshot_skipped <<- TRUE cl <- net$clustering(3)[[1]] invokeRestart("muffle_cran_snapshot") mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, }, skip = handle_skip, warning = handle_warning, message = handle_message, clusterInit = cl) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), mySBM_missSBM$doVEM() end_test = function() { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 28: 0.95)test_code(code, parent.frame()) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)29: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", 0.1) { expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), sampler_directed_nocov$rNetwork(store = TRUE) 0.2) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), "bernoulli", TRUE) 0.95) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, }) plot = FALSE))
mySBM_sbm$setModel(3)30: net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)eval(code, test_env) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData,
clusterInit = cl)31: mySBM_missSBM$doVEM()eval(code, test_env) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
32: withCallingHandlers({ 0.1) eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), new_expectations <- the$test_expectations > starting_expectations 0.95) if (snapshot_skipped) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() } 0.01)}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), if (on_cran()) { 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), skip(paste0("{", e$package, "} is not installed.")) 0.2) } expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), }, snapshot_on_cran = function(cnd) { 0.95) snapshot_skipped <<- TRUE }) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
30: 33: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler)
31: 34: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: withCallingHandlers({35: tryCatchList(expr, classes, parentenv, handlers) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {36: skip("On CRAN")tryCatch(withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$test_expectations > starting_expectations skip_empty() if (snapshot_skipped) { } skip("On CRAN")}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) { else if (!new_expectations && skip_on_empty) { skip(paste0("{", e$package, "} is not installed.")) skip_empty() } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE33: invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])37:
doWithOneRestart(return(expr), restart)35:
tryCatchList(expr, classes, parentenv, handlers)38:
withOneRestart(expr, restarts[[1L]])36:
tryCatch(withCallingHandlers({39: eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty()}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), error = handle_error, interrupt = handle_interrupt), error = handle_fatal) end_test = function() {
})37:
doWithOneRestart(return(expr), restart)40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 38: StopReporter$new())withOneRestart(expr, restarts[[1L]])
41: 39: source_file(path, env = env(env), desc = desc, shuffle = shuffle, withRestarts(tryCatch(withCallingHandlers({ error_call = error_call) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations42: if (snapshot_skipped) {FUN(X[[i]], ...) skip("On CRAN")
}43: else if (!new_expectations && skip_on_empty) {lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, skip_empty() error_call = error_call) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {44: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
}45: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")46: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {47: })tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")40: NULLtest_code(code = exprs, env = env, reporter = get_reporter() %||% }) StopReporter$new())
48: 41: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 42: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, FUN(X[[i]], ...) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 43: error_call = error_call)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 44: reporter = reporter, load_helpers = load_helpers, env = env, doTryCatch(return(expr), name, parentenv, handler) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])51:
test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
46: An irrecoverable exception occurred. R is aborting now ...
tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-44.R
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-explore-block-count.R:4:3',
'test-missSBM_collection-degenerate.R:80:3',
'test-missSBM_collection-estimate_chain.R:64:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-sbm-bernoulli-with-covariates.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-with-covariates.R:46:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:46:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:44:3'): SimpleSBM_fit 'Bernoulli' model, directed, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:44:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64