Last updated on 2026-10-20 21:58:43 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 | 56.44 | 240.34 | 296.78 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 57.00 | 247.35 | 304.35 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 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 | 85.58 | 342.08 | 427.66 | 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 | ERROR | ||||
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 119.00 | 528.00 | 647.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [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."))
Traceback:
} 1: }, snapshot_on_cran = function(cnd) {dispatcher(membership_name, membership_init$to_cc(), model_name, snapshot_skipped <<- TRUE .self$network_to_cc(), TRUE) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 2: error = handle_error, interrupt = handle_interrupt)FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: 21: doTryCatch(return(expr), name, parentenv, handler)
doTryCatch(return(expr), name, parentenv, handler) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
23:
tryCatchList(expr, classes, parentenv, handlers) 7:
tryCatch(expr, error = function(e) {24: call <- conditionCall(e)tryCatch(withCallingHandlers({ if (!is.null(call)) { eval(code, test_env) if (identical(call[[1L]], quote(doTryCatch))) new_expectations <- the$test_expectations > starting_expectations call <- sys.call(-4L) if (snapshot_skipped) { dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") skip("On CRAN") LONG <- 75L } else if (!new_expectations && skip_on_empty) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] skip_empty() w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (is.na(w)) skip(paste0("{", e$package, "} is not installed.")) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b")}, snapshot_on_cran = function(cnd) { if (w > LONG) snapshot_skipped <<- TRUE prefix <- paste0(prefix, "\n ") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")25: .Internal(seterrmessage(msg[1L]))doWithOneRestart(return(expr), restart) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile) .Internal(printDeferredWarnings())26: }withOneRestart(expr, restarts[[1L]]) invisible(structure(msg, class = "try-error", condition = e))})
8: 27: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
withRestarts(tryCatch(withCallingHandlers({ 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations10: if (snapshot_skipped) {FUN(X[[i]], ...)
skip("On CRAN")11: }lapply(seq_len(cores), inner.do) else if (!new_expectations && skip_on_empty) {
skip_empty()12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, }}, expectation = handle_expectation, packageNotFoundError = function(e) { mc.silent = TRUE) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))13: }parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, }, snapshot_on_cran = function(cnd) { verbose = (verbosity > 4)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")14: }, skip = handle_skip, warning = handle_warning, message = handle_message, .self$do_with_inits(inits, Q, reinitialization_effort) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {15: }).self$estim_ascend(reinitialization_effort, changing_effort)
28: 16: test_code(code, parent.frame())private$BMobject$estimate()
29: 17: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) {
sampler_undirected_cov$rNetwork(store = TRUE)18: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, eval(code, test_env) "bernoulli", FALSE, covarList = covarList_undirected)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 19: plot = FALSE))eval(code, test_env) mySBM_sbm$setModel(Q)
20: net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, withCallingHandlers({ covariates = covarList_undirected) eval(code, test_env) cls <- net$clustering(1:(2 * Q)) new_expectations <- the$test_expectations > starting_expectations cl <- cls[[Q]] if (snapshot_skipped) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) skip("On CRAN") mySBM_missSBM$doVEM() } expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), else if (!new_expectations && skip_on_empty) { 0.05) skip_empty() expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }}, expectation = handle_expectation, packageNotFoundError = function(e) { 0.8) if (on_cran()) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), skip(paste0("{", e$package, "} is not installed.")) 0.01) } expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), }, snapshot_on_cran = function(cnd) { 0.1) snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), invokeRestart("muffle_cran_snapshot") 0.1)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), error = handle_error, interrupt = handle_interrupt) 0.85)
})21:
doTryCatch(return(expr), name, parentenv, handler)30:
eval(code, test_env)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])31: eval(code, test_env)
23: 32: tryCatchList(expr, classes, parentenv, handlers)
withCallingHandlers({24: eval(code, test_env)tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
33: 25: doTryCatch(return(expr), name, parentenv, handler)doWithOneRestart(return(expr), restart)
34: 26: tryCatchOne(expr, names, parentenv, handlers[[1L]])withOneRestart(expr, restarts[[1L]])
35: 27: tryCatchList(expr, classes, parentenv, handlers)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)36: new_expectations <- the$test_expectations > starting_expectationstryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } 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) { skip(paste0("{", e$package, "} is not installed.")) if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, snapshot_on_cran = function(cnd) { invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, skip = handle_skip, warning = handle_warning, message = handle_message, end_test = function() { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) })
37: 28: doWithOneRestart(return(expr), restart)test_code(code, parent.frame())
29: 38: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", withOneRestart(expr, restarts[[1L]])
{39: sampler_undirected_cov$rNetwork(store = TRUE)withRestarts(tryCatch(withCallingHandlers({ mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations "bernoulli", FALSE, covarList = covarList_undirected) if (snapshot_skipped) { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, skip("On CRAN") plot = FALSE)) } mySBM_sbm$setModel(Q) else if (!new_expectations && skip_on_empty) { net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, skip_empty() covariates = covarList_undirected) } cls <- net$clustering(1:(2 * Q))}, expectation = handle_expectation, packageNotFoundError = function(e) { cl <- cls[[Q]] if (on_cran()) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, skip(paste0("{", e$package, "} is not installed.")) clusterInit = cl, covarList = covarList_undirected) }}, snapshot_on_cran = function(cnd) { mySBM_missSBM$doVEM() snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), invokeRestart("muffle_cran_snapshot") 0.05)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 0.8) end_test = function() { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), }) 0.01)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 40: 0.1)test_code(code = exprs, env = env, reporter = get_reporter() %||% expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), StopReporter$new()) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 41: 0.85)source_file(path, env = env(env), desc = desc, shuffle = shuffle, }) error_call = error_call)
30: 42: eval(code, test_env)FUN(X[[i]], ...)
31: 43: eval(code, test_env)
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 32: error_call = error_call)withCallingHandlers({
eval(code, test_env)44: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
45: skip("On CRAN")tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
else if (!new_expectations && skip_on_empty) {46: skip_empty()tryCatchList(expr, classes, parentenv, handlers) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {47: if (on_cran()) {tryCatch(code, testthat_abort_reporter = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) cat(conditionMessage(cnd), "\n") } NULL}, snapshot_on_cran = function(cnd) {}) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")48: }, skip = handle_skip, warning = handle_warning, message = handle_message, with_reporter(reporters$multi, lapply(test_paths, test_one_file, error = handle_error, interrupt = handle_interrupt) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
33: 49: test_files_serial(test_dir = test_dir, test_package = test_package, doTryCatch(return(expr), name, parentenv, handler) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 34: desc = desc, load_package = load_package, shuffle = shuffle, tryCatchOne(expr, names, parentenv, handlers[[1L]]) error_call = error_call)
50: 35: tryCatchList(expr, classes, parentenv, handlers)test_files(test_dir = path, test_paths = test_paths, test_package = package,
36: reporter = reporter, load_helpers = load_helpers, env = env, tryCatch(withCallingHandlers({ stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, eval(code, test_env) load_package = load_package, parallel = parallel, shuffle = shuffle) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {51: skip("On CRAN")test_dir("testthat", package = package, reporter = reporter, } ..., load_package = "installed") else if (!new_expectations && skip_on_empty) {
skip_empty()52: }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {test_check("missSBM")
skip(paste0("{", e$package, "} is not installed."))An irrecoverable exception occurred. R is aborting now ...
}}, 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]], ...)
Traceback:
1: 11: dispatcher(membership_name, membership_init$to_cc(), model_name, lapply(seq_len(cores), inner.do) .self$network_to_cc(), TRUE)
12: 2: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, FUN(X[[i]], ...) mc.silent = TRUE)
3: 13: lapply(X = S, FUN = FUN, ...)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4)) 4:
doTryCatch(return(expr), name, parentenv, handler)
14: 5: .self$do_with_inits(inits, Q, reinitialization_effort)tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: 6: .self$estim_ascend(reinitialization_effort, changing_effort)tryCatchList(expr, classes, parentenv, handlers)
16: 7: private$BMobject$estimate()tryCatch(expr, error = function(e) {
call <- conditionCall(e)17: if (!is.null(call)) {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)18: dcall <- deparse(call, nlines = 1L)eval(code, test_env) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L19: sm <- strsplit(conditionMessage(e), "\n")[[1L]]eval(code, test_env) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 20: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], withCallingHandlers({ type = "b") eval(code, test_env) if (w > LONG) new_expectations <- the$test_expectations > starting_expectations prefix <- paste0(prefix, "\n ") if (snapshot_skipped) { } skip("On CRAN") else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n") else if (!new_expectations && skip_on_empty) { .Internal(seterrmessage(msg[1L])) skip_empty() if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile)}, expectation = handle_expectation, packageNotFoundError = function(e) { .Internal(printDeferredWarnings()) if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) invisible(structure(msg, class = "try-error", condition = e)) }}, snapshot_on_cran = function(cnd) {}) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 8: }, skip = handle_skip, warning = handle_warning, message = handle_message, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) error = handle_error, interrupt = handle_interrupt)
9: 21: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))doTryCatch(return(expr), name, parentenv, handler)
10: 22: FUN(X[[i]], ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: lapply(seq_len(cores), inner.do)23:
tryCatchList(expr, classes, parentenv, handlers)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 24: mc.silent = TRUE)tryCatch(withCallingHandlers({
eval(code, test_env)13: new_expectations <- the$test_expectations > starting_expectationsparallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4)) if (snapshot_skipped) {
skip("On CRAN")14: }.self$do_with_inits(inits, Q, reinitialization_effort) else if (!new_expectations && skip_on_empty) {
skip_empty()15: }.self$estim_ascend(reinitialization_effort, changing_effort)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {16: skip(paste0("{", e$package, "} is not installed."))private$BMobject$estimate() }
}, snapshot_on_cran = function(cnd) {17: snapshot_skipped <<- TRUEmySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
18: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)eval(code, test_env)
25: 19: doWithOneRestart(return(expr), restart)eval(code, test_env)
26: 20: withOneRestart(expr, restarts[[1L]])withCallingHandlers({
eval(code, test_env)27: new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) snapshot_skipped <<- TRUE 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]])
28: 23: test_code(code, parent.frame())
tryCatchList(expr, classes, parentenv, handlers)
29: 24: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", tryCatch(withCallingHandlers({ { eval(code, test_env) sampler_directed_cov$rNetwork(store = TRUE) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, skip("On CRAN") "bernoulli", TRUE, covarList = covarList_directed) } mySBM_sbm$optimize(estimOptions = list(verbosity = 0, else if (!new_expectations && skip_on_empty) { plot = FALSE)) skip_empty() mySBM_sbm$setModel(Q) } net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, }, expectation = handle_expectation, packageNotFoundError = function(e) { covariates = covarList_directed) if (on_cran()) { cls <- net$clustering(1:(2 * Q)) skip(paste0("{", e$package, "} is not installed.")) cl <- cls[[Q]] } mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, }, snapshot_on_cran = function(cnd) { clusterInit = cl, covarList = covarList_directed) snapshot_skipped <<- TRUE mySBM_missSBM$doVEM(trace = TRUE) invokeRestart("muffle_cran_snapshot") expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.1) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.8)25: doWithOneRestart(return(expr), restart) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.05)26: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), withOneRestart(expr, restarts[[1L]]) 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships),
0.85)27: })withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)30: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
skip("On CRAN")31: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()32: }withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() {}, expectation = handle_expectation, packageNotFoundError = function(e) { }) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))28: }test_code(code, parent.frame())}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE29: invokeRestart("muffle_cran_snapshot")test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", }, skip = handle_skip, warning = handle_warning, message = handle_message, { error = handle_error, interrupt = handle_interrupt) sampler_directed_cov$rNetwork(store = TRUE)
mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, 33: "bernoulli", TRUE, covarList = covarList_directed)doTryCatch(return(expr), name, parentenv, handler) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))34: mySBM_sbm$setModel(Q)tryCatchOne(expr, names, parentenv, handlers[[1L]]) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData,
covariates = covarList_directed)35: cls <- net$clustering(1:(2 * Q))tryCatchList(expr, classes, parentenv, handlers) cl <- cls[[Q]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, 36: clusterInit = cl, covarList = covarList_directed)tryCatch(withCallingHandlers({ mySBM_missSBM$doVEM(trace = TRUE) eval(code, test_env) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), new_expectations <- the$test_expectations > starting_expectations 0.1) if (snapshot_skipped) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), skip("On CRAN") 0.8) } expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), else if (!new_expectations && skip_on_empty) { 0.05) skip_empty() expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), } 0.1)}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 0.85) if (on_cran()) { }) skip(paste0("{", e$package, "} is not installed."))
}30: }, snapshot_on_cran = function(cnd) {eval(code, test_env) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")31: eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)32:
withCallingHandlers({37: eval(code, test_env)doWithOneRestart(return(expr), restart) new_expectations <- the$test_expectations > starting_expectations
38: if (snapshot_skipped) {withOneRestart(expr, restarts[[1L]]) skip("On CRAN")
}39: else if (!new_expectations && skip_on_empty) {withRestarts(tryCatch(withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip(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: }, snapshot_on_cran = function(cnd) {doTryCatch(return(expr), name, parentenv, handler) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")34: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {35: })tryCatchList(expr, classes, parentenv, handlers)
40: 36: test_code(code = exprs, env = env, reporter = get_reporter() %||% 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) { error_call = error_call) skip("On CRAN")
}42: else if (!new_expectations && skip_on_empty) {FUN(X[[i]], ...) skip_empty()
}}, expectation = handle_expectation, packageNotFoundError = function(e) {43: if (on_cran()) {lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, skip(paste0("{", e$package, "} is not installed.")) error_call = error_call) }
}, snapshot_on_cran = function(cnd) {44: snapshot_skipped <<- TRUEdoTryCatch(return(expr), name, parentenv, handler) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 45: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)tryCatchOne(expr, names, parentenv, handlers[[1L]])
37: 46: tryCatchList(expr, classes, parentenv, handlers)doWithOneRestart(return(expr), restart)
38: 47: withOneRestart(expr, restarts[[1L]])tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")39: NULLwithRestarts(tryCatch(withCallingHandlers({}) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations48: if (snapshot_skipped) { skip("On CRAN")with_reporter(reporters$multi, lapply(test_paths, test_one_file, } env = env, desc = desc, shuffle = shuffle, error_call = error_call)) else if (!new_expectations && skip_on_empty) {
skip_empty()49: test_files_serial(test_dir = test_dir, test_package = test_package, } test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, }, expectation = handle_expectation, packageNotFoundError = function(e) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, if (on_cran()) { desc = desc, load_package = load_package, shuffle = shuffle, skip(paste0("{", e$package, "} is not installed.")) error_call = error_call) }
}, snapshot_on_cran = function(cnd) {50: snapshot_skipped <<- TRUEtest_files(test_dir = path, test_paths = test_paths, test_package = package, invokeRestart("muffle_cran_snapshot") reporter = reporter, load_helpers = load_helpers, env = env, }, skip = handle_skip, warning = handle_warning, message = handle_message, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), load_package = load_package, parallel = parallel, shuffle = shuffle) end_test = function() {
51: })test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 52: StopReporter$new())test_check("missSBM")
41: An irrecoverable exception occurred. R is aborting now ...
source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$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])) 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)
Traceback:
1:
12: dispatcher(membership_name, membership_init$to_cc(), model_name, parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, .self$network_to_cc(), TRUE) mc.silent = TRUE)
2: 13: FUN(X[[i]], ...)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4)) 3:
lapply(X = S, FUN = FUN, ...)14:
4: .self$do_with_inits(inits, Q, reinitialization_effort)doTryCatch(return(expr), name, parentenv, handler)
15: 5: .self$estim_ascend(reinitialization_effort, changing_effort)tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: 6: private$BMobject$estimate()tryCatchList(expr, classes, parentenv, handlers)
17: 7: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))tryCatch(expr, error = function(e) {
call <- conditionCall(e) if (!is.null(call)) {18: if (identical(call[[1L]], quote(doTryCatch))) eval(code, test_env) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)19: prefix <- paste("Error in", dcall, ": ")eval(code, test_env) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]20: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")withCallingHandlers({ if (is.na(w)) eval(code, test_env) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], new_expectations <- the$test_expectations > starting_expectations type = "b") if (snapshot_skipped) { if (w > LONG) skip("On CRAN") prefix <- paste0(prefix, "\n ") } } else if (!new_expectations && skip_on_empty) { else prefix <- "Error : " skip_empty() msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L]))}, expectation = handle_expectation, packageNotFoundError = function(e) { if (!silent && isTRUE(getOption("show.error.messages"))) { if (on_cran()) { cat(msg, file = outFile) skip(paste0("{", e$package, "} is not installed.")) .Internal(printDeferredWarnings()) } }}, snapshot_on_cran = function(cnd) { invisible(structure(msg, class = "try-error", condition = e)) snapshot_skipped <<- TRUE}) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 8: error = handle_error, interrupt = handle_interrupt)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
21: 9: doTryCatch(return(expr), name, parentenv, handler)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
22: 10: tryCatchOne(expr, names, parentenv, handlers[[1L]])FUN(X[[i]], ...)
23: 11: tryCatchList(expr, classes, parentenv, handlers)lapply(seq_len(cores), inner.do)
24: 12: tryCatch(withCallingHandlers({parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, eval(code, test_env) mc.silent = TRUE) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {13: skip("On CRAN") } else if (!new_expectations && skip_on_empty) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, skip_empty() verbose = (verbosity > 4)) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {14: if (on_cran()) {.self$do_with_inits(inits, Q, reinitialization_effort) skip(paste0("{", e$package, "} is not installed."))
}15: }, snapshot_on_cran = function(cnd) {.self$estim_ascend(reinitialization_effort, changing_effort) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")16: }, skip = handle_skip, warning = handle_warning, message = handle_message, private$BMobject$estimate() error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
17: 25: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))doWithOneRestart(return(expr), restart)
18: 26: eval(code, test_env)withOneRestart(expr, restarts[[1L]])
19: 27: eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)20: new_expectations <- the$test_expectations > starting_expectationswithCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } else if (!new_expectations && skip_on_empty) { } skip_empty()}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip(paste0("{", e$package, "} is not installed.")) if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, snapshot_on_cran = function(cnd) { invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, skip = handle_skip, warning = handle_warning, message = handle_message, end_test = function() { error = handle_error, interrupt = handle_interrupt) })
21: 28: doTryCatch(return(expr), name, parentenv, handler)test_code(code, parent.frame())
22: 29: tryCatchOne(expr, names, parentenv, handlers[[1L]])test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate",
{23: sampler_undirected_nocov$rNetwork(store = TRUE)tryCatchList(expr, classes, parentenv, handlers) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData,
"bernoulli", FALSE)24: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, tryCatch(withCallingHandlers({ plot = FALSE)) eval(code, test_env) mySBM_sbm$setModel(3) new_expectations <- the$test_expectations > starting_expectations net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) if (snapshot_skipped) { cl <- net$clustering(3)[[1]] skip("On CRAN") mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, } clusterInit = cl) else if (!new_expectations && skip_on_empty) { mySBM_missSBM$doVEM() skip_empty() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), } 0.05)}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), if (on_cran()) { 0.95) skip(paste0("{", e$package, "} is not installed.")) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), } 0.01)}, snapshot_on_cran = function(cnd) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), snapshot_skipped <<- TRUE 0.05) invokeRestart("muffle_cran_snapshot") expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.95) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) })
25: 30: doWithOneRestart(return(expr), restart)eval(code, test_env)
26: 31: withOneRestart(expr, restarts[[1L]])eval(code, test_env)
27: 32: withRestarts(tryCatch(withCallingHandlers({withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { else if (!new_expectations && skip_on_empty) { skip_empty() skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } if (on_cran()) { skip(paste0("{", e$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) end_test = function() {
})33:
doTryCatch(return(expr), name, parentenv, handler)28:
test_code(code, parent.frame())34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", 35: {tryCatchList(expr, classes, parentenv, handlers)
sampler_undirected_nocov$rNetwork(store = TRUE)36: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, tryCatch(withCallingHandlers({ "bernoulli", FALSE) eval(code, test_env) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { plot = FALSE)) skip("On CRAN") mySBM_sbm$setModel(3) } net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) else if (!new_expectations && skip_on_empty) { cl <- net$clustering(3)[[1]] skip_empty() mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, } clusterInit = cl)}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_missSBM$doVEM() if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), } 0.05)}, snapshot_on_cran = function(cnd) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), snapshot_skipped <<- TRUE 0.95) invokeRestart("muffle_cran_snapshot") expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 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)37:
doWithOneRestart(return(expr), restart)31:
eval(code, test_env)38:
withOneRestart(expr, restarts[[1L]])32: withCallingHandlers({
eval(code, test_env)39: new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") } new_expectations <- the$test_expectations > starting_expectations 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$package, "} is not installed.")) } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$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 <<- 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: end_test = function() {tryCatchOne(expr, names, parentenv, handlers[[1L]]) })
35: 40: tryCatchList(expr, classes, parentenv, handlers)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())36:
tryCatch(withCallingHandlers({41: eval(code, test_env)source_file(path, env = env(env), desc = desc, shuffle = shuffle, new_expectations <- the$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) {43: skip_empty()lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } error_call = error_call)
}, expectation = handle_expectation, packageNotFoundError = function(e) {44: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
}45: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")46: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
47: 37: tryCatch(code, testthat_abort_reporter = function(cnd) {doWithOneRestart(return(expr), restart) cat(conditionMessage(cnd), "\n")
NULL38: })withOneRestart(expr, restarts[[1L]])
48: 39: with_reporter(reporters$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, } stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }, snapshot_on_cran = function(cnd) { load_package = load_package, parallel = parallel, shuffle = shuffle) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")51: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_dir("testthat", package = package, reporter = reporter, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), ..., load_package = "installed") end_test = function() {
})52:
test_check("missSBM")40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% An irrecoverable exception occurred. R is aborting now ...
StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
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, no covariate", { sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.2) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
Traceback:
1: 33: doTryCatch(return(expr), name, parentenv, handler)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE)34:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 2:
FUN(X[[i]], ...)35:
tryCatchList(expr, classes, parentenv, handlers) 3:
lapply(X = S, FUN = FUN, ...)36:
tryCatch(withCallingHandlers({ 4: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler)
new_expectations <- the$test_expectations > starting_expectations 5: if (snapshot_skipped) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip("On CRAN")
} 6: else if (!new_expectations && skip_on_empty) {tryCatchList(expr, classes, parentenv, handlers) skip_empty()
}}, expectation = handle_expectation, packageNotFoundError = function(e) { 7: if (on_cran()) {tryCatch(expr, error = function(e) { skip(paste0("{", e$package, "} is not installed.")) call <- conditionCall(e) } if (!is.null(call)) {}, snapshot_on_cran = function(cnd) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) snapshot_skipped <<- TRUE dcall <- deparse(call, nlines = 1L) invokeRestart("muffle_cran_snapshot") prefix <- paste("Error in", dcall, ": ")}, skip = handle_skip, warning = handle_warning, message = handle_message, LONG <- 75L error = handle_error, interrupt = handle_interrupt), error = handle_fatal) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) 37: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], doWithOneRestart(return(expr), restart) type = "b")
if (w > LONG) 38: prefix <- paste0(prefix, "\n ")withOneRestart(expr, restarts[[1L]]) }
else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")39: .Internal(seterrmessage(msg[1L]))withRestarts(tryCatch(withCallingHandlers({ if (!silent && isTRUE(getOption("show.error.messages"))) { eval(code, test_env) cat(msg, file = outFile) new_expectations <- the$test_expectations > starting_expectations .Internal(printDeferredWarnings()) if (snapshot_skipped) { } skip("On CRAN") invisible(structure(msg, class = "try-error", condition = e)) }}) else if (!new_expectations && skip_on_empty) {
skip_empty() 8: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { 9: skip(paste0("{", e$package, "} is not installed."))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
}, snapshot_on_cran = function(cnd) {10: snapshot_skipped <<- TRUEFUN(X[[i]], ...) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 11: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), lapply(seq_len(cores), inner.do) end_test = function() {
})12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 40: test_code(code = exprs, env = env, reporter = get_reporter() %||% mc.silent = TRUE) StopReporter$new())
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 41: verbose = (verbosity > 4))source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)14: .self$do_with_inits(inits, Q, reinitialization_effort)
42: 15: FUN(X[[i]], ...)
.self$estim_ascend(reinitialization_effort, changing_effort)43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 16: error_call = error_call)private$BMobject$estimate()
44: 17: doTryCatch(return(expr), name, parentenv, handler)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
45: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(code, test_env)
46: 19: tryCatchList(expr, classes, parentenv, handlers)eval(code, test_env)
47: 20: tryCatch(code, testthat_abort_reporter = function(cnd) {withCallingHandlers({ eval(code, test_env) cat(conditionMessage(cnd), "\n") new_expectations <- the$test_expectations > starting_expectations NULL if (snapshot_skipped) {})
skip("On CRAN")48: }with_reporter(reporters$multi, lapply(test_paths, test_one_file, else if (!new_expectations && skip_on_empty) { env = env, desc = desc, shuffle = shuffle, error_call = error_call)) skip_empty()
}49: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_files_serial(test_dir = test_dir, test_package = test_package, if (on_cran()) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, skip(paste0("{", e$package, "} is not installed.")) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, } error_call = error_call)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE50: invokeRestart("muffle_cran_snapshot")test_files(test_dir = path, test_paths = test_paths, test_package = package, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 21: load_package = load_package, parallel = parallel, shuffle = shuffle)doTryCatch(return(expr), name, parentenv, handler)
51: 22: test_dir("testthat", package = package, reporter = reporter, tryCatchOne(expr, names, parentenv, handlers[[1L]]) ..., load_package = "installed")
23: 52: tryCatchList(expr, classes, parentenv, handlers)test_check("missSBM")
24: An irrecoverable exception occurred. R is aborting now ...
tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", { sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) 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_directed_nocov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.2) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: 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-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