Last updated on 2026-10-20 01:50:16 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 88.36 | 352.66 | 441.02 | 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 | 95.00 | 449.00 | 544.00 | 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’ [39s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missSBM)
>
> test_check("missSBM")
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 3 model(s).
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degreeTested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degree
sampling: dyad new better on connectivity
node
double-standard
block-node new better on mixture
Adjusting Variational EM for Stochastic Block Model
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'node' network-sampling process
Initialization of 1 model(s).
Performing VEM inference
Model with 3 blocks.
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 2 model(s).
Performing VEM inference
Model with 2 blocks.
Model with 1 blocks.
Polishing (node-swap)
Looking for better solutions
Pass 1 Going forward +
Pass 1 Going backward +
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L
Traceback:
sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 1: if (is.na(w)) dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") 2: if (w > LONG) FUN(X[[i]], ...) prefix <- paste0(prefix, "\n ")
} 3: else prefix <- "Error : "lapply(X = S, FUN = FUN, ...) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { 4: cat(msg, file = outFile)doTryCatch(return(expr), name, parentenv, handler) .Internal(printDeferredWarnings())
5: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) invisible(structure(msg, class = "try-error", condition = e))
}) 6: tryCatchList(expr, classes, parentenv, handlers)
7:
tryCatch(expr, error = function(e) { 8: call <- conditionCall(e)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 9: call <- sys.call(-4L)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") LONG <- 75L10: sm <- strsplit(conditionMessage(e), "\n")[[1L]]FUN(X[[i]], ...) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 11: lapply(seq_len(cores), inner.do) type = "b")
if (w > LONG) prefix <- paste0(prefix, "\n ")12: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")13: .Internal(seterrmessage(msg[1L]))parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) verbose = (verbosity > 4)) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error", condition = e))14: }).self$do_with_inits(inits, Q, reinitialization_effort)
15: 8: .self$estim_ascend(reinitialization_effort, changing_effort)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: 9: private$BMobject$estimate()sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: 10: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))FUN(X[[i]], ...)
18: 11: eval(code, test_env)lapply(seq_len(cores), inner.do)
19: 12: eval(code, test_env)
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 20: withCallingHandlers({ mc.silent = TRUE) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {13: skip("On CRAN")parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, } verbose = (verbosity > 4)) else if (!new_expectations && skip_on_empty) { skip_empty()
14: }.self$do_with_inits(inits, Q, reinitialization_effort)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))15: }.self$estim_ascend(reinitialization_effort, changing_effort)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE16: invokeRestart("muffle_cran_snapshot")private$BMobject$estimate()}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))21:
doTryCatch(return(expr), name, parentenv, handler)18:
eval(code, test_env)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])19:
eval(code, test_env)23:
tryCatchList(expr, classes, parentenv, handlers)20:
withCallingHandlers({24: eval(code, test_env)tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) new_expectations <- the$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()) { 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")}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)21:
doTryCatch(return(expr), name, parentenv, handler)25:
doWithOneRestart(return(expr), restart)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])26:
withOneRestart(expr, restarts[[1L]])23:
tryCatchList(expr, classes, parentenv, handlers)27:
withRestarts(tryCatch(withCallingHandlers({24: eval(code, test_env)tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { } skip(paste0("{", e$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) })
25: 28: doWithOneRestart(return(expr), restart)test_code(code, parent.frame())
26:
withOneRestart(expr, restarts[[1L]])29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate",
27: {withRestarts(tryCatch(withCallingHandlers({ sampler_undirected_cov$rNetwork(store = TRUE) eval(code, test_env) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, new_expectations <- the$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) { skip_empty() net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, } covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q))}, expectation = handle_expectation, packageNotFoundError = function(e) { cl <- cls[[Q]] if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, } clusterInit = cl, covarList = covarList_undirected)}, snapshot_on_cran = function(cnd) { mySBM_missSBM$doVEM() snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) invokeRestart("muffle_cran_snapshot") expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 0.01) end_test = function() { 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)28: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85)test_code(code, parent.frame()) })
29: 30: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", eval(code, test_env) { sampler_undirected_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData,
"bernoulli", FALSE, covarList = covarList_undirected)31: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, eval(code, test_env) plot = FALSE))
mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, 32: covariates = covarList_undirected)withCallingHandlers({ cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] eval(code, test_env) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, new_expectations <- the$test_expectations > starting_expectations clusterInit = cl, covarList = covarList_undirected) if (snapshot_skipped) { mySBM_missSBM$doVEM() skip("On CRAN") expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), } 0.05) else if (!new_expectations && skip_on_empty) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) skip_empty() expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) }}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), if (on_cran()) { 0.1) skip(paste0("{", e$package, "} is not installed.")) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), } 0.1)}, snapshot_on_cran = function(cnd) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85) snapshot_skipped <<- TRUE }) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 30: error = handle_error, interrupt = handle_interrupt)eval(code, test_env)
33: 31: doTryCatch(return(expr), name, parentenv, handler)eval(code, test_env)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])32:
withCallingHandlers({ eval(code, test_env)35: tryCatchList(expr, classes, parentenv, handlers) 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 <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, 33: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)doTryCatch(return(expr), name, parentenv, handler)
37: 34: doWithOneRestart(return(expr), restart)tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: 38: tryCatchList(expr, classes, parentenv, handlers)
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) { } 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) {}, 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_fatal), error = handle_error, interrupt = handle_interrupt), error = handle_fatal) end_test = function() {
})
37: 40: doWithOneRestart(return(expr), restart)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())38:
withOneRestart(expr, restarts[[1L]])41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 39: error_call = error_call)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)42: new_expectations <- the$test_expectations > starting_expectationsFUN(X[[i]], ...) if (snapshot_skipped) {
skip("On CRAN")43: }lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, else if (!new_expectations && skip_on_empty) { error_call = error_call) skip_empty()
}44: }, expectation = handle_expectation, packageNotFoundError = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))45: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE46: invokeRestart("muffle_cran_snapshot")tryCatchList(expr, classes, parentenv, handlers)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 47: end_test = function() {tryCatch(code, testthat_abort_reporter = function(cnd) { }) cat(conditionMessage(cnd), "\n")
NULL40: })test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 41: env = env, desc = desc, shuffle = shuffle, error_call = error_call))source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 42: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, FUN(X[[i]], ...) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 43: error_call = error_call)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 44: reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, doTryCatch(return(expr), name, parentenv, handler) load_package = load_package, parallel = parallel, shuffle = shuffle)
51: 45: test_dir("testthat", package = package, reporter = reporter, tryCatchOne(expr, names, parentenv, handlers[[1L]]) ..., load_package = "installed")
46: 52: tryCatchList(expr, classes, parentenv, handlers)test_check("missSBM")
47: An irrecoverable exception occurred. R is aborting now ...
tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty()
Traceback:
} 1: }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {dispatcher(membership_name, membership_init$to_cc(), model_name, skip(paste0("{", e$package, "} is not installed.")) .self$network_to_cc(), TRUE) }
}, snapshot_on_cran = function(cnd) { 2: snapshot_skipped <<- TRUEFUN(X[[i]], ...)
invokeRestart("muffle_cran_snapshot") 3: }, skip = handle_skip, warning = handle_warning, message = handle_message, lapply(X = S, FUN = FUN, ...) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() { 4: })doTryCatch(return(expr), name, parentenv, handler)
5: 28: tryCatchOne(expr, names, parentenv, handlers[[1L]])test_code(code, parent.frame())
6: 29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", tryCatchList(expr, classes, parentenv, handlers)
7: {tryCatch(expr, error = function(e) { sampler_directed_cov$rNetwork(store = TRUE) call <- conditionCall(e) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, "bernoulli", TRUE, covarList = covarList_directed) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, call <- sys.call(-4L) plot = FALSE)) dcall <- deparse(call, nlines = 1L) mySBM_sbm$setModel(Q) prefix <- paste("Error in", dcall, ": ") net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, LONG <- 75L covariates = covarList_directed) sm <- strsplit(conditionMessage(e), "\n")[[1L]] cls <- net$clustering(1:(2 * Q)) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") cl <- cls[[Q]] if (is.na(w)) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], clusterInit = cl, covarList = covarList_directed) type = "b") mySBM_missSBM$doVEM(trace = TRUE) if (w > LONG) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), prefix <- paste0(prefix, "\n ") 0.1) } else prefix <- "Error : " expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), msg <- paste0(prefix, conditionMessage(e), "\n") 0.8) .Internal(seterrmessage(msg[1L])) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), if (!silent && isTRUE(getOption("show.error.messages"))) { 0.05) cat(msg, file = outFile) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), .Internal(printDeferredWarnings()) 0.1) } expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), invisible(structure(msg, class = "try-error", condition = e)) 0.85)}) })
30: 8: eval(code, test_env)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
31: 9: eval(code, test_env)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
32: 10: withCallingHandlers({FUN(X[[i]], ...) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations11: if (snapshot_skipped) {lapply(seq_len(cores), inner.do)
skip("On CRAN")12: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, else if (!new_expectations && skip_on_empty) { mc.silent = TRUE) skip_empty()
}13: }, expectation = handle_expectation, packageNotFoundError = function(e) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, if (on_cran()) { verbose = (verbosity > 4)) skip(paste0("{", e$package, "} is not installed."))
}14: }, snapshot_on_cran = function(cnd) {.self$do_with_inits(inits, Q, reinitialization_effort) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")15: }, skip = handle_skip, warning = handle_warning, message = handle_message, .self$estim_ascend(reinitialization_effort, changing_effort) error = handle_error, interrupt = handle_interrupt)
16: 33: private$BMobject$estimate()doTryCatch(return(expr), name, parentenv, handler)
17: 34: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: eval(code, test_env)35:
tryCatchList(expr, classes, parentenv, handlers)19:
eval(code, test_env)36:
tryCatch(withCallingHandlers({20: eval(code, test_env)withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) new_expectations <- the$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()) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE}, 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)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
21: 37: doTryCatch(return(expr), name, parentenv, handler)
doWithOneRestart(return(expr), restart)22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: 23: withOneRestart(expr, restarts[[1L]])tryCatchList(expr, classes, parentenv, handlers)
39: 24: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) 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) { 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$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { }}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, snapshot_on_cran = function(cnd) { end_test = function() { snapshot_skipped <<- TRUE }) invokeRestart("muffle_cran_snapshot")
40: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_code(code = exprs, env = env, reporter = get_reporter() %||% error = handle_error, interrupt = handle_interrupt), error = handle_fatal) StopReporter$new())
25: 41: doWithOneRestart(return(expr), restart)source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
26: 42: withOneRestart(expr, restarts[[1L]])FUN(X[[i]], ...)
27: 43: withRestarts(tryCatch(withCallingHandlers({lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, eval(code, test_env) error_call = error_call) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {44: skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler) }
else if (!new_expectations && skip_on_empty) {45: skip_empty()tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {46: if (on_cran()) {tryCatchList(expr, classes, parentenv, handlers) skip(paste0("{", e$package, "} is not installed."))
}47: }, snapshot_on_cran = function(cnd) {tryCatch(code, testthat_abort_reporter = function(cnd) { snapshot_skipped <<- TRUE cat(conditionMessage(cnd), "\n") invokeRestart("muffle_cran_snapshot") NULL}, skip = handle_skip, warning = handle_warning, message = handle_message, }) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {48: })with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))28:
test_code(code, parent.frame())49:
test_files_serial(test_dir = test_dir, test_package = test_package, 29: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", desc = desc, load_package = load_package, shuffle = shuffle, { sampler_directed_cov$rNetwork(store = TRUE) error_call = error_call) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData,
50: "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, test_files(test_dir = path, test_paths = test_paths, test_package = package, plot = FALSE)) mySBM_sbm$setModel(Q) reporter = reporter, load_helpers = load_helpers, env = env, net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, covariates = covarList_directed) load_package = load_package, parallel = parallel, shuffle = shuffle) cls <- net$clustering(1:(2 * Q))
cl <- cls[[Q]]51: mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") clusterInit = cl, covarList = covarList_directed) mySBM_missSBM$doVEM(trace = TRUE)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 52: 0.1)test_check("missSBM") expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), An irrecoverable exception occurred. R is aborting now ...
0.05) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 0.85) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) 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)
Traceback:
new_expectations <- the$test_expectations > starting_expectations 1: if (snapshot_skipped) {dispatcher(membership_name, membership_init$to_cc(), model_name, skip("On CRAN") .self$network_to_cc(), TRUE) }
2: else if (!new_expectations && skip_on_empty) {FUN(X[[i]], ...) skip_empty()
} 3: }, expectation = handle_expectation, packageNotFoundError = function(e) {lapply(X = S, FUN = FUN, ...) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 4: }doTryCatch(return(expr), name, parentenv, handler)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") 5: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = handle_error, interrupt = handle_interrupt)
6: 21: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
7: 22: tryCatch(expr, error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) call <- conditionCall(e)
if (!is.null(call)) {23: if (identical(call[[1L]], quote(doTryCatch))) tryCatchList(expr, classes, parentenv, handlers) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)24: prefix <- paste("Error in", dcall, ": ")tryCatch(withCallingHandlers({ LONG <- 75L eval(code, test_env) sm <- strsplit(conditionMessage(e), "\n")[[1L]] new_expectations <- the$test_expectations > starting_expectations w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (snapshot_skipped) { if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], skip("On CRAN") type = "b") } if (w > LONG) prefix <- paste0(prefix, "\n ") else if (!new_expectations && skip_on_empty) { } skip_empty() else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n")}, expectation = handle_expectation, packageNotFoundError = function(e) { .Internal(seterrmessage(msg[1L])) if (on_cran()) { if (!silent && isTRUE(getOption("show.error.messages"))) { skip(paste0("{", e$package, "} is not installed.")) cat(msg, file = outFile) .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), error = handle_fatal)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
25: 9: doWithOneRestart(return(expr), restart)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
26: 10: withOneRestart(expr, restarts[[1L]])FUN(X[[i]], ...)
27: 11: withRestarts(tryCatch(withCallingHandlers({lapply(seq_len(cores), inner.do) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations12: if (snapshot_skipped) {parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, skip("On CRAN") mc.silent = TRUE) }
else if (!new_expectations && skip_on_empty) {13: parallel_lapply(inits, .self$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$estim_ascend(reinitialization_effort, changing_effort) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")16: private$BMobject$estimate()}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 17: end_test = function() {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) })
18: 28: eval(code, test_env)test_code(code, parent.frame())
19: 29: eval(code, test_env)test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate",
{20: sampler_undirected_nocov$rNetwork(store = TRUE)withCallingHandlers({ mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, eval(code, test_env) "bernoulli", FALSE) new_expectations <- the$test_expectations > starting_expectations mySBM_sbm$optimize(estimOptions = list(verbosity = 0, if (snapshot_skipped) { plot = FALSE)) skip("On CRAN") mySBM_sbm$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$doVEM() if (on_cran()) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), skip(paste0("{", e$package, "} is not installed.")) 0.05) } expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }, snapshot_on_cran = function(cnd) { 0.95) snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), invokeRestart("muffle_cran_snapshot") 0.01)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), error = handle_error, interrupt = handle_interrupt) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 21: 0.95) })doTryCatch(return(expr), name, parentenv, handler)
30: 22: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: 23: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers)
32: 24: withCallingHandlers({tryCatch(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()) { 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$test_expectations > starting_expectationstryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) new_expectations <- the$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) { 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())
38: 29: withOneRestart(expr, restarts[[1L]])test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate",
{39: sampler_undirected_nocov$rNetwork(store = TRUE)withRestarts(tryCatch(withCallingHandlers({ mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) eval(code, test_env) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, new_expectations <- the$test_expectations > starting_expectations plot = FALSE)) if (snapshot_skipped) { mySBM_sbm$setModel(3) skip("On CRAN") net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) } cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, else if (!new_expectations && skip_on_empty) { clusterInit = cl) skip_empty() mySBM_missSBM$doVEM() } expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { 0.05) skip(paste0("{", e$package, "} is not installed.")) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), } 0.95)}, snapshot_on_cran = function(cnd) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), invokeRestart("muffle_cran_snapshot") 0.05)}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), end_test = function() { 0.95) }) })
40: 30: test_code(code = exprs, env = env, reporter = get_reporter() %||% eval(code, test_env) StopReporter$new())
31: 41: eval(code, test_env)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
32: error_call = error_call)withCallingHandlers({
eval(code, test_env)42: new_expectations <- the$test_expectations > starting_expectationsFUN(X[[i]], ...) if (snapshot_skipped) {
skip("On CRAN")43: }lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, else if (!new_expectations && skip_on_empty) { error_call = error_call) skip_empty()
}44: }, expectation = handle_expectation, packageNotFoundError = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))45: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE46: invokeRestart("muffle_cran_snapshot")tryCatchList(expr, classes, parentenv, handlers)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)47:
tryCatch(code, testthat_abort_reporter = function(cnd) {33: cat(conditionMessage(cnd), "\n")doTryCatch(return(expr), name, parentenv, handler) NULL
})34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
48: 35: with_reporter(reporters$multi, lapply(test_paths, test_one_file, tryCatchList(expr, classes, parentenv, handlers) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, 36: tryCatch(withCallingHandlers({ test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, eval(code, test_env) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { desc = desc, load_package = load_package, shuffle = shuffle, skip("On CRAN") error_call = error_call) }
50: else if (!new_expectations && skip_on_empty) {test_files(test_dir = path, test_paths = test_paths, test_package = package, skip_empty() reporter = reporter, load_helpers = load_helpers, env = env, } stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }, expectation = handle_expectation, packageNotFoundError = function(e) { load_package = load_package, parallel = parallel, shuffle = shuffle) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))51: }test_dir("testthat", package = package, reporter = reporter, }, snapshot_on_cran = function(cnd) { ..., load_package = "installed") snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)52:
37: test_check("missSBM")
doWithOneRestart(return(expr), restart)An irrecoverable exception occurred. R is aborting now ...
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch)))
Traceback:
call <- sys.call(-4L) 1: dcall <- deparse(call, nlines = 1L)dispatcher(membership_name, membership_init$to_cc(), model_name, prefix <- paste("Error in", dcall, ": ") .self$network_to_cc(), TRUE) LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 2: if (is.na(w)) FUN(X[[i]], ...) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") 3: if (w > LONG) lapply(X = S, FUN = FUN, ...) prefix <- paste0(prefix, "\n ")
} 4: else prefix <- "Error : "doTryCatch(return(expr), name, parentenv, handler) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) 5: if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) cat(msg, file = outFile)
.Internal(printDeferredWarnings()) 6: }tryCatchList(expr, classes, parentenv, handlers) invisible(structure(msg, class = "try-error", condition = e))})
8: 7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatch(expr, error = function(e) {
call <- conditionCall(e) 9: if (!is.null(call)) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")10: LONG <- 75LFUN(X[[i]], ...) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
11: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")lapply(seq_len(cores), inner.do) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 12: type = "b")parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, if (w > LONG) mc.silent = TRUE) prefix <- paste0(prefix, "\n ")
13: } else prefix <- "Error : "parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { verbose = (verbosity > 4)) cat(msg, file = outFile) .Internal(printDeferredWarnings())
14: }.self$do_with_inits(inits, Q, reinitialization_effort) invisible(structure(msg, class = "try-error", condition = e))
})15:
.self$estim_ascend(reinitialization_effort, changing_effort) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)16:
private$BMobject$estimate() 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))10:
FUN(X[[i]], ...)18:
eval(code, test_env)11:
lapply(seq_len(cores), inner.do)19:
eval(code, test_env)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 20: mc.silent = TRUE)withCallingHandlers({
eval(code, test_env)13: new_expectations <- the$test_expectations > starting_expectationsparallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, if (snapshot_skipped) { verbose = (verbosity > 4)) skip("On CRAN")
}14: else if (!new_expectations && skip_on_empty) {.self$do_with_inits(inits, Q, reinitialization_effort) skip_empty()
}15: }, expectation = handle_expectation, packageNotFoundError = function(e) {.self$estim_ascend(reinitialization_effort, changing_effort) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))16: }private$BMobject$estimate()}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE17: invokeRestart("muffle_cran_snapshot")mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)18:
eval(code, test_env)
19: 21: doTryCatch(return(expr), name, parentenv, handler)eval(code, test_env)
22: 20: tryCatchOne(expr, names, parentenv, handlers[[1L]])withCallingHandlers({
eval(code, test_env)23: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {tryCatchList(expr, classes, parentenv, handlers) skip("On CRAN")
}24: else if (!new_expectations && skip_on_empty) {tryCatch(withCallingHandlers({ skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { }}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {21: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$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$test_expectations > starting_expectations
if (snapshot_skipped) {26: skip("On CRAN")withOneRestart(expr, restarts[[1L]]) }
else if (!new_expectations && skip_on_empty) {27: skip_empty()withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { new_expectations <- the$test_expectations > starting_expectations if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN") }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))25: }doWithOneRestart(return(expr), restart)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE26: invokeRestart("muffle_cran_snapshot")withOneRestart(expr, restarts[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 27: end_test = function() {withRestarts(tryCatch(withCallingHandlers({ }) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations28: if (snapshot_skipped) {test_code(code, parent.frame()) skip("On CRAN")
}29: else if (!new_expectations && skip_on_empty) {test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", skip_empty() { } sampler_directed_nocov$rNetwork(store = TRUE)}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, if (on_cran()) { "bernoulli", TRUE) skip(paste0("{", e$package, "} is not installed.")) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, } plot = FALSE))}, snapshot_on_cran = function(cnd) { mySBM_sbm$setModel(3) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]]}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), clusterInit = cl) end_test = function() { mySBM_missSBM$doVEM() }) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
0.1)28: test_code(code, parent.frame()) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.95)29: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01)test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), { 0.1) sampler_directed_nocov$rNetwork(store = TRUE) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, 0.2) "bernoulli", TRUE) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 0.95) plot = FALSE)) }) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)
cl <- net$clustering(3)[[1]]30: mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl)eval(code, test_env) mySBM_missSBM$doVEM()
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 31: 0.1)eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.95)32: withCallingHandlers({ expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), eval(code, test_env) 0.01) new_expectations <- the$test_expectations > starting_expectations expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), if (snapshot_skipped) { 0.1) skip("On CRAN") expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), } 0.2) else if (!new_expectations && skip_on_empty) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.95) skip_empty() }) }
30: }, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))31: }eval(code, test_env)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE32: invokeRestart("muffle_cran_snapshot")withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {33: skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler) }
else if (!new_expectations && skip_on_empty) { skip_empty()34: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {35: skip(paste0("{", e$package, "} is not installed."))tryCatchList(expr, classes, parentenv, handlers) }
}, snapshot_on_cran = function(cnd) {36: snapshot_skipped <<- TRUEtryCatch(withCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt) if (snapshot_skipped) {
skip("On CRAN")33: }doTryCatch(return(expr), name, parentenv, handler) else if (!new_expectations && skip_on_empty) {
skip_empty()34: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {35: skip(paste0("{", e$package, "} is not installed."))tryCatchList(expr, classes, parentenv, handlers) }
36: }, snapshot_on_cran = function(cnd) {tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip("On CRAN")
}37: else if (!new_expectations && skip_on_empty) {doWithOneRestart(return(expr), restart) skip_empty()
}38: }, expectation = handle_expectation, packageNotFoundError = function(e) {withOneRestart(expr, restarts[[1L]]) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))39: }withRestarts(tryCatch(withCallingHandlers({}, snapshot_on_cran = function(cnd) { eval(code, test_env) snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
37: else if (!new_expectations && skip_on_empty) {doWithOneRestart(return(expr), restart)
skip_empty() }38: }, expectation = handle_expectation, packageNotFoundError = function(e) {withOneRestart(expr, restarts[[1L]]) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
}39: }, snapshot_on_cran = function(cnd) {withRestarts(tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip("On CRAN") end_test = function() { } }) else if (!new_expectations && skip_on_empty) {
skip_empty()40: }test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {41: skip(paste0("{", e$package, "} is not installed."))source_file(path, env = env(env), desc = desc, shuffle = shuffle, } error_call = error_call)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE42: invokeRestart("muffle_cran_snapshot")FUN(X[[i]], ...)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 43: end_test = function() {lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, }) error_call = error_call)
40: 44: test_code(code = exprs, env = env, reporter = get_reporter() %||% doTryCatch(return(expr), name, parentenv, handler) StopReporter$new())
45: 41: tryCatchOne(expr, names, parentenv, handlers[[1L]])source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)46:
tryCatchList(expr, classes, parentenv, handlers)42:
FUN(X[[i]], ...)47:
tryCatch(code, testthat_abort_reporter = function(cnd) {43: cat(conditionMessage(cnd), "\n")lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, NULL error_call = error_call)})
44: 48: doTryCatch(return(expr), name, parentenv, handler)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])49:
test_files_serial(test_dir = test_dir, test_package = test_package, 46: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, tryCatchList(expr, classes, parentenv, handlers) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 47: error_call = error_call)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")50: NULLtest_files(test_dir = path, test_paths = test_paths, test_package = package, }) reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 48: load_package = load_package, parallel = parallel, shuffle = shuffle)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))51:
test_dir("testthat", package = package, reporter = reporter, 49: ..., load_package = "installed")test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 52: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_check("missSBM") desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)An irrecoverable exception occurred. R is aborting now ...
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