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Last updated on 2026-10-24 05:51:20 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 82.72 | 340.58 | 423.30 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 59.05 | 235.58 | 294.63 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 59.00 | 271.80 | 330.80 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 237.71 | 301.71 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 420.00 | 511.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 87.75 | 330.28 | 418.03 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 86.79 | 329.37 | 416.16 | OK | |
| r-release-macos-arm64 | 1.1.0 | 17.00 | 92.00 | 109.00 | OK | |
| r-release-macos-x86_64 | 1.1.0 | 59.00 | 456.00 | 515.00 | OK | |
| r-release-windows-x86_64 | 1.1.0 | 96.00 | 347.00 | 443.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 20.00 | 95.00 | 115.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 118.00 | 481.00 | 599.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [37s/33s]
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:
Traceback:
1: 1: dispatcher(membership_name, membership_init$to_cc(), model_name, dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) .self$network_to_cc(), TRUE)
2: 2: FUN(X[[i]], ...)FUN(X[[i]], ...)
3: 3: lapply(X = S, FUN = FUN, ...)lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler) 4: doTryCatch(return(expr), name, parentenv, handler)
5: 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 6: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
7: 7: tryCatch(expr, error = function(e) {tryCatch(expr, error = function(e) { call <- conditionCall(e) call <- conditionCall(e) if (!is.null(call)) { if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") prefix <- paste("Error in", dcall, ": ") LONG <- 75L LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") type = "b") if (w > LONG) if (w > LONG) prefix <- paste0(prefix, "\n ") prefix <- paste0(prefix, "\n ") } } else prefix <- "Error : " else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) cat(msg, file = outFile) .Internal(printDeferredWarnings()) } .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) invisible(structure(msg, class = "try-error", condition = e))})
8:
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: 10: FUN(X[[i]], ...)FUN(X[[i]], ...)
11: 11: lapply(seq_len(cores), inner.do)lapply(seq_len(cores), inner.do)
12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, mc.silent = TRUE)
verbose = (verbosity > 4))
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 14: .self$do_with_inits(inits, Q, reinitialization_effort) verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)15:
15: .self$estim_ascend(reinitialization_effort, changing_effort)
.self$estim_ascend(reinitialization_effort, changing_effort)16:
private$BMobject$estimate()16:
private$BMobject$estimate()17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: 18: eval(code, test_env)eval(code, test_env)
19: 19: eval(code, test_env)eval(code, test_env)
20: 20: 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()) { 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)
21: 21: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])23:
tryCatchList(expr, classes, parentenv, handlers)23:
tryCatchList(expr, classes, parentenv, handlers)24:
tryCatch(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) { } 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,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)25:
doWithOneRestart(return(expr), restart)25:
doWithOneRestart(return(expr), restart)26:
withOneRestart(expr, restarts[[1L]])
26: 27: withOneRestart(expr, restarts[[1L]])withRestarts(tryCatch(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()) { }}, 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_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() { end_test = function() { }) })
28: 28: test_code(code, parent.frame())test_code(code, parent.frame())
29: 29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", { { sampler_undirected_cov$rNetwork(store = TRUE) sampler_undirected_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, "bernoulli", FALSE, covarList = covarList_undirected) "bernoulli", FALSE, covarList = covarList_undirected) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) plot = FALSE)) mySBM_sbm$setModel(Q) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected) covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM() mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 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) 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) 0.85) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), }) 0.85)
})
30: 30: eval(code, test_env)eval(code, test_env)
31: 31: eval(code, test_env)eval(code, test_env)
32: 32: withCallingHandlers({withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") if (snapshot_skipped) { skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { 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) { 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, 33: error = handle_error, interrupt = handle_interrupt)doTryCatch(return(expr), name, parentenv, handler)
33: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
34: 35: tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
36:
35: tryCatch(withCallingHandlers({ eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {36: tryCatch(withCallingHandlers({ skip("On CRAN") } eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { else if (!new_expectations && skip_on_empty) { skip_empty() skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE37: invokeRestart("muffle_cran_snapshot")doWithOneRestart(return(expr), restart)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)38:
withOneRestart(expr, restarts[[1L]])
37: 39: doWithOneRestart(return(expr), restart)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)38: new_expectations <- the$test_expectations > starting_expectationswithOneRestart(expr, restarts[[1L]]) if (snapshot_skipped) {
skip("On CRAN")39: withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { 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), error = handle_fatal), }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE end_test = function() { }) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 40: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_code(code = exprs, env = env, reporter = get_reporter() %||% end_test = function() { StopReporter$new()) })
41: 40: test_code(code = exprs, env = env, reporter = get_reporter() %||% source_file(path, env = env(env), desc = desc, shuffle = shuffle, StopReporter$new()) error_call = error_call)
41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)42:
FUN(X[[i]], ...)42:
FUN(X[[i]], ...)43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 43: error_call = error_call)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)44:
doTryCatch(return(expr), name, parentenv, handler)44:
doTryCatch(return(expr), name, parentenv, handler)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: 46: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
47: 47: tryCatch(code, testthat_abort_reporter = function(cnd) {tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") cat(conditionMessage(cnd), "\n") NULL NULL})})
48: 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: 49: test_files_serial(test_dir = test_dir, test_package = test_package, test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) error_call = error_call)
50: 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle) load_package = load_package, parallel = parallel, shuffle = shuffle)
51: 51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")52:
test_check("missSBM")52:
test_check("missSBM")An irrecoverable exception occurred. R is aborting now ...
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 ") }
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .self$network_to_cc(), TRUE)
.Internal(seterrmessage(msg[1L])) 2: if (!silent && isTRUE(getOption("show.error.messages"))) {FUN(X[[i]], ...) cat(msg, file = outFile)
.Internal(printDeferredWarnings()) 3: }lapply(X = S, FUN = FUN, ...) invisible(structure(msg, class = "try-error", condition = e))})
4: 8: doTryCatch(return(expr), name, parentenv, handler)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
5: 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: 6: FUN(X[[i]], ...)
tryCatchList(expr, classes, parentenv, handlers)11:
lapply(seq_len(cores), inner.do) 7:
tryCatch(expr, error = function(e) {12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, call <- conditionCall(e) mc.silent = TRUE) if (!is.null(call)) {
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, if (identical(call[[1L]], quote(doTryCatch))) verbose = (verbosity > 4)) call <- sys.call(-4L)
14: dcall <- deparse(call, nlines = 1L).self$do_with_inits(inits, Q, reinitialization_effort) prefix <- paste("Error in", dcall, ": ")
15: LONG <- 75L.self$estim_ascend(reinitialization_effort, changing_effort) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
16: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) private$BMobject$estimate() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")17: if (w > LONG) prefix <- paste0(prefix, "\n ")mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) } else prefix <- "Error : "
18: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))eval(code, test_env) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)19: .Internal(printDeferredWarnings()) }eval(code, test_env)
invisible(structure(msg, class = "try-error", condition = e))20: })withCallingHandlers({ eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations 8: if (snapshot_skipped) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) skip("On CRAN")
} else if (!new_expectations && skip_on_empty) { 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) skip_empty()
}}, expectation = handle_expectation, packageNotFoundError = function(e) {10: if (on_cran()) {FUN(X[[i]], ...)
skip(paste0("{", e$package, "} is not installed."))11: }lapply(seq_len(cores), inner.do)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE12: invokeRestart("muffle_cran_snapshot")parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, }, skip = handle_skip, warning = handle_warning, message = handle_message, mc.silent = TRUE) error = handle_error, interrupt = handle_interrupt)
13: 21: doTryCatch(return(expr), name, parentenv, handler)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: .self$do_with_inits(inits, Q, reinitialization_effort)23:
tryCatchList(expr, classes, parentenv, handlers)15:
.self$estim_ascend(reinitialization_effort, changing_effort)24:
tryCatch(withCallingHandlers({16: eval(code, test_env)private$BMobject$estimate() new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { skip("On CRAN")17: }mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
else if (!new_expectations && skip_on_empty) {18: skip_empty()eval(code, test_env) }
19: }, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env) if (on_cran()) {
20: skip(paste0("{", e$package, "} is not installed."))withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") } else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
}25: doWithOneRestart(return(expr), restart)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {26: skip(paste0("{", e$package, "} is not installed."))withOneRestart(expr, restarts[[1L]])
}27: }, snapshot_on_cran = function(cnd) {withRestarts(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$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt) if (snapshot_skipped) {
21: skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler) }
else if (!new_expectations && skip_on_empty) {22: skip_empty()tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {23: if (on_cran()) {tryCatchList(expr, classes, parentenv, handlers) skip(paste0("{", e$package, "} is not installed."))
}24: }, snapshot_on_cran = function(cnd) {tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip("On CRAN") end_test = function() { } }) else if (!new_expectations && skip_on_empty) { skip_empty()
}28: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_code(code, parent.frame()) if (on_cran()) {
29: skip(paste0("{", e$package, "} is not installed."))test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", } {}, snapshot_on_cran = function(cnd) { sampler_directed_cov$rNetwork(store = TRUE) snapshot_skipped <<- TRUE mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, invokeRestart("muffle_cran_snapshot") "bernoulli", TRUE, covarList = covarList_directed)}, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) plot = FALSE))
mySBM_sbm$setModel(Q)25: net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, doWithOneRestart(return(expr), restart) covariates = covarList_directed)
cls <- net$clustering(1:(2 * Q))26: cl <- cls[[Q]]withOneRestart(expr, restarts[[1L]]) mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net,
27: clusterInit = cl, covarList = covarList_directed)withRestarts(tryCatch(withCallingHandlers({ mySBM_missSBM$doVEM(trace = TRUE) eval(code, test_env) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { 0.1) skip("On CRAN") expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), } 0.8) else if (!new_expectations && skip_on_empty) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), skip_empty() 0.05) } expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.1) if (on_cran()) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), skip(paste0("{", e$package, "} is not installed.")) 0.85) } })}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")30: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), eval(code, test_env) end_test = function() {
})31: eval(code, test_env)
28:
test_code(code, parent.frame())32:
withCallingHandlers({29: eval(code, test_env)test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", new_expectations <- the$test_expectations > starting_expectations { if (snapshot_skipped) { sampler_directed_cov$rNetwork(store = TRUE) skip("On CRAN") mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, } "bernoulli", TRUE, covarList = covarList_directed) else if (!new_expectations && skip_on_empty) { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, skip_empty() plot = FALSE)) } mySBM_sbm$setModel(Q)}, expectation = handle_expectation, packageNotFoundError = function(e) { net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, if (on_cran()) { covariates = covarList_directed) skip(paste0("{", e$package, "} is not installed.")) cls <- net$clustering(1:(2 * Q)) } cl <- cls[[Q]]}, snapshot_on_cran = function(cnd) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, snapshot_skipped <<- TRUE clusterInit = cl, covarList = covarList_directed) invokeRestart("muffle_cran_snapshot") mySBM_missSBM$doVEM(trace = TRUE)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), error = handle_error, interrupt = handle_interrupt) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 33: 0.8)doTryCatch(return(expr), name, parentenv, handler)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 34: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0.05)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 35: 0.1)tryCatchList(expr, classes, parentenv, handlers) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships),
0.85)36: })tryCatch(withCallingHandlers({
30: eval(code, test_env) new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
skip("On CRAN")31: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()32: withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { new_expectations <- the$test_expectations > starting_expectations if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE }}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) } error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")37: }, skip = handle_skip, warning = handle_warning, message = handle_message, doWithOneRestart(return(expr), restart) error = handle_error, interrupt = handle_interrupt)
38: 33: withOneRestart(expr, restarts[[1L]])doTryCatch(return(expr), name, parentenv, handler)
34: 39: tryCatchOne(expr, names, parentenv, handlers[[1L]])withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations35: tryCatchList(expr, classes, parentenv, handlers) if (snapshot_skipped) { skip("On CRAN")
36: } else if (!new_expectations && skip_on_empty) { skip_empty()tryCatch(withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN") }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, expectation = handle_expectation, packageNotFoundError = function(e) { end_test = function() { if (on_cran()) { }) skip(paste0("{", e$package, "} is not installed."))
40: }test_code(code = exprs, env = env, reporter = get_reporter() %||% }, snapshot_on_cran = function(cnd) { StopReporter$new()) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")41: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)37:
doWithOneRestart(return(expr), restart)42:
FUN(X[[i]], ...)38:
withOneRestart(expr, restarts[[1L]])43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 39: error_call = error_call)withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env)
new_expectations <- the$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$package, "} is not installed."))
}47: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")tryCatch(code, testthat_abort_reporter = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), cat(conditionMessage(cnd), "\n") end_test = function() { NULL })})
40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 48: StopReporter$new())with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 49: error_call = error_call)test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 42: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, FUN(X[[i]], ...) desc = desc, load_package = load_package, shuffle = shuffle,
43: error_call = error_call)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 44: reporter = reporter, load_helpers = load_helpers, env = env, doTryCatch(return(expr), name, parentenv, handler) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
51: 46: test_dir("testthat", package = package, reporter = reporter, tryCatchList(expr, classes, parentenv, handlers) ..., load_package = "installed")
47:
tryCatch(code, testthat_abort_reporter = function(cnd) {52: cat(conditionMessage(cnd), "\n")test_check("missSBM") NULL
})An irrecoverable exception occurred. R is aborting now ...
48: with_reporter(reporters$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) {
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
call <- conditionCall(e) 2: if (!is.null(call)) {FUN(X[[i]], ...) if (identical(call[[1L]], quote(doTryCatch)))
3: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)lapply(X = S, FUN = FUN, ...) 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)) 4: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], doTryCatch(return(expr), name, parentenv, handler)
5: type = "b")tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (w > LONG)
prefix <- paste0(prefix, "\n ") 6: }tryCatchList(expr, classes, parentenv, handlers) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n") 7: .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatch(expr, error = function(e) { cat(msg, file = outFile) call <- conditionCall(e) .Internal(printDeferredWarnings()) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) invisible(structure(msg, class = "try-error", condition = e)) dcall <- deparse(call, nlines = 1L)}) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L 8: sm <- strsplit(conditionMessage(e), "\n")[[1L]]try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (is.na(w))
10: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")FUN(X[[i]], ...)
11: if (w > LONG) prefix <- paste0(prefix, "\n ")lapply(seq_len(cores), inner.do) }
else prefix <- "Error : "12: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, if (!silent && isTRUE(getOption("show.error.messages"))) { mc.silent = TRUE) cat(msg, file = outFile) .Internal(printDeferredWarnings())
13: }parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, invisible(structure(msg, class = "try-error", condition = e)) verbose = (verbosity > 4))})
14: 8: .self$do_with_inits(inits, Q, reinitialization_effort)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)15:
.self$estim_ascend(reinitialization_effort, changing_effort) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))16:
private$BMobject$estimate()10:
FUN(X[[i]], ...)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))11: lapply(seq_len(cores), inner.do)
18: 12: eval(code, test_env)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE,
mc.silent = TRUE)19:
eval(code, test_env)
13: 20: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, withCallingHandlers({ verbose = (verbosity > 4)) eval(code, test_env)
14: new_expectations <- the$test_expectations > starting_expectations.self$do_with_inits(inits, Q, reinitialization_effort) if (snapshot_skipped) {
skip("On CRAN")15: }.self$estim_ascend(reinitialization_effort, changing_effort) else if (!new_expectations && skip_on_empty) {
skip_empty()16: }}, expectation = handle_expectation, packageNotFoundError = function(e) {private$BMobject$estimate() if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))17: }mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE18: invokeRestart("muffle_cran_snapshot")eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)19: eval(code, test_env)
21: 20: doTryCatch(return(expr), name, parentenv, handler)
withCallingHandlers({22: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {23: skip("On CRAN")tryCatchList(expr, classes, parentenv, handlers) }
else if (!new_expectations && skip_on_empty) {24: skip_empty()tryCatch(withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { new_expectations <- the$test_expectations > starting_expectations if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))21: }doTryCatch(return(expr), name, parentenv, handler)
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE22: invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)23:
25: tryCatchList(expr, classes, parentenv, handlers)doWithOneRestart(return(expr), restart)
24: 26: withOneRestart(expr, restarts[[1L]])tryCatch(withCallingHandlers({
eval(code, test_env)27: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {withRestarts(tryCatch(withCallingHandlers({ skip("On CRAN") eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() 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")}, 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() {25: })doWithOneRestart(return(expr), restart)
28: 26: test_code(code, parent.frame())withOneRestart(expr, restarts[[1L]])
27: 29: withRestarts(tryCatch(withCallingHandlers({test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", eval(code, test_env) { new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { sampler_undirected_nocov$rNetwork(store = TRUE) skip("On CRAN") mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, } "bernoulli", FALSE) else if (!new_expectations && skip_on_empty) { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, skip_empty() } plot = FALSE))}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_sbm$setModel(3) if (on_cran()) { net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) skip(paste0("{", e$package, "} is not installed.")) cl <- net$clustering(3)[[1]] } mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, }, snapshot_on_cran = function(cnd) { clusterInit = cl) snapshot_skipped <<- TRUE mySBM_missSBM$doVEM() invokeRestart("muffle_cran_snapshot") expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.05) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), end_test = function() { 0.95) }) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)28: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 0.05)test_code(code, parent.frame()) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships),
0.95)29: })
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", 30: { sampler_undirected_nocov$rNetwork(store = TRUE)eval(code, test_env) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData,
"bernoulli", FALSE)31: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, eval(code, test_env) plot = FALSE))
mySBM_sbm$setModel(3)32: net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData)withCallingHandlers({ cl <- net$clustering(3)[[1]] eval(code, test_env) mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, new_expectations <- the$test_expectations > starting_expectations clusterInit = cl) if (snapshot_skipped) { mySBM_missSBM$doVEM() skip("On CRAN") expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), } 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), else if (!new_expectations && skip_on_empty) { 0.95) skip_empty() expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), } 0.01)}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), if (on_cran()) { 0.05) skip(paste0("{", e$package, "} is not installed.")) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), } 0.95)}, snapshot_on_cran = function(cnd) { }) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")30: }, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt)
31: 33: doTryCatch(return(expr), name, parentenv, handler)eval(code, test_env)
34: 32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
withCallingHandlers({35: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN")36: } else if (!new_expectations && skip_on_empty) {tryCatch(withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) { skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt) skip(paste0("{", e$package, "} is not installed.")) }
}, snapshot_on_cran = function(cnd) {33: snapshot_skipped <<- TRUEdoTryCatch(return(expr), name, parentenv, handler) 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)
35: tryCatchList(expr, classes, parentenv, handlers)37:
doWithOneRestart(return(expr), restart)36:
38: tryCatch(withCallingHandlers({withOneRestart(expr, restarts[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations39: if (snapshot_skipped) {withRestarts(tryCatch(withCallingHandlers({ skip("On CRAN") } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$test_expectations > starting_expectations skip_empty() if (snapshot_skipped) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, }}, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")37: }, skip = handle_skip, warning = handle_warning, message = handle_message, doWithOneRestart(return(expr), restart)
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 38: end_test = function() {withOneRestart(expr, restarts[[1L]]) })
39: 40: withRestarts(tryCatch(withCallingHandlers({test_code(code = exprs, env = env, reporter = get_reporter() %||% eval(code, test_env) StopReporter$new()) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {41: skip("On CRAN")source_file(path, env = env(env), desc = desc, shuffle = shuffle, } error_call = error_call) else if (!new_expectations && skip_on_empty) {
skip_empty()42: }FUN(X[[i]], ...)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {43: skip(paste0("{", e$package, "} is not installed."))lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } error_call = error_call)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE44: invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 45: end_test = function() {tryCatchOne(expr, names, parentenv, handlers[[1L]]) })
46: 40: tryCatchList(expr, classes, parentenv, handlers)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())47:
41: tryCatch(code, testthat_abort_reporter = function(cnd) {source_file(path, env = env(env), desc = desc, shuffle = shuffle, cat(conditionMessage(cnd), "\n") error_call = error_call) NULL
})42:
FUN(X[[i]], ...)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 43: env = env, desc = desc, shuffle = shuffle, error_call = error_call))lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
49: error_call = error_call)test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 44: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, doTryCatch(return(expr), name, parentenv, handler) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
50: 46: test_files(test_dir = path, test_paths = test_paths, test_package = package, tryCatchList(expr, classes, parentenv, handlers) reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)47:
tryCatch(code, testthat_abort_reporter = function(cnd) {51: cat(conditionMessage(cnd), "\n")test_dir("testthat", package = package, reporter = reporter, NULL ..., load_package = "installed")
})52:
test_check("missSBM")48: with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))An irrecoverable exception occurred. R is aborting now ...
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)
Traceback:
1: new_expectations <- the$test_expectations > starting_expectationsdispatcher(membership_name, membership_init$to_cc(), model_name, if (snapshot_skipped) { .self$network_to_cc(), TRUE)
skip("On CRAN") } 2: else if (!new_expectations && skip_on_empty) { skip_empty()FUN(X[[i]], ...) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { 3: if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))lapply(X = S, FUN = FUN, ...) }
}, snapshot_on_cran = function(cnd) { 4: snapshot_skipped <<- TRUEdoTryCatch(return(expr), name, parentenv, handler)
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), error = handle_fatal),
end_test = function() { 6: })tryCatchList(expr, classes, parentenv, handlers)
7: 28: test_code(code, parent.frame())tryCatch(expr, error = function(e) {
call <- conditionCall(e) if (!is.null(call)) {29: if (identical(call[[1L]], quote(doTryCatch))) test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) { sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] "bernoulli", TRUE) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") mySBM_sbm$optimize(estimOptions = list(verbosity = 0, if (is.na(w)) plot = FALSE)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) type = "b") cl <- net$clustering(3)[[1]] if (w > LONG) mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, prefix <- paste0(prefix, "\n ") clusterInit = cl) mySBM_missSBM$doVEM() } else prefix <- "Error : " expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) 0.1) if (!silent && isTRUE(getOption("show.error.messages"))) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), cat(msg, file = outFile) .Internal(printDeferredWarnings()) } 0.95) invisible(structure(msg, class = "try-error", condition = e)) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), }) 0.01)
8: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam),
0.2) 9: expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 0.95)
10: })FUN(X[[i]], ...)
30:
eval(code, test_env)11: lapply(seq_len(cores), inner.do)
31:
eval(code, test_env)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 32: mc.silent = TRUE)withCallingHandlers({
eval(code, test_env)13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, new_expectations <- the$test_expectations > starting_expectations verbose = (verbosity > 4))
if (snapshot_skipped) {14: skip("On CRAN").self$do_with_inits(inits, Q, reinitialization_effort) }
else if (!new_expectations && skip_on_empty) {15: skip_empty() }.self$estim_ascend(reinitialization_effort, changing_effort)}, expectation = handle_expectation, packageNotFoundError = function(e) {
16: if (on_cran()) {private$BMobject$estimate() skip(paste0("{", e$package, "} is not installed."))
}17: }, snapshot_on_cran = function(cnd) {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")18: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)eval(code, test_env)
33: 19: doTryCatch(return(expr), name, parentenv, handler)
34: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: 20: tryCatchList(expr, classes, parentenv, handlers)withCallingHandlers({
eval(code, test_env)36: new_expectations <- the$test_expectations > starting_expectationstryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE21: invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)
}, skip = handle_skip, warning = handle_warning, message = handle_message, 22: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)tryCatchOne(expr, names, parentenv, handlers[[1L]])
37: 23: doWithOneRestart(return(expr), restart)tryCatchList(expr, classes, parentenv, handlers)
38:
24: withOneRestart(expr, restarts[[1L]])tryCatch(withCallingHandlers({
eval(code, test_env)39: new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { } skip_empty() } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 25: doWithOneRestart(return(expr), restart) end_test = function() {
})26:
withOneRestart(expr, restarts[[1L]])40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 27: StopReporter$new())withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations41: if (snapshot_skipped) {source_file(path, env = env(env), desc = desc, shuffle = shuffle, skip("On CRAN") error_call = error_call) }
else if (!new_expectations && skip_on_empty) {42: skip_empty()FUN(X[[i]], ...) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {43: skip(paste0("{", e$package, "} is not installed."))lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } error_call = error_call)
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE44: doTryCatch(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]])
end_test = function() {46: tryCatchList(expr, classes, parentenv, handlers) })
28: test_code(code, parent.frame())
47: tryCatch(code, testthat_abort_reporter = function(cnd) {29: cat(conditionMessage(cnd), "\n")test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", NULL})
{48: sampler_directed_nocov$rNetwork(store = TRUE)with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData,
"bernoulli", TRUE)49: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, plot = FALSE)) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, mySBM_sbm$setModel(3) desc = desc, load_package = load_package, shuffle = shuffle, net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) error_call = error_call) cl <- net$clustering(3)[[1]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, 50: clusterInit = cl)test_files(test_dir = path, test_paths = test_paths, test_package = package, mySBM_missSBM$doVEM() reporter = reporter, load_helpers = load_helpers, env = env, expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 0.1) load_package = load_package, parallel = parallel, shuffle = shuffle)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 51: 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), test_dir("testthat", package = package, reporter = reporter, 0.01) ..., load_package = "installed")
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 52: test_check("missSBM") 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam),
An irrecoverable exception occurred. R is aborting now ...
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
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