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Last updated on 2026-10-15 12:06:56 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 80.54 | 363.82 | 444.36 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 57.45 | 245.68 | 303.13 | 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 | 63.00 | 247.59 | 310.59 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 446.00 | 537.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 85.58 | 342.08 | 427.66 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 74.39 | 345.64 | 420.03 | 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 | 95.00 | 361.00 | 456.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 19.00 | 102.00 | 121.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 119.00 | 528.00 | 647.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [37s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missSBM)
>
> test_check("missSBM")
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 3 model(s).
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degreeTested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degree
sampling: dyad new better on connectivity
node
double-standard
block-node new better on mixture
Adjusting Variational EM for Stochastic Block Model
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'node' network-sampling process
Initialization of 1 model(s).
Performing VEM inference
Model with 3 blocks.
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 2 model(s).
Performing VEM inference
Model with 2 blocks.
Model with 1 blocks.
Polishing (node-swap)
Looking for better solutions
Pass 1 Going forward +
Pass 1 Going backward +
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", { sampler_undirected_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, "bernoulli", FALSE, covarList = covarList_undirected) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") }
Traceback:
else if (!new_expectations && skip_on_empty) { 1: skip_empty()dispatcher(membership_name, membership_init$to_cc(), model_name, } .self$network_to_cc(), TRUE)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) 2: }}, snapshot_on_cran = function(cnd) {FUN(X[[i]], ...) snapshot_skipped <<- TRUE
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)
4: 37: doTryCatch(return(expr), name, parentenv, handler)doWithOneRestart(return(expr), restart)
5: 38: tryCatchOne(expr, names, parentenv, handlers[[1L]])withOneRestart(expr, restarts[[1L]])
6:
tryCatchList(expr, classes, parentenv, handlers)
39: 7: withRestarts(tryCatch(withCallingHandlers({tryCatch(expr, error = function(e) { eval(code, test_env) call <- conditionCall(e) new_expectations <- the$test_expectations > starting_expectations if (!is.null(call)) { if (snapshot_skipped) { if (identical(call[[1L]], quote(doTryCatch))) skip("On CRAN") call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) } prefix <- paste("Error in", dcall, ": ") LONG <- 75L else if (!new_expectations && skip_on_empty) { skip_empty() sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } if (is.na(w)) }, expectation = handle_expectation, packageNotFoundError = function(e) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (on_cran()) { type = "b") skip(paste0("{", e$package, "} is not installed.")) if (w > LONG) }}, snapshot_on_cran = function(cnd) { prefix <- paste0(prefix, "\n ") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else prefix <- "Error : "}, skip = handle_skip, warning = handle_warning, message = handle_message, msg <- paste0(prefix, conditionMessage(e), "\n") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), .Internal(seterrmessage(msg[1L])) end_test = function() { if (!silent && isTRUE(getOption("show.error.messages"))) { }) cat(msg, file = outFile)
.Internal(printDeferredWarnings())40: } invisible(structure(msg, class = "try-error", condition = e))test_code(code = exprs, env = env, reporter = get_reporter() %||% }) StopReporter$new())
8: 41: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call) 9:
42: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...)
10: 43: FUN(X[[i]], ...)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)11:
lapply(seq_len(cores), inner.do)44:
doTryCatch(return(expr), name, parentenv, handler)
12: 45: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, tryCatchOne(expr, names, parentenv, handlers[[1L]]) mc.silent = TRUE)
46:
tryCatchList(expr, classes, parentenv, handlers)
47: 13: tryCatch(code, testthat_abort_reporter = function(cnd) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, cat(conditionMessage(cnd), "\n") verbose = (verbosity > 4)) NULL
})14:
.self$do_with_inits(inits, Q, reinitialization_effort)48: with_reporter(reporters$multi, lapply(test_paths, test_one_file,
15: env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: .self$estim_ascend(reinitialization_effort, changing_effort)
test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)16:
private$BMobject$estimate()50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 17: reporter = reporter, load_helpers = load_helpers, env = env, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)18:
eval(code, test_env)51:
test_dir("testthat", package = package, reporter = reporter, 19: ..., load_package = "installed")
eval(code, test_env)52:
20: test_check("missSBM")withCallingHandlers({
An irrecoverable exception occurred. R is aborting now ...
eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", { sampler_undirected_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, "bernoulli", FALSE, covarList = covarList_undirected) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, covariates = covarList_undirected) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_undirected) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 0.85) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: 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$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
Traceback:
14: 1: .self$do_with_inits(inits, Q, reinitialization_effort)
dispatcher(membership_name, membership_init$to_cc(), model_name, 15: .self$network_to_cc(), TRUE).self$estim_ascend(reinitialization_effort, changing_effort)
2: 16: FUN(X[[i]], ...)private$BMobject$estimate()
17: 3: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
lapply(X = S, FUN = FUN, ...)18:
4: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler)
5: 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(code, test_env)
6: 20: tryCatchList(expr, classes, parentenv, handlers)withCallingHandlers({
7: eval(code, test_env)tryCatch(expr, error = function(e) { new_expectations <- the$test_expectations > starting_expectations call <- conditionCall(e) if (snapshot_skipped) { if (!is.null(call)) { skip("On CRAN") if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) else if (!new_expectations && skip_on_empty) { prefix <- paste("Error in", dcall, ": ") skip_empty() LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, expectation = handle_expectation, packageNotFoundError = function(e) { if (is.na(w)) if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b")}, snapshot_on_cran = function(cnd) { if (w > LONG) snapshot_skipped <<- TRUE prefix <- paste0(prefix, "\n ") invokeRestart("muffle_cran_snapshot") } else prefix <- "Error : "}, skip = handle_skip, warning = handle_warning, message = handle_message, msg <- paste0(prefix, conditionMessage(e), "\n") error = handle_error, interrupt = handle_interrupt) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {21: cat(msg, file = outFile)doTryCatch(return(expr), name, parentenv, handler) .Internal(printDeferredWarnings())
}22: tryCatchOne(expr, names, parentenv, handlers[[1L]]) invisible(structure(msg, class = "try-error", condition = e))
})
23: 8: tryCatchList(expr, classes, parentenv, handlers)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
24: 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatch(withCallingHandlers({
eval(code, test_env)10: new_expectations <- the$test_expectations > starting_expectationsFUN(X[[i]], ...) if (snapshot_skipped) {
skip("On CRAN")11: }lapply(seq_len(cores), inner.do) else if (!new_expectations && skip_on_empty) {
skip_empty()12: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, }, expectation = handle_expectation, packageNotFoundError = function(e) { mc.silent = TRUE) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))13: }parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, }, snapshot_on_cran = function(cnd) { verbose = (verbosity > 4))
snapshot_skipped <<- TRUE14: .self$do_with_inits(inits, Q, reinitialization_effort) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 15: error = handle_error, interrupt = handle_interrupt), error = handle_fatal).self$estim_ascend(reinitialization_effort, changing_effort)
25: 16: private$BMobject$estimate()doWithOneRestart(return(expr), restart)
17: 26: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))withOneRestart(expr, restarts[[1L]])
18: eval(code, test_env)27:
withRestarts(tryCatch(withCallingHandlers({19: eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { skip("On CRAN")20: }withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() {}, snapshot_on_cran = function(cnd) { }) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")28: test_code(code, parent.frame())}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
29: 21: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", doTryCatch(return(expr), name, parentenv, handler) {
sampler_directed_cov$rNetwork(store = TRUE)22: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, tryCatchOne(expr, names, parentenv, handlers[[1L]]) "bernoulli", TRUE, covarList = covarList_directed)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 23: plot = FALSE))tryCatchList(expr, classes, parentenv, handlers) mySBM_sbm$setModel(Q)
net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, covariates = covarList_directed)24: cls <- net$clustering(1:(2 * Q))tryCatch(withCallingHandlers({ 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_directed) if (snapshot_skipped) { mySBM_missSBM$doVEM(trace = TRUE) skip("On CRAN") expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), } 0.1) else if (!new_expectations && skip_on_empty) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), skip_empty() 0.8) } expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.05) if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), } 0.1)}, snapshot_on_cran = function(cnd) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), snapshot_skipped <<- TRUE 0.85) invokeRestart("muffle_cran_snapshot") })}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)30:
eval(code, test_env)25: doWithOneRestart(return(expr), restart)
26: 31: withOneRestart(expr, restarts[[1L]])eval(code, test_env)
27:
withRestarts(tryCatch(withCallingHandlers({32: 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_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: end_test = function() {doTryCatch(return(expr), name, parentenv, handler) })
34: 28: tryCatchOne(expr, names, parentenv, handlers[[1L]])test_code(code, parent.frame())
35: 29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", tryCatchList(expr, classes, parentenv, handlers) {
sampler_directed_cov$rNetwork(store = TRUE)36: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, tryCatch(withCallingHandlers({ "bernoulli", TRUE, covarList = covarList_directed) eval(code, test_env) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, new_expectations <- the$test_expectations > starting_expectations plot = FALSE)) if (snapshot_skipped) { mySBM_sbm$setModel(Q) skip("On CRAN") net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, } covariates = covarList_directed) else if (!new_expectations && skip_on_empty) { cls <- net$clustering(1:(2 * Q)) skip_empty() cl <- cls[[Q]] } mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { clusterInit = cl, covarList = covarList_directed) skip(paste0("{", e$package, "} is not installed.")) mySBM_missSBM$doVEM(trace = TRUE) } expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, snapshot_on_cran = function(cnd) { 0.1) snapshot_skipped <<- TRUE expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), invokeRestart("muffle_cran_snapshot") 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) 0.05)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 37: 0.1)doWithOneRestart(return(expr), restart) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships),
0.85)38: withOneRestart(expr, restarts[[1L]]) })
39: 30: withRestarts(tryCatch(withCallingHandlers({eval(code, test_env) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations31: if (snapshot_skipped) {eval(code, test_env) skip("On CRAN")
}32: else if (!new_expectations && skip_on_empty) {withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() {}, snapshot_on_cran = function(cnd) { }) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, 40: error = handle_error, interrupt = handle_interrupt)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())33:
doTryCatch(return(expr), name, parentenv, handler)41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 34: error_call = error_call)tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: 35: FUN(X[[i]], ...)tryCatchList(expr, classes, parentenv, handlers)
43: 36: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, tryCatch(withCallingHandlers({ error_call = error_call) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations44: if (snapshot_skipped) { 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$package, "} is not installed."))47: }tryCatch(code, testthat_abort_reporter = function(cnd) {}, snapshot_on_cran = function(cnd) { cat(conditionMessage(cnd), "\n") snapshot_skipped <<- TRUE NULL invokeRestart("muffle_cran_snapshot")})}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 37: env = env, desc = desc, shuffle = shuffle, error_call = error_call))doWithOneRestart(return(expr), restart)
49: 38: test_files_serial(test_dir = test_dir, test_package = test_package, withOneRestart(expr, restarts[[1L]]) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 39: desc = desc, load_package = load_package, shuffle = shuffle, withRestarts(tryCatch(withCallingHandlers({ error_call = error_call) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {50: test_files(test_dir = path, test_paths = test_paths, test_package = package, skip("On CRAN") reporter = reporter, load_helpers = load_helpers, env = env, } stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, else if (!new_expectations && skip_on_empty) { load_package = load_package, parallel = parallel, shuffle = shuffle) skip_empty()
}51: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_dir("testthat", package = package, reporter = reporter, if (on_cran()) { ..., load_package = "installed") skip(paste0("{", e$package, "} is not installed."))
52: }test_check("missSBM")}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUEAn irrecoverable exception occurred. R is aborting now ...
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) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", { sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE
Traceback:
invokeRestart("muffle_cran_snapshot") 1: }, skip = handle_skip, warning = handle_warning, message = handle_message, dispatcher(membership_name, membership_init$to_cc(), model_name, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), .self$network_to_cc(), TRUE) end_test = function() {
}) 2:
FUN(X[[i]], ...)40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 3: StopReporter$new())lapply(X = S, FUN = FUN, ...)
41: 4: source_file(path, env = env(env), desc = desc, shuffle = shuffle, doTryCatch(return(expr), name, parentenv, handler) error_call = error_call)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
42:
FUN(X[[i]], ...) 6:
tryCatchList(expr, classes, parentenv, handlers)43:
7: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)tryCatch(expr, error = function(e) {
44: call <- conditionCall(e)doTryCatch(return(expr), name, parentenv, handler) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 45: call <- sys.call(-4L)tryCatchOne(expr, names, parentenv, handlers[[1L]]) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")46: LONG <- 75LtryCatchList(expr, classes, parentenv, handlers) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")47: tryCatch(code, testthat_abort_reporter = function(cnd) { if (is.na(w)) cat(conditionMessage(cnd), "\n") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], NULL type = "b")}) if (w > LONG)
prefix <- paste0(prefix, "\n ")48: }with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) else prefix <- "Error : "
49: msg <- paste0(prefix, conditionMessage(e), "\n")test_files_serial(test_dir = test_dir, test_package = test_package, .Internal(seterrmessage(msg[1L])) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, if (!silent && isTRUE(getOption("show.error.messages"))) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, cat(msg, file = outFile) desc = desc, load_package = load_package, shuffle = shuffle, .Internal(printDeferredWarnings()) error_call = error_call) }
invisible(structure(msg, class = "try-error", condition = e))50: })test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 8: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) load_package = load_package, parallel = parallel, shuffle = shuffle)
9: 51: test_dir("testthat", package = package, reporter = reporter, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) ..., load_package = "installed")
10: 52: FUN(X[[i]], ...)test_check("missSBM")
11: An irrecoverable exception occurred. R is aborting now ...
lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", { sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
Traceback:
1: 7: tryCatch(expr, error = function(e) { call <- conditionCall(e)dispatcher(membership_name, membership_init$to_cc(), model_name, if (!is.null(call)) { .self$network_to_cc(), TRUE) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) 2: prefix <- paste("Error in", dcall, ": ") LONG <- 75LFUN(X[[i]], ...) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 3: if (is.na(w)) lapply(X = S, FUN = FUN, ...) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") 4: if (w > LONG) doTryCatch(return(expr), name, parentenv, handler) prefix <- paste0(prefix, "\n ")
} else prefix <- "Error : " 5: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile) 6: .Internal(printDeferredWarnings()) }tryCatchList(expr, classes, parentenv, handlers)
invisible(structure(msg, class = "try-error", condition = e))}) 7:
tryCatch(expr, error = function(e) { 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) call <- conditionCall(e)
if (!is.null(call)) { 9: if (identical(call[[1L]], quote(doTryCatch))) sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)
10: prefix <- paste("Error in", dcall, ": ")FUN(X[[i]], ...)
LONG <- 75L11: sm <- strsplit(conditionMessage(e), "\n")[[1L]]lapply(seq_len(cores), inner.do) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w))
12: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE) type = "b")
if (w > LONG) 13: prefix <- paste0(prefix, "\n ")parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, } verbose = (verbosity > 4)) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")14: .Internal(seterrmessage(msg[1L])).self$do_with_inits(inits, Q, reinitialization_effort) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)15: .Internal(printDeferredWarnings()).self$estim_ascend(reinitialization_effort, changing_effort) }
16: invisible(structure(msg, class = "try-error", condition = e))private$BMobject$estimate()})
17: 8: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
18: 9: eval(code, test_env)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
19: 10: eval(code, test_env)FUN(X[[i]], ...)
20: 11: withCallingHandlers({ eval(code, test_env)lapply(seq_len(cores), inner.do) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {12: skip("On CRAN")parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, } mc.silent = TRUE) else if (!new_expectations && skip_on_empty) {
skip_empty()13: }parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, }, expectation = handle_expectation, packageNotFoundError = function(e) { verbose = (verbosity > 4)) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))14: }.self$do_with_inits(inits, Q, reinitialization_effort)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE15: invokeRestart("muffle_cran_snapshot").self$estim_ascend(reinitialization_effort, changing_effort)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)16:
private$BMobject$estimate()21:
doTryCatch(return(expr), name, parentenv, handler)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
22: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(code, test_env)
23: 19: tryCatchList(expr, classes, parentenv, handlers)eval(code, test_env)
24: 20: tryCatch(withCallingHandlers({withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { else if (!new_expectations && skip_on_empty) { skip_empty() skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { 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)
21: 25: doTryCatch(return(expr), name, parentenv, handler)doWithOneRestart(return(expr), restart)
22: 26: tryCatchOne(expr, names, parentenv, handlers[[1L]])withOneRestart(expr, restarts[[1L]])
23: 27: tryCatchList(expr, classes, parentenv, handlers)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)24: 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() } }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() skip(paste0("{", e$package, "} is not installed.")) } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), snapshot_skipped <<- TRUE end_test = function() { invokeRestart("muffle_cran_snapshot") })}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)28:
25: test_code(code, parent.frame())doWithOneRestart(return(expr), restart)
29: 26: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", withOneRestart(expr, restarts[[1L]]) {
sampler_directed_nocov$rNetwork(store = TRUE)27: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, withRestarts(tryCatch(withCallingHandlers({ "bernoulli", TRUE) eval(code, test_env) mySBM_sbm$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$new(sampler_directed_nocov$networkData) } cl <- net$clustering(3)[[1]] else if (!new_expectations && skip_on_empty) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, skip_empty() clusterInit = cl) }}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_missSBM$doVEM() if (on_cran()) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), skip(paste0("{", e$package, "} is not installed.")) 0.1) } expect_gt(ARI(mySBM_missSBM$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$mean, sampler_directed_nocov$connectParam$mean), error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 0.1) end_test = function() { expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), }) 0.2)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.95)28: })test_code(code, parent.frame())
30: 29: eval(code, test_env)test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate",
{ sampler_directed_nocov$rNetwork(store = TRUE)31: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, eval(code, test_env) "bernoulli", TRUE)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 32: plot = FALSE))withCallingHandlers({ mySBM_sbm$setModel(3) eval(code, test_env) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) new_expectations <- the$test_expectations > starting_expectations cl <- net$clustering(3)[[1]] if (snapshot_skipped) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl) skip("On CRAN") mySBM_missSBM$doVEM() } expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), else if (!new_expectations && skip_on_empty) { 0.1) skip_empty() expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), } 0.95)}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), if (on_cran()) { 0.01) skip(paste0("{", e$package, "} is not installed.")) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), } 0.1)}, snapshot_on_cran = function(cnd) { expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), snapshot_skipped <<- TRUE 0.2) invokeRestart("muffle_cran_snapshot") expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.95) error = handle_error, interrupt = handle_interrupt) })
33: 30: doTryCatch(return(expr), name, parentenv, handler)eval(code, test_env)
34: 31: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(code, test_env)
35: 32: 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 } else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() skip(paste0("{", e$package, "} is not installed.")) } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")33: }, skip = handle_skip, warning = handle_warning, message = handle_message, doTryCatch(return(expr), name, parentenv, handler) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
34: 37: tryCatchOne(expr, names, parentenv, handlers[[1L]])doWithOneRestart(return(expr), restart)
35: 38: tryCatchList(expr, classes, parentenv, handlers)withOneRestart(expr, restarts[[1L]])
36: 39: tryCatch(withCallingHandlers({withRestarts(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_fatal), error = handle_error, interrupt = handle_interrupt), error = handle_fatal) end_test = function() {
})37:
doWithOneRestart(return(expr), restart)40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 38: StopReporter$new())withOneRestart(expr, restarts[[1L]])
41: 39: source_file(path, env = env(env), desc = desc, shuffle = shuffle, withRestarts(tryCatch(withCallingHandlers({ error_call = error_call) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations42: if (snapshot_skipped) {FUN(X[[i]], ...) skip("On CRAN")
}43: else if (!new_expectations && skip_on_empty) {lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, skip_empty() error_call = error_call) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {44: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
}}, snapshot_on_cran = function(cnd) {45: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 46: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), tryCatchList(expr, classes, parentenv, handlers) end_test = function() {
})47:
tryCatch(code, testthat_abort_reporter = function(cnd) {40: cat(conditionMessage(cnd), "\n")test_code(code = exprs, env = env, reporter = get_reporter() %||% NULL StopReporter$new())})
48: 41: with_reporter(reporters$multi, lapply(test_paths, test_one_file, source_file(path, env = env(env), desc = desc, shuffle = shuffle, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) error_call = error_call)
49: 42: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, FUN(X[[i]], ...) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 43: error_call = error_call)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 44: reporter = reporter, load_helpers = load_helpers, env = env, doTryCatch(return(expr), name, parentenv, handler) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])51:
test_dir("testthat", package = package, reporter = reporter, 46: ..., load_package = "installed")tryCatchList(expr, classes, parentenv, handlers)
52: 47: test_check("missSBM")tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")An irrecoverable exception occurred. R is aborting now ...
NULL})
48: with_reporter(reporters$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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