Last updated on 2026-10-21 07:54:46 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 80.98 | 341.84 | 422.82 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 59.05 | 240.46 | 299.51 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 57.00 | 247.35 | 304.35 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 237.71 | 301.71 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 420.00 | 511.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 85.58 | 342.08 | 427.66 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 86.79 | 329.37 | 416.16 | OK | |
| r-release-macos-arm64 | 1.1.0 | 17.00 | 92.00 | 109.00 | OK | |
| r-release-macos-x86_64 | 1.1.0 | 59.00 | 456.00 | 515.00 | OK | |
| r-release-windows-x86_64 | 1.1.0 | 93.00 | 345.00 | 438.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 20.00 | 91.00 | 111.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 121.00 | 474.00 | 595.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [40s/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
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iteration #: 13
iteration #: 14
iteration #: 15
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iteration #: 17
iteration #: 18
iteration #: 19
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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))
Traceback:
mySBM_sbm$setModel(Q) 1: net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, dispatcher(membership_name, membership_init$to_cc(), model_name, covariates = covarList_undirected) .self$network_to_cc(), TRUE) cls <- net$clustering(1:(2 * Q))
cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, 2: clusterInit = cl, covarList = covarList_undirected)FUN(X[[i]], ...) mySBM_missSBM$doVEM()
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 3: 0.05)lapply(X = S, FUN = FUN, ...) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
4: 0.8)doTryCatch(return(expr), name, parentenv, handler) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01) 5: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam),
0.1) 6: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), tryCatchList(expr, classes, parentenv, handlers) 0.85)
}) 7:
tryCatch(expr, error = function(e) {30: call <- conditionCall(e)eval(code, test_env)
if (!is.null(call)) {31: eval(code, test_env) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)32: dcall <- deparse(call, nlines = 1L)withCallingHandlers({ prefix <- paste("Error in", dcall, ": ") eval(code, test_env) LONG <- 75L new_expectations <- the$test_expectations > starting_expectations sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (snapshot_skipped) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") skip("On CRAN") if (is.na(w)) } else if (!new_expectations && skip_on_empty) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], skip_empty() type = "b") } if (w > LONG) }, expectation = handle_expectation, packageNotFoundError = function(e) { prefix <- paste0(prefix, "\n ") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n")}, snapshot_on_cran = function(cnd) { .Internal(seterrmessage(msg[1L])) snapshot_skipped <<- TRUE if (!silent && isTRUE(getOption("show.error.messages"))) { invokeRestart("muffle_cran_snapshot") cat(msg, file = outFile)}, skip = handle_skip, warning = handle_warning, message = handle_message, .Internal(printDeferredWarnings()) error = handle_error, interrupt = handle_interrupt) }
invisible(structure(msg, class = "try-error", condition = e))33: })doTryCatch(return(expr), name, parentenv, handler)
8: 34: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: 35: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchList(expr, classes, parentenv, handlers)
10: 36: FUN(X[[i]], ...)tryCatch(withCallingHandlers({
eval(code, test_env)11: new_expectations <- the$test_expectations > starting_expectationslapply(seq_len(cores), inner.do) if (snapshot_skipped) {
skip("On CRAN")12: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, else if (!new_expectations && skip_on_empty) { mc.silent = TRUE) skip_empty()
}}, expectation = handle_expectation, packageNotFoundError = function(e) {13: if (on_cran()) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, skip(paste0("{", e$package, "} is not installed.")) verbose = (verbosity > 4)) }
}, snapshot_on_cran = function(cnd) {14: snapshot_skipped <<- TRUE.self$do_with_inits(inits, Q, reinitialization_effort) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 15: .self$estim_ascend(reinitialization_effort, changing_effort) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
16: 37: private$BMobject$estimate()doWithOneRestart(return(expr), restart)
17: 38: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))withOneRestart(expr, restarts[[1L]])
18:
eval(code, test_env)
39: 19: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {20: skip("On CRAN")withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) { skip(paste0("{", e$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) { end_test = function() { 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$new())21:
doTryCatch(return(expr), name, parentenv, handler)41: source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])42:
FUN(X[[i]], ...)23:
tryCatchList(expr, classes, parentenv, handlers)43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 24: error_call = error_call)tryCatch(withCallingHandlers({
eval(code, test_env)44: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
skip("On CRAN")45: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()46: }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {47: skip(paste0("{", e$package, "} is not installed."))tryCatch(code, testthat_abort_reporter = function(cnd) { } cat(conditionMessage(cnd), "\n")}, snapshot_on_cran = function(cnd) { NULL snapshot_skipped <<- TRUE}) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 48: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))25:
doWithOneRestart(return(expr), restart)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 26: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, withOneRestart(expr, restarts[[1L]]) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 27: error_call = error_call)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)50: new_expectations <- the$test_expectations > starting_expectationstest_files(test_dir = path, test_paths = test_paths, test_package = package, if (snapshot_skipped) { reporter = reporter, load_helpers = load_helpers, env = env, skip("On CRAN") stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } load_package = load_package, parallel = parallel, shuffle = shuffle) else if (!new_expectations && skip_on_empty) {
skip_empty()51: }test_dir("testthat", package = package, reporter = reporter, }, expectation = handle_expectation, packageNotFoundError = function(e) { ..., load_package = "installed") if (on_cran()) {
skip(paste0("{", e$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() { })
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$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$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$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) {
Traceback:
skip_empty() 1: }dispatcher(membership_name, membership_init$to_cc(), model_name, }, expectation = handle_expectation, packageNotFoundError = function(e) { .self$network_to_cc(), TRUE) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 2: }FUN(X[[i]], ...)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE 3: lapply(X = S, FUN = FUN, ...) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 4: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)doTryCatch(return(expr), name, parentenv, handler)
25: 5: doWithOneRestart(return(expr), restart)tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: 6: withOneRestart(expr, restarts[[1L]])tryCatchList(expr, classes, parentenv, handlers)
27: 7: withRestarts(tryCatch(withCallingHandlers({tryCatch(expr, error = function(e) { eval(code, test_env) call <- conditionCall(e) new_expectations <- the$test_expectations > starting_expectations if (!is.null(call)) { if (snapshot_skipped) { if (identical(call[[1L]], quote(doTryCatch))) skip("On CRAN") call <- sys.call(-4L) } dcall <- deparse(call, nlines = 1L) else if (!new_expectations && skip_on_empty) { prefix <- paste("Error in", dcall, ": ") skip_empty() LONG <- 75L } sm <- strsplit(conditionMessage(e), "\n")[[1L]]}, expectation = handle_expectation, packageNotFoundError = function(e) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (on_cran()) { if (is.na(w)) skip(paste0("{", e$package, "} is not installed.")) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b")}, snapshot_on_cran = function(cnd) { if (w > LONG) snapshot_skipped <<- TRUE prefix <- paste0(prefix, "\n ") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else prefix <- "Error : " error = handle_error, interrupt = handle_interrupt), error = handle_fatal), msg <- paste0(prefix, conditionMessage(e), "\n") end_test = function() { .Internal(seterrmessage(msg[1L])) }) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)28: .Internal(printDeferredWarnings())test_code(code, parent.frame()) }
invisible(structure(msg, class = "try-error", condition = e))29: })test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate",
{ 8: sampler_directed_cov$rNetwork(store = TRUE)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData,
"bernoulli", TRUE, covarList = covarList_directed) 9: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) plot = FALSE)) mySBM_sbm$setModel(Q)
net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, 10: covariates = covarList_directed)FUN(X[[i]], ...) cls <- net$clustering(1:(2 * Q))
cl <- cls[[Q]]11: mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, lapply(seq_len(cores), inner.do) clusterInit = cl, covarList = covarList_directed)
mySBM_missSBM$doVEM(trace = TRUE)12: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 0.1) mc.silent = TRUE) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.8)13: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 0.05) verbose = (verbosity > 4)) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean),
0.1)14: expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), .self$do_with_inits(inits, Q, reinitialization_effort) 0.85)
})15:
.self$estim_ascend(reinitialization_effort, changing_effort)30:
eval(code, test_env)16:
private$BMobject$estimate()31:
eval(code, test_env)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))32:
withCallingHandlers({18: eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {19: skip("On CRAN")eval(code, test_env) }
else if (!new_expectations && skip_on_empty) {20: skip_empty()withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { new_expectations <- the$test_expectations > starting_expectations if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {33: skip(paste0("{", e$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) {34: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)35:
tryCatchList(expr, classes, parentenv, handlers)21:
doTryCatch(return(expr), name, parentenv, handler)36:
tryCatch(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$package, "} is not installed.")) skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))37: }doWithOneRestart(return(expr), restart)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE38: invokeRestart("muffle_cran_snapshot")withOneRestart(expr, restarts[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)39:
withRestarts(tryCatch(withCallingHandlers({25: eval(code, test_env)doWithOneRestart(return(expr), restart) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {26: withOneRestart(expr, restarts[[1L]]) skip("On CRAN")
}27: else if (!new_expectations && skip_on_empty) {withRestarts(tryCatch(withCallingHandlers({ skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip(paste0("{", e$package, "} is not installed.")) end_test = function() { }}, snapshot_on_cran = function(cnd) { }) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")40: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_code(code = exprs, env = env, reporter = get_reporter() %||% error = handle_error, interrupt = handle_interrupt), error = handle_fatal), StopReporter$new()) end_test = function() {
})41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 28: error_call = error_call)test_code(code, parent.frame())
42: 29: FUN(X[[i]], ...)test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate",
{43: sampler_directed_cov$rNetwork(store = TRUE)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, error_call = error_call) "bernoulli", TRUE, covarList = covarList_directed)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 44: plot = FALSE))doTryCatch(return(expr), name, parentenv, handler) mySBM_sbm$setModel(Q)
net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, 45: covariates = covarList_directed)tryCatchOne(expr, names, parentenv, handlers[[1L]]) cls <- net$clustering(1:(2 * Q))
cl <- cls[[Q]]46: mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, tryCatchList(expr, classes, parentenv, handlers) clusterInit = cl, covarList = covarList_directed)
mySBM_missSBM$doVEM(trace = TRUE)47: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), tryCatch(code, testthat_abort_reporter = function(cnd) { 0.1) cat(conditionMessage(cnd), "\n") expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), NULL 0.8)}) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.05)48: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), with_reporter(reporters$multi, lapply(test_paths, test_one_file, 0.1) env = env, desc = desc, shuffle = shuffle, error_call = error_call)) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships),
49: test_files_serial(test_dir = test_dir, test_package = test_package, 0.85) }) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 30: desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)eval(code, test_env)
50: 31: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, eval(code, test_env) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)32: withCallingHandlers({
eval(code, test_env)51: new_expectations <- the$test_expectations > starting_expectationstest_dir("testthat", package = package, reporter = reporter, if (snapshot_skipped) { ..., load_package = "installed") skip("On CRAN")
52: }test_check("missSBM") else if (!new_expectations && skip_on_empty) {
skip_empty()An irrecoverable exception occurred. R is aborting now ...
}}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1:
Traceback:
dispatcher(membership_name, membership_init$to_cc(), model_name, 1: .self$network_to_cc(), TRUE)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE) 2:
FUN(X[[i]], ...) 2:
FUN(X[[i]], ...) 3:
lapply(X = S, FUN = FUN, ...) 3:
lapply(X = S, FUN = FUN, ...) 4:
doTryCatch(return(expr), name, parentenv, handler) 4:
doTryCatch(return(expr), name, parentenv, handler) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
6: 7: tryCatchList(expr, classes, parentenv, handlers)tryCatch(expr, error = function(e) {
call <- conditionCall(e) 7: if (!is.null(call)) {tryCatch(expr, error = function(e) { if (identical(call[[1L]], quote(doTryCatch))) call <- conditionCall(e) if (!is.null(call)) { call <- sys.call(-4L) if (identical(call[[1L]], quote(doTryCatch))) dcall <- deparse(call, nlines = 1L) call <- sys.call(-4L) prefix <- paste("Error in", dcall, ": ") dcall <- deparse(call, nlines = 1L) LONG <- 75L prefix <- paste("Error in", dcall, ": ") sm <- strsplit(conditionMessage(e), "\n")[[1L]] LONG <- 75L w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (is.na(w)) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (is.na(w)) type = "b") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (w > LONG) type = "b") prefix <- paste0(prefix, "\n ") if (w > LONG) } prefix <- paste0(prefix, "\n ") else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n") else prefix <- "Error : " .Internal(seterrmessage(msg[1L])) msg <- paste0(prefix, conditionMessage(e), "\n") if (!silent && isTRUE(getOption("show.error.messages"))) { .Internal(seterrmessage(msg[1L])) cat(msg, file = outFile) if (!silent && isTRUE(getOption("show.error.messages"))) { .Internal(printDeferredWarnings()) cat(msg, file = outFile) } .Internal(printDeferredWarnings()) invisible(structure(msg, class = "try-error", condition = e)) }}) invisible(structure(msg, class = "try-error", condition = e))
}) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: 10: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...)
10: 11: FUN(X[[i]], ...)lapply(seq_len(cores), inner.do)
11: 12: lapply(seq_len(cores), inner.do)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: mc.silent = TRUE)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 14: verbose = (verbosity > 4)).self$do_with_inits(inits, Q, reinitialization_effort)
14: 15: .self$do_with_inits(inits, Q, reinitialization_effort).self$estim_ascend(reinitialization_effort, changing_effort)
15: 16: .self$estim_ascend(reinitialization_effort, changing_effort)private$BMobject$estimate()
16: 17: private$BMobject$estimate()mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
17: 18: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))eval(code, test_env)
18: 19: eval(code, test_env)eval(code, test_env)
19: 20: eval(code, test_env)withCallingHandlers({
eval(code, test_env)20: new_expectations <- the$test_expectations > starting_expectationswithCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, 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) {}, skip = handle_skip, warning = handle_warning, message = handle_message, snapshot_skipped <<- TRUE error = handle_error, interrupt = handle_interrupt) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 21: error = handle_error, interrupt = handle_interrupt)doTryCatch(return(expr), name, parentenv, handler)
21: 22: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
23: 24: tryCatchList(expr, classes, parentenv, handlers)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() } } 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) {}, skip = handle_skip, warning = handle_warning, message = handle_message, snapshot_skipped <<- TRUE error = handle_error, interrupt = handle_interrupt), error = handle_fatal) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 25: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
doWithOneRestart(return(expr), restart)25:
doWithOneRestart(return(expr), restart)26:
withOneRestart(expr, restarts[[1L]])26:
withOneRestart(expr, restarts[[1L]])27:
withRestarts(tryCatch(withCallingHandlers({27: eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { 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() { end_test = function() { }) })
28: 28: test_code(code, parent.frame())test_code(code, parent.frame())
29: 29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", { { sampler_undirected_nocov$rNetwork(store = TRUE) sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) plot = FALSE)) mySBM_sbm$setModel(3) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) cl <- net$clustering(3)[[1]] cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl) clusterInit = cl) 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), 0.95) 0.95) 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_nocov$connectParam$mean), expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 0.05) 0.05) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.95) 0.95) }) })
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) 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)
33: 33: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
34: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: 35: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
36: 36: tryCatch(withCallingHandlers({tryCatch(withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { else if (!new_expectations && skip_on_empty) { skip_empty() skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: 37: doWithOneRestart(return(expr), restart)doWithOneRestart(return(expr), restart)
38: 38: withOneRestart(expr, restarts[[1L]])withOneRestart(expr, restarts[[1L]])
39: 39: withRestarts(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() { end_test = function() { }) })
40: 40: test_code(code = exprs, env = env, reporter = get_reporter() %||% test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) StopReporter$new())
41: 41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) error_call = error_call)
42: 42: FUN(X[[i]], ...)FUN(X[[i]], ...)
43: 43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) error_call = error_call)
44: 44: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
45: 45: tryCatchOne(expr, names, parentenv, handlers[[1L]])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, test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") ..., load_package = "installed")
52: 52: test_check("missSBM")test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
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$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
Traceback:
14: 1: .self$do_with_inits(inits, Q, reinitialization_effort)dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
15: 2: .self$estim_ascend(reinitialization_effort, changing_effort)FUN(X[[i]], ...)
16:
private$BMobject$estimate() 3:
17: lapply(X = S, FUN = FUN, ...)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env) 4: doTryCatch(return(expr), name, parentenv, handler)
19:
eval(code, test_env) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])20:
withCallingHandlers({ eval(code, test_env) 6: new_expectations <- the$test_expectations > starting_expectationstryCatchList(expr, classes, parentenv, handlers) if (snapshot_skipped) {
7: skip("On CRAN")tryCatch(expr, error = function(e) { } else if (!new_expectations && skip_on_empty) { call <- conditionCall(e) skip_empty() if (!is.null(call)) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (identical(call[[1L]], quote(doTryCatch))) if (on_cran()) { call <- sys.call(-4L) skip(paste0("{", e$package, "} is not installed.")) dcall <- deparse(call, nlines = 1L) } prefix <- paste("Error in", dcall, ": ")}, snapshot_on_cran = function(cnd) { LONG <- 75L snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") sm <- strsplit(conditionMessage(e), "\n")[[1L]]}, skip = handle_skip, warning = handle_warning, message = handle_message, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") error = handle_error, interrupt = handle_interrupt) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")21: if (w > LONG) doTryCatch(return(expr), name, parentenv, handler) prefix <- paste0(prefix, "\n ") }
22: else prefix <- "Error : "tryCatchOne(expr, names, parentenv, handlers[[1L]]) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))23: if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)tryCatchList(expr, classes, parentenv, handlers) .Internal(printDeferredWarnings())
24: }tryCatch(withCallingHandlers({ invisible(structure(msg, class = "try-error", condition = e)) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations}) if (snapshot_skipped) {
skip("On CRAN") 8: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) else if (!new_expectations && skip_on_empty) {
skip_empty() 9: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {10: skip(paste0("{", e$package, "} is not installed.")) }FUN(X[[i]], ...)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE11: invokeRestart("muffle_cran_snapshot")lapply(seq_len(cores), inner.do)}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
12: 25: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, doWithOneRestart(return(expr), restart) mc.silent = TRUE)
26: withOneRestart(expr, restarts[[1L]])13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 27: withRestarts(tryCatch(withCallingHandlers({ verbose = (verbosity > 4)) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {14: skip("On CRAN").self$do_with_inits(inits, Q, reinitialization_effort) } else if (!new_expectations && skip_on_empty) {
skip_empty()15: }.self$estim_ascend(reinitialization_effort, changing_effort)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {16: skip(paste0("{", e$package, "} is not installed.")) }private$BMobject$estimate()}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE17: invokeRestart("muffle_cran_snapshot")mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 18: end_test = function() {eval(code, test_env) })
19: 28: test_code(code, parent.frame())eval(code, test_env)
29: 20: withCallingHandlers({test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", eval(code, test_env) { new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { sampler_directed_nocov$rNetwork(store = TRUE) skip("On CRAN") mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, } "bernoulli", TRUE) else if (!new_expectations && skip_on_empty) { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, skip_empty() } plot = FALSE)) mySBM_sbm$setModel(3)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) skip(paste0("{", e$package, "} is not installed.")) cl <- net$clustering(3)[[1]] } mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE clusterInit = cl) invokeRestart("muffle_cran_snapshot") mySBM_missSBM$doVEM()}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), error = handle_error, interrupt = handle_interrupt) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 21: 0.95)doTryCatch(return(expr), name, parentenv, handler) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)22: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam),
0.2)23: expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), tryCatchList(expr, classes, parentenv, handlers) 0.95)
})24:
tryCatch(withCallingHandlers({30: eval(code, test_env) eval(code, test_env)
new_expectations <- the$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) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, snapshot_on_cran = function(cnd) {25: snapshot_skipped <<- TRUEdoWithOneRestart(return(expr), restart) invokeRestart("muffle_cran_snapshot")
26: }, skip = handle_skip, warning = handle_warning, message = handle_message, withOneRestart(expr, restarts[[1L]]) error = handle_error, interrupt = handle_interrupt)
27: 33: withRestarts(tryCatch(withCallingHandlers({doTryCatch(return(expr), name, parentenv, handler)
eval(code, test_env)34: new_expectations <- the$test_expectations > starting_expectationstryCatchOne(expr, names, parentenv, handlers[[1L]]) if (snapshot_skipped) { skip("On CRAN") }
else if (!new_expectations && skip_on_empty) {35: skip_empty()tryCatchList(expr, classes, parentenv, handlers) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {36: if (on_cran()) {tryCatch(withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() {}, expectation = handle_expectation, packageNotFoundError = function(e) { }) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))28: }test_code(code, parent.frame())}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE29: invokeRestart("muffle_cran_snapshot")test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", }, skip = handle_skip, warning = handle_warning, message = handle_message, { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) sampler_directed_nocov$rNetwork(store = TRUE)
mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, 37: "bernoulli", TRUE)doWithOneRestart(return(expr), restart) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))38: mySBM_sbm$setModel(3)withOneRestart(expr, restarts[[1L]]) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)
cl <- net$clustering(3)[[1]]39: mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, withRestarts(tryCatch(withCallingHandlers({ clusterInit = cl) eval(code, test_env) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), new_expectations <- the$test_expectations > starting_expectations 0.1) if (snapshot_skipped) { skip("On CRAN") expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), } 0.95) else if (!new_expectations && skip_on_empty) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), skip_empty() 0.01) } expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.1) if (on_cran()) { expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), skip(paste0("{", e$package, "} is not installed.")) 0.2) } expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), }, snapshot_on_cran = function(cnd) { 0.95) snapshot_skipped <<- TRUE }) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 30: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), eval(code, test_env) end_test = function() {
})31:
eval(code, test_env)40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 32: StopReporter$new())withCallingHandlers({
eval(code, test_env)41: new_expectations <- the$test_expectations > starting_expectationssource_file(path, env = env(env), desc = desc, shuffle = shuffle, if (snapshot_skipped) { error_call = error_call) skip("On CRAN")
}42: else if (!new_expectations && skip_on_empty) {FUN(X[[i]], ...)
skip_empty()43: }lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, }, expectation = handle_expectation, packageNotFoundError = function(e) { error_call = error_call) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))44: doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) {45: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 46: error = handle_error, interrupt = handle_interrupt)tryCatchList(expr, classes, parentenv, handlers)
33: 47: doTryCatch(return(expr), name, parentenv, handler)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")34: NULLtryCatchOne(expr, names, parentenv, handlers[[1L]])})
35: 48: tryCatchList(expr, classes, parentenv, handlers)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))36:
tryCatch(withCallingHandlers({49: eval(code, test_env)test_files_serial(test_dir = test_dir, test_package = test_package, new_expectations <- the$test_expectations > starting_expectations test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, if (snapshot_skipped) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, skip("On CRAN") desc = desc, load_package = load_package, shuffle = shuffle, } error_call = error_call) else if (!new_expectations && skip_on_empty) {
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, skip_empty() reporter = reporter, load_helpers = load_helpers, env = env, } stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }, expectation = handle_expectation, packageNotFoundError = function(e) { load_package = load_package, parallel = parallel, shuffle = shuffle) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))51: }test_dir("testthat", package = package, reporter = reporter, }, snapshot_on_cran = function(cnd) { ..., load_package = "installed") snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, 52: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)test_check("missSBM")
37: An irrecoverable exception occurred. R is aborting now ...
doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-44.R
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-explore-block-count.R:4:3',
'test-missSBM_collection-degenerate.R:80:3',
'test-missSBM_collection-estimate_chain.R:64:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-sbm-bernoulli-with-covariates.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-with-covariates.R:46:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:46:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:44:3'): SimpleSBM_fit 'Bernoulli' model, directed, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:44:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64