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Last updated on 2026-11-13 17:51:52 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 74.27 | 371.31 | 445.58 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 58.86 | 260.29 | 319.15 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 60.00 | 254.27 | 314.27 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 257.44 | 321.44 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 422.00 | 513.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 80.59 | 359.22 | 439.81 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 78.58 | 329.18 | 407.76 | 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 | 99.00 | 414.00 | 513.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | ERROR | ||||
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 117.00 | 542.00 | 659.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [38s/31s]
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]])
Traceback:
23: 1: tryCatchList(expr, classes, parentenv, handlers)dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE)24:
tryCatch(withCallingHandlers({ 2: eval(code, test_env)FUN(X[[i]], ...) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { 3: skip("On CRAN")lapply(X = S, FUN = FUN, ...) }
else if (!new_expectations && skip_on_empty) { 4: skip_empty()doTryCatch(return(expr), name, parentenv, handler) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { 5: if (on_cran()) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip(paste0("{", e$package, "} is not installed."))
} 6: }, snapshot_on_cran = function(cnd) {tryCatchList(expr, classes, parentenv, handlers) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 7: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatch(expr, error = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) call <- conditionCall(e)
if (!is.null(call)) {25: if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)doWithOneRestart(return(expr), restart) dcall <- deparse(call, nlines = 1L)
26: prefix <- paste("Error in", dcall, ": ")withOneRestart(expr, restarts[[1L]]) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]27: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")withRestarts(tryCatch(withCallingHandlers({ if (is.na(w)) eval(code, test_env) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], new_expectations <- the$test_expectations > starting_expectations type = "b") if (snapshot_skipped) { if (w > LONG) skip("On CRAN") } prefix <- paste0(prefix, "\n ") else if (!new_expectations && skip_on_empty) { } skip_empty() else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n")}, expectation = handle_expectation, packageNotFoundError = function(e) { .Internal(seterrmessage(msg[1L])) if (on_cran()) { if (!silent && isTRUE(getOption("show.error.messages"))) { skip(paste0("{", e$package, "} is not installed.")) cat(msg, file = outFile) } .Internal(printDeferredWarnings())}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE invisible(structure(msg, class = "try-error", condition = e)) invokeRestart("muffle_cran_snapshot")})}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 8: end_test = function() {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) })
9: 28: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))test_code(code, parent.frame())
10: 29: FUN(X[[i]], ...)test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate",
{11: sampler_undirected_cov$rNetwork(store = TRUE)lapply(seq_len(cores), inner.do) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData,
"bernoulli", FALSE, covarList = covarList_undirected)12: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, plot = FALSE)) mc.silent = TRUE) mySBM_sbm$setModel(Q)
net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, 13: covariates = covarList_undirected)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, cls <- net$clustering(1:(2 * Q)) verbose = (verbosity > 4)) cl <- cls[[Q]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, 14: clusterInit = cl, covarList = covarList_undirected).self$do_with_inits(inits, Q, reinitialization_effort) mySBM_missSBM$doVEM()
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 15: 0.05).self$estim_ascend(reinitialization_effort, changing_effort) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.8)16: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), private$BMobject$estimate() 0.01)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 17: 0.1)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam),
0.1)18: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), eval(code, test_env) 0.85)
})19:
eval(code, test_env)30:
eval(code, test_env)20:
withCallingHandlers({31: eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {32: skip("On CRAN")withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt) }
}, snapshot_on_cran = function(cnd) {21: snapshot_skipped <<- TRUEdoTryCatch(return(expr), name, parentenv, handler) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 22: error = handle_error, interrupt = handle_interrupt)tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: 23: doTryCatch(return(expr), name, parentenv, handler)tryCatchList(expr, classes, parentenv, handlers)
34: 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch(withCallingHandlers({
eval(code, test_env)35: new_expectations <- the$test_expectations > starting_expectationstryCatchList(expr, classes, parentenv, handlers) if (snapshot_skipped) {
skip("On CRAN")36: }tryCatch(withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip(paste0("{", e$package, "} is not installed."))
}}, snapshot_on_cran = function(cnd) {25: snapshot_skipped <<- TRUEdoWithOneRestart(return(expr), restart) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 26: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)withOneRestart(expr, restarts[[1L]])
37: 27: doWithOneRestart(return(expr), restart)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)38: new_expectations <- the$test_expectations > starting_expectationswithOneRestart(expr, restarts[[1L]]) if (snapshot_skipped) {
skip("On CRAN")39: }withRestarts(tryCatch(withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$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: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })test_code(code, parent.frame())
40: test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", 41: {source_file(path, env = env(env), desc = desc, shuffle = shuffle, sampler_undirected_cov$rNetwork(store = TRUE) error_call = error_call) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData,
"bernoulli", FALSE, covarList = covarList_undirected)42: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, FUN(X[[i]], ...) plot = FALSE))
mySBM_sbm$setModel(Q)43: net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, covariates = covarList_undirected) error_call = error_call) cls <- net$clustering(1:(2 * Q))
cl <- cls[[Q]]44: mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, doTryCatch(return(expr), name, parentenv, handler) clusterInit = cl, covarList = covarList_undirected)
mySBM_missSBM$doVEM()45: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 46: 0.8)tryCatchList(expr, classes, parentenv, handlers) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01)47: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), tryCatch(code, testthat_abort_reporter = function(cnd) { 0.1) cat(conditionMessage(cnd), "\n") expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), NULL 0.1)}) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships),
0.85) })
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, 30: env = env, desc = desc, shuffle = shuffle, error_call = error_call))
eval(code, test_env)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 31: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, eval(code, test_env) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 32: error_call = error_call)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)
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)
Traceback:
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 1: mc.silent = TRUE)dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4)) 2:
FUN(X[[i]], ...)14:
.self$do_with_inits(inits, Q, reinitialization_effort) 3:
lapply(X = S, FUN = FUN, ...)15:
.self$estim_ascend(reinitialization_effort, changing_effort) 4:
doTryCatch(return(expr), name, parentenv, handler)16:
private$BMobject$estimate() 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) 6:
tryCatchList(expr, classes, parentenv, handlers)18:
eval(code, test_env) 7:
tryCatch(expr, error = function(e) {19: call <- conditionCall(e)eval(code, test_env) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 20: call <- sys.call(-4L)withCallingHandlers({ dcall <- deparse(call, nlines = 1L) eval(code, test_env) prefix <- paste("Error in", dcall, ": ") new_expectations <- the$test_expectations > starting_expectations LONG <- 75L if (snapshot_skipped) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] skip("On CRAN") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } if (is.na(w)) else if (!new_expectations && skip_on_empty) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], skip_empty() type = "b") } if (w > LONG) }, expectation = handle_expectation, packageNotFoundError = function(e) { prefix <- paste0(prefix, "\n ") if (on_cran()) { } skip(paste0("{", e$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))21: })doTryCatch(return(expr), name, parentenv, handler)
8: 22: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: 23: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchList(expr, classes, parentenv, handlers)
10: 24: FUN(X[[i]], ...)tryCatch(withCallingHandlers({
eval(code, test_env)11: new_expectations <- the$test_expectations > starting_expectationslapply(seq_len(cores), inner.do) if (snapshot_skipped) {
skip("On CRAN")12: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, else if (!new_expectations && skip_on_empty) { mc.silent = TRUE) skip_empty()
}13: }, expectation = handle_expectation, packageNotFoundError = function(e) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, if (on_cran()) { verbose = (verbosity > 4)) skip(paste0("{", e$package, "} is not installed."))
}14: }, snapshot_on_cran = function(cnd) {.self$do_with_inits(inits, Q, reinitialization_effort) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")15: }, skip = handle_skip, warning = handle_warning, message = handle_message, .self$estim_ascend(reinitialization_effort, changing_effort)
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)16:
private$BMobject$estimate()25:
doWithOneRestart(return(expr), restart)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))26:
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$test_expectations > starting_expectations
if (snapshot_skipped) {20: skip("On CRAN")withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$test_expectations > starting_expectations skip_empty() if (snapshot_skipped) { } skip("On CRAN")}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) { else if (!new_expectations && skip_on_empty) { skip(paste0("{", e$package, "} is not installed.")) skip_empty() } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), 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, 28: error = handle_error, interrupt = handle_interrupt)
test_code(code, parent.frame())21:
doTryCatch(return(expr), name, parentenv, handler)29:
22: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", tryCatchOne(expr, names, parentenv, handlers[[1L]]) {
sampler_directed_cov$rNetwork(store = TRUE)23: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, tryCatchList(expr, classes, parentenv, handlers) "bernoulli", TRUE, covarList = covarList_directed)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))24: mySBM_sbm$setModel(Q)tryCatch(withCallingHandlers({ net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, eval(code, test_env) covariates = covarList_directed) new_expectations <- the$test_expectations > starting_expectations cls <- net$clustering(1:(2 * Q)) if (snapshot_skipped) { cl <- cls[[Q]] skip("On CRAN") mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, } clusterInit = cl, covarList = covarList_directed) else if (!new_expectations && skip_on_empty) { mySBM_missSBM$doVEM(trace = TRUE) skip_empty() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), } 0.1)}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), if (on_cran()) { 0.8) skip(paste0("{", e$package, "} is not installed.")) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), } 0.05)}, snapshot_on_cran = function(cnd) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), snapshot_skipped <<- TRUE 0.1) invokeRestart("muffle_cran_snapshot") expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.85) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) })
25: 30: doWithOneRestart(return(expr), restart)eval(code, test_env)
26: 31: withOneRestart(expr, restarts[[1L]])eval(code, test_env)
27: 32: withRestarts(tryCatch(withCallingHandlers({withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { else if (!new_expectations && skip_on_empty) { skip_empty() skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { 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) end_test = function() {
})33:
28: doTryCatch(return(expr), name, parentenv, handler)test_code(code, parent.frame())
34: 29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", tryCatchOne(expr, names, parentenv, handlers[[1L]]) {
sampler_directed_cov$rNetwork(store = TRUE)35: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, tryCatchList(expr, classes, parentenv, handlers) "bernoulli", TRUE, covarList = covarList_directed)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 36: plot = FALSE))tryCatch(withCallingHandlers({ mySBM_sbm$setModel(Q) eval(code, test_env) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, new_expectations <- the$test_expectations > starting_expectations covariates = covarList_directed) if (snapshot_skipped) { cls <- net$clustering(1:(2 * Q)) skip("On CRAN") cl <- cls[[Q]] } mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, else if (!new_expectations && skip_on_empty) { clusterInit = cl, covarList = covarList_directed) skip_empty() mySBM_missSBM$doVEM(trace = TRUE) } expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.1) if (on_cran()) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), skip(paste0("{", e$package, "} is not installed.")) 0.8) } expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), }, snapshot_on_cran = function(cnd) { 0.05) snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), invokeRestart("muffle_cran_snapshot") 0.1)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 0.85)
})37:
doWithOneRestart(return(expr), restart)30:
eval(code, test_env)38:
withOneRestart(expr, restarts[[1L]])31:
eval(code, test_env)39:
withRestarts(tryCatch(withCallingHandlers({32: eval(code, test_env)withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty()}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip(paste0("{", e$package, "} is not installed.")) if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, snapshot_on_cran = function(cnd) { invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, skip = handle_skip, warning = handle_warning, message = handle_message, end_test = function() { error = handle_error, interrupt = handle_interrupt) })
33: 40: doTryCatch(return(expr), name, parentenv, handler)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 35: error_call = error_call)tryCatchList(expr, classes, parentenv, handlers)
42: FUN(X[[i]], ...)36:
tryCatch(withCallingHandlers({43: eval(code, test_env)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, new_expectations <- the$test_expectations > starting_expectations error_call = error_call) if (snapshot_skipped) {
skip("On CRAN")44: }doTryCatch(return(expr), name, parentenv, handler) else if (!new_expectations && skip_on_empty) {
skip_empty()45: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {46: skip(paste0("{", e$package, "} is not installed."))tryCatchList(expr, classes, parentenv, handlers) }
}, snapshot_on_cran = function(cnd) {47: snapshot_skipped <<- TRUEtryCatch(code, testthat_abort_reporter = function(cnd) { invokeRestart("muffle_cran_snapshot") cat(conditionMessage(cnd), "\n")}, skip = handle_skip, warning = handle_warning, message = handle_message, NULL error = handle_error, interrupt = handle_interrupt), error = handle_fatal)})
37: 48: doWithOneRestart(return(expr), restart)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))38:
withOneRestart(expr, restarts[[1L]])49:
test_files_serial(test_dir = test_dir, test_package = test_package, 39: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, withRestarts(tryCatch(withCallingHandlers({ env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, eval(code, test_env) desc = desc, load_package = load_package, shuffle = shuffle, new_expectations <- the$test_expectations > starting_expectations error_call = error_call) if (snapshot_skipped) {
skip("On CRAN")50: }test_files(test_dir = path, test_paths = test_paths, test_package = package, else if (!new_expectations && skip_on_empty) { reporter = reporter, load_helpers = load_helpers, env = env, skip_empty() stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } load_package = load_package, parallel = parallel, shuffle = shuffle)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {51: skip(paste0("{", e$package, "} is not installed."))test_dir("testthat", package = package, reporter = reporter, } ..., load_package = "installed")}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE52: invokeRestart("muffle_cran_snapshot")test_check("missSBM")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), An irrecoverable exception occurred. R is aborting now ...
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:
Traceback:
doWithOneRestart(return(expr), restart) 1:
dispatcher(membership_name, membership_init$to_cc(), model_name, 26: .self$network_to_cc(), TRUE)withOneRestart(expr, restarts[[1L]])
2: 27: FUN(X[[i]], ...)withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations 3: if (snapshot_skipped) {lapply(X = S, FUN = FUN, ...) skip("On CRAN")
} 4: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler) skip_empty()
} 5: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 6: }tryCatchList(expr, classes, parentenv, handlers)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE 7: invokeRestart("muffle_cran_snapshot")tryCatch(expr, error = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, call <- conditionCall(e) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) end_test = function() { call <- sys.call(-4L) }) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")28: LONG <- 75Ltest_code(code, parent.frame()) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")29: if (is.na(w)) test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], { type = "b") sampler_undirected_nocov$rNetwork(store = TRUE) if (w > LONG) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, prefix <- paste0(prefix, "\n ") "bernoulli", FALSE) } mySBM_sbm$optimize(estimOptions = list(verbosity = 0, else prefix <- "Error : " plot = FALSE)) msg <- paste0(prefix, conditionMessage(e), "\n") mySBM_sbm$setModel(3) .Internal(seterrmessage(msg[1L])) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) if (!silent && isTRUE(getOption("show.error.messages"))) { cl <- net$clustering(3)[[1]] cat(msg, file = outFile) mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl) .Internal(printDeferredWarnings()) mySBM_missSBM$doVEM() } expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), invisible(structure(msg, class = "try-error", condition = e)) 0.05)}) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.95) 8: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 0.01)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 9: 0.05)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships),
0.95)10: })FUN(X[[i]], ...)
30: 11: eval(code, test_env)lapply(seq_len(cores), inner.do)
12: 31: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, eval(code, test_env) mc.silent = TRUE)
32: 13: withCallingHandlers({parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations verbose = (verbosity > 4)) if (snapshot_skipped) {
skip("On CRAN")14: }.self$do_with_inits(inits, Q, reinitialization_effort) else if (!new_expectations && skip_on_empty) {
skip_empty()15: }}, expectation = handle_expectation, packageNotFoundError = function(e) {.self$estim_ascend(reinitialization_effort, changing_effort) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))16: }private$BMobject$estimate()}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE17: invokeRestart("muffle_cran_snapshot")mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)18:
eval(code, test_env)33:
doTryCatch(return(expr), name, parentenv, handler)19:
eval(code, test_env)34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])20:
withCallingHandlers({35: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {36: skip("On CRAN")tryCatch(withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$test_expectations > starting_expectations skip_empty() if (snapshot_skipped) { } skip("On CRAN")}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) { else if (!new_expectations && skip_on_empty) { skip(paste0("{", e$package, "} is not installed.")) skip_empty() } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE21: invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])37:
23: doWithOneRestart(return(expr), restart)tryCatchList(expr, classes, parentenv, handlers)
24: 38: tryCatch(withCallingHandlers({withOneRestart(expr, restarts[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations39: withRestarts(tryCatch(withCallingHandlers({ if (snapshot_skipped) { skip("On CRAN") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() skip(paste0("{", e$package, "} is not installed.")) }}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$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")25: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), doWithOneRestart(return(expr), restart) end_test = function() {
})26:
withOneRestart(expr, restarts[[1L]])40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 27: StopReporter$new())withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, new_expectations <- the$test_expectations > starting_expectations error_call = error_call) if (snapshot_skipped) { skip("On CRAN")
} else if (!new_expectations && skip_on_empty) {42: skip_empty()FUN(X[[i]], ...) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {43: skip(paste0("{", e$package, "} is not installed."))lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, }}, snapshot_on_cran = function(cnd) { error_call = error_call) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")44: }, skip = handle_skip, warning = handle_warning, message = handle_message, doTryCatch(return(expr), name, parentenv, handler) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
45: end_test = function() {tryCatchOne(expr, names, parentenv, handlers[[1L]]) })
46: 28: test_code(code, parent.frame())tryCatchList(expr, classes, parentenv, handlers)
29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", 47: { sampler_undirected_nocov$rNetwork(store = TRUE)tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, NULL "bernoulli", FALSE)}) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))48: mySBM_sbm$setModel(3)with_reporter(reporters$multi, lapply(test_paths, test_one_file, net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) env = env, desc = desc, shuffle = shuffle, error_call = error_call)) cl <- net$clustering(3)[[1]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl)49: mySBM_missSBM$doVEM()test_files_serial(test_dir = test_dir, test_package = test_package, expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 0.95) desc = desc, load_package = load_package, shuffle = shuffle, expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), error_call = error_call) 0.01)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 50: 0.05)test_files(test_dir = path, test_paths = test_paths, test_package = package, expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), reporter = reporter, load_helpers = load_helpers, env = env, 0.95) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }) load_package = load_package, parallel = parallel, shuffle = shuffle)
51: 30: test_dir("testthat", package = package, reporter = reporter, eval(code, test_env) ..., load_package = "installed")
31: 52: eval(code, test_env)test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
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)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", { sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.2) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
Traceback:
1: end_test = function() {dispatcher(membership_name, membership_init$to_cc(), model_name, }) .self$network_to_cc(), TRUE)
40: 2: test_code(code = exprs, env = env, reporter = get_reporter() %||% FUN(X[[i]], ...) StopReporter$new())
3: 41: lapply(X = S, FUN = FUN, ...)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call) 4:
doTryCatch(return(expr), name, parentenv, handler)42:
FUN(X[[i]], ...) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) 6:
tryCatchList(expr, classes, parentenv, handlers)44:
doTryCatch(return(expr), name, parentenv, handler) 7:
tryCatch(expr, error = function(e) { call <- conditionCall(e)45: if (!is.null(call)) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)46: dcall <- deparse(call, nlines = 1L)tryCatchList(expr, classes, parentenv, handlers) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L47: sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatch(code, testthat_abort_reporter = function(cnd) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") cat(conditionMessage(cnd), "\n") if (is.na(w)) NULL w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }) type = "b")
if (w > LONG) 48: prefix <- paste0(prefix, "\n ")with_reporter(reporters$multi, lapply(test_paths, test_one_file, } env = env, desc = desc, shuffle = shuffle, error_call = error_call)) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")49: .Internal(seterrmessage(msg[1L]))test_files_serial(test_dir = test_dir, test_package = test_package, if (!silent && isTRUE(getOption("show.error.messages"))) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, cat(msg, file = outFile) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, .Internal(printDeferredWarnings()) desc = desc, load_package = load_package, shuffle = shuffle, } error_call = error_call) invisible(structure(msg, class = "try-error", condition = e))
})50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 8: reporter = reporter, load_helpers = load_helpers, env = env, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))51:
test_dir("testthat", package = package, reporter = reporter, 10: ..., load_package = "installed")FUN(X[[i]], ...)
52: 11: test_check("missSBM")lapply(seq_len(cores), inner.do)
An irrecoverable exception occurred. R is aborting now ...
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", { sampler_directed_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 0.1) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.2) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-without-covariate-44.R
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-explore-block-count.R:4:3',
'test-missSBM_collection-degenerate.R:80:3',
'test-missSBM_collection-estimate_chain.R:64:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-sbm-bernoulli-with-covariates.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-with-covariates.R:46:3'): SimpleSBM_fit 'Bernoulli' model, directed, one covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-with-covariates.R:46:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:16:3'): SimpleSBM_fit 'Bernoulli' model, undirected, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:16:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
── Error ('test-sbm-bernoulli-without-covariate.R:44:3'): SimpleSBM_fit 'Bernoulli' model, directed, no covariate ──
Error: invalid assignment for reference class field 'Z', should be from class "matrix" or a subclass (was class "NULL")
Backtrace:
▆
1. ├─mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) at test-sbm-bernoulli-without-covariate.R:44:3
2. │ └─private$BMobject$estimate()
3. │ └─.self$estim_ascend(reinitialization_effort, changing_effort)
4. │ └─.self$do_with_inits(inits, Q, reinitialization_effort)
5. │ └─base::sapply(...)
6. │ └─base::lapply(X = X, FUN = FUN, ...)
7. │ └─blockmodels (local) FUN(X[[i]], ...)
8. │ └─getRefClass(membership_name)(from_cc = r$membership)
9. │ └─methods::new(`<chr>`, ...)
10. │ ├─methods::initialize(value, ...)
11. │ └─methods::initialize(value, ...)
12. │ └─.Object$initialize(...)
13. └─blockmodels (local) `<dfltBndF>`(base::quote(NULL))
14. └─methods:::.setDummyField(...)
[ FAIL 4 | WARN 4 | SKIP 3 | PASS 531 ]
Error:
! Test failures.
Execution halted
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