Last updated on 2026-10-11 04:51:03 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 86.78 | 353.63 | 440.41 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 56.73 | 254.44 | 311.17 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 58.00 | 243.36 | 301.36 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 62.00 | 246.59 | 308.59 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 450.00 | 541.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 82.95 | 348.35 | 431.30 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 74.39 | 345.64 | 420.03 | OK | |
| r-release-macos-arm64 | 1.1.0 | 17.00 | 92.00 | 109.00 | OK | |
| r-release-macos-x86_64 | 1.1.0 | 59.00 | 456.00 | 515.00 | OK | |
| r-release-windows-x86_64 | 1.1.0 | 91.00 | 364.00 | 455.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 21.00 | 103.00 | 124.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 114.00 | 492.00 | 606.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [37s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missSBM)
>
> test_check("missSBM")
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 3 model(s).
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degreeTested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degree
sampling: dyad new better on connectivity
node
double-standard
block-node new better on mixture
Adjusting Variational EM for Stochastic Block Model
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'node' network-sampling process
Initialization of 1 model(s).
Performing VEM inference
Model with 3 blocks.
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 2 model(s).
Performing VEM inference
Model with 2 blocks.
Model with 1 blocks.
Polishing (node-swap)
Looking for better solutions
Pass 1 Going forward +
Pass 1 Going backward +
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
Traceback:
1: 7: dispatcher(membership_name, membership_init$to_cc(), model_name, tryCatch(expr, error = function(e) { .self$network_to_cc(), TRUE)
2: call <- conditionCall(e)FUN(X[[i]], ...)
if (!is.null(call)) { 3: if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)lapply(X = S, FUN = FUN, ...) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") 4: LONG <- 75LdoTryCatch(return(expr), name, parentenv, handler)
sm <- strsplit(conditionMessage(e), "\n")[[1L]] 5: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") 6: if (w > LONG) tryCatchList(expr, classes, parentenv, handlers)
prefix <- paste0(prefix, "\n ") } 7: tryCatch(expr, error = function(e) { else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) call <- conditionCall(e) if (!silent && isTRUE(getOption("show.error.messages"))) { if (!is.null(call)) { cat(msg, file = outFile) if (identical(call[[1L]], quote(doTryCatch))) .Internal(printDeferredWarnings()) call <- sys.call(-4L) } dcall <- deparse(call, nlines = 1L) invisible(structure(msg, class = "try-error", condition = e)) prefix <- paste("Error in", dcall, ": ")})
LONG <- 75L 8: sm <- strsplit(conditionMessage(e), "\n")[[1L]]try(lapply(X = S, FUN = FUN, ...), silent = TRUE) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 9: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (w > LONG) prefix <- paste0(prefix, "\n ")
}10: else prefix <- "Error : "FUN(X[[i]], ...) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))11: if (!silent && isTRUE(getOption("show.error.messages"))) {lapply(seq_len(cores), inner.do) cat(msg, file = outFile)
.Internal(printDeferredWarnings())12: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, invisible(structure(msg, class = "try-error", condition = e)) mc.silent = TRUE)})
8: 13: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
9: 14: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)).self$do_with_inits(inits, Q, reinitialization_effort)
15: 10: .self$estim_ascend(reinitialization_effort, changing_effort)FUN(X[[i]], ...)
11: 16: lapply(seq_len(cores), inner.do)private$BMobject$estimate()
12: 17: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mc.silent = TRUE)
13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 18: verbose = (verbosity > 4))eval(code, test_env)
14: 19: .self$do_with_inits(inits, Q, reinitialization_effort)eval(code, test_env)
15:
20: .self$estim_ascend(reinitialization_effort, changing_effort)withCallingHandlers({
eval(code, test_env)16: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {private$BMobject$estimate() skip("On CRAN")
} else if (!new_expectations && skip_on_empty) {17: skip_empty()mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
}}, expectation = handle_expectation, packageNotFoundError = function(e) {18: if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))eval(code, test_env) }
}, snapshot_on_cran = function(cnd) {19: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")
20: }, skip = handle_skip, warning = handle_warning, message = handle_message, withCallingHandlers({ error = handle_error, interrupt = handle_interrupt) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations21: if (snapshot_skipped) {doTryCatch(return(expr), name, parentenv, handler) skip("On CRAN")
}22: else if (!new_expectations && skip_on_empty) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip_empty()
}23: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))24: }tryCatch(withCallingHandlers({}, snapshot_on_cran = function(cnd) { eval(code, test_env) snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") } error = handle_error, interrupt = handle_interrupt) else if (!new_expectations && skip_on_empty) {
skip_empty()21: }doTryCatch(return(expr), name, parentenv, handler)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {22: skip(paste0("{", e$package, "} is not installed."))tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, snapshot_on_cran = function(cnd) {23: snapshot_skipped <<- TRUEtryCatchList(expr, classes, parentenv, handlers) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 24: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)tryCatch(withCallingHandlers({
eval(code, test_env)25: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {doWithOneRestart(return(expr), restart) skip("On CRAN")
}26: else if (!new_expectations && skip_on_empty) {withOneRestart(expr, restarts[[1L]]) skip_empty()
}27: }, expectation = handle_expectation, packageNotFoundError = function(e) {withRestarts(tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
skip("On CRAN")25: }doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()27: }withRestarts(tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, expectation = handle_expectation, packageNotFoundError = function(e) { end_test = function() { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } })}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE28: invokeRestart("muffle_cran_snapshot")test_code(code, parent.frame())}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 29: end_test = function() {test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", }) {
sampler_undirected_cov$rNetwork(store = TRUE)28: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, test_code(code, parent.frame()) "bernoulli", FALSE, covarList = covarList_undirected)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 29: plot = FALSE))test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", mySBM_sbm$setModel(Q) { net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, sampler_undirected_cov$rNetwork(store = TRUE) covariates = covarList_undirected) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, cls <- net$clustering(1:(2 * Q)) "bernoulli", FALSE, covarList = covarList_undirected) cl <- cls[[Q]] mySBM_sbm$optimize(estimOptions = list(verbosity = 0, mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, plot = FALSE)) clusterInit = cl, covarList = covarList_undirected) mySBM_sbm$setModel(Q) mySBM_missSBM$doVEM() net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), covariates = covarList_undirected) 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), cls <- net$clustering(1:(2 * Q)) 0.8) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), clusterInit = cl, covarList = covarList_undirected) 0.01) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) 0.05) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.1) 0.8) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.85) 0.01) }) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean),
0.1)30: expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), eval(code, test_env) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 31: 0.85) })eval(code, test_env)
32: 30: eval(code, test_env)withCallingHandlers({
eval(code, test_env)31: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
skip("On CRAN")32: }withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt) skip(paste0("{", e$package, "} is not installed."))
}33: }, snapshot_on_cran = function(cnd) {doTryCatch(return(expr), name, parentenv, handler)
34: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 35: error = handle_error, interrupt = handle_interrupt)tryCatchList(expr, classes, parentenv, handlers)
36: 33: tryCatch(withCallingHandlers({doTryCatch(return(expr), name, parentenv, handler) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations34: if (snapshot_skipped) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip("On CRAN")
}35: else if (!new_expectations && skip_on_empty) {tryCatchList(expr, classes, parentenv, handlers) skip_empty()
}36: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip_empty()
37: doWithOneRestart(return(expr), restart) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {38: if (on_cran()) {withOneRestart(expr, restarts[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}39: }, snapshot_on_cran = function(cnd) {withRestarts(tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip("On CRAN")
}37: else if (!new_expectations && skip_on_empty) {doWithOneRestart(return(expr), restart)
38: skip_empty()withOneRestart(expr, restarts[[1L]]) }}, expectation = handle_expectation, packageNotFoundError = function(e) {
39: withRestarts(tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }, expectation = handle_expectation, packageNotFoundError = function(e) { end_test = function() { if (on_cran()) { }) skip(paste0("{", e$package, "} is not installed.")) }
}, snapshot_on_cran = function(cnd) {40: snapshot_skipped <<- TRUEtest_code(code = exprs, env = env, reporter = get_reporter() %||% invokeRestart("muffle_cran_snapshot") StopReporter$new())}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 41: end_test = function() {source_file(path, env = env(env), desc = desc, shuffle = shuffle, }) error_call = error_call)
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% 42: FUN(X[[i]], ...) StopReporter$new())
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: 41: tryCatchOne(expr, names, parentenv, handlers[[1L]])source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)46:
tryCatchList(expr, classes, parentenv, handlers)42:
FUN(X[[i]], ...)47:
tryCatch(code, testthat_abort_reporter = function(cnd) {43: cat(conditionMessage(cnd), "\n")lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, NULL error_call = error_call)})
44: 48: doTryCatch(return(expr), name, parentenv, handler)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)49:
test_files_serial(test_dir = test_dir, test_package = test_package, 47: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, tryCatch(code, testthat_abort_reporter = function(cnd) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, cat(conditionMessage(cnd), "\n") desc = desc, load_package = load_package, shuffle = shuffle, NULL error_call = error_call)})
50:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 48: reporter = reporter, load_helpers = load_helpers, env = env, with_reporter(reporters$multi, lapply(test_paths, test_one_file, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) load_package = load_package, parallel = parallel, shuffle = shuffle)
49: 51: test_files_serial(test_dir = test_dir, test_package = test_package, test_dir("testthat", package = package, 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, desc = desc, load_package = load_package, shuffle = shuffle, ..., load_package = "installed") error_call = error_call)
52: 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, test_check("missSBM") stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)An irrecoverable exception occurred. R is aborting now ...
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty()
Traceback:
} 1: }, expectation = handle_expectation, packageNotFoundError = function(e) {dispatcher(membership_name, membership_init$to_cc(), model_name, if (on_cran()) { .self$network_to_cc(), TRUE) skip(paste0("{", e$package, "} is not installed."))
} 2: }, snapshot_on_cran = function(cnd) {FUN(X[[i]], ...) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 3: lapply(X = S, FUN = FUN, ...)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 4: end_test = function() {doTryCatch(return(expr), name, parentenv, handler)
}) 5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])28:
test_code(code, parent.frame()) 6:
tryCatchList(expr, classes, parentenv, handlers)29:
7: tryCatch(expr, error = function(e) {test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", call <- conditionCall(e) if (!is.null(call)) { { sampler_directed_cov$rNetwork(store = TRUE) if (identical(call[[1L]], quote(doTryCatch))) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, call <- sys.call(-4L) "bernoulli", TRUE, covarList = covarList_directed) dcall <- deparse(call, nlines = 1L) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) prefix <- paste("Error in", dcall, ": ") mySBM_sbm$setModel(Q) LONG <- 75L net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, sm <- strsplit(conditionMessage(e), "\n")[[1L]] covariates = covarList_directed) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") cls <- net$clustering(1:(2 * Q)) if (is.na(w)) cl <- cls[[Q]] w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") clusterInit = cl, covarList = covarList_directed) } else prefix <- "Error : " mySBM_missSBM$doVEM(trace = TRUE) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), msg <- paste0(prefix, conditionMessage(e), "\n") 0.1) .Internal(seterrmessage(msg[1L])) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), if (!silent && isTRUE(getOption("show.error.messages"))) { 0.8) cat(msg, file = outFile) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), .Internal(printDeferredWarnings()) 0.05) } expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), invisible(structure(msg, class = "try-error", condition = e)) 0.1)}) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships),
0.85) 8: })
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)30:
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))eval(code, test_env)
10: FUN(X[[i]], ...)31:
eval(code, test_env)11: lapply(seq_len(cores), inner.do)
32:
withCallingHandlers({12: eval(code, test_env)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {13: skip("On CRAN")parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, } verbose = (verbosity > 4)) else if (!new_expectations && skip_on_empty) {
skip_empty()14: .self$do_with_inits(inits, Q, reinitialization_effort) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {15: if (on_cran()) {.self$estim_ascend(reinitialization_effort, changing_effort)
16: skip(paste0("{", e$package, "} is not installed."))private$BMobject$estimate() }
}, snapshot_on_cran = function(cnd) {17: snapshot_skipped <<- TRUEmySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
18: eval(code, test_env) error = handle_error, interrupt = handle_interrupt)
19: 33: eval(code, test_env)
20: doTryCatch(return(expr), name, parentenv, handler)withCallingHandlers({
eval(code, test_env)34: new_expectations <- the$test_expectations > starting_expectationstryCatchOne(expr, names, parentenv, handlers[[1L]]) if (snapshot_skipped) {
skip("On CRAN")35: }tryCatchList(expr, classes, parentenv, handlers)
else if (!new_expectations && skip_on_empty) {36: skip_empty()tryCatch(withCallingHandlers({ eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, }}, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))21: }doTryCatch(return(expr), name, parentenv, handler)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE22: invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)23:
tryCatchList(expr, classes, parentenv, handlers)37:
doWithOneRestart(return(expr), restart)24:
tryCatch(withCallingHandlers({38: eval(code, test_env)withOneRestart(expr, restarts[[1L]])
39: new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") } else if (!new_expectations && skip_on_empty) { 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$package, "} is not installed.")) skip_empty() } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) } error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE25: invokeRestart("muffle_cran_snapshot")}, 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: 40: withOneRestart(expr, restarts[[1L]])test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, 27: withRestarts(tryCatch(withCallingHandlers({ error_call = error_call) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations42: FUN(X[[i]], ...) if (snapshot_skipped) {
skip("On CRAN")43: }lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, else if (!new_expectations && skip_on_empty) { error_call = error_call) skip_empty()
44: }doTryCatch(return(expr), name, parentenv, handler)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {45: skip(paste0("{", e$package, "} is not installed."))tryCatchOne(expr, names, parentenv, handlers[[1L]]) }}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE46: invokeRestart("muffle_cran_snapshot")tryCatchList(expr, classes, parentenv, handlers)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 47: end_test = function() {tryCatch(code, testthat_abort_reporter = function(cnd) { }) cat(conditionMessage(cnd), "\n")
NULL28: })
test_code(code, parent.frame())48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 29: env = env, desc = desc, shuffle = shuffle, error_call = error_call))test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate",
{ sampler_directed_cov$rNetwork(store = TRUE)49: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, test_files_serial(test_dir = test_dir, test_package = test_package, "bernoulli", TRUE, covarList = covarList_directed) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, plot = FALSE)) desc = desc, load_package = load_package, shuffle = shuffle, mySBM_sbm$setModel(Q) error_call = error_call) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData,
covariates = covarList_directed) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]]50: mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, test_files(test_dir = path, test_paths = test_paths, test_package = package, clusterInit = cl, covarList = covarList_directed) reporter = reporter, load_helpers = load_helpers, env = env, mySBM_missSBM$doVEM(trace = TRUE) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), load_package = load_package, parallel = parallel, shuffle = shuffle) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 51: 0.8)test_dir("testthat", package = package, reporter = reporter, expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), ..., load_package = "installed") 0.05)
52: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), test_check("missSBM") 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 0.85)An irrecoverable exception occurred. R is aborting now ...
})
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
Traceback:
1: 1: dispatcher(membership_name, membership_init$to_cc(), model_name, dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) .self$network_to_cc(), TRUE)
2: 2: FUN(X[[i]], ...)FUN(X[[i]], ...)
3: 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:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6:
tryCatchList(expr, classes, parentenv, handlers) 6:
tryCatchList(expr, classes, parentenv, handlers) 7:
tryCatch(expr, error = function(e) { call <- conditionCall(e) 7: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) tryCatch(expr, error = function(e) { call <- conditionCall(e) call <- sys.call(-4L) if (!is.null(call)) { dcall <- deparse(call, nlines = 1L) if (identical(call[[1L]], quote(doTryCatch))) prefix <- paste("Error in", dcall, ": ") call <- sys.call(-4L) LONG <- 75L dcall <- deparse(call, nlines = 1L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] prefix <- paste("Error in", dcall, ": ") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") LONG <- 75L if (is.na(w)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") type = "b") if (is.na(w)) if (w > LONG) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], prefix <- paste0(prefix, "\n ") type = "b") } if (w > LONG) else prefix <- "Error : " prefix <- paste0(prefix, "\n ") msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) else prefix <- "Error : " 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"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) .Internal(printDeferredWarnings()) } } invisible(structure(msg, class = "try-error", condition = e)) invisible(structure(msg, class = "try-error", condition = e))})})
8: 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: 10: FUN(X[[i]], ...)FUN(X[[i]], ...)
11: 11: lapply(seq_len(cores), inner.do)lapply(seq_len(cores), inner.do)
12: 12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE) mc.silent = TRUE)
13: 13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4)) verbose = (verbosity > 4))
14: 14: .self$do_with_inits(inits, Q, reinitialization_effort).self$do_with_inits(inits, Q, reinitialization_effort)
15: 15: .self$estim_ascend(reinitialization_effort, changing_effort).self$estim_ascend(reinitialization_effort, changing_effort)
16: 16: private$BMobject$estimate()private$BMobject$estimate()
17: 17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: 18: eval(code, test_env)eval(code, test_env)
19: 19: eval(code, test_env)eval(code, test_env)
20: 20: withCallingHandlers({withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } else if (!new_expectations && skip_on_empty) { } 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)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)21:
doTryCatch(return(expr), name, parentenv, handler)21:
doTryCatch(return(expr), name, parentenv, handler)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])23:
tryCatchList(expr, classes, parentenv, handlers)23:
tryCatchList(expr, classes, parentenv, handlers)24:
tryCatch(withCallingHandlers({24: eval(code, test_env)tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { skip_empty() } } else if (!new_expectations && skip_on_empty) {}, 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")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")25: }, skip = handle_skip, warning = handle_warning, message = handle_message, doWithOneRestart(return(expr), restart) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
26: 25: withOneRestart(expr, restarts[[1L]])doWithOneRestart(return(expr), restart)
27: 26: withRestarts(tryCatch(withCallingHandlers({withOneRestart(expr, restarts[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations27: if (snapshot_skipped) {withRestarts(tryCatch(withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() skip(paste0("{", e$package, "} is not installed.")) } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), snapshot_skipped <<- TRUE end_test = function() { invokeRestart("muffle_cran_snapshot") })}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 28: end_test = function() {test_code(code, parent.frame()) })
29: 28: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", test_code(code, parent.frame()) {
sampler_undirected_nocov$rNetwork(store = TRUE)29: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", "bernoulli", FALSE) { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, sampler_undirected_nocov$rNetwork(store = TRUE) plot = FALSE)) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, mySBM_sbm$setModel(3) "bernoulli", FALSE) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, cl <- net$clustering(3)[[1]] plot = FALSE)) mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, mySBM_sbm$setModel(3) clusterInit = cl) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) mySBM_missSBM$doVEM() cl <- net$clustering(3)[[1]] expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, 0.05) clusterInit = cl) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), mySBM_missSBM$doVEM() 0.95) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.05) 0.01) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 0.95) 0.05) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.01) 0.95) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), }) 0.05)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 30: 0.95)eval(code, test_env) })
31: 30: eval(code, test_env)eval(code, test_env)
32: 31: withCallingHandlers({eval(code, test_env) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations32: if (snapshot_skipped) {withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() skip(paste0("{", e$package, "} is not installed.")) } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")33: }, skip = handle_skip, warning = handle_warning, message = handle_message, doTryCatch(return(expr), name, parentenv, handler) error = handle_error, interrupt = handle_interrupt)
34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])33:
doTryCatch(return(expr), name, parentenv, handler)35:
tryCatchList(expr, classes, parentenv, handlers)34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])36:
tryCatch(withCallingHandlers({35: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers)
new_expectations <- the$test_expectations > starting_expectations36: if (snapshot_skipped) {tryCatch(withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") } }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() skip(paste0("{", e$package, "} is not installed.")) } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")37: }, skip = handle_skip, warning = handle_warning, message = handle_message, doWithOneRestart(return(expr), restart) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
38: withOneRestart(expr, restarts[[1L]])37:
doWithOneRestart(return(expr), restart)39:
withRestarts(tryCatch(withCallingHandlers({38: eval(code, test_env)withOneRestart(expr, restarts[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {39: skip("On CRAN")withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { skip_empty() new_expectations <- the$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), error = handle_fatal), } end_test = function() {}, snapshot_on_cran = function(cnd) { }) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 40: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_code(code = exprs, env = env, reporter = get_reporter() %||% end_test = function() { StopReporter$new()) })
41: 40: source_file(path, env = env(env), desc = desc, shuffle = shuffle, test_code(code = exprs, env = env, reporter = get_reporter() %||% error_call = error_call) StopReporter$new())
42: 41: FUN(X[[i]], ...)source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 42: error_call = error_call)FUN(X[[i]], ...)
44: 43: doTryCatch(return(expr), name, parentenv, handler)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
45: 44: tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
46: 45: tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: 47: tryCatchList(expr, classes, parentenv, handlers)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")47: NULLtryCatch(code, testthat_abort_reporter = function(cnd) {}) cat(conditionMessage(cnd), "\n")
NULL48: })with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 49: env = env, desc = desc, shuffle = shuffle, error_call = error_call))test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 49: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_files_serial(test_dir = test_dir, test_package = test_package, desc = desc, load_package = load_package, shuffle = shuffle, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, error_call = error_call) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 50: error_call = error_call)test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 50: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_files(test_dir = path, test_paths = test_paths, test_package = package, load_package = load_package, parallel = parallel, shuffle = shuffle) reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 51: load_package = load_package, parallel = parallel, shuffle = shuffle)test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")51:
test_dir("testthat", package = package, reporter = reporter, 52: ..., load_package = "installed")test_check("missSBM")
52: An irrecoverable exception occurred. R is aborting now ...
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)
Traceback:
new_expectations <- the$test_expectations > starting_expectations 1: if (snapshot_skipped) {dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) skip("On CRAN")
2: } else if (!new_expectations && skip_on_empty) {FUN(X[[i]], ...) skip_empty()
} 3: }, expectation = handle_expectation, packageNotFoundError = function(e) {lapply(X = S, FUN = FUN, ...) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
} 4: doTryCatch(return(expr), name, parentenv, handler)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE 5: invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
6: error = handle_error, interrupt = handle_interrupt)tryCatchList(expr, classes, parentenv, handlers)
21: 7: doTryCatch(return(expr), name, parentenv, handler)tryCatch(expr, error = function(e) {
call <- conditionCall(e) if (!is.null(call)) {22: if (identical(call[[1L]], quote(doTryCatch))) tryCatchOne(expr, names, parentenv, handlers[[1L]]) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")23: LONG <- 75LtryCatchList(expr, classes, parentenv, handlers) 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], 24: type = "b")tryCatch(withCallingHandlers({ if (w > LONG) prefix <- paste0(prefix, "\n ") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else prefix <- "Error : " if (snapshot_skipped) { msg <- paste0(prefix, conditionMessage(e), "\n") skip("On CRAN") .Internal(seterrmessage(msg[1L])) } if (!silent && isTRUE(getOption("show.error.messages"))) { else if (!new_expectations && skip_on_empty) { cat(msg, file = outFile) skip_empty() } .Internal(printDeferredWarnings()) }}, expectation = handle_expectation, packageNotFoundError = function(e) { invisible(structure(msg, class = "try-error", condition = e)) if (on_cran()) {}) skip(paste0("{", e$package, "} is not installed."))
} 8: }, snapshot_on_cran = function(cnd) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
snapshot_skipped <<- TRUE 9: invokeRestart("muffle_cran_snapshot")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
10: 25: FUN(X[[i]], ...)doWithOneRestart(return(expr), restart)
11: 26: lapply(seq_len(cores), inner.do)withOneRestart(expr, restarts[[1L]])
12: 27: withRestarts(tryCatch(withCallingHandlers({parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, eval(code, test_env) mc.silent = TRUE) new_expectations <- the$test_expectations > starting_expectations
13: if (snapshot_skipped) {parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, skip("On CRAN") verbose = (verbosity > 4)) }
else if (!new_expectations && skip_on_empty) {14: skip_empty().self$do_with_inits(inits, Q, reinitialization_effort) }}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {15: skip(paste0("{", e$package, "} is not installed.")).self$estim_ascend(reinitialization_effort, changing_effort) }
}, snapshot_on_cran = function(cnd) {16: snapshot_skipped <<- TRUEprivate$BMobject$estimate() invokeRestart("muffle_cran_snapshot")
17: }, skip = handle_skip, warning = handle_warning, message = handle_message, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {18: })eval(code, test_env)
28: test_code(code, parent.frame())19:
eval(code, test_env)29:
20: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", withCallingHandlers({ { eval(code, test_env) sampler_directed_nocov$rNetwork(store = TRUE) new_expectations <- the$test_expectations > starting_expectations mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, if (snapshot_skipped) { "bernoulli", TRUE) skip("On CRAN") mySBM_sbm$optimize(estimOptions = list(verbosity = 0, } plot = FALSE)) else if (!new_expectations && skip_on_empty) { mySBM_sbm$setModel(3) skip_empty() net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) } cl <- net$clustering(3)[[1]]}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, if (on_cran()) { clusterInit = cl) skip(paste0("{", e$package, "} is not installed.")) } mySBM_missSBM$doVEM()}, snapshot_on_cran = function(cnd) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) snapshot_skipped <<- TRUE expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), invokeRestart("muffle_cran_snapshot") 0.95)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), error = handle_error, interrupt = handle_interrupt) 0.01)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 21: 0.1)doTryCatch(return(expr), name, parentenv, handler) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam),
0.2)22: expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0.95)
23: })tryCatchList(expr, classes, parentenv, handlers)
24: 30: tryCatch(withCallingHandlers({ eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { skip("On CRAN")31: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()32: }withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))25: }doWithOneRestart(return(expr), restart)
}, snapshot_on_cran = function(cnd) {26: snapshot_skipped <<- TRUEwithOneRestart(expr, restarts[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 27: withRestarts(tryCatch(withCallingHandlers({ error = handle_error, interrupt = handle_interrupt) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations33: doTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
skip("On CRAN")34: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()35: }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {36: skip(paste0("{", e$package, "} is not installed."))tryCatch(withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { invokeRestart("muffle_cran_snapshot") skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), else if (!new_expectations && skip_on_empty) { end_test = function() { skip_empty() }) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {28: test_code(code, parent.frame()) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))29: }test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", }, snapshot_on_cran = function(cnd) { { snapshot_skipped <<- TRUE sampler_directed_nocov$rNetwork(store = TRUE) invokeRestart("muffle_cran_snapshot") mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, }, skip = handle_skip, warning = handle_warning, message = handle_message, "bernoulli", TRUE) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))37: mySBM_sbm$setModel(3)doWithOneRestart(return(expr), restart) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData)
38: cl <- net$clustering(3)[[1]]withOneRestart(expr, restarts[[1L]]) mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData,
clusterInit = cl)39: mySBM_missSBM$doVEM()withRestarts(tryCatch(withCallingHandlers({ expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), eval(code, test_env) 0.1) new_expectations <- the$test_expectations > starting_expectations expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), if (snapshot_skipped) { 0.95) skip("On CRAN") expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), } 0.01) else if (!new_expectations && skip_on_empty) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), skip_empty() 0.1) } expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 0.2)}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), if (on_cran()) { 0.95) skip(paste0("{", e$package, "} is not installed.")) }) }
}, snapshot_on_cran = function(cnd) {30: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 31: end_test = function() {eval(code, test_env) })
32: withCallingHandlers({40: eval(code, test_env)test_code(code = exprs, env = env, reporter = get_reporter() %||% new_expectations <- the$test_expectations > starting_expectations StopReporter$new()) if (snapshot_skipped) { skip("On CRAN")
}41: else if (!new_expectations && skip_on_empty) {source_file(path, env = env(env), desc = desc, shuffle = shuffle, skip_empty() error_call = error_call) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {42: skip(paste0("{", e$package, "} is not installed."))FUN(X[[i]], ...) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")43: }, skip = handle_skip, warning = handle_warning, message = handle_message, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error = handle_error, interrupt = handle_interrupt) error_call = error_call)
33: 44: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
45: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
tryCatchOne(expr, names, parentenv, handlers[[1L]])46:
tryCatchList(expr, classes, parentenv, handlers)35:
tryCatchList(expr, classes, parentenv, handlers)47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n")
NULL36: })tryCatch(withCallingHandlers({
48: eval(code, test_env)with_reporter(reporters$multi, lapply(test_paths, test_one_file, new_expectations <- the$test_expectations > starting_expectations env = env, desc = desc, shuffle = shuffle, error_call = error_call)) if (snapshot_skipped) {
skip("On CRAN")49: } else if (!new_expectations && skip_on_empty) { skip_empty()test_files_serial(test_dir = test_dir, test_package = test_package, } test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, }, expectation = handle_expectation, packageNotFoundError = function(e) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, if (on_cran()) { error_call = error_call) skip(paste0("{", e$package, "} is not installed."))
}50: }, snapshot_on_cran = function(cnd) {test_files(test_dir = path, test_paths = test_paths, test_package = package, snapshot_skipped <<- TRUE reporter = reporter, load_helpers = load_helpers, env = env, invokeRestart("muffle_cran_snapshot") stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }, skip = handle_skip, warning = handle_warning, message = handle_message, load_package = load_package, parallel = parallel, shuffle = shuffle) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
51: 37: test_dir("testthat", package = package, reporter = reporter, doWithOneRestart(return(expr), restart) ..., load_package = "installed")
52: 38: test_check("missSBM")withOneRestart(expr, restarts[[1L]])
An irrecoverable exception occurred. R is aborting now ...
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