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Last updated on 2026-09-24 17:50:55 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 89.37 | 358.05 | 447.42 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 57.55 | 243.49 | 301.04 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 59.00 | 243.15 | 302.15 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 248.05 | 312.05 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 452.00 | 543.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 83.11 | 346.95 | 430.06 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 90.56 | 343.79 | 434.35 | 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 | 98.00 | 361.00 | 459.00 | 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 | 115.00 | 505.00 | 620.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [38s/29s]
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")
Traceback:
1: if (w > LONG) dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) prefix <- paste0(prefix, "\n ")
2: } else prefix <- "Error : "FUN(X[[i]], ...) msg <- paste0(prefix, conditionMessage(e), "\n")
3: .Internal(seterrmessage(msg[1L]))lapply(X = S, FUN = FUN, ...) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile) 4: .Internal(printDeferredWarnings())doTryCatch(return(expr), name, parentenv, handler) }
invisible(structure(msg, class = "try-error", condition = e)) 5: })tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: 6: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchList(expr, classes, parentenv, handlers)
9: 7: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatch(expr, error = function(e) {
call <- conditionCall(e)10: if (!is.null(call)) {FUN(X[[i]], ...) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)11: dcall <- deparse(call, nlines = 1L)lapply(seq_len(cores), inner.do) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L12: sm <- strsplit(conditionMessage(e), "\n")[[1L]]parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") mc.silent = TRUE) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 13: type = "b")parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, if (w > LONG) verbose = (verbosity > 4)) prefix <- paste0(prefix, "\n ")
}14: else prefix <- "Error : ".self$do_with_inits(inits, Q, reinitialization_effort) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))15: if (!silent && isTRUE(getOption("show.error.messages"))) {.self$estim_ascend(reinitialization_effort, changing_effort) cat(msg, file = outFile)
.Internal(printDeferredWarnings())16: }private$BMobject$estimate() invisible(structure(msg, class = "try-error", condition = e))
})17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)18:
eval(code, test_env) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))19:
eval(code, test_env)10:
FUN(X[[i]], ...)20:
withCallingHandlers({11: eval(code, test_env)lapply(seq_len(cores), inner.do) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {12: skip("On CRAN")parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, } mc.silent = TRUE) else if (!new_expectations && skip_on_empty) {
skip_empty()13: }parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, }, expectation = handle_expectation, packageNotFoundError = function(e) { verbose = (verbosity > 4)) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))14: }.self$do_with_inits(inits, Q, reinitialization_effort)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE15: invokeRestart("muffle_cran_snapshot").self$estim_ascend(reinitialization_effort, changing_effort)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)16:
private$BMobject$estimate()21:
doTryCatch(return(expr), name, parentenv, handler)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])18:
eval(code, test_env)23:
tryCatchList(expr, classes, parentenv, handlers)19:
eval(code, test_env)24:
tryCatch(withCallingHandlers({20: 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,
error = handle_error, interrupt = handle_interrupt)25:
doWithOneRestart(return(expr), restart)21:
doTryCatch(return(expr), name, parentenv, handler)26:
withOneRestart(expr, restarts[[1L]])22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])27:
withRestarts(tryCatch(withCallingHandlers({23: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {24: skip("On CRAN")tryCatch(withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$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), 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), error = handle_fatal)test_code(code, parent.frame())
25: 29: doWithOneRestart(return(expr), restart)test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate",
{26: sampler_undirected_cov$rNetwork(store = TRUE)withOneRestart(expr, restarts[[1L]]) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData,
"bernoulli", FALSE, covarList = covarList_undirected)27: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, withRestarts(tryCatch(withCallingHandlers({ plot = FALSE)) eval(code, test_env) mySBM_sbm$setModel(Q) new_expectations <- the$test_expectations > starting_expectations net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, if (snapshot_skipped) { covariates = covarList_undirected) skip("On CRAN") cls <- net$clustering(1:(2 * Q)) } cl <- cls[[Q]] else if (!new_expectations && skip_on_empty) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, skip_empty() clusterInit = cl, covarList = covarList_undirected) } mySBM_missSBM$doVEM()}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), if (on_cran()) { 0.05) skip(paste0("{", e$package, "} is not installed.")) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), } 0.8)}, snapshot_on_cran = function(cnd) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), snapshot_skipped <<- TRUE 0.01) invokeRestart("muffle_cran_snapshot") expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.1) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), end_test = function() { 0.1) }) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships),
0.85)28: })test_code(code, parent.frame())
30: 29: eval(code, test_env)test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate",
{31: sampler_undirected_cov$rNetwork(store = TRUE)eval(code, test_env) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData,
"bernoulli", FALSE, covarList = covarList_undirected)32: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, withCallingHandlers({ plot = FALSE)) eval(code, test_env) mySBM_sbm$setModel(Q) new_expectations <- the$test_expectations > starting_expectations net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, if (snapshot_skipped) { covariates = covarList_undirected) skip("On CRAN") cls <- net$clustering(1:(2 * Q)) } cl <- cls[[Q]] else if (!new_expectations && skip_on_empty) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, skip_empty() clusterInit = cl, covarList = covarList_undirected) } mySBM_missSBM$doVEM()}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), if (on_cran()) { 0.05) skip(paste0("{", e$package, "} is not installed.")) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), } 0.8)}, snapshot_on_cran = function(cnd) { expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), snapshot_skipped <<- TRUE 0.01) invokeRestart("muffle_cran_snapshot") expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.1) error = handle_error, interrupt = handle_interrupt) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam),
0.1)33: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), doTryCatch(return(expr), name, parentenv, handler) 0.85)
})34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])30:
eval(code, test_env)35:
tryCatchList(expr, classes, parentenv, handlers)31:
eval(code, test_env)36:
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,
error = handle_error, interrupt = handle_interrupt)37:
doWithOneRestart(return(expr), restart)33:
doTryCatch(return(expr), name, parentenv, handler)38:
withOneRestart(expr, restarts[[1L]])34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])39:
withRestarts(tryCatch(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), error = handle_fatal), }, snapshot_on_cran = function(cnd) { end_test = function() { snapshot_skipped <<- TRUE }) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 40: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())37:
doWithOneRestart(return(expr), restart)41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 38: error_call = error_call)withOneRestart(expr, restarts[[1L]])
42: 39: FUN(X[[i]], ...)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)43: new_expectations <- the$test_expectations > starting_expectationslapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, if (snapshot_skipped) { error_call = error_call) skip("On CRAN")
}44: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler) skip_empty()
}45: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))46: }tryCatchList(expr, classes, parentenv, handlers)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE47: invokeRestart("muffle_cran_snapshot")tryCatch(code, testthat_abort_reporter = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, cat(conditionMessage(cnd), "\n") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), NULL end_test = function() {}) })
48: 40: with_reporter(reporters$multi, lapply(test_paths, test_one_file, test_code(code = exprs, env = env, reporter = get_reporter() %||% env = env, desc = desc, shuffle = shuffle, error_call = error_call)) StopReporter$new())
49: 41: test_files_serial(test_dir = test_dir, test_package = test_package, source_file(path, env = env(env), desc = desc, shuffle = shuffle, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, error_call = error_call) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 42: error_call = error_call)FUN(X[[i]], ...)
50: 43: test_files(test_dir = path, test_paths = test_paths, test_package = package, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, reporter = reporter, load_helpers = load_helpers, env = env, error_call = error_call) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)44:
doTryCatch(return(expr), name, parentenv, handler)51:
test_dir("testthat", package = package, reporter = reporter, 45: ..., load_package = "installed")tryCatchOne(expr, names, parentenv, handlers[[1L]])
52: 46: test_check("missSBM")tryCatchList(expr, classes, parentenv, handlers)
An irrecoverable exception occurred. R is aborting now ...
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$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:
Traceback:
1: 1: dispatcher(membership_name, membership_init$to_cc(), model_name, dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE) .self$network_to_cc(), TRUE)
2: 2: FUN(X[[i]], ...)FUN(X[[i]], ...)
3: 3: lapply(X = S, FUN = FUN, ...)lapply(X = S, FUN = FUN, ...)
4: 4: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
5: 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 6: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
7: 7: tryCatch(expr, error = function(e) { call <- conditionCall(e)tryCatch(expr, error = function(e) { if (!is.null(call)) { call <- conditionCall(e) if (identical(call[[1L]], quote(doTryCatch))) if (!is.null(call)) { call <- sys.call(-4L) if (identical(call[[1L]], quote(doTryCatch))) dcall <- deparse(call, nlines = 1L) call <- sys.call(-4L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L dcall <- deparse(call, nlines = 1L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") prefix <- paste("Error in", dcall, ": ") if (is.na(w)) LONG <- 75L w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], sm <- strsplit(conditionMessage(e), "\n")[[1L]] type = "b") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (w > LONG) if (is.na(w)) prefix <- paste0(prefix, "\n ") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b") else prefix <- "Error : " if (w > LONG) msg <- paste0(prefix, conditionMessage(e), "\n") prefix <- paste0(prefix, "\n ") } .Internal(seterrmessage(msg[1L])) else prefix <- "Error : " if (!silent && isTRUE(getOption("show.error.messages"))) { msg <- paste0(prefix, conditionMessage(e), "\n") cat(msg, file = outFile) .Internal(seterrmessage(msg[1L])) .Internal(printDeferredWarnings()) if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile) invisible(structure(msg, class = "try-error", condition = e)) .Internal(printDeferredWarnings())}) }
invisible(structure(msg, class = "try-error", condition = e)) 8: })try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
8: 9: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: 9: FUN(X[[i]], ...)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
11: 10: lapply(seq_len(cores), inner.do)FUN(X[[i]], ...)
12: 11: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, lapply(seq_len(cores), inner.do) mc.silent = TRUE)
13: 12: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, verbose = (verbosity > 4)) mc.silent = TRUE)
14: 13: .self$do_with_inits(inits, Q, reinitialization_effort)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores,
verbose = (verbosity > 4))15: .self$estim_ascend(reinitialization_effort, changing_effort)
14: .self$do_with_inits(inits, Q, reinitialization_effort)16:
private$BMobject$estimate()15:
.self$estim_ascend(reinitialization_effort, changing_effort)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))16:
private$BMobject$estimate()18:
eval(code, test_env)17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))19:
eval(code, test_env)18: eval(code, test_env)
20: 19: withCallingHandlers({ eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {20: skip("On CRAN")withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$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$package, "} is not installed.")) skip_empty() } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$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]])
23: 21: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
22: 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch(withCallingHandlers({
eval(code, test_env)23: new_expectations <- the$test_expectations > starting_expectationstryCatchList(expr, classes, parentenv, handlers) if (snapshot_skipped) {
skip("On CRAN")24: }tryCatch(withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$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) }
}, 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]])
25: 27: doWithOneRestart(return(expr), restart)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)26: new_expectations <- the$test_expectations > starting_expectationswithOneRestart(expr, restarts[[1L]]) if (snapshot_skipped) {
27: skip("On CRAN")withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$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$package, "} is not installed.")) skip_empty() } }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$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, directed, one covariate", test_code(code, parent.frame()) {
sampler_directed_cov$rNetwork(store = TRUE)29: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", "bernoulli", TRUE, covarList = covarList_directed) { mySBM_sbm$optimize(estimOptions = list(verbosity = 0, sampler_directed_cov$rNetwork(store = TRUE) plot = FALSE)) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, mySBM_sbm$setModel(Q) "bernoulli", TRUE, covarList = covarList_directed) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, mySBM_sbm$optimize(estimOptions = list(verbosity = 0, covariates = covarList_directed) plot = FALSE)) cls <- net$clustering(1:(2 * Q)) mySBM_sbm$setModel(Q) cl <- cls[[Q]] net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, covariates = covarList_directed) clusterInit = cl, covarList = covarList_directed) cls <- net$clustering(1:(2 * Q)) mySBM_missSBM$doVEM(trace = TRUE) cl <- cls[[Q]] expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, 0.1) clusterInit = cl, covarList = covarList_directed) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), mySBM_missSBM$doVEM(trace = TRUE) 0.8) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.1) 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 0.8) 0.1) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 0.05) 0.85) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 0.1) }) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships),
0.85) })30:
eval(code, test_env)30:
eval(code, test_env)31:
eval(code, test_env)31:
eval(code, test_env)32:
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)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)33: doTryCatch(return(expr), name, parentenv, handler)
33: 34: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: 35: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
35: 36: tryCatchList(expr, classes, parentenv, handlers)tryCatch(withCallingHandlers({
eval(code, test_env)36: new_expectations <- the$test_expectations > starting_expectationstryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, snapshot_on_cran = function(cnd) { invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)37:
doWithOneRestart(return(expr), restart)37:
doWithOneRestart(return(expr), restart)38:
withOneRestart(expr, restarts[[1L]])38:
withOneRestart(expr, restarts[[1L]])39:
withRestarts(tryCatch(withCallingHandlers({39: eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } 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), error = handle_fatal), }) end_test = function() {
})40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 40: StopReporter$new())test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 41: error_call = error_call)source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: 42: FUN(X[[i]], ...)FUN(X[[i]], ...)
43: 43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) error_call = error_call)
44: 44: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
45: 45: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: 46: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
47: 47: tryCatch(code, testthat_abort_reporter = function(cnd) {tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") cat(conditionMessage(cnd), "\n") NULL NULL})})
48: 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: 49: test_files_serial(test_dir = test_dir, test_package = test_package, test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) error_call = error_call)
50: 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle) load_package = load_package, parallel = parallel, shuffle = shuffle)
51: 51: test_dir("testthat", package = package, reporter = reporter, test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") ..., load_package = "installed")
52: 52: test_check("missSBM")test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-46.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", { sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE 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$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42:
Traceback:
FUN(X[[i]], ...) 1:
dispatcher(membership_name, membership_init$to_cc(), model_name, 43: .self$network_to_cc(), TRUE)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call) 2:
FUN(X[[i]], ...)44:
doTryCatch(return(expr), name, parentenv, handler) 3:
lapply(X = S, FUN = FUN, ...)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: doTryCatch(return(expr), name, parentenv, handler)
5:
tryCatchOne(expr, names, parentenv, handlers[[1L]])46:
tryCatchList(expr, classes, parentenv, handlers) 6:
47: tryCatchList(expr, classes, parentenv, handlers)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n") 7: NULLtryCatch(expr, error = function(e) {}) call <- conditionCall(e)
if (!is.null(call)) {48: if (identical(call[[1L]], quote(doTryCatch))) with_reporter(reporters$multi, lapply(test_paths, test_one_file, call <- sys.call(-4L) env = env, desc = desc, shuffle = shuffle, error_call = error_call)) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")49: LONG <- 75Ltest_files_serial(test_dir = test_dir, test_package = test_package, sm <- strsplit(conditionMessage(e), "\n")[[1L]] test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, if (is.na(w)) desc = desc, load_package = load_package, shuffle = shuffle, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], error_call = error_call) type = "b")
if (w > LONG) 50: prefix <- paste0(prefix, "\n ")test_files(test_dir = path, test_paths = test_paths, test_package = package, } reporter = reporter, load_helpers = load_helpers, env = env, else prefix <- "Error : " stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, msg <- paste0(prefix, conditionMessage(e), "\n") load_package = load_package, parallel = parallel, shuffle = shuffle) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {51: cat(msg, file = outFile)test_dir("testthat", package = package, reporter = reporter, .Internal(printDeferredWarnings()) ..., load_package = "installed") }
invisible(structure(msg, class = "try-error", condition = e))52: })test_check("missSBM")
8: An irrecoverable exception occurred. R is aborting now ...
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", { sampler_undirected_nocov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, "bernoulli", FALSE) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.01) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), 0.05) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE 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$memberships), 0.95) })
30: eval(code, test_env)
31: eval(code, test_env)
32:
Traceback:
1: withCallingHandlers({dispatcher(membership_name, membership_init$to_cc(), model_name, eval(code, test_env) .self$network_to_cc(), TRUE) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { 2: skip("On CRAN")FUN(X[[i]], ...) }
else if (!new_expectations && skip_on_empty) { skip_empty() 3: }lapply(X = S, FUN = FUN, ...)
}, expectation = handle_expectation, packageNotFoundError = function(e) { 4: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
} 5: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 6: error = handle_error, interrupt = handle_interrupt)tryCatchList(expr, classes, parentenv, handlers)
33:
doTryCatch(return(expr), name, parentenv, handler) 7:
tryCatch(expr, error = function(e) {34: call <- conditionCall(e)tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 35: call <- sys.call(-4L)tryCatchList(expr, classes, parentenv, handlers) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")36: LONG <- 75LtryCatch(withCallingHandlers({ sm <- strsplit(conditionMessage(e), "\n")[[1L]] eval(code, test_env) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") new_expectations <- the$test_expectations > starting_expectations if (is.na(w)) if (snapshot_skipped) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") skip("On CRAN") } if (w > LONG) else if (!new_expectations && skip_on_empty) { prefix <- paste0(prefix, "\n ") skip_empty() } else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n")}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { .Internal(seterrmessage(msg[1L])) skip(paste0("{", e$package, "} is not installed.")) if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile)}, snapshot_on_cran = function(cnd) { .Internal(printDeferredWarnings()) } snapshot_skipped <<- TRUE invisible(structure(msg, class = "try-error", condition = e)) invokeRestart("muffle_cran_snapshot")})}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
8: 37: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)doWithOneRestart(return(expr), restart)
38: 9: withOneRestart(expr, restarts[[1L]])sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: 39: FUN(X[[i]], ...)withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations11: lapply(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) { snapshot_skipped <<- TRUE.self$do_with_inits(inits, Q, reinitialization_effort) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 15: end_test = function() {.self$estim_ascend(reinitialization_effort, changing_effort) })
40: 16: test_code(code = exprs, env = env, reporter = get_reporter() %||% private$BMobject$estimate() StopReporter$new())
17: 41: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)18:
42: eval(code, test_env)FUN(X[[i]], ...)
19: 43: eval(code, test_env)
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)20:
withCallingHandlers({44: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip("On CRAN") }
else if (!new_expectations && skip_on_empty) {46: skip_empty() }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))47: }tryCatch(code, testthat_abort_reporter = function(cnd) {}, snapshot_on_cran = function(cnd) { cat(conditionMessage(cnd), "\n") snapshot_skipped <<- TRUE NULL invokeRestart("muffle_cran_snapshot")})}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 21: env = env, desc = desc, shuffle = shuffle, error_call = error_call))doTryCatch(return(expr), name, parentenv, handler)
49: 22: test_files_serial(test_dir = test_dir, test_package = test_package, tryCatchOne(expr, names, parentenv, handlers[[1L]]) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 23: desc = desc, load_package = load_package, shuffle = shuffle, tryCatchList(expr, classes, parentenv, handlers) error_call = error_call)
24: 50: tryCatch(withCallingHandlers({test_files(test_dir = path, test_paths = test_paths, test_package = package, eval(code, test_env) reporter = reporter, load_helpers = load_helpers, env = env, new_expectations <- the$test_expectations > starting_expectations stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, if (snapshot_skipped) { load_package = load_package, parallel = parallel, shuffle = shuffle) skip("On CRAN")
}51: else if (!new_expectations && skip_on_empty) {test_dir("testthat", package = package, reporter = reporter, skip_empty() ..., load_package = "installed") }
}, expectation = handle_expectation, packageNotFoundError = function(e) {52: if (on_cran()) {test_check("missSBM") skip(paste0("{", e$package, "} is not installed."))
}An irrecoverable exception occurred. R is aborting now ...
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$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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