Last updated on 2026-11-06 04:00:37 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 81.92 | 340.67 | 422.59 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 57.81 | 235.89 | 293.70 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 57.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 64.00 | 239.38 | 303.38 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 91.00 | 417.00 | 508.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | OK | ||||
| r-release-linux-x86_64 | 1.1.0 | 78.27 | 331.21 | 409.48 | 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 | 101.00 | 348.00 | 449.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 19.00 | 103.00 | 122.00 | 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 | 475.00 | 589.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [36s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missSBM)
>
> test_check("missSBM")
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'dyad' network-sampling process
iteration #: 2
iteration #: 3
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'covar-node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 3 model(s).
Tested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degreeTested sampling:
- dyad
- node
- double-standard
- block-node
- block-dyad
- degree
sampling: dyad new better on connectivity
node
double-standard
block-node new better on mixture
Adjusting Variational EM for Stochastic Block Model
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'node' network-sampling process
Initialization of 1 model(s).
Performing VEM inference
Model with 3 blocks.
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 2 model(s).
Performing VEM inference
Model with 2 blocks.
Model with 1 blocks.
Polishing (node-swap)
Looking for better solutions
Pass 1 Going forward +
Pass 1 Going backward +
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
Traceback:
if (is.na(w)) 1: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], dispatcher(membership_name, membership_init$to_cc(), model_name, type = "b") .self$network_to_cc(), TRUE) if (w > LONG)
prefix <- paste0(prefix, "\n ") 2: }FUN(X[[i]], ...) else prefix <- "Error : "
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: doTryCatch(return(expr), name, parentenv, handler) .Internal(printDeferredWarnings())
} 5: invisible(structure(msg, class = "try-error", condition = e))tryCatchOne(expr, names, parentenv, handlers[[1L]])})
6: 8: tryCatchList(expr, classes, parentenv, handlers)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
7: 9: tryCatch(expr, error = function(e) { call <- conditionCall(e)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 10: call <- sys.call(-4L)FUN(X[[i]], ...) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")11: lapply(seq_len(cores), inner.do) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]12: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, if (is.na(w)) mc.silent = TRUE) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")13: if (w > LONG) parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, prefix <- paste0(prefix, "\n ") } verbose = (verbosity > 4)) else prefix <- "Error : "
14: msg <- paste0(prefix, conditionMessage(e), "\n").self$do_with_inits(inits, Q, reinitialization_effort) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {15: cat(msg, file = outFile).self$estim_ascend(reinitialization_effort, changing_effort) .Internal(printDeferredWarnings())
}16: invisible(structure(msg, class = "try-error", condition = e))private$BMobject$estimate()})
8: 17: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
9: 18: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))eval(code, test_env)
19: 10: eval(code, test_env)FUN(X[[i]], ...)
20: 11: withCallingHandlers({lapply(seq_len(cores), inner.do) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations12: if (snapshot_skipped) {parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, skip("On CRAN") mc.silent = TRUE) }
else if (!new_expectations && skip_on_empty) {13: skip_empty()parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, }}, expectation = handle_expectation, packageNotFoundError = function(e) { verbose = (verbosity > 4))
if (on_cran()) {14: skip(paste0("{", e$package, "} is not installed.")).self$do_with_inits(inits, Q, reinitialization_effort) }
}, snapshot_on_cran = function(cnd) {15: snapshot_skipped <<- TRUE.self$estim_ascend(reinitialization_effort, changing_effort) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 16: error = handle_error, interrupt = handle_interrupt)private$BMobject$estimate()
21: 17: doTryCatch(return(expr), name, parentenv, handler)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
22: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(code, test_env)
19: 23: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers)
20: 24: withCallingHandlers({tryCatch(withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { else if (!new_expectations && skip_on_empty) { skip_empty() skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) error = handle_error, interrupt = handle_interrupt)
25: 21: doWithOneRestart(return(expr), restart)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",
{ sampler_undirected_cov$rNetwork(store = TRUE)26: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, withOneRestart(expr, restarts[[1L]]) "bernoulli", FALSE, covarList = covarList_undirected)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 27: plot = FALSE)) mySBM_sbm$setModel(Q)withRestarts(tryCatch(withCallingHandlers({ net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations covariates = covarList_undirected) if (snapshot_skipped) { cls <- net$clustering(1:(2 * Q)) skip("On CRAN") cl <- cls[[Q]] } mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, else if (!new_expectations && skip_on_empty) { clusterInit = cl, covarList = covarList_undirected) skip_empty() mySBM_missSBM$doVEM() } expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), }, expectation = handle_expectation, packageNotFoundError = function(e) { 0.05) if (on_cran()) { expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), skip(paste0("{", e$package, "} is not installed.")) 0.8) } expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), }, snapshot_on_cran = function(cnd) { 0.01) snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), invokeRestart("muffle_cran_snapshot") 0.1)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 0.1) end_test = function() { expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), }) 0.85)
})28:
test_code(code, parent.frame())30:
eval(code, test_env)29:
test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", 31: {eval(code, test_env) sampler_undirected_cov$rNetwork(store = TRUE)
mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, 32: "bernoulli", FALSE, covarList = covarList_undirected)withCallingHandlers({ mySBM_sbm$optimize(estimOptions = list(verbosity = 0, eval(code, test_env) plot = FALSE)) new_expectations <- the$test_expectations > starting_expectations mySBM_sbm$setModel(Q) if (snapshot_skipped) { net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, skip("On CRAN") covariates = covarList_undirected) } cls <- net$clustering(1:(2 * Q)) else if (!new_expectations && skip_on_empty) { cl <- cls[[Q]] skip_empty() mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, } 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), 33: 0.1)doTryCatch(return(expr), name, parentenv, handler) expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships),
0.85)34: })tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: 35: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers)
31: 36: eval(code, test_env)tryCatch(withCallingHandlers({
eval(code, test_env)32: new_expectations <- the$test_expectations > starting_expectationswithCallingHandlers({ eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$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$test_expectations > starting_expectations
if (snapshot_skipped) {36: skip("On CRAN")tryCatch(withCallingHandlers({ } eval(code, test_env) new_expectations <- the$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) { } if (on_cran()) { else if (!new_expectations && skip_on_empty) { skip(paste0("{", e$package, "} is not installed.")) skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) snapshot_skipped <<- TRUE }}, snapshot_on_cran = function(cnd) { invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), error = handle_error, interrupt = handle_interrupt), error = handle_fatal) end_test = function() {
})37:
doWithOneRestart(return(expr), restart)40:
38: test_code(code = exprs, env = env, reporter = get_reporter() %||% withOneRestart(expr, restarts[[1L]]) StopReporter$new())
39: 41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, withRestarts(tryCatch(withCallingHandlers({ error_call = error_call)
eval(code, test_env)42: new_expectations <- the$test_expectations > starting_expectationsFUN(X[[i]], ...) if (snapshot_skipped) { skip("On CRAN")
} else if (!new_expectations && skip_on_empty) {43: skip_empty()lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } error_call = error_call)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {44: doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed.")) }
}, snapshot_on_cran = function(cnd) {45: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 46: end_test = function() {tryCatchList(expr, classes, parentenv, handlers) })
47: 40: tryCatch(code, testthat_abort_reporter = function(cnd) {test_code(code = exprs, env = env, reporter = get_reporter() %||% cat(conditionMessage(cnd), "\n") StopReporter$new()) NULL
})41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 48: error_call = error_call)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))42:
49: FUN(X[[i]], ...)test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 43: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) error_call = error_call)
44: 50: doTryCatch(return(expr), name, parentenv, handler)test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 45: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, tryCatchOne(expr, names, parentenv, handlers[[1L]]) load_package = load_package, parallel = parallel, shuffle = shuffle)
46: 51: tryCatchList(expr, classes, parentenv, handlers)test_dir("testthat", package = package, reporter = reporter,
47: ..., load_package = "installed")tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")52: NULLtest_check("missSBM")})
An irrecoverable exception occurred. R is aborting now ...
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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, one covariate", { sampler_directed_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, covariates = covarList_directed) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_directed) mySBM_missSBM$doVEM(trace = TRUE) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.05) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships),
Traceback:
0.85) 1: })dispatcher(membership_name, membership_init$to_cc(), model_name,
.self$network_to_cc(), TRUE)30:
eval(code, test_env) 2:
FUN(X[[i]], ...)31:
eval(code, test_env) 3:
lapply(X = S, FUN = FUN, ...)32:
withCallingHandlers({ 4: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { 5: skip("On CRAN")tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
else if (!new_expectations && skip_on_empty) { 6: skip_empty()tryCatchList(expr, classes, parentenv, handlers) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { 7: if (on_cran()) {tryCatch(expr, error = function(e) { skip(paste0("{", e$package, "} is not installed.")) call <- conditionCall(e) } if (!is.null(call)) {}, snapshot_on_cran = function(cnd) { if (identical(call[[1L]], quote(doTryCatch))) snapshot_skipped <<- TRUE call <- sys.call(-4L) invokeRestart("muffle_cran_snapshot") dcall <- deparse(call, nlines = 1L)}, skip = handle_skip, warning = handle_warning, message = handle_message, prefix <- paste("Error in", dcall, ": ") error = handle_error, interrupt = handle_interrupt) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]33: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")doTryCatch(return(expr), name, parentenv, handler) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 34: type = "b")tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (w > LONG)
prefix <- paste0(prefix, "\n ")35: }tryCatchList(expr, classes, parentenv, handlers) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")36: .Internal(seterrmessage(msg[1L]))tryCatch(withCallingHandlers({ if (!silent && isTRUE(getOption("show.error.messages"))) { eval(code, test_env) cat(msg, file = outFile) new_expectations <- the$test_expectations > starting_expectations .Internal(printDeferredWarnings()) if (snapshot_skipped) { } skip("On CRAN") invisible(structure(msg, class = "try-error", condition = e)) }}) else if (!new_expectations && skip_on_empty) {
skip_empty() 8: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { 9: skip(paste0("{", e$package, "} is not installed."))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
}, snapshot_on_cran = function(cnd) {10: snapshot_skipped <<- TRUEFUN(X[[i]], ...) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 11: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)lapply(seq_len(cores), inner.do)
37: 12: doWithOneRestart(return(expr), restart)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE,
mc.silent = TRUE)38:
withOneRestart(expr, restarts[[1L]])13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 39: verbose = (verbosity > 4))withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)14: new_expectations <- the$test_expectations > starting_expectations.self$do_with_inits(inits, Q, reinitialization_effort) if (snapshot_skipped) {
skip("On CRAN")15: }.self$estim_ascend(reinitialization_effort, changing_effort) else if (!new_expectations && skip_on_empty) {
skip_empty()16: }private$BMobject$estimate()}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {17: skip(paste0("{", e$package, "} is not installed."))mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) }
}, snapshot_on_cran = function(cnd) {18: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 19: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), eval(code, test_env) end_test = function() {
})20:
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: source_file(path, env = env(env), desc = desc, shuffle = shuffle, } error_call = error_call) else if (!new_expectations && skip_on_empty) {
skip_empty()42: }FUN(X[[i]], ...)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {43: skip(paste0("{", e$package, "} is not installed."))lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } error_call = error_call)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE44: invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)45:
tryCatchOne(expr, names, parentenv, handlers[[1L]])21:
doTryCatch(return(expr), name, parentenv, handler)46:
tryCatchList(expr, classes, parentenv, handlers)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])47:
tryCatch(code, testthat_abort_reporter = function(cnd) {23: cat(conditionMessage(cnd), "\n")tryCatchList(expr, classes, parentenv, handlers) NULL
})24:
tryCatch(withCallingHandlers({48: eval(code, test_env)with_reporter(reporters$multi, lapply(test_paths, test_one_file, new_expectations <- the$test_expectations > starting_expectations env = env, desc = desc, shuffle = shuffle, error_call = error_call)) if (snapshot_skipped) {
skip("On CRAN")49: }test_files_serial(test_dir = test_dir, test_package = test_package, else if (!new_expectations && skip_on_empty) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, skip_empty() env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } desc = desc, load_package = load_package, shuffle = shuffle, }, expectation = handle_expectation, packageNotFoundError = function(e) { error_call = error_call) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))50: }test_files(test_dir = path, test_paths = test_paths, test_package = package, }, snapshot_on_cran = function(cnd) { reporter = reporter, load_helpers = load_helpers, env = env, snapshot_skipped <<- TRUE stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, invokeRestart("muffle_cran_snapshot") load_package = load_package, parallel = parallel, shuffle = shuffle)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)51:
test_dir("testthat", package = package, reporter = reporter, 25: ..., load_package = "installed")doWithOneRestart(return(expr), restart)
52: 26: test_check("missSBM")withOneRestart(expr, restarts[[1L]])
An irrecoverable exception occurred. R is aborting now ...
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, one covariate", { sampler_directed_cov$rNetwork(store = TRUE) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, "bernoulli", TRUE, covarList = covarList_directed) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) mySBM_sbm$setModel(Q) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, covariates = covarList_directed) cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, clusterInit = cl, covarList = covarList_directed) mySBM_missSBM$doVEM(trace = TRUE) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), 0.8) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 0.05) 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)
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:
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$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$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 ...
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$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$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:
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: 5: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 5: tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
7:
tryCatch(expr, error = function(e) { 6: call <- conditionCall(e)tryCatchList(expr, classes, parentenv, handlers) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 7: call <- sys.call(-4L)tryCatch(expr, error = function(e) { dcall <- deparse(call, nlines = 1L) call <- conditionCall(e) prefix <- paste("Error in", dcall, ": ") LONG <- 75L if (!is.null(call)) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (identical(call[[1L]], quote(doTryCatch))) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) call <- sys.call(-4L) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], dcall <- deparse(call, nlines = 1L) type = "b") prefix <- paste("Error in", dcall, ": ") if (w > LONG) LONG <- 75L prefix <- paste0(prefix, "\n ") sm <- strsplit(conditionMessage(e), "\n")[[1L]] } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") else prefix <- "Error : " if (is.na(w)) msg <- paste0(prefix, conditionMessage(e), "\n") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], .Internal(seterrmessage(msg[1L])) type = "b") if (!silent && isTRUE(getOption("show.error.messages"))) { if (w > LONG) cat(msg, file = outFile) prefix <- paste0(prefix, "\n ") .Internal(printDeferredWarnings()) } } else prefix <- "Error : " invisible(structure(msg, class = "try-error", condition = e)) msg <- paste0(prefix, conditionMessage(e), "\n")}) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) { 8: cat(msg, file = outFile)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) .Internal(printDeferredWarnings())
} 9: invisible(structure(msg, class = "try-error", condition = e))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))})
10:
FUN(X[[i]], ...) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)11:
9: lapply(seq_len(cores), inner.do)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: 12: FUN(X[[i]], ...)parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE,
mc.silent = TRUE)11:
lapply(seq_len(cores), inner.do)13:
parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 12: verbose = (verbosity > 4))parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE,
mc.silent = TRUE)14:
.self$do_with_inits(inits, Q, reinitialization_effort)
13: 15: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, .self$estim_ascend(reinitialization_effort, changing_effort)
verbose = (verbosity > 4))16:
private$BMobject$estimate()
14: 17: .self$do_with_inits(inits, Q, reinitialization_effort)mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
15: 18: .self$estim_ascend(reinitialization_effort, changing_effort)eval(code, test_env)
16: 19: private$BMobject$estimate()eval(code, test_env)
17: 20: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))withCallingHandlers({
eval(code, test_env)18: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
skip("On CRAN")19: } else if (!new_expectations && skip_on_empty) {eval(code, test_env) skip_empty() }
}, expectation = handle_expectation, packageNotFoundError = function(e) {20: withCallingHandlers({ if (on_cran()) { eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {21: skip(paste0("{", e$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) {22: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 23: error = handle_error, interrupt = handle_interrupt)tryCatchList(expr, classes, parentenv, handlers)
21: 24: doTryCatch(return(expr), name, parentenv, handler)tryCatch(withCallingHandlers({
eval(code, test_env)22: new_expectations <- the$test_expectations > starting_expectationstryCatchOne(expr, names, parentenv, handlers[[1L]]) if (snapshot_skipped) {
skip("On CRAN")23: } else if (!new_expectations && skip_on_empty) {tryCatchList(expr, classes, parentenv, handlers) skip_empty()
24: }tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations }}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip_empty()
}25: doWithOneRestart(return(expr), restart)}, expectation = handle_expectation, packageNotFoundError = function(e) {
26: if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))withOneRestart(expr, restarts[[1L]]) }
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE27: invokeRestart("muffle_cran_snapshot")withRestarts(tryCatch(withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) new_expectations <- the$test_expectations > starting_expectations
25: if (snapshot_skipped) {doWithOneRestart(return(expr), restart) skip("On CRAN")
}26: else if (!new_expectations && skip_on_empty) {withOneRestart(expr, restarts[[1L]]) skip_empty()
27: }withRestarts(tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip_empty() end_test = function() { }) }}, expectation = handle_expectation, packageNotFoundError = function(e) {
28: if (on_cran()) {test_code(code, parent.frame()) skip(paste0("{", e$package, "} is not installed."))
}}, snapshot_on_cran = function(cnd) {29: snapshot_skipped <<- TRUEtest_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", invokeRestart("muffle_cran_snapshot") {}, skip = handle_skip, warning = handle_warning, message = handle_message, sampler_directed_nocov$rNetwork(store = TRUE) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData,
"bernoulli", TRUE)28: test_code(code, parent.frame()) mySBM_sbm$optimize(estimOptions = list(verbosity = 0,
plot = FALSE))29: mySBM_sbm$setModel(3)test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) { sampler_directed_nocov$rNetwork(store = TRUE) cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_nocov$networkData, "bernoulli", TRUE) clusterInit = cl) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), plot = FALSE)) mySBM_sbm$setModel(3) 0.1) net <- missSBM:::partlyObservedNetwork$new(sampler_directed_nocov$networkData) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), cl <- net$clustering(3)[[1]] mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(sampler_directed_nocov$networkData, 0.95) clusterInit = cl) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 0.01) 0.1) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), 0.95) 0.1) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), 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({ 0.2) eval(code, test_env) expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), new_expectations <- the$test_expectations > starting_expectations 0.95) if (snapshot_skipped) { })
skip("On CRAN") } else if (!new_expectations && skip_on_empty) {30: eval(code, test_env) skip_empty() }
31: }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {eval(code, test_env)
skip(paste0("{", e$package, "} is not installed."))32: }}, snapshot_on_cran = function(cnd) {withCallingHandlers({ eval(code, test_env) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") error = handle_error, interrupt = handle_interrupt)
} else if (!new_expectations && skip_on_empty) {33: skip_empty() }doTryCatch(return(expr), name, parentenv, handler)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {34: tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}35: tryCatchList(expr, classes, parentenv, handlers)}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE
36: invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatch(withCallingHandlers({ error = handle_error, interrupt = handle_interrupt) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {33: doTryCatch(return(expr), name, parentenv, handler) skip("On CRAN") }
34: else if (!new_expectations && skip_on_empty) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip_empty()
}}, expectation = handle_expectation, packageNotFoundError = function(e) {35: if (on_cran()) {tryCatchList(expr, classes, parentenv, handlers) skip(paste0("{", e$package, "} is not installed."))
}36: }, snapshot_on_cran = function(cnd) {tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
skip("On CRAN")37: }doWithOneRestart(return(expr), restart)
else if (!new_expectations && skip_on_empty) {38: skip_empty() }withOneRestart(expr, restarts[[1L]])}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))39: }}, snapshot_on_cran = function(cnd) {withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip("On CRAN") }
37: else if (!new_expectations && skip_on_empty) {doWithOneRestart(return(expr), restart)
skip_empty()38: }}, expectation = handle_expectation, packageNotFoundError = function(e) {withOneRestart(expr, restarts[[1L]])
if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))39: }withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip("On CRAN") } error = handle_error, interrupt = handle_interrupt), error = handle_fatal), else if (!new_expectations && skip_on_empty) { end_test = function() { }) skip_empty()
}40: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_code(code = exprs, env = env, reporter = get_reporter() %||% if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) StopReporter$new()) }}, snapshot_on_cran = function(cnd) {
41: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() { })42:
40: FUN(X[[i]], ...)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())
43: 41: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) error_call = error_call)
42: 44: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)
45: 43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, tryCatchOne(expr, names, parentenv, handlers[[1L]])
error_call = error_call)
46: tryCatchList(expr, classes, parentenv, handlers)44: doTryCatch(return(expr), name, parentenv, handler)
47:
45: tryCatch(code, testthat_abort_reporter = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) cat(conditionMessage(cnd), "\n") NULL
})46:
tryCatchList(expr, classes, parentenv, handlers)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 47: env = env, desc = desc, shuffle = shuffle, error_call = error_call))
tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n")49: test_files_serial(test_dir = test_dir, test_package = test_package, NULL}) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 48: desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, reporter = reporter, load_helpers = load_helpers, env = env, 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, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) load_package = load_package, parallel = parallel, shuffle = shuffle)
51:
test_dir("testthat", package = package, reporter = reporter, 50: ..., load_package = "installed")test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env,
52: 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-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