Last updated on 2026-09-24 02:52:20 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 | 58.00 | 245.06 | 303.06 | 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 | 20.00 | 113.00 | 133.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 59.00 | 679.00 | 738.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 115.00 | 505.00 | 620.00 | 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
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iteration #: 17
iteration #: 18
iteration #: 19
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iteration #: 21
iteration #: 22
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iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Dyads are distributed according to a 'undirected' SBM.
Imputation assumes a 'node' network-sampling process
iteration #: 2
iteration #: 3
iteration #: 4
iteration #: 5
iteration #: 6
iteration #: 7
iteration #: 8
iteration #: 9
iteration #: 10
iteration #: 11
iteration #: 12
iteration #: 13
iteration #: 14
iteration #: 15
iteration #: 16
iteration #: 17
iteration #: 18
iteration #: 19
iteration #: 20
iteration #: 21
iteration #: 22
iteration #: 23
iteration #: 24
iteration #: 25
iteration #: 26
iteration #: 27
iteration #: 28
iteration #: 29
iteration #: 30
iteration #: 31
iteration #: 32
iteration #: 33
iteration #: 34
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'node' network-sampling process
Initialization of 1 model(s).
Performing VEM inference
Model with 3 blocks.
Adjusting Variational EM for Stochastic Block Model
Imputation assumes a 'dyad' network-sampling process
Initialization of 2 model(s).
Performing VEM inference
Model with 2 blocks.
Model with 1 blocks.
Polishing (node-swap)
Looking for better solutions
Pass 1 Going forward +
Pass 1 Going backward +
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)
13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4))
14: .self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: private$BMobject$estimate()
17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: eval(code, test_env)
19: eval(code, test_env)
20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env)
Traceback:
1: new_expectations <- the$test_expectations > starting_expectationsdispatcher(membership_name, membership_init$to_cc(), model_name, if (snapshot_skipped) { .self$network_to_cc(), TRUE) skip("On CRAN")
} 2: else if (!new_expectations && skip_on_empty) {FUN(X[[i]], ...) skip_empty()
} 3: }, expectation = handle_expectation, packageNotFoundError = function(e) {lapply(X = S, FUN = FUN, ...) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
} 4: }, snapshot_on_cran = function(cnd) {doTryCatch(return(expr), name, parentenv, handler)
snapshot_skipped <<- TRUE 5: invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 6:
tryCatchList(expr, classes, parentenv, handlers)25:
doWithOneRestart(return(expr), restart) 7:
tryCatch(expr, error = function(e) {26: call <- conditionCall(e)withOneRestart(expr, restarts[[1L]])
if (!is.null(call)) {27: withRestarts(tryCatch(withCallingHandlers({ if (identical(call[[1L]], quote(doTryCatch))) eval(code, test_env) call <- sys.call(-4L) new_expectations <- the$test_expectations > starting_expectations dcall <- deparse(call, nlines = 1L) if (snapshot_skipped) { prefix <- paste("Error in", dcall, ": ") skip("On CRAN") LONG <- 75L } sm <- strsplit(conditionMessage(e), "\n")[[1L]] else if (!new_expectations && skip_on_empty) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") skip_empty() if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }, expectation = handle_expectation, packageNotFoundError = function(e) { type = "b") if (on_cran()) { if (w > LONG) skip(paste0("{", e$package, "} is not installed.")) prefix <- paste0(prefix, "\n ") } }}, snapshot_on_cran = function(cnd) { else prefix <- "Error : " snapshot_skipped <<- TRUE msg <- paste0(prefix, conditionMessage(e), "\n") invokeRestart("muffle_cran_snapshot") .Internal(seterrmessage(msg[1L]))}, skip = handle_skip, warning = handle_warning, message = handle_message, if (!silent && isTRUE(getOption("show.error.messages"))) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), cat(msg, file = outFile) end_test = function() { .Internal(printDeferredWarnings()) }) }
invisible(structure(msg, class = "try-error", condition = e))28: })test_code(code, parent.frame())
8: 29: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate",
{ 9: sampler_undirected_cov$rNetwork(store = TRUE)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData,
"bernoulli", FALSE, covarList = covarList_undirected)10: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, FUN(X[[i]], ...) plot = FALSE))
mySBM_sbm$setModel(Q)11: net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData, lapply(seq_len(cores), inner.do) covariates = covarList_undirected)
cls <- net$clustering(1:(2 * Q))12: cl <- cls[[Q]]parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, mc.silent = TRUE) clusterInit = cl, covarList = covarList_undirected)
mySBM_missSBM$doVEM()13: expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, 0.05) verbose = (verbosity > 4)) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships),
0.8)14: expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), .self$do_with_inits(inits, Q, reinitialization_effort) 0.01)
expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), 15: 0.1).self$estim_ascend(reinitialization_effort, changing_effort) expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam),
0.1)16: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), private$BMobject$estimate() 0.85)
})17:
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))30:
eval(code, test_env)18:
eval(code, test_env)31:
eval(code, test_env)19:
eval(code, test_env)32:
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)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)33:
doTryCatch(return(expr), name, parentenv, handler)21:
doTryCatch(return(expr), name, parentenv, handler)34:
tryCatchOne(expr, names, parentenv, handlers[[1L]])22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])35:
tryCatchList(expr, classes, parentenv, handlers)23:
tryCatchList(expr, classes, parentenv, handlers)36:
tryCatch(withCallingHandlers({24: eval(code, test_env)tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { } 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), error = handle_fatal)37:
doWithOneRestart(return(expr), restart)25:
doWithOneRestart(return(expr), restart)38:
withOneRestart(expr, restarts[[1L]])26:
withOneRestart(expr, restarts[[1L]])39:
withRestarts(tryCatch(withCallingHandlers({27: eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } 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() %||% 28: StopReporter$new())test_code(code, parent.frame())
41: 29: source_file(path, env = env(env), desc = desc, shuffle = shuffle, test_that("SimpleSBM_fit 'Bernoulli' model, undirected, one covariate", error_call = error_call) {
sampler_undirected_cov$rNetwork(store = TRUE)42: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_cov$networkData, FUN(X[[i]], ...) "bernoulli", FALSE, covarList = covarList_undirected)
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 43: plot = FALSE))lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, mySBM_sbm$setModel(Q) error_call = error_call) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_cov$networkData,
covariates = covarList_undirected)44: cls <- net$clustering(1:(2 * Q))doTryCatch(return(expr), name, parentenv, handler) cl <- cls[[Q]]
mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, 45: clusterInit = cl, covarList = covarList_undirected)tryCatchOne(expr, names, parentenv, handlers[[1L]]) mySBM_missSBM$doVEM() expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean),
0.05)46: expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), tryCatchList(expr, classes, parentenv, handlers) 0.8)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 47: 0.01)tryCatch(code, testthat_abort_reporter = function(cnd) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_cov$connectParam$mean), cat(conditionMessage(cnd), "\n") 0.1) NULL expect_lt(rmse(mySBM_missSBM$covarParam, sampler_undirected_cov$covarParam), }) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_cov$memberships), 48: 0.85)with_reporter(reporters$multi, lapply(test_paths, test_one_file, }) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
30: 49: eval(code, test_env)test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 31: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, eval(code, test_env) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)32:
withCallingHandlers({50: eval(code, test_env)test_files(test_dir = path, test_paths = test_paths, test_package = package, new_expectations <- the$test_expectations > starting_expectations reporter = reporter, load_helpers = load_helpers, env = env, if (snapshot_skipped) { stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, skip("On CRAN") load_package = load_package, parallel = parallel, shuffle = shuffle) }
else if (!new_expectations && skip_on_empty) {51: skip_empty()test_dir("testthat", package = package, reporter = reporter, } ..., load_package = "installed")}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {52: skip(paste0("{", e$package, "} is not installed."))test_check("missSBM") }
}, snapshot_on_cran = function(cnd) {An irrecoverable exception occurred. R is aborting now ...
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...)
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
52: test_check("missSBM")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-sbm-bernoulli-with-covariates-16.R
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e)
Traceback:
1: if (!is.null(call)) {dispatcher(membership_name, membership_init$to_cc(), model_name, if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) .self$network_to_cc(), TRUE) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") 2: LONG <- 75LFUN(X[[i]], ...) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 3: if (is.na(w)) lapply(X = S, FUN = FUN, ...) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") if (w > LONG) 4: prefix <- paste0(prefix, "\n ")doTryCatch(return(expr), name, parentenv, handler) }
else prefix <- "Error : " 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) 6: if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatchList(expr, classes, parentenv, handlers) cat(msg, file = outFile)
.Internal(printDeferredWarnings()) 7: }tryCatch(expr, error = function(e) { invisible(structure(msg, class = "try-error", condition = e)) call <- conditionCall(e)}) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 8: call <- sys.call(-4L)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") LONG <- 75L 9: sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
if (is.na(w)) 10: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], FUN(X[[i]], ...)
11: type = "b")lapply(seq_len(cores), inner.do) if (w > LONG)
prefix <- paste0(prefix, "\n ")12: } else prefix <- "Error : "parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, msg <- paste0(prefix, conditionMessage(e), "\n") mc.silent = TRUE) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {13: cat(msg, file = outFile)parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, .Internal(printDeferredWarnings()) verbose = (verbosity > 4)) }
invisible(structure(msg, class = "try-error", condition = e))})14:
.self$do_with_inits(inits, Q, reinitialization_effort) 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15: 9: .self$estim_ascend(reinitialization_effort, changing_effort)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
16: 10: private$BMobject$estimate()FUN(X[[i]], ...)
17: 11: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))lapply(seq_len(cores), inner.do)
18:
eval(code, test_env)12:
parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, 19: eval(code, test_env) mc.silent = TRUE)
13: 20: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, withCallingHandlers({ verbose = (verbosity > 4)) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations14: if (snapshot_skipped) {.self$do_with_inits(inits, Q, reinitialization_effort) skip("On CRAN")
} else if (!new_expectations && skip_on_empty) {15: skip_empty().self$estim_ascend(reinitialization_effort, changing_effort) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {16: if (on_cran()) {private$BMobject$estimate() skip(paste0("{", e$package, "} is not installed."))
17: }mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")18: }, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt)
19: 21: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler)
20: 22: tryCatchOne(expr, names, parentenv, handlers[[1L]])withCallingHandlers({
eval(code, test_env)23: new_expectations <- the$test_expectations > starting_expectationstryCatchList(expr, classes, parentenv, handlers)
if (snapshot_skipped) {24: skip("On CRAN")tryCatch(withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$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$package, "} is not installed.")) skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")21: }, skip = handle_skip, warning = handle_warning, message = handle_message, doTryCatch(return(expr), name, parentenv, handler) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
22: 25: tryCatchOne(expr, names, parentenv, handlers[[1L]])doWithOneRestart(return(expr), restart)
26: 23: withOneRestart(expr, restarts[[1L]])tryCatchList(expr, classes, parentenv, handlers)
27: withRestarts(tryCatch(withCallingHandlers({24: eval(code, test_env)tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations skip("On CRAN") } 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()) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { skip(paste0("{", e$package, "} is not installed.")) } if (on_cran()) {}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 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: doWithOneRestart(return(expr), restart)29:
26: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", withOneRestart(expr, restarts[[1L]]) {
sampler_directed_cov$rNetwork(store = TRUE)27: mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, withRestarts(tryCatch(withCallingHandlers({ "bernoulli", TRUE, covarList = covarList_directed) eval(code, test_env) mySBM_sbm$optimize(estimOptions = list(verbosity = 0, new_expectations <- the$test_expectations > starting_expectations plot = FALSE)) mySBM_sbm$setModel(Q) if (snapshot_skipped) { net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, skip("On CRAN") covariates = covarList_directed) } cls <- net$clustering(1:(2 * Q)) cl <- cls[[Q]] else if (!new_expectations && skip_on_empty) { skip_empty() mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, } clusterInit = cl, covarList = covarList_directed)}, expectation = handle_expectation, packageNotFoundError = function(e) { mySBM_missSBM$doVEM(trace = TRUE) if (on_cran()) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), skip(paste0("{", e$package, "} is not installed.")) 0.1) } expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }, snapshot_on_cran = function(cnd) { 0.8) snapshot_skipped <<- TRUE expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), invokeRestart("muffle_cran_snapshot") 0.05)}, skip = handle_skip, warning = handle_warning, message = handle_message, expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 0.1) end_test = function() { expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), }) 0.85)
})
28: 30: test_code(code, parent.frame())eval(code, test_env)
29: 31: test_that("SimpleSBM_fit 'Bernoulli' model, directed, one covariate", eval(code, test_env) { sampler_directed_cov$rNetwork(store = TRUE)
32: withCallingHandlers({ mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_directed_cov$networkData, eval(code, test_env) "bernoulli", TRUE, covarList = covarList_directed) new_expectations <- the$test_expectations > starting_expectations mySBM_sbm$optimize(estimOptions = list(verbosity = 0, if (snapshot_skipped) { plot = FALSE)) skip("On CRAN") mySBM_sbm$setModel(Q) } net <- missSBM:::partlyObservedNetwork$new(sampler_directed_cov$networkData, else if (!new_expectations && skip_on_empty) { covariates = covarList_directed) skip_empty() cls <- net$clustering(1:(2 * Q)) }}, expectation = handle_expectation, packageNotFoundError = function(e) { cl <- cls[[Q]] if (on_cran()) { mySBM_missSBM <- missSBM:::SimpleSBM_fit_withCov$new(net, skip(paste0("{", e$package, "} is not installed.")) clusterInit = cl, covarList = covarList_directed) } mySBM_missSBM$doVEM(trace = TRUE)}, snapshot_on_cran = function(cnd) { expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), snapshot_skipped <<- TRUE 0.1) invokeRestart("muffle_cran_snapshot") expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }, skip = handle_skip, warning = handle_warning, message = handle_message, 0.8) error = handle_error, interrupt = handle_interrupt) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.05)33: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_cov$connectParam$mean), doTryCatch(return(expr), name, parentenv, handler) 0.1)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_cov$memberships), 34: 0.85)tryCatchOne(expr, names, parentenv, handlers[[1L]]) })
35: 30: tryCatchList(expr, classes, parentenv, handlers)eval(code, test_env)
36: tryCatch(withCallingHandlers({31: eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {32: skip("On CRAN")withCallingHandlers({ } eval(code, test_env) else if (!new_expectations && skip_on_empty) { new_expectations <- the$test_expectations > starting_expectations skip_empty() if (snapshot_skipped) { } skip("On CRAN")}, expectation = handle_expectation, packageNotFoundError = function(e) { } 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) {
snapshot_skipped <<- TRUE37: invokeRestart("muffle_cran_snapshot")doWithOneRestart(return(expr), restart)
}, skip = handle_skip, warning = handle_warning, message = handle_message, 38: error = handle_error, interrupt = handle_interrupt)withOneRestart(expr, restarts[[1L]])
33: 39: doTryCatch(return(expr), name, parentenv, handler)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)34: new_expectations <- the$test_expectations > starting_expectationstryCatchOne(expr, names, parentenv, handlers[[1L]]) if (snapshot_skipped) { skip("On CRAN")
}35: else if (!new_expectations && skip_on_empty) {tryCatchList(expr, classes, parentenv, handlers) skip_empty()
}36: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip_empty() end_test = function() { } })}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {40: skip(paste0("{", e$package, "} is not installed."))test_code(code = exprs, env = env, reporter = get_reporter() %||% } StopReporter$new())}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE41: invokeRestart("muffle_cran_snapshot")source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
42: 37: FUN(X[[i]], ...)
doWithOneRestart(return(expr), restart)43:
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 38: error_call = error_call)withOneRestart(expr, restarts[[1L]])
39: 44: withRestarts(tryCatch(withCallingHandlers({doTryCatch(return(expr), name, parentenv, handler) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations45: if (snapshot_skipped) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip("On CRAN")
}46: else if (!new_expectations && skip_on_empty) {tryCatchList(expr, classes, parentenv, handlers) skip_empty()
}47: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatch(code, testthat_abort_reporter = function(cnd) { if (on_cran()) { cat(conditionMessage(cnd), "\n") skip(paste0("{", e$package, "} is not installed.")) NULL }})}, snapshot_on_cran = function(cnd) {
48: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")with_reporter(reporters$multi, lapply(test_paths, test_one_file, }, skip = handle_skip, warning = handle_warning, message = handle_message, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {49: })
test_files_serial(test_dir = test_dir, test_package = test_package, 40: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, test_code(code = exprs, env = env, reporter = get_reporter() %||% env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, StopReporter$new()) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 50: error_call = error_call)test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 42: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, FUN(X[[i]], ...) load_package = load_package, parallel = parallel, shuffle = shuffle)
43: 51: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, test_dir("testthat", package = package, reporter = reporter, error_call = error_call) ..., load_package = "installed")
44: 52: doTryCatch(return(expr), name, parentenv, handler)test_check("missSBM")
45: An irrecoverable exception occurred. R is aborting now ...
tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$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:
Traceback:
1: lapply(X = S, FUN = FUN, ...)dispatcher(membership_name, membership_init$to_cc(), model_name, .self$network_to_cc(), TRUE)
4: 2: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)
3: 5: lapply(X = S, FUN = FUN, ...)
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: doTryCatch(return(expr), name, parentenv, handler)
6: 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
6: 7: tryCatchList(expr, classes, parentenv, handlers)tryCatch(expr, error = function(e) {
call <- conditionCall(e) 7: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) tryCatch(expr, error = function(e) { call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) call <- conditionCall(e) if (!is.null(call)) { prefix <- paste("Error in", dcall, ": ") if (identical(call[[1L]], quote(doTryCatch))) LONG <- 75L call <- sys.call(-4L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] dcall <- deparse(call, nlines = 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]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") type = "b") if (w > LONG) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], prefix <- paste0(prefix, "\n ") type = "b") if (w > LONG) } else prefix <- "Error : " prefix <- paste0(prefix, "\n ") } msg <- paste0(prefix, conditionMessage(e), "\n") else prefix <- "Error : " .Internal(seterrmessage(msg[1L])) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) cat(msg, file = outFile) } .Internal(printDeferredWarnings()) invisible(structure(msg, class = "try-error", condition = e)) }}) invisible(structure(msg, class = "try-error", condition = e))
}) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 8:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 9:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))10:
FUN(X[[i]], ...)
10: FUN(X[[i]], ...)11:
lapply(seq_len(cores), inner.do)11: lapply(seq_len(cores), inner.do)
12: 12: parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE) mc.silent = TRUE)
13: 13: parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, verbose = (verbosity > 4)) verbose = (verbosity > 4))
14: 14: .self$do_with_inits(inits, Q, reinitialization_effort).self$do_with_inits(inits, Q, reinitialization_effort)
15: .self$estim_ascend(reinitialization_effort, changing_effort)15: .self$estim_ascend(reinitialization_effort, changing_effort)
16: 16: private$BMobject$estimate()private$BMobject$estimate()
17: 17: mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE))
18: 18: eval(code, test_env)eval(code, test_env)
19: 19: eval(code, test_env)eval(code, test_env)
20:
withCallingHandlers({20: eval(code, test_env)withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() skip("On CRAN") }}, expectation = handle_expectation, packageNotFoundError = function(e) { } else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip_empty() } skip(paste0("{", e$package, "} is not installed.")) }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE error = handle_error, interrupt = handle_interrupt) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
21: error = handle_error, interrupt = handle_interrupt)
doTryCatch(return(expr), name, parentenv, handler)
21: doTryCatch(return(expr), name, parentenv, handler)22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])22:
tryCatchOne(expr, names, parentenv, handlers[[1L]])23:
tryCatchList(expr, classes, parentenv, handlers)
23: 24: tryCatch(withCallingHandlers({tryCatchList(expr, classes, parentenv, handlers) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {24: skip("On CRAN")tryCatch(withCallingHandlers({ } else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))25: }doWithOneRestart(return(expr), restart)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE26: withOneRestart(expr, restarts[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
27: withRestarts(tryCatch(withCallingHandlers({25: eval(code, test_env)doWithOneRestart(return(expr), restart) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN")26: } else if (!new_expectations && skip_on_empty) {withOneRestart(expr, restarts[[1L]]) skip_empty()
}27: }, expectation = handle_expectation, packageNotFoundError = function(e) {withRestarts(tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { skip_empty() }) }
28: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_code(code, parent.frame()) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))29: }test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", }, snapshot_on_cran = function(cnd) { { sampler_undirected_nocov$rNetwork(store = TRUE) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, end_test = function() { "bernoulli", FALSE) })
mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 28: plot = FALSE))test_code(code, parent.frame()) mySBM_sbm$setModel(3)
net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData)29: cl <- net$clustering(3)[[1]]test_that("SimpleSBM_fit 'Bernoulli' model, undirected, no covariate", { mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, sampler_undirected_nocov$rNetwork(store = TRUE) clusterInit = cl) mySBM_sbm <- sbm::SimpleSBM_fit$new(sampler_undirected_nocov$networkData, mySBM_missSBM$doVEM() "bernoulli", FALSE) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), mySBM_sbm$optimize(estimOptions = list(verbosity = 0, 0.05) plot = FALSE)) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), mySBM_sbm$setModel(3) net <- missSBM:::partlyObservedNetwork$new(sampler_undirected_nocov$networkData) 0.95) cl <- net$clustering(3)[[1]] expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), mySBM_missSBM <- missSBM:::SimpleSBM_fit_noCov$new(net, 0.01) clusterInit = cl) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean), mySBM_missSBM$doVEM() 0.05) expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), 0.05) 0.95) expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), }) 0.95)
expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik), 30: 0.01)eval(code, test_env) expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_undirected_nocov$connectParam$mean),
0.05)31: expect_gt(ARI(mySBM_missSBM$memberships, sampler_undirected_nocov$memberships), eval(code, test_env) 0.95)
})32:
withCallingHandlers({30: eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN")31: }eval(code, test_env)
else if (!new_expectations && skip_on_empty) { skip_empty()32: }withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {33: skip(paste0("{", e$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) {34: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 35: error = handle_error, interrupt = handle_interrupt)tryCatchList(expr, classes, parentenv, handlers)
36: 33: tryCatch(withCallingHandlers({doTryCatch(return(expr), name, parentenv, handler) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations34: tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (snapshot_skipped) {
skip("On CRAN")35: }tryCatchList(expr, classes, parentenv, handlers) else if (!new_expectations && skip_on_empty) {
skip_empty()36: }tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { }}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {37: if (on_cran()) {doWithOneRestart(return(expr), restart) skip(paste0("{", e$package, "} is not installed."))
}38: }, snapshot_on_cran = function(cnd) {withOneRestart(expr, restarts[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")39: }, skip = handle_skip, warning = handle_warning, message = handle_message, withRestarts(tryCatch(withCallingHandlers({ error = handle_error, interrupt = handle_interrupt), error = handle_fatal) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations37: if (snapshot_skipped) {doWithOneRestart(return(expr), restart) skip("On CRAN")
}38: else if (!new_expectations && skip_on_empty) {withOneRestart(expr, restarts[[1L]]) skip_empty()
}39: }, expectation = handle_expectation, packageNotFoundError = function(e) {withRestarts(tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() {}, expectation = handle_expectation, packageNotFoundError = function(e) { }) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))40: }test_code(code = exprs, env = env, reporter = get_reporter() %||% }, snapshot_on_cran = function(cnd) { StopReporter$new()) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")41: }, skip = handle_skip, warning = handle_warning, message = handle_message, source_file(path, env = env(env), desc = desc, shuffle = shuffle, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), error_call = error_call) end_test = function() {
})42:
FUN(X[[i]], ...)40:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 43: StopReporter$new())lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)41:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 44: error_call = error_call)doTryCatch(return(expr), name, parentenv, handler)
42: 45: FUN(X[[i]], ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
43: 46: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, tryCatchList(expr, classes, parentenv, handlers) error_call = error_call)
47: 44: tryCatch(code, testthat_abort_reporter = function(cnd) {doTryCatch(return(expr), name, parentenv, handler) cat(conditionMessage(cnd), "\n")
NULL45: tryCatchOne(expr, names, parentenv, handlers[[1L]])})
46: 48: tryCatchList(expr, classes, parentenv, handlers)with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))47:
49: tryCatch(code, testthat_abort_reporter = function(cnd) {test_files_serial(test_dir = test_dir, test_package = test_package, cat(conditionMessage(cnd), "\n") test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, NULL env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)48:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 50: env = env, desc = desc, shuffle = shuffle, error_call = error_call))test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 49: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_files_serial(test_dir = test_dir, test_package = test_package, load_package = load_package, parallel = parallel, shuffle = shuffle) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 51: desc = desc, load_package = load_package, shuffle = shuffle, test_dir("testthat", package = package, reporter = reporter, error_call = error_call) ..., load_package = "installed")
50: 52: test_files(test_dir = path, test_paths = test_paths, test_package = package, test_check("missSBM") reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, An irrecoverable exception occurred. R is aborting now ...
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$doVEM()
Traceback:
expect_lt(rmse(mySBM_missSBM$connectParam$mean, mySBM_sbm$connectParam$mean), 1: 0.1)dispatcher(membership_name, membership_init$to_cc(), model_name, expect_gt(ARI(mySBM_missSBM$memberships, mySBM_sbm$memberships), .self$network_to_cc(), TRUE) 0.95) expect_lt(rmse(mySBM_missSBM$loglik, mySBM_sbm$loglik),
0.01) 2: expect_lt(rmse(mySBM_missSBM$connectParam$mean, sampler_directed_nocov$connectParam$mean), FUN(X[[i]], ...)
0.1) 3: expect_lt(rmse(mySBM_missSBM$covarParam, sampler_directed_cov$covarParam), lapply(X = S, FUN = FUN, ...) 0.2)
expect_gt(ARI(mySBM_missSBM$memberships, sampler_directed_nocov$memberships), 4: 0.95) })doTryCatch(return(expr), name, parentenv, handler)
30: 5: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]])
31:
eval(code, test_env) 6:
tryCatchList(expr, classes, parentenv, handlers)32:
withCallingHandlers({ 7: tryCatch(expr, error = function(e) { eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations call <- conditionCall(e) if (snapshot_skipped) { skip("On CRAN") if (!is.null(call)) { } if (identical(call[[1L]], quote(doTryCatch))) else if (!new_expectations && skip_on_empty) { call <- sys.call(-4L) skip_empty() dcall <- deparse(call, nlines = 1L) } prefix <- paste("Error in", dcall, ": ")}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { LONG <- 75L skip(paste0("{", e$package, "} is not installed.")) sm <- strsplit(conditionMessage(e), "\n")[[1L]] } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) }, snapshot_on_cran = function(cnd) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], snapshot_skipped <<- TRUE type = "b") invokeRestart("muffle_cran_snapshot") if (w > LONG) }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) prefix <- paste0(prefix, "\n ")
}33: else prefix <- "Error : "doTryCatch(return(expr), name, parentenv, handler) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))
34: if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) cat(msg, file = outFile)
.Internal(printDeferredWarnings())35: }tryCatchList(expr, classes, parentenv, handlers) invisible(structure(msg, class = "try-error", condition = e))
})36:
tryCatch(withCallingHandlers({ 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations 9: if (snapshot_skipped) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) skip("On CRAN")
}10: else if (!new_expectations && skip_on_empty) {FUN(X[[i]], ...) skip_empty()
}11: }, expectation = handle_expectation, packageNotFoundError = function(e) {lapply(seq_len(cores), inner.do) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
12: }parallel::mclapply(X, FUN, ..., mc.cores = mc.cores, mc.set.seed = FALSE, mc.silent = TRUE)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE13: invokeRestart("muffle_cran_snapshot")parallel_lapply(inits, .self$do_one_estim, mc.cores = ncores, }, skip = handle_skip, warning = handle_warning, message = handle_message, verbose = (verbosity > 4)) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
14: 37: .self$do_with_inits(inits, Q, reinitialization_effort)doWithOneRestart(return(expr), restart)
15: 38: .self$estim_ascend(reinitialization_effort, changing_effort)withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations16: if (snapshot_skipped) {private$BMobject$estimate() skip("On CRAN")
}17: else if (!new_expectations && skip_on_empty) {mySBM_sbm$optimize(estimOptions = list(verbosity = 0, plot = FALSE)) skip_empty()
}18: }, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env) if (on_cran()) {
19: skip(paste0("{", e$package, "} is not installed."))eval(code, test_env)
}20: }, snapshot_on_cran = function(cnd) {withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { skip("On CRAN") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } else if (!new_expectations && skip_on_empty) { end_test = function() { skip_empty() }) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {40: if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))test_code(code = exprs, env = env, reporter = get_reporter() %||% } StopReporter$new())}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, invokeRestart("muffle_cran_snapshot") error_call = error_call)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)42:
FUN(X[[i]], ...)21: doTryCatch(return(expr), name, parentenv, handler)
43: 22: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, tryCatchOne(expr, names, parentenv, handlers[[1L]])
error_call = error_call)23:
tryCatchList(expr, classes, parentenv, handlers)44:
doTryCatch(return(expr), name, parentenv, handler)24:
tryCatch(withCallingHandlers({45: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {46: skip("On CRAN")tryCatchList(expr, classes, parentenv, handlers)
47: }tryCatch(code, testthat_abort_reporter = function(cnd) { else if (!new_expectations && skip_on_empty) { cat(conditionMessage(cnd), "\n") skip_empty() NULL }})}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {48: skip(paste0("{", e$package, "} is not installed."))with_reporter(reporters$multi, lapply(test_paths, test_one_file, } env = env, desc = desc, shuffle = shuffle, error_call = error_call))}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE49: test_files_serial(test_dir = test_dir, test_package = test_package, invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)25:
doWithOneRestart(return(expr), restart)50:
26: withOneRestart(expr, restarts[[1L]])test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 27: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, withRestarts(tryCatch(withCallingHandlers({ load_package = load_package, parallel = parallel, shuffle = shuffle) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {51: skip("On CRAN") }test_dir("testthat", package = package, reporter = reporter, else if (!new_expectations && skip_on_empty) { ..., load_package = "installed")
skip_empty() }52: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_check("missSBM") if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) }An irrecoverable exception occurred. R is aborting now ...
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
28: test_code(code, parent.frame())
29: test_that("SimpleSBM_fit 'Bernoulli' model, directed, no covariate", { sampler_directed_nocov$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
Flavor: r-oldrel-macos-arm64