Last updated on 2026-11-04 01:52:12 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4.3 | 7.95 | 72.68 | 80.63 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4.3 | 6.21 | 56.77 | 62.98 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.4.3 | 54.29 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.4.3 | 53.80 | OK | |||
| r-devel-windows-x86_64 | 1.4.3 | 9.00 | 87.00 | 96.00 | OK | |
| r-patched-linux-x86_64 | 1.4.3 | 7.75 | 67.23 | 74.98 | OK | |
| r-release-linux-x86_64 | 1.4.3 | 7.18 | 66.83 | 74.01 | OK | |
| r-release-macos-arm64 | 1.4.3 | 2.00 | 21.00 | 23.00 | OK | |
| r-release-macos-x86_64 | 1.4.3 | 6.00 | 65.00 | 71.00 | OK | |
| r-release-windows-x86_64 | 1.4.3 | 9.00 | 81.00 | 90.00 | OK | |
| r-oldrel-macos-arm64 | 1.4.3 | 3.00 | 59.00 | 62.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.4.3 | 5.00 | 77.00 | 82.00 | OK | |
| r-oldrel-windows-x86_64 | 1.4.3 | 11.00 | 100.00 | 111.00 | OK |
Version: 1.4.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scTenifoldNet)
>
> test_check("scTenifoldNet")
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: FUN(X[[i]], ...)
2: lapply(X = S, FUN = FUN, ...)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: 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))})
7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: FUN(X[[i]], ...)
10: lapply(seq_len(cores), inner.do)
11: parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, mc.preschedule = TRUE)
12: .pcNetCoefficients(basis$Z, basis$d, nComp, nCores)
13: pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)
14: eval_bare(expr, quo_get_env(quo))
15: quasi_label(enquo(object), label)
16: expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))
17: eval(code, test_env)
18: eval(code, test_env)
19: 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)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
Traceback:
24: doWithOneRestart(return(expr), restart) 1:
FUN(X[[i]], ...)25:
withOneRestart(expr, restarts[[1L]]) 2:
lapply(X = S, FUN = FUN, ...)26:
withRestarts(tryCatch(withCallingHandlers({ 3: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { 4: skip("On CRAN")tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
else if (!new_expectations && skip_on_empty) { 5: skip_empty()tryCatchList(expr, classes, parentenv, handlers) }
6: }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {tryCatch(expr, error = function(e) { skip(paste0("{", e$package, "} is not installed.")) call <- conditionCall(e) if (!is.null(call)) { } if (identical(call[[1L]], quote(doTryCatch))) }, snapshot_on_cran = function(cnd) { call <- sys.call(-4L) snapshot_skipped <<- TRUE dcall <- deparse(call, nlines = 1L) invokeRestart("muffle_cran_snapshot") prefix <- paste("Error in", dcall, ": ")}, skip = handle_skip, warning = handle_warning, message = handle_message, LONG <- 75L error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
sm <- strsplit(conditionMessage(e), "\n")[[1L]]27: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")test_code(code, parent.frame()) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 28: test_that("pcNet matches per-gene SVD principal component regression", type = "b") if (w > LONG) { nCells <- 200 prefix <- paste0(prefix, "\n ") nGenes <- 100 } nComp <- 3 else prefix <- "Error : " set.seed(42) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), msg <- paste0(prefix, conditionMessage(e), "\n") nrow = nGenes, ncol = nCells) .Internal(seterrmessage(msg[1L])) rownames(X) <- paste0("Gene", seq_len(nGenes)) if (!silent && isTRUE(getOption("show.error.messages"))) { X_std <- scale(Matrix::t(X)) cat(msg, file = outFile) reference <- matrix(0, nGenes, nGenes) .Internal(printDeferredWarnings()) for (K in seq_len(nGenes)) { } design_matrix <- X_std[, -K] invisible(structure(msg, class = "try-error", condition = e))}) principal_components <- svd(design_matrix, nu = 0, nv = nComp)$v
pc_scores <- design_matrix %*% principal_components 7: pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) reference[K, -K] <- principal_components %*% pc_coefficients
} 8: xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) verbose = FALSE)
expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) 9: expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, FUN(X[[i]], ...)
nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))10: lapply(seq_len(cores), inner.do) })
11: 29: parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, eval(code, test_env) nComp = nComp, secular_weights = secular_weights, mc.cores = nCores,
mc.preschedule = TRUE)30: eval(code, test_env)
12: 31: .pcNetCoefficients(basis$Z, basis$d, nComp, nCores)
13: withCallingHandlers({pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations14: if (snapshot_skipped) {eval_bare(expr, quo_get_env(quo)) skip("On CRAN")
}15: else if (!new_expectations && skip_on_empty) {quasi_label(enquo(object), label) skip_empty()
}16: }, expectation = handle_expectation, packageNotFoundError = function(e) {expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), if (on_cran()) { pcNet(X, nComp = nComp, verbose = FALSE)) skip(paste0("{", e$package, "} is not installed."))
}17: }, snapshot_on_cran = function(cnd) {eval(code, test_env) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")18: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)eval(code, test_env)
32: 19: doTryCatch(return(expr), name, parentenv, handler)withCallingHandlers({
eval(code, test_env)33: new_expectations <- the$test_expectations > starting_expectationstryCatchOne(expr, names, parentenv, handlers[[1L]]) if (snapshot_skipped) {
skip("On CRAN")34: }tryCatchList(expr, classes, parentenv, handlers) else if (!new_expectations && skip_on_empty) {
skip_empty()35: }tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {20: skip(paste0("{", e$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE21: invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)22:
tryCatchList(expr, classes, parentenv, handlers)36:
23: doWithOneRestart(return(expr), restart)tryCatch(withCallingHandlers({
eval(code, test_env)37: new_expectations <- the$test_expectations > starting_expectationswithOneRestart(expr, restarts[[1L]]) if (snapshot_skipped) {
skip("On CRAN")38: } else if (!new_expectations && skip_on_empty) {withRestarts(tryCatch(withCallingHandlers({ skip_empty() eval(code, test_env) } 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.")) } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE24: invokeRestart("muffle_cran_snapshot")doWithOneRestart(return(expr), restart)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 25: end_test = function() {withOneRestart(expr, restarts[[1L]]) })
39:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 26: StopReporter$new())withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)40: new_expectations <- the$test_expectations > starting_expectationssource_file(path, env = env(env), desc = desc, shuffle = shuffle, if (snapshot_skipped) { error_call = error_call) skip("On CRAN") }
41: else if (!new_expectations && skip_on_empty) { skip_empty()FUN(X[[i]], ...) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {42: if (on_cran()) {lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, skip(paste0("{", e$package, "} is not installed.")) error_call = error_call) }
}, snapshot_on_cran = function(cnd) {43: snapshot_skipped <<- TRUEdoTryCatch(return(expr), name, parentenv, handler) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 44: end_test = function() {tryCatchOne(expr, names, parentenv, handlers[[1L]]) })
45: 27: tryCatchList(expr, classes, parentenv, handlers)test_code(code, parent.frame())
46:
tryCatch(code, testthat_abort_reporter = function(cnd) {28: cat(conditionMessage(cnd), "\n")test_that("pcNet matches per-gene SVD principal component regression", NULL {}) nCells <- 200
nGenes <- 10047: nComp <- 3with_reporter(reporters$multi, lapply(test_paths, test_one_file, set.seed(42) env = env, desc = desc, shuffle = shuffle, error_call = error_call)) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98),
nrow = nGenes, ncol = nCells)48: rownames(X) <- paste0("Gene", seq_len(nGenes))test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, X_std <- scale(Matrix::t(X)) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, reference <- matrix(0, nGenes, nGenes) for (K in seq_len(nGenes)) { desc = desc, load_package = load_package, shuffle = shuffle, design_matrix <- X_std[, -K] error_call = error_call) principal_components <- svd(design_matrix, nu = 0,
nv = nComp)$v49: pc_scores <- design_matrix %*% principal_componentstest_files(test_dir = path, test_paths = test_paths, test_package = package, pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) reporter = reporter, load_helpers = load_helpers, env = env, reference[K, -K] <- principal_components %*% pc_coefficients stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, } load_package = load_package, parallel = parallel, shuffle = shuffle)
xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, 50: verbose = FALSE)test_dir("testthat", package = package, reporter = reporter, expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) ..., load_package = "installed") expect_equal(pcNet(X, nComp = nComp, verbose = FALSE,
nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))51: })test_check("scTenifoldNet")
29: An irrecoverable exception occurred. R is aborting now ...
eval(code, test_env)
30: eval(code, test_env)
31: 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)
32: doTryCatch(return(expr), name, parentenv, handler)
33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: tryCatchList(expr, classes, parentenv, handlers)
35: 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)
36: doWithOneRestart(return(expr), restart)
37: withOneRestart(expr, restarts[[1L]])
38: 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() { })
39: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
40: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
41: FUN(X[[i]], ...)
42: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
43: doTryCatch(return(expr), name, parentenv, handler)
44: tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
47: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
48: 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)
49: 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)
50: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
51: test_check("scTenifoldNet")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-pcNet-89.R
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 66 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-pcNet.R:88:3'): pcNet matches per-gene SVD principal component regression ──
Error in `.pcNetCoefficients(basis$Z, basis$d, nComp, nCores)`: Parallel computation failed:
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-pcNet.R:88:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─scTenifoldNet::pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)
5. └─scTenifoldNet:::.pcNetCoefficients(basis$Z, basis$d, nComp, nCores)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 66 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64