Last updated on 2026-11-04 22:56:26 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 | 6.04 | 55.84 | 61.88 | 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 | 41.00 | 44.00 | 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’ [2s/2s]
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)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: 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.")) }
Traceback:
}, snapshot_on_cran = function(cnd) { 1: snapshot_skipped <<- TRUEFUN(X[[i]], ...) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 2: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), lapply(X = S, FUN = FUN, ...) end_test = function() {
}) 3:
doTryCatch(return(expr), name, parentenv, handler)27:
test_code(code, parent.frame()) 4:
tryCatchOne(expr, names, parentenv, handlers[[1L]])28:
test_that("pcNet matches per-gene SVD principal component regression", 5: {tryCatchList(expr, classes, parentenv, handlers) nCells <- 200
nGenes <- 100 6: nComp <- 3tryCatch(expr, error = function(e) { set.seed(42) call <- conditionCall(e) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), if (!is.null(call)) { nrow = nGenes, ncol = nCells) if (identical(call[[1L]], quote(doTryCatch))) rownames(X) <- paste0("Gene", seq_len(nGenes)) call <- sys.call(-4L) X_std <- scale(Matrix::t(X)) dcall <- deparse(call, nlines = 1L) reference <- matrix(0, nGenes, nGenes) prefix <- paste("Error in", dcall, ": ") for (K in seq_len(nGenes)) { LONG <- 75L design_matrix <- X_std[, -K] sm <- strsplit(conditionMessage(e), "\n")[[1L]] principal_components <- svd(design_matrix, nu = 0, nv = nComp)$v w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") pc_scores <- design_matrix %*% principal_components if (is.na(w)) pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], reference[K, -K] <- principal_components %*% pc_coefficients type = "b") } if (w > LONG) xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, prefix <- paste0(prefix, "\n ") verbose = FALSE) } expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) else prefix <- "Error : " expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, msg <- paste0(prefix, conditionMessage(e), "\n") nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) .Internal(seterrmessage(msg[1L])) }) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)29: .Internal(printDeferredWarnings())eval(code, test_env) }
invisible(structure(msg, class = "try-error", condition = e))30: })eval(code, test_env)
7: 31: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)withCallingHandlers({
eval(code, test_env) 8: new_expectations <- the$test_expectations > starting_expectationssendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (snapshot_skipped) {
skip("On CRAN") 9: }FUN(X[[i]], ...) else if (!new_expectations && skip_on_empty) {
skip_empty()10: }lapply(seq_len(cores), inner.do)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {11: skip(paste0("{", e$package, "} is not installed."))parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, } nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, }, snapshot_on_cran = function(cnd) { mc.preschedule = TRUE) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, 12: error = handle_error, interrupt = handle_interrupt).pcNetCoefficients(basis$Z, basis$d, nComp, nCores)
32: 13: doTryCatch(return(expr), name, parentenv, handler)pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)
33: 14: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval_bare(expr, quo_get_env(quo))
34: 15: tryCatchList(expr, classes, parentenv, handlers)quasi_label(enquo(object), label)
35: 16: tryCatch(withCallingHandlers({expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), eval(code, test_env) pcNet(X, nComp = nComp, verbose = FALSE)) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {17: skip("On CRAN")eval(code, test_env) }
else if (!new_expectations && skip_on_empty) {18: skip_empty()eval(code, test_env) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {19: if (on_cran()) {withCallingHandlers({ skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip_empty()
}36: }, expectation = handle_expectation, packageNotFoundError = function(e) {doWithOneRestart(return(expr), restart) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))37: }withOneRestart(expr, restarts[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE38: invokeRestart("muffle_cran_snapshot")withRestarts(tryCatch(withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {20: skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler) }
else if (!new_expectations && skip_on_empty) {21: skip_empty()tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {22: if (on_cran()) {tryCatchList(expr, classes, parentenv, handlers) skip(paste0("{", e$package, "} is not installed."))
}23: }, snapshot_on_cran = function(cnd) {tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip("On CRAN") end_test = function() { } }) else if (!new_expectations && skip_on_empty) {
skip_empty()39: }test_code(code = exprs, env = env, reporter = get_reporter() %||% }, expectation = handle_expectation, packageNotFoundError = function(e) { StopReporter$new()) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))40: }source_file(path, env = env(env), desc = desc, shuffle = shuffle, }, snapshot_on_cran = function(cnd) { error_call = error_call) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")41: }, skip = handle_skip, warning = handle_warning, message = handle_message, FUN(X[[i]], ...) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
42: 24: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, doWithOneRestart(return(expr), restart) error_call = error_call)
25: 43: withOneRestart(expr, restarts[[1L]])doTryCatch(return(expr), name, parentenv, handler)
26: 44: withRestarts(tryCatch(withCallingHandlers({tryCatchOne(expr, names, parentenv, handlers[[1L]]) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations45: if (snapshot_skipped) {tryCatchList(expr, classes, parentenv, handlers) skip("On CRAN")
}46: else if (!new_expectations && skip_on_empty) {tryCatch(code, testthat_abort_reporter = function(cnd) { skip_empty() cat(conditionMessage(cnd), "\n") } NULL}, expectation = handle_expectation, packageNotFoundError = function(e) {}) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))47: }with_reporter(reporters$multi, lapply(test_paths, test_one_file, }, snapshot_on_cran = function(cnd) { env = env, desc = desc, shuffle = shuffle, error_call = error_call)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")48: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_files_serial(test_dir = test_dir, test_package = test_package, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, end_test = function() { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)27:
test_code(code, parent.frame())49:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 28: reporter = reporter, load_helpers = load_helpers, env = env, test_that("pcNet matches per-gene SVD principal component regression", stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, { load_package = load_package, parallel = parallel, shuffle = shuffle) nCells <- 200
nGenes <- 10050: nComp <- 3test_dir("testthat", package = package, reporter = reporter, set.seed(42) ..., load_package = "installed") X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98),
nrow = nGenes, ncol = nCells)51: rownames(X) <- paste0("Gene", seq_len(nGenes))test_check("scTenifoldNet") X_std <- scale(Matrix::t(X))
reference <- matrix(0, nGenes, nGenes)An irrecoverable exception occurred. R is aborting now ...
for (K in seq_len(nGenes)) { design_matrix <- X_std[, -K] principal_components <- svd(design_matrix, nu = 0, nv = nComp)$v pc_scores <- design_matrix %*% principal_components pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) reference[K, -K] <- principal_components %*% pc_coefficients } xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, verbose = FALSE) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) })
29: 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