Last updated on 2026-11-08 03:54:48 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4.3 | 8.08 | 72.55 | 80.63 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4.3 | 5.13 | 56.71 | 61.84 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.4.3 | 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 | OK | ||||
| r-release-linux-x86_64 | 1.4.3 | 7.03 | 66.71 | 73.74 | 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 | 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 | 102.00 | 113.00 | 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]])
Traceback:
22: tryCatchList(expr, classes, parentenv, handlers) 1:
FUN(X[[i]], ...)23:
tryCatch(withCallingHandlers({ 2: eval(code, test_env)lapply(X = S, FUN = FUN, ...) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { 3: skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler) }
else if (!new_expectations && skip_on_empty) { 4: skip_empty()tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
5: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 6: }tryCatch(expr, error = function(e) {}, snapshot_on_cran = function(cnd) { call <- conditionCall(e) snapshot_skipped <<- TRUE if (!is.null(call)) { invokeRestart("muffle_cran_snapshot") if (identical(call[[1L]], quote(doTryCatch))) }, skip = handle_skip, warning = handle_warning, message = handle_message, call <- sys.call(-4L) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")24: LONG <- 75LdoWithOneRestart(return(expr), restart) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")25: if (is.na(w)) withOneRestart(expr, restarts[[1L]]) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")26: if (w > LONG) withRestarts(tryCatch(withCallingHandlers({ prefix <- paste0(prefix, "\n ") } eval(code, test_env) else prefix <- "Error : " new_expectations <- the$test_expectations > starting_expectations msg <- paste0(prefix, conditionMessage(e), "\n") if (snapshot_skipped) { .Internal(seterrmessage(msg[1L])) skip("On CRAN") if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile) else if (!new_expectations && skip_on_empty) { .Internal(printDeferredWarnings()) skip_empty() } } invisible(structure(msg, class = "try-error", condition = e))}, expectation = handle_expectation, packageNotFoundError = function(e) {}) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 7: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE 8: invokeRestart("muffle_cran_snapshot")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 9: end_test = function() {FUN(X[[i]], ...) })
10: 27: lapply(seq_len(cores), inner.do)test_code(code, parent.frame())
11: 28: parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, test_that("pcNet matches per-gene SVD principal component regression", nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, { mc.preschedule = TRUE) nCells <- 200
nGenes <- 10012: nComp <- 3.pcNetCoefficients(basis$Z, basis$d, nComp, nCores) set.seed(42)
X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), 13: nrow = nGenes, ncol = nCells)pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) rownames(X) <- paste0("Gene", seq_len(nGenes))
X_std <- scale(Matrix::t(X))14: reference <- matrix(0, nGenes, nGenes)eval_bare(expr, quo_get_env(quo)) for (K in seq_len(nGenes)) {
design_matrix <- X_std[, -K]15: principal_components <- svd(design_matrix, nu = 0, quasi_label(enquo(object), label) nv = nComp)$v
pc_scores <- design_matrix %*% principal_components16: pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), reference[K, -K] <- principal_components %*% pc_coefficients pcNet(X, nComp = nComp, verbose = FALSE)) }
17: eval(code, test_env) xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE,
verbose = FALSE)18: expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)eval(code, test_env)
expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, 19: nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))withCallingHandlers({ }) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations29: if (snapshot_skipped) {eval(code, test_env) skip("On CRAN")
}30: else if (!new_expectations && skip_on_empty) {eval(code, test_env) skip_empty()
}31: }, expectation = handle_expectation, packageNotFoundError = function(e) {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) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {20: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
}21: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")22: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt)
23: 32: tryCatch(withCallingHandlers({doTryCatch(return(expr), name, parentenv, handler) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations33: if (snapshot_skipped) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip("On CRAN")
}34: else if (!new_expectations && skip_on_empty) {tryCatchList(expr, classes, parentenv, handlers) skip_empty()
}35: }, 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()
}24: }, expectation = handle_expectation, packageNotFoundError = function(e) {doWithOneRestart(return(expr), restart) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))25: }withOneRestart(expr, restarts[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE26: invokeRestart("muffle_cran_snapshot")withRestarts(tryCatch(withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {36: skip("On CRAN")doWithOneRestart(return(expr), restart) }
else if (!new_expectations && skip_on_empty) {37: skip_empty()withOneRestart(expr, restarts[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {38: if (on_cran()) {withRestarts(tryCatch(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() end_test = function() { } })}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {27: skip(paste0("{", e$package, "} is not installed."))test_code(code, parent.frame()) }
}, snapshot_on_cran = function(cnd) {28: snapshot_skipped <<- TRUEtest_that("pcNet matches per-gene SVD principal component regression", invokeRestart("muffle_cran_snapshot") {}, skip = handle_skip, warning = handle_warning, message = handle_message, nCells <- 200 error = handle_error, interrupt = handle_interrupt), error = handle_fatal), nGenes <- 100 end_test = function() { nComp <- 3 }) set.seed(42)
X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), 39: nrow = nGenes, ncol = nCells)test_code(code = exprs, env = env, reporter = get_reporter() %||% rownames(X) <- paste0("Gene", seq_len(nGenes)) StopReporter$new()) X_std <- scale(Matrix::t(X))
reference <- matrix(0, nGenes, nGenes)40: for (K in seq_len(nGenes)) {source_file(path, env = env(env), desc = desc, shuffle = shuffle, design_matrix <- X_std[, -K] error_call = error_call) principal_components <- svd(design_matrix, nu = 0,
nv = nComp)$v41: pc_scores <- design_matrix %*% principal_componentsFUN(X[[i]], ...) pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)
reference[K, -K] <- principal_components %*% pc_coefficients42: }lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, error_call = error_call) verbose = FALSE)
expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)43: expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, doTryCatch(return(expr), name, parentenv, handler) nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))
})44:
tryCatchOne(expr, names, parentenv, handlers[[1L]])29:
eval(code, test_env)45:
tryCatchList(expr, classes, parentenv, handlers)30:
eval(code, test_env)46:
tryCatch(code, testthat_abort_reporter = function(cnd) {31: cat(conditionMessage(cnd), "\n")withCallingHandlers({ NULL eval(code, test_env)}) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {47: skip("On CRAN")with_reporter(reporters$multi, lapply(test_paths, test_one_file, } env = env, desc = desc, shuffle = shuffle, error_call = error_call)) else if (!new_expectations && skip_on_empty) {
skip_empty()48: }test_files_serial(test_dir = test_dir, test_package = test_package, }, expectation = handle_expectation, packageNotFoundError = function(e) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, if (on_cran()) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, skip(paste0("{", e$package, "} is not installed.")) desc = desc, load_package = load_package, shuffle = shuffle, } error_call = error_call)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE49: invokeRestart("muffle_cran_snapshot")test_files(test_dir = path, test_paths = test_paths, test_package = package, }, skip = handle_skip, warning = handle_warning, message = handle_message, reporter = reporter, load_helpers = load_helpers, env = env, error = handle_error, interrupt = handle_interrupt) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)32:
doTryCatch(return(expr), name, parentenv, handler)50:
test_dir("testthat", package = package, reporter = reporter, 33: ..., load_package = "installed")tryCatchOne(expr, names, parentenv, handlers[[1L]])
51: 34: test_check("scTenifoldNet")tryCatchList(expr, classes, parentenv, handlers)
An irrecoverable exception occurred. R is aborting now ...
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