Last updated on 2026-11-07 00:50:31 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 | 5.05 | 54.69 | 59.74 | 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 | 7.18 | 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 | 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’ [3s/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)
Traceback:
new_expectations <- the$test_expectations > starting_expectations 1: if (snapshot_skipped) {FUN(X[[i]], ...) skip("On CRAN")
2: }lapply(X = S, FUN = FUN, ...) else if (!new_expectations && skip_on_empty) {
skip_empty() 3: }doTryCatch(return(expr), name, parentenv, handler)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { 4: skip(paste0("{", e$package, "} is not installed."))tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, snapshot_on_cran = function(cnd) { 5: snapshot_skipped <<- TRUEtryCatchList(expr, classes, parentenv, handlers) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 6: error = handle_error, interrupt = handle_interrupt)tryCatch(expr, error = function(e) {
call <- conditionCall(e)20: if (!is.null(call)) {doTryCatch(return(expr), name, parentenv, handler) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)21: prefix <- paste("Error in", dcall, ": ")tryCatchOne(expr, names, parentenv, handlers[[1L]]) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]22: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) tryCatchList(expr, classes, parentenv, handlers)
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")23: if (w > LONG) tryCatch(withCallingHandlers({ prefix <- paste0(prefix, "\n ") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") if (snapshot_skipped) { .Internal(seterrmessage(msg[1L])) skip("On CRAN") if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile) else if (!new_expectations && skip_on_empty) { .Internal(printDeferredWarnings()) skip_empty() } } invisible(structure(msg, class = "try-error", condition = e))}, expectation = handle_expectation, packageNotFoundError = function(e) {})
if (on_cran()) { 7: skip(paste0("{", e$package, "} is not installed."))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))
9: }, skip = handle_skip, warning = handle_warning, message = handle_message, FUN(X[[i]], ...) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
10: lapply(seq_len(cores), inner.do)24:
doWithOneRestart(return(expr), restart)11:
parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, 25: nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, withOneRestart(expr, restarts[[1L]]) mc.preschedule = TRUE)
26: 12: withRestarts(tryCatch(withCallingHandlers({.pcNetCoefficients(basis$Z, basis$d, nComp, nCores) eval(code, test_env)
13: new_expectations <- the$test_expectations > starting_expectationspcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)
if (snapshot_skipped) {14: skip("On CRAN")eval_bare(expr, quo_get_env(quo)) }
else if (!new_expectations && skip_on_empty) { skip_empty()15: }quasi_label(enquo(object), label)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {16: skip(paste0("{", e$package, "} is not installed.")) }expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), }, snapshot_on_cran = function(cnd) { pcNet(X, nComp = nComp, verbose = FALSE)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")17: }, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {18: })eval(code, test_env)
27: 19: test_code(code, parent.frame())
withCallingHandlers({28: test_that("pcNet matches per-gene SVD principal component regression", eval(code, test_env) { new_expectations <- the$test_expectations > starting_expectations nCells <- 200 if (snapshot_skipped) { nGenes <- 100 skip("On CRAN") nComp <- 3 } set.seed(42) else if (!new_expectations && skip_on_empty) { X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), skip_empty() nrow = nGenes, ncol = nCells) } rownames(X) <- paste0("Gene", seq_len(nGenes))}, expectation = handle_expectation, packageNotFoundError = function(e) { X_std <- scale(Matrix::t(X)) if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) reference <- matrix(0, nGenes, nGenes) } for (K in seq_len(nGenes)) {}, snapshot_on_cran = function(cnd) { design_matrix <- X_std[, -K] snapshot_skipped <<- TRUE principal_components <- svd(design_matrix, nu = 0, invokeRestart("muffle_cran_snapshot") nv = nComp)$v}, skip = handle_skip, warning = handle_warning, message = handle_message, pc_scores <- design_matrix %*% principal_components error = handle_error, interrupt = handle_interrupt) pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)
reference[K, -K] <- principal_components %*% pc_coefficients20: }doTryCatch(return(expr), name, parentenv, handler) xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE,
verbose = FALSE)21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)22: expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, tryCatchList(expr, classes, parentenv, handlers) nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))
})
23: 29: tryCatch(withCallingHandlers({eval(code, test_env) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations30: if (snapshot_skipped) { skip("On CRAN")eval(code, test_env) } else if (!new_expectations && skip_on_empty) {
skip_empty() }31: }, expectation = handle_expectation, packageNotFoundError = function(e) {withCallingHandlers({ if (on_cran()) { 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") 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: doWithOneRestart(return(expr), restart) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {25: if (on_cran()) {withOneRestart(expr, restarts[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}26: }, snapshot_on_cran = function(cnd) {withRestarts(tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt) skip("On CRAN")
}32: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler)
skip_empty()33: tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {34: if (on_cran()) {tryCatchList(expr, classes, parentenv, handlers) skip(paste0("{", e$package, "} is not installed."))
}35: }, snapshot_on_cran = function(cnd) {tryCatch(withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$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() }
}, expectation = handle_expectation, packageNotFoundError = function(e) {27: if (on_cran()) {test_code(code, parent.frame()) skip(paste0("{", e$package, "} is not installed."))
}28: }, snapshot_on_cran = function(cnd) {test_that("pcNet matches per-gene SVD principal component regression", snapshot_skipped <<- TRUE { invokeRestart("muffle_cran_snapshot") nCells <- 200}, skip = handle_skip, warning = handle_warning, message = handle_message, nGenes <- 100 error = handle_error, interrupt = handle_interrupt), error = handle_fatal) nComp <- 3
set.seed(42)36: doWithOneRestart(return(expr), restart) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98),
nrow = nGenes, ncol = nCells)37: rownames(X) <- paste0("Gene", seq_len(nGenes))withOneRestart(expr, restarts[[1L]]) X_std <- scale(Matrix::t(X))
reference <- matrix(0, nGenes, nGenes)38: for (K in seq_len(nGenes)) {withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) design_matrix <- X_std[, -K] new_expectations <- the$test_expectations > starting_expectations principal_components <- svd(design_matrix, nu = 0, if (snapshot_skipped) { nv = nComp)$v skip("On CRAN") pc_scores <- design_matrix %*% principal_components } pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) else if (!new_expectations && skip_on_empty) { reference[K, -K] <- principal_components %*% pc_coefficients skip_empty() } } xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, }, expectation = handle_expectation, packageNotFoundError = function(e) { verbose = FALSE) if (on_cran()) { expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) skip(paste0("{", e$package, "} is not installed.")) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) } })
}, snapshot_on_cran = function(cnd) {29: snapshot_skipped <<- TRUEeval(code, test_env)
30: eval(code, test_env) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 31: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), withCallingHandlers({ end_test = function() { eval(code, test_env) }) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {39: skip("On CRAN")test_code(code = exprs, env = env, reporter = get_reporter() %||% } StopReporter$new()) else if (!new_expectations && skip_on_empty) {
40: skip_empty()source_file(path, env = env(env), desc = desc, shuffle = shuffle, } error_call = error_call)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {41: skip(paste0("{", e$package, "} is not installed."))FUN(X[[i]], ...) }
}, snapshot_on_cran = function(cnd) {42: snapshot_skipped <<- TRUElapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, invokeRestart("muffle_cran_snapshot") error_call = error_call)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)43:
doTryCatch(return(expr), name, parentenv, handler)32:
doTryCatch(return(expr), name, parentenv, handler)44:
tryCatchOne(expr, names, parentenv, handlers[[1L]])33:
tryCatchOne(expr, names, parentenv, handlers[[1L]])45:
tryCatchList(expr, classes, parentenv, handlers)34:
tryCatchList(expr, classes, parentenv, handlers)46:
tryCatch(code, testthat_abort_reporter = function(cnd) {35: cat(conditionMessage(cnd), "\n")tryCatch(withCallingHandlers({ NULL eval(code, test_env)}) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {47: skip("On CRAN")with_reporter(reporters$multi, lapply(test_paths, test_one_file, } env = env, desc = desc, shuffle = shuffle, error_call = error_call))
else if (!new_expectations && skip_on_empty) {48: skip_empty()test_files_serial(test_dir = test_dir, test_package = test_package, } test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, }, expectation = handle_expectation, packageNotFoundError = function(e) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, if (on_cran()) { desc = desc, load_package = load_package, shuffle = shuffle, skip(paste0("{", e$package, "} is not installed.")) error_call = error_call) }
}, snapshot_on_cran = function(cnd) {49: snapshot_skipped <<- TRUEtest_files(test_dir = path, test_paths = test_paths, test_package = package, invokeRestart("muffle_cran_snapshot") reporter = reporter, load_helpers = load_helpers, env = env, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
load_package = load_package, parallel = parallel, shuffle = shuffle)
36: doWithOneRestart(return(expr), restart)50:
test_dir("testthat", package = package, reporter = reporter, 37: ..., load_package = "installed")withOneRestart(expr, restarts[[1L]])
51: 38: test_check("scTenifoldNet")withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectationsAn irrecoverable exception occurred. R is aborting now ...
if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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