Last updated on 2026-11-03 04:54:48 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4.3 | 8.16 | 72.89 | 81.05 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4.3 | 6.41 | 55.38 | 61.79 | 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 | 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$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) {
Traceback:
if (on_cran()) { 1: skip(paste0("{", e$package, "} is not installed."))FUN(X[[i]], ...) }
}, snapshot_on_cran = function(cnd) { 2: snapshot_skipped <<- TRUElapply(X = S, FUN = FUN, ...) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 3: error = handle_error, interrupt = handle_interrupt)doTryCatch(return(expr), name, parentenv, handler)
20: 4: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
22: 6: tryCatchList(expr, classes, parentenv, handlers)tryCatch(expr, error = function(e) { call <- conditionCall(e)
if (!is.null(call)) {23: if (identical(call[[1L]], quote(doTryCatch))) tryCatch(withCallingHandlers({ call <- sys.call(-4L) eval(code, test_env) dcall <- deparse(call, nlines = 1L) new_expectations <- the$test_expectations > starting_expectations prefix <- paste("Error in", dcall, ": ") if (snapshot_skipped) { LONG <- 75L skip("On CRAN") sm <- strsplit(conditionMessage(e), "\n")[[1L]] } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") else if (!new_expectations && skip_on_empty) { if (is.na(w)) skip_empty() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b")}, expectation = handle_expectation, packageNotFoundError = function(e) { if (w > LONG) if (on_cran()) { prefix <- paste0(prefix, "\n ") skip(paste0("{", e$package, "} is not installed.")) } } else prefix <- "Error : "}, snapshot_on_cran = function(cnd) { msg <- paste0(prefix, conditionMessage(e), "\n") snapshot_skipped <<- TRUE .Internal(seterrmessage(msg[1L])) invokeRestart("muffle_cran_snapshot") if (!silent && isTRUE(getOption("show.error.messages"))) {}, skip = handle_skip, warning = handle_warning, message = handle_message, cat(msg, file = outFile) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) .Internal(printDeferredWarnings())
}24: invisible(structure(msg, class = "try-error", condition = e))doWithOneRestart(return(expr), restart)})
25: 7: withOneRestart(expr, restarts[[1L]])try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
26: 8: withRestarts(tryCatch(withCallingHandlers({sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations 9: FUN(X[[i]], ...) if (snapshot_skipped) {
skip("On CRAN")10: }lapply(seq_len(cores), inner.do) else if (!new_expectations && skip_on_empty) {
skip_empty()11: }parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, }, expectation = handle_expectation, packageNotFoundError = function(e) { nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, if (on_cran()) { mc.preschedule = TRUE) skip(paste0("{", e$package, "} is not installed."))
}12: }, snapshot_on_cran = function(cnd) {.pcNetCoefficients(basis$Z, basis$d, nComp, nCores) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")13: }, skip = handle_skip, warning = handle_warning, message = handle_message, pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() { })14:
eval_bare(expr, quo_get_env(quo))27:
test_code(code, parent.frame())15:
quasi_label(enquo(object), label)28:
test_that("pcNet matches per-gene SVD principal component regression", 16: {expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), nCells <- 200 pcNet(X, nComp = nComp, verbose = FALSE)) nGenes <- 100
nComp <- 317: set.seed(42)eval(code, test_env) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98),
nrow = nGenes, ncol = nCells)18: rownames(X) <- paste0("Gene", seq_len(nGenes))eval(code, test_env) X_std <- scale(Matrix::t(X))
reference <- matrix(0, nGenes, nGenes)19: for (K in seq_len(nGenes)) {withCallingHandlers({ design_matrix <- X_std[, -K] eval(code, test_env) principal_components <- svd(design_matrix, nu = 0, new_expectations <- the$test_expectations > starting_expectations nv = nComp)$v if (snapshot_skipped) { pc_scores <- design_matrix %*% principal_components skip("On CRAN") pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) } reference[K, -K] <- principal_components %*% pc_coefficients } else if (!new_expectations && skip_on_empty) { xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, skip_empty() verbose = FALSE) } expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, if (on_cran()) { nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) skip(paste0("{", e$package, "} is not installed.")) }) }
}, snapshot_on_cran = function(cnd) {29: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 30: eval(code, test_env)
error = handle_error, interrupt = handle_interrupt)31: withCallingHandlers({
eval(code, test_env)20: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
skip("On CRAN")21: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) {
skip_empty()22: }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {23: skip(paste0("{", e$package, "} is not installed."))tryCatch(withCallingHandlers({ eval(code, test_env) } new_expectations <- the$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) skip_empty()
}32: }, expectation = handle_expectation, packageNotFoundError = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))33: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")34: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
35: 24: tryCatch(withCallingHandlers({doWithOneRestart(return(expr), restart) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations25: if (snapshot_skipped) {withOneRestart(expr, restarts[[1L]]) skip("On CRAN")
}26: 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 } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, snapshot_on_cran = function(cnd) {36: snapshot_skipped <<- TRUEdoWithOneRestart(return(expr), restart) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 37: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), withOneRestart(expr, restarts[[1L]]) end_test = function() {
})38:
withRestarts(tryCatch(withCallingHandlers({27: eval(code, test_env)test_code(code, parent.frame()) new_expectations <- the$test_expectations > starting_expectations
28: if (snapshot_skipped) {test_that("pcNet matches per-gene SVD principal component regression", skip("On CRAN") { } nCells <- 200 else if (!new_expectations && skip_on_empty) { nGenes <- 100 skip_empty() nComp <- 3 } set.seed(42)}, expectation = handle_expectation, packageNotFoundError = function(e) { X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), if (on_cran()) { nrow = nGenes, ncol = nCells) skip(paste0("{", e$package, "} is not installed.")) rownames(X) <- paste0("Gene", seq_len(nGenes)) } X_std <- scale(Matrix::t(X))}, snapshot_on_cran = function(cnd) { reference <- matrix(0, nGenes, nGenes) for (K in seq_len(nGenes)) { snapshot_skipped <<- TRUE design_matrix <- X_std[, -K] invokeRestart("muffle_cran_snapshot") principal_components <- svd(design_matrix, nu = 0, }, skip = handle_skip, warning = handle_warning, message = handle_message, nv = nComp)$v error = handle_error, interrupt = handle_interrupt), error = handle_fatal), pc_scores <- design_matrix %*% principal_components end_test = function() { pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) }) reference[K, -K] <- principal_components %*% pc_coefficients
}39: xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, test_code(code = exprs, env = env, reporter = get_reporter() %||% verbose = FALSE) StopReporter$new()) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)
expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, 40: nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))source_file(path, env = env(env), desc = desc, shuffle = shuffle, }) error_call = error_call)
29: 41: eval(code, test_env)FUN(X[[i]], ...)
30: 42: eval(code, test_env)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)31:
withCallingHandlers({43: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {44: skip("On CRAN")tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
else if (!new_expectations && skip_on_empty) {45: skip_empty()tryCatchList(expr, classes, parentenv, handlers) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {46: if (on_cran()) {tryCatch(code, testthat_abort_reporter = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) cat(conditionMessage(cnd), "\n") } NULL}, snapshot_on_cran = function(cnd) {}) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")47: }, skip = handle_skip, warning = handle_warning, message = handle_message, with_reporter(reporters$multi, lapply(test_paths, test_one_file, error = handle_error, interrupt = handle_interrupt) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
32: 48: doTryCatch(return(expr), name, parentenv, handler)test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 33: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, tryCatchOne(expr, names, parentenv, handlers[[1L]]) desc = desc, load_package = load_package, shuffle = shuffle,
error_call = error_call)34:
tryCatchList(expr, classes, parentenv, handlers)49:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 35: reporter = reporter, load_helpers = load_helpers, env = env, tryCatch(withCallingHandlers({ stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, eval(code, test_env) load_package = load_package, parallel = parallel, shuffle = shuffle) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {50: skip("On CRAN")test_dir("testthat", package = package, reporter = reporter, } ..., load_package = "installed") else if (!new_expectations && skip_on_empty) {
skip_empty()51: }test_check("scTenifoldNet")}, expectation = handle_expectation, packageNotFoundError = function(e) {
An irrecoverable exception occurred. R is aborting now ...
if (on_cran()) { skip(paste0("{", e$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