Last updated on 2026-11-14 12:50:36 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4.3 | 6.71 | 72.97 | 79.68 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4.3 | 5.69 | 54.55 | 60.24 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.4.3 | 54.23 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.4.3 | 53.85 | OK | |||
| r-devel-windows-x86_64 | 1.4.3 | 10.00 | 88.00 | 98.00 | OK | |
| r-patched-linux-x86_64 | 1.4.3 | 7.72 | 66.52 | 74.24 | 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 | 103.00 | 112.00 | 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 | 172.00 | 183.00 | 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.")) }}, 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() { })
27: test_code(code, parent.frame())
28:
Traceback:
test_that("pcNet matches per-gene SVD principal component regression", { 1: nCells <- 200FUN(X[[i]], ...) nGenes <- 100
nComp <- 3 2: set.seed(42)lapply(X = S, FUN = FUN, ...) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98),
nrow = nGenes, ncol = nCells) 3: rownames(X) <- paste0("Gene", seq_len(nGenes))doTryCatch(return(expr), name, parentenv, handler) X_std <- scale(Matrix::t(X))
reference <- matrix(0, nGenes, nGenes) 4: for (K in seq_len(nGenes)) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) design_matrix <- X_std[, -K]
5: principal_components <- svd(design_matrix, nu = 0, tryCatchList(expr, classes, parentenv, handlers) nv = nComp)$v
pc_scores <- design_matrix %*% principal_components 6: pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)tryCatch(expr, error = function(e) { reference[K, -K] <- principal_components %*% pc_coefficients call <- conditionCall(e) } if (!is.null(call)) { xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, if (identical(call[[1L]], quote(doTryCatch))) verbose = FALSE) call <- sys.call(-4L) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) dcall <- deparse(call, nlines = 1L) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, prefix <- paste("Error in", dcall, ": ") nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) LONG <- 75L }) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")29: if (is.na(w)) eval(code, test_env) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")30: if (w > LONG) eval(code, test_env) prefix <- paste0(prefix, "\n ")
}31: else prefix <- "Error : "withCallingHandlers({ msg <- paste0(prefix, conditionMessage(e), "\n") eval(code, test_env) .Internal(seterrmessage(msg[1L])) new_expectations <- the$test_expectations > starting_expectations if (!silent && isTRUE(getOption("show.error.messages"))) { if (snapshot_skipped) { cat(msg, file = outFile) skip("On CRAN") .Internal(printDeferredWarnings()) } } else if (!new_expectations && skip_on_empty) { invisible(structure(msg, class = "try-error", condition = e)) skip_empty()}) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { 7: if (on_cran()) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) skip(paste0("{", e$package, "} is not installed."))
} 8: }, snapshot_on_cran = function(cnd) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 9: }, skip = handle_skip, warning = handle_warning, message = handle_message, FUN(X[[i]], ...) error = handle_error, interrupt = handle_interrupt)
10: 32: lapply(seq_len(cores), inner.do)doTryCatch(return(expr), name, parentenv, handler)
11: 33: parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, tryCatchOne(expr, names, parentenv, handlers[[1L]]) nComp = nComp, secular_weights = secular_weights, mc.cores = nCores,
mc.preschedule = TRUE)34:
tryCatchList(expr, classes, parentenv, handlers)12:
.pcNetCoefficients(basis$Z, basis$d, nComp, nCores)35:
tryCatch(withCallingHandlers({13: eval(code, test_env)pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {14: skip("On CRAN")eval_bare(expr, quo_get_env(quo)) }
else if (!new_expectations && skip_on_empty) {15: skip_empty()quasi_label(enquo(object), label) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {16: if (on_cran()) {expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), skip(paste0("{", e$package, "} is not installed.")) pcNet(X, nComp = nComp, verbose = FALSE)) }
}, snapshot_on_cran = function(cnd) {17: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
36: 18: doWithOneRestart(return(expr), restart)
eval(code, test_env)
37: 19: withOneRestart(expr, restarts[[1L]])withCallingHandlers({
eval(code, test_env)38: new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE skip(paste0("{", e$package, "} is not installed.")) invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, snapshot_on_cran = function(cnd) { error = handle_error, interrupt = handle_interrupt) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")20: }, skip = handle_skip, warning = handle_warning, message = handle_message, doTryCatch(return(expr), name, parentenv, handler) error = handle_error, interrupt = handle_interrupt), error = handle_fatal),
end_test = function() {21: })tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: 22: test_code(code = exprs, env = env, reporter = get_reporter() %||% tryCatchList(expr, classes, parentenv, handlers) StopReporter$new())
23: 40: tryCatch(withCallingHandlers({source_file(path, env = env(env), desc = desc, shuffle = shuffle, eval(code, test_env) error_call = error_call) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {41: skip("On CRAN")FUN(X[[i]], ...) }
else if (!new_expectations && skip_on_empty) {42: skip_empty()lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } error_call = error_call)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {43: skip(paste0("{", e$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) {44: snapshot_skipped <<- TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 45: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)tryCatchList(expr, classes, parentenv, handlers)
46: 24: tryCatch(code, testthat_abort_reporter = function(cnd) {doWithOneRestart(return(expr), restart) cat(conditionMessage(cnd), "\n")
NULL25: })withOneRestart(expr, restarts[[1L]])
47: 26: with_reporter(reporters$multi, lapply(test_paths, test_one_file, withRestarts(tryCatch(withCallingHandlers({ env = env, desc = desc, shuffle = shuffle, error_call = error_call)) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations48: if (snapshot_skipped) {test_files_serial(test_dir = test_dir, test_package = test_package, skip("On CRAN") test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, } env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, else if (!new_expectations && skip_on_empty) { desc = desc, load_package = load_package, shuffle = shuffle, skip_empty() error_call = error_call) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {49: if (on_cran()) {test_files(test_dir = path, test_paths = test_paths, test_package = package, skip(paste0("{", e$package, "} is not installed.")) reporter = reporter, load_helpers = load_helpers, env = env, } stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }, snapshot_on_cran = function(cnd) { load_package = load_package, parallel = parallel, shuffle = shuffle) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")50: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_dir("testthat", package = package, reporter = reporter, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), ..., load_package = "installed") end_test = function() {
})51:
test_check("scTenifoldNet")27:
test_code(code, parent.frame())An irrecoverable exception occurred. R is aborting now ...
28: test_that("pcNet matches per-gene SVD principal component regression", { nCells <- 200 nGenes <- 100 nComp <- 3 set.seed(42) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), nrow = nGenes, ncol = nCells) rownames(X) <- paste0("Gene", seq_len(nGenes)) X_std <- scale(Matrix::t(X)) reference <- matrix(0, nGenes, nGenes) for (K in seq_len(nGenes)) { design_matrix <- X_std[, -K] principal_components <- svd(design_matrix, nu = 0, nv = nComp)$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