Last updated on 2026-11-02 09:52:57 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 | 5.90 | 54.63 | 60.53 | 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 | 4.00 | 48.00 | 52.00 | 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 | 97.00 | 108.00 | OK |
Version: 1.4.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/3s]
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:
Traceback:
eval(code, test_env)
19: 1: withCallingHandlers({FUN(X[[i]], ...) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations 2: if (snapshot_skipped) {lapply(X = S, FUN = FUN, ...) skip("On CRAN")
} 3: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler) skip_empty()
} 4: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_cran()) {
5: skip(paste0("{", e$package, "} is not installed.")) }tryCatchList(expr, classes, parentenv, handlers)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") 6: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatch(expr, error = function(e) { error = handle_error, interrupt = handle_interrupt) call <- conditionCall(e) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 20: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)doTryCatch(return(expr), name, parentenv, handler) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L21: sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatchOne(expr, names, parentenv, handlers[[1L]])
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")22: 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$test_expectations > starting_expectations else prefix <- "Error : " if (snapshot_skipped) { msg <- paste0(prefix, conditionMessage(e), "\n") skip("On CRAN") } .Internal(seterrmessage(msg[1L])) else if (!new_expectations && skip_on_empty) { if (!silent && isTRUE(getOption("show.error.messages"))) { skip_empty() cat(msg, file = outFile) } .Internal(printDeferredWarnings())}, expectation = handle_expectation, packageNotFoundError = function(e) { } invisible(structure(msg, class = "try-error", condition = e)) if (on_cran()) {}) skip(paste0("{", e$package, "} is not installed.")) }
}, snapshot_on_cran = function(cnd) { 7: snapshot_skipped <<- TRUEtry(lapply(X = S, FUN = FUN, ...), silent = TRUE) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
8: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
24: 9: doWithOneRestart(return(expr), restart)FUN(X[[i]], ...)
25: 10: withOneRestart(expr, restarts[[1L]])lapply(seq_len(cores), inner.do)
26:
11: parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, withRestarts(tryCatch(withCallingHandlers({ mc.preschedule = TRUE) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations12: .pcNetCoefficients(basis$Z, basis$d, nComp, nCores) if (snapshot_skipped) {
skip("On CRAN")13: pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) }
else if (!new_expectations && skip_on_empty) {14: skip_empty()eval_bare(expr, quo_get_env(quo))
}}, expectation = handle_expectation, packageNotFoundError = function(e) {15: quasi_label(enquo(object), label) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) }16: }, snapshot_on_cran = function(cnd) {expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), snapshot_skipped <<- TRUE pcNet(X, nComp = nComp, verbose = FALSE)) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 17: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() {eval(code, test_env) })
18: 27: eval(code, test_env)test_code(code, parent.frame())
28: 19: test_that("pcNet matches per-gene SVD principal component regression", withCallingHandlers({ { eval(code, test_env) nCells <- 200 new_expectations <- the$test_expectations > starting_expectations nGenes <- 100 if (snapshot_skipped) { nComp <- 3 skip("On CRAN") set.seed(42) } X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), nrow = nGenes, ncol = nCells) else if (!new_expectations && skip_on_empty) { rownames(X) <- paste0("Gene", seq_len(nGenes)) skip_empty() X_std <- scale(Matrix::t(X)) } reference <- matrix(0, nGenes, nGenes)}, expectation = handle_expectation, packageNotFoundError = function(e) { for (K in seq_len(nGenes)) { if (on_cran()) { design_matrix <- X_std[, -K] skip(paste0("{", e$package, "} is not installed.")) principal_components <- svd(design_matrix, nu = 0, nv = nComp)$v } pc_scores <- design_matrix %*% principal_components}, snapshot_on_cran = function(cnd) { pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) snapshot_skipped <<- TRUE reference[K, -K] <- principal_components %*% pc_coefficients invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, verbose = FALSE) error = handle_error, interrupt = handle_interrupt) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)
expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, 20: nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))doTryCatch(return(expr), name, parentenv, handler) })
21: 29: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: eval(code, test_env)
22: 31: tryCatchList(expr, classes, parentenv, handlers)withCallingHandlers({
eval(code, test_env)23: new_expectations <- the$test_expectations > starting_expectationstryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { if (on_cran()) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") skip(paste0("{", e$package, "} is not installed."))}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE32: invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
33: 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])doWithOneRestart(return(expr), restart)
34: 25: tryCatchList(expr, classes, parentenv, handlers)withOneRestart(expr, restarts[[1L]])
26: 35: withRestarts(tryCatch(withCallingHandlers({tryCatch(withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { else if (!new_expectations && skip_on_empty) { skip_empty() skip_empty() } }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip(paste0("{", e$package, "} is not installed.")) } }}, snapshot_on_cran = function(cnd) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, snapshot_skipped <<- TRUE error = handle_error, interrupt = handle_interrupt), error = handle_fatal), invokeRestart("muffle_cran_snapshot") end_test = function() {}, skip = handle_skip, warning = handle_warning, message = handle_message, }) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
27: 36: test_code(code, parent.frame())doWithOneRestart(return(expr), restart)
28: 37: test_that("pcNet matches per-gene SVD principal component regression", withOneRestart(expr, restarts[[1L]]) {
nCells <- 200 nGenes <- 10038: nComp <- 3withRestarts(tryCatch(withCallingHandlers({ set.seed(42) eval(code, test_env) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { nrow = nGenes, ncol = nCells) skip("On CRAN") rownames(X) <- paste0("Gene", seq_len(nGenes)) } X_std <- scale(Matrix::t(X)) else if (!new_expectations && skip_on_empty) { skip_empty() reference <- matrix(0, nGenes, nGenes) } for (K in seq_len(nGenes)) {}, expectation = handle_expectation, packageNotFoundError = function(e) { design_matrix <- X_std[, -K] if (on_cran()) { principal_components <- svd(design_matrix, nu = 0, skip(paste0("{", e$package, "} is not installed.")) } nv = nComp)$v}, snapshot_on_cran = function(cnd) { pc_scores <- design_matrix %*% principal_components snapshot_skipped <<- TRUE pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) invokeRestart("muffle_cran_snapshot") reference[K, -K] <- principal_components %*% pc_coefficients }}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, verbose = FALSE) end_test = function() { 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))39: })test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())29: eval(code, test_env)
40: 30: source_file(path, env = env(env), desc = desc, shuffle = shuffle, eval(code, test_env) error_call = error_call)
31:
41: withCallingHandlers({FUN(X[[i]], ...) eval(code, test_env)
42: new_expectations <- the$test_expectations > starting_expectationslapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, if (snapshot_skipped) { skip("On CRAN") error_call = error_call) }
43: else if (!new_expectations && skip_on_empty) { skip_empty()doTryCatch(return(expr), name, parentenv, handler) }}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))44: }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")45: tryCatchList(expr, classes, parentenv, handlers)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)46: tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")32: NULLdoTryCatch(return(expr), name, parentenv, handler)})
47: 33: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: 48: tryCatchList(expr, classes, parentenv, handlers)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, 35: tryCatch(withCallingHandlers({ desc = desc, load_package = load_package, shuffle = shuffle, eval(code, test_env) error_call = error_call)
new_expectations <- the$test_expectations > starting_expectations49: if (snapshot_skipped) {test_files(test_dir = path, test_paths = test_paths, test_package = package, skip("On CRAN") reporter = reporter, load_helpers = load_helpers, env = env, } else if (!new_expectations && skip_on_empty) { stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, skip_empty() load_package = load_package, parallel = parallel, shuffle = shuffle) }
50: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_dir("testthat", package = package, reporter = reporter, if (on_cran()) { ..., load_package = "installed") skip(paste0("{", e$package, "} is not installed.")) }
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE51: test_check("scTenifoldNet")
invokeRestart("muffle_cran_snapshot")An irrecoverable exception occurred. R is aborting now ...
}, 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