Last updated on 2026-10-30 19:51:24 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 | 5.89 | 57.20 | 63.09 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.4.3 | 54.29 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.4.3 | 53.53 | 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 | 7.03 | 67.07 | 74.10 | 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 | 12.00 | 91.00 | 103.00 | 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$test_expectations > starting_expectations
Traceback:
if (snapshot_skipped) { 1: FUN(X[[i]], ...) skip("On CRAN")
} 2: else if (!new_expectations && skip_on_empty) {lapply(X = S, FUN = FUN, ...) skip_empty()
} 3: doTryCatch(return(expr), name, parentenv, handler)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { 4: skip(paste0("{", e$package, "} is not installed."))tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, snapshot_on_cran = function(cnd) { 5: tryCatchList(expr, classes, parentenv, handlers) 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), error = handle_fatal), call <- conditionCall(e) end_test = function() { if (!is.null(call)) { }) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)27: dcall <- deparse(call, nlines = 1L)test_code(code, parent.frame()) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L28: sm <- strsplit(conditionMessage(e), "\n")[[1L]]test_that("pcNet matches per-gene SVD principal component regression", w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") { if (is.na(w)) nCells <- 200 w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], nGenes <- 100 type = "b") nComp <- 3 if (w > LONG) set.seed(42) prefix <- paste0(prefix, "\n ") X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), } nrow = nGenes, ncol = nCells) else prefix <- "Error : " rownames(X) <- paste0("Gene", seq_len(nGenes)) msg <- paste0(prefix, conditionMessage(e), "\n") X_std <- scale(Matrix::t(X)) .Internal(seterrmessage(msg[1L])) reference <- matrix(0, nGenes, nGenes) if (!silent && isTRUE(getOption("show.error.messages"))) { for (K in seq_len(nGenes)) { cat(msg, file = outFile) design_matrix <- X_std[, -K] .Internal(printDeferredWarnings()) principal_components <- svd(design_matrix, nu = 0, } nv = nComp)$v invisible(structure(msg, class = "try-error", condition = e)) pc_scores <- design_matrix %*% principal_components}) pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)
reference[K, -K] <- principal_components %*% pc_coefficients 7: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE,
verbose = FALSE) 8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, 9: nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) })FUN(X[[i]], ...)
29: 10: lapply(seq_len(cores), inner.do)eval(code, test_env)
11: 30: parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, eval(code, test_env) nComp = nComp, secular_weights = secular_weights, mc.cores = nCores,
mc.preschedule = TRUE)31:
withCallingHandlers({12: .pcNetCoefficients(basis$Z, basis$d, nComp, nCores) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {13: skip("On CRAN")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) { if (on_cran()) {15: skip(paste0("{", e$package, "} is not installed.")) }quasi_label(enquo(object), label)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE16: invokeRestart("muffle_cran_snapshot")expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), }, skip = handle_skip, warning = handle_warning, message = handle_message, pcNet(X, nComp = nComp, verbose = FALSE)) error = handle_error, interrupt = handle_interrupt)
17: 32: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler)
18: 33: eval(code, test_env)tryCatchOne(expr, names, parentenv, handlers[[1L]])
19:
withCallingHandlers({34: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { skip("On CRAN")35: }tryCatch(withCallingHandlers({ eval(code, test_env) else if (!new_expectations && skip_on_empty) { skip_empty() } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } } 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) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt) skip(paste0("{", e$package, "} is not installed."))
}20: }, snapshot_on_cran = function(cnd) {doTryCatch(return(expr), name, parentenv, handler) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")21: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
22: 36: tryCatchList(expr, classes, parentenv, handlers)doWithOneRestart(return(expr), restart)
23: 37: withOneRestart(expr, restarts[[1L]])
38: withRestarts(tryCatch(withCallingHandlers({tryCatch(withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") if (snapshot_skipped) { } skip("On CRAN") else if (!new_expectations && skip_on_empty) { } skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty()}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, snapshot_on_cran = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, snapshot_skipped <<- TRUE error = handle_error, interrupt = handle_interrupt), error = handle_fatal), invokeRestart("muffle_cran_snapshot") end_test = function() {}, skip = handle_skip, warning = handle_warning, message = handle_message, }) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
24: 39: doWithOneRestart(return(expr), restart)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())
25: 40: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
41: withOneRestart(expr, restarts[[1L]])FUN(X[[i]], ...)
26: 42: withRestarts(tryCatch(withCallingHandlers({lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations43: doTryCatch(return(expr), name, parentenv, handler)
if (snapshot_skipped) {44: skip("On CRAN")tryCatchOne(expr, names, parentenv, handlers[[1L]]) } else if (!new_expectations && skip_on_empty) {
skip_empty()45: }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {46: skip(paste0("{", e$package, "} is not installed."))tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") } NULL}, snapshot_on_cran = function(cnd) {}) snapshot_skipped <<- TRUE
47: with_reporter(reporters$multi, lapply(test_paths, test_one_file, invokeRestart("muffle_cran_snapshot") env = env, desc = desc, shuffle = shuffle, error_call = error_call))}, skip = handle_skip, warning = handle_warning, message = handle_message,
48: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_files_serial(test_dir = test_dir, test_package = test_package, end_test = function() { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, }) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 27: error_call = error_call)test_code(code, parent.frame())
49: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, 28: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_that("pcNet matches per-gene SVD principal component regression", load_package = load_package, parallel = parallel, shuffle = shuffle) {
nCells <- 200 nGenes <- 10050: test_dir("testthat", package = package, reporter = reporter, nComp <- 3 ..., load_package = "installed") set.seed(42)
X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), 51: nrow = nGenes, ncol = nCells)test_check("scTenifoldNet") rownames(X) <- paste0("Gene", seq_len(nGenes))
X_std <- scale(Matrix::t(X))An irrecoverable exception occurred. R is aborting now ...
reference <- matrix(0, nGenes, nGenes) for (K in seq_len(nGenes)) { design_matrix <- X_std[, -K] principal_components <- svd(design_matrix, nu = 0, nv = nComp)$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