Last updated on 2026-11-01 18:53:19 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 | 5.18 | 54.09 | 59.27 | 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 | 7.18 | 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 | 3.00 | 49.00 | 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’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scTenifoldNet)
>
> test_check("scTenifoldNet")
*** caught segfault ***
*** caught segfault ***
address 0x110, cause 'invalid permissions'
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)
Traceback:
if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) 1: FUN(X[[i]], ...) call <- sys.call(-4L)
2: dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")lapply(X = S, FUN = FUN, ...)
LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] 3: doTryCatch(return(expr), name, parentenv, handler) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w))
4: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatchOne(expr, names, parentenv, handlers[[1L]])
type = "b") 5: tryCatchList(expr, classes, parentenv, handlers) if (w > LONG) prefix <- paste0(prefix, "\n ")
6: tryCatch(expr, error = function(e) { } else prefix <- "Error : " call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) if (!silent && isTRUE(getOption("show.error.messages"))) { prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") cat(msg, file = outFile) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], .Internal(printDeferredWarnings()) } type = "b") if (w > LONG) invisible(structure(msg, class = "try-error", condition = e)) 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) 7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) .Internal(printDeferredWarnings()) }
8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) invisible(structure(msg, class = "try-error", condition = e))})
9:
7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)FUN(X[[i]], ...)
8: 10: lapply(seq_len(cores), inner.do)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
11: 9: FUN(X[[i]], ...)parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, nComp = nComp, secular_weights = secular_weights, mc.cores = nCores,
mc.preschedule = TRUE)
10: lapply(seq_len(cores), inner.do)
12: .pcNetCoefficients(basis$Z, basis$d, nComp, nCores)11: parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, nComp = nComp, secular_weights = secular_weights, mc.cores = nCores,
13: mc.preschedule = TRUE)
12: pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2).pcNetCoefficients(basis$Z, basis$d, nComp, nCores)
14: 13: pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)
eval_bare(expr, quo_get_env(quo))
14: eval_bare(expr, quo_get_env(quo))15:
quasi_label(enquo(object), label)
15: quasi_label(enquo(object), label)16:
expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))16: expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2),
pcNet(X, nComp = nComp, verbose = FALSE))17:
eval(code, test_env)17:
eval(code, test_env)18:
eval(code, test_env)
18: eval(code, test_env)19:
19: withCallingHandlers({ eval(code, test_env)withCallingHandlers({ 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 snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) error = handle_error, interrupt = handle_interrupt)
20: 20: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
21: 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: 22: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
23: 23: 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") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)24: doWithOneRestart(return(expr), restart)
24: doWithOneRestart(return(expr), restart)25: withOneRestart(expr, restarts[[1L]])
25: 26: withOneRestart(expr, restarts[[1L]])withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)26: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) skip("On CRAN") new_expectations <- the$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) { 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 snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }) end_test = function() {
})27:
test_code(code, parent.frame())27:
test_code(code, parent.frame())28:
test_that("pcNet matches per-gene SVD principal component regression", 28: test_that("pcNet matches per-gene SVD principal component regression", { { nCells <- 200 nCells <- 200 nGenes <- 100 nComp <- 3 nGenes <- 100 set.seed(42) nComp <- 3 set.seed(42) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), nrow = nGenes, ncol = nCells) nrow = nGenes, ncol = nCells) rownames(X) <- paste0("Gene", seq_len(nGenes)) rownames(X) <- paste0("Gene", seq_len(nGenes)) X_std <- scale(Matrix::t(X)) X_std <- scale(Matrix::t(X)) reference <- matrix(0, nGenes, nGenes) reference <- matrix(0, nGenes, nGenes) for (K in seq_len(nGenes)) { for (K in seq_len(nGenes)) { design_matrix <- X_std[, -K] design_matrix <- X_std[, -K] principal_components <- svd(design_matrix, nu = 0, principal_components <- svd(design_matrix, nu = 0, nv = nComp)$v nv = nComp)$v pc_scores <- design_matrix %*% principal_components pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) pc_scores <- design_matrix %*% principal_components reference[K, -K] <- principal_components %*% pc_coefficients } pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, reference[K, -K] <- principal_components %*% pc_coefficients } verbose = FALSE) xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) verbose = FALSE) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, }) nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))
})29:
eval(code, test_env)29:
eval(code, test_env)
30: 30: eval(code, test_env)eval(code, test_env)
31:
withCallingHandlers({ eval(code, test_env)31: withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { if (snapshot_skipped) { skip("On CRAN") skip("On CRAN") } } else if (!new_expectations && skip_on_empty) { skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty()}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, expectation = handle_expectation, packageNotFoundError = function(e) { 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 snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) error = handle_error, interrupt = handle_interrupt)
32: 32: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
33: 33: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: 34: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
35: 35: 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) { } skip_empty() else if (!new_expectations && skip_on_empty) { } skip_empty()}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip(paste0("{", e$package, "} is not installed.")) if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, snapshot_on_cran = function(cnd) { invokeRestart("muffle_cran_snapshot") snapshot_skipped <<- TRUE}, skip = handle_skip, warning = handle_warning, message = handle_message, invokeRestart("muffle_cran_snapshot") error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)36:
doWithOneRestart(return(expr), restart)36:
doWithOneRestart(return(expr), restart)37:
withOneRestart(expr, restarts[[1L]])37:
withOneRestart(expr, restarts[[1L]])38:
withRestarts(tryCatch(withCallingHandlers({38: eval(code, test_env)withRestarts(tryCatch(withCallingHandlers({ new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) if (snapshot_skipped) { new_expectations <- the$test_expectations > starting_expectations 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()) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip(paste0("{", e$package, "} is not installed.")) if (on_cran()) { }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE skip(paste0("{", e$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), error = handle_fatal), snapshot_skipped <<- TRUE end_test = function() { invokeRestart("muffle_cran_snapshot") })}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 39: end_test = function() {test_code(code = exprs, env = env, reporter = get_reporter() %||% }) StopReporter$new())
39: 40: test_code(code = exprs, env = env, reporter = get_reporter() %||% source_file(path, env = env(env), desc = desc, shuffle = shuffle, StopReporter$new()) error_call = error_call)
40: 41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, FUN(X[[i]], ...) error_call = error_call)
42: 41: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, FUN(X[[i]], ...) error_call = error_call)
42: 43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, doTryCatch(return(expr), name, parentenv, handler) error_call = error_call)
44: 43: tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
45: 44: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
45: 46: tryCatchList(expr, classes, parentenv, handlers)tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")46: NULLtryCatch(code, testthat_abort_reporter = function(cnd) {}) cat(conditionMessage(cnd), "\n")
NULL47: })with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, desc = desc, shuffle = shuffle, error_call = error_call))47:
48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, test_files_serial(test_dir = test_dir, test_package = test_package, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 48: test_files_serial(test_dir = test_dir, test_package = test_package, desc = desc, load_package = load_package, shuffle = shuffle, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, error_call = error_call) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 49: error_call = error_call)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, 49: load_package = load_package, parallel = parallel, shuffle = shuffle)test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 50: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_dir("testthat", package = package, reporter = reporter, load_package = load_package, parallel = parallel, shuffle = shuffle) ..., load_package = "installed")
50: 51: test_dir("testthat", package = package, reporter = reporter, test_check("scTenifoldNet") ..., load_package = "installed")
An irrecoverable exception occurred. R is aborting now ...
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