CRAN Package Check Results for Package scTenifoldNet

Last updated on 2026-10-26 23:52:23 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.4.3	7.82	72.46	80.28	OK
r-devel-linux-x86_64-debian-gcc	1.4.3	5.66	54.72	60.38	OK
r-devel-linux-x86_64-fedora-clang	1.4.3			78.47	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	6.88	66.12	73.00	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	82.00	91.00	OK
r-oldrel-macos-arm64	1.4.3	3.00	52.00	55.00	ERROR
r-oldrel-macos-x86_64	1.4.3	5.00	77.00	82.00	OK
r-oldrel-windows-x86_64	1.4.3	12.00	91.00	103.00	OK

Check Details

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 *** *** 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) 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) Traceback: 1: .Internal(printDeferredWarnings())FUN(X[[i]], ...) } invisible(structure(msg, class = "try-error", condition = e)) 2: }) lapply(X = S, FUN = FUN, ...) 7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 3: 8: doTryCatch(return(expr), name, parentenv, handler)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 4: 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])FUN(X[[i]], ...) 10: 5: lapply(seq_len(cores), inner.do)tryCatchList(expr, classes, parentenv, handlers) 11: 6: parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, tryCatch(expr, error = function(e) { nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, call <- conditionCall(e) mc.preschedule = TRUE) if (!is.null(call)) {12: if (identical(call[[1L]], quote(doTryCatch))) .pcNetCoefficients(basis$Z, basis$d, nComp, nCores) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)13: prefix <- paste("Error in", dcall, ": ") LONG <- 75LpcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")14: if (is.na(w)) eval_bare(expr, quo_get_env(quo)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")15: if (w > LONG) quasi_label(enquo(object), label) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : "16: msg <- paste0(prefix, conditionMessage(e), "\n")expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), .Internal(seterrmessage(msg[1L])) pcNet(X, nComp = nComp, verbose = FALSE)) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings())17: }eval(code, test_env) invisible(structure(msg, class = "try-error", condition = e)) })18: eval(code, test_env) 7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)19: withCallingHandlers({ 8: eval(code, test_env)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) new_expectations <- the$test_expectations > starting_expectations 9: FUN(X[[i]], ...) if (snapshot_skipped) { skip("On CRAN")10: }lapply(seq_len(cores), inner.do) else if (!new_expectations && skip_on_empty) { skip_empty() }11: }, expectation = handle_expectation, packageNotFoundError = function(e) {parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, if (on_cran()) { nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, skip(paste0("{", e$package, "} is not installed.")) mc.preschedule = TRUE) } }, snapshot_on_cran = function(cnd) {12: snapshot_skipped <<- TRUE.pcNetCoefficients(basis$Z, basis$d, nComp, nCores) invokeRestart("muffle_cran_snapshot") }, skip = handle_skip, warning = handle_warning, message = handle_message, 13: error = handle_error, interrupt = handle_interrupt) pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)20: doTryCatch(return(expr), name, parentenv, handler)14: eval_bare(expr, quo_get_env(quo))21: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15: 22: quasi_label(enquo(object), label)tryCatchList(expr, classes, parentenv, handlers) 16: 23: expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), tryCatch(withCallingHandlers({ pcNet(X, nComp = nComp, verbose = FALSE)) eval(code, test_env) 17: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) { skip("On CRAN")18: }eval(code, test_env) else if (!new_expectations && skip_on_empty) { skip_empty()19: }withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal) } }, expectation = handle_expectation, packageNotFoundError = function(e) {24: if (on_cran()) {doWithOneRestart(return(expr), restart) skip(paste0("{", e$package, "} is not installed.")) }25: }, snapshot_on_cran = function(cnd) {withOneRestart(expr, restarts[[1L]]) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")26: }, skip = handle_skip, warning = handle_warning, message = handle_message, withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) error = handle_error, interrupt = handle_interrupt) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {20: skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler) } else if (!new_expectations && skip_on_empty) {21: tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip_empty() }22: tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {23: tryCatch(withCallingHandlers({ eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations }}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") } else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() {}, expectation = handle_expectation, packageNotFoundError = function(e) { }) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))27: }test_code(code, parent.frame())}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE28: invokeRestart("muffle_cran_snapshot")test_that("pcNet matches per-gene SVD principal component regression", {}, skip = handle_skip, warning = handle_warning, message = handle_message, nCells <- 200 error = handle_error, interrupt = handle_interrupt), error = handle_fatal) nGenes <- 100 nComp <- 324: set.seed(42)doWithOneRestart(return(expr), restart) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), 25: nrow = nGenes, ncol = nCells)withOneRestart(expr, restarts[[1L]]) rownames(X) <- paste0("Gene", seq_len(nGenes)) X_std <- scale(Matrix::t(X))26: reference <- matrix(0, nGenes, nGenes)withRestarts(tryCatch(withCallingHandlers({ for (K in seq_len(nGenes)) { eval(code, test_env) design_matrix <- X_std[, -K] new_expectations <- the$test_expectations > starting_expectations principal_components <- svd(design_matrix, nu = 0, if (snapshot_skipped) { skip("On CRAN") nv = nComp)$v } else if (!new_expectations && skip_on_empty) { pc_scores <- design_matrix %*% principal_components skip_empty() pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) reference[K, -K] <- principal_components %*% pc_coefficients } }}, expectation = handle_expectation, packageNotFoundError = function(e) { xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, if (on_cran()) { verbose = FALSE) skip(paste0("{", e$package, "} is not installed.")) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) } expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, }, snapshot_on_cran = function(cnd) { nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) snapshot_skipped <<- TRUE }) invokeRestart("muffle_cran_snapshot") }, skip = handle_skip, warning = handle_warning, message = handle_message, 29: eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })30: eval(code, test_env)27: test_code(code, parent.frame())31: withCallingHandlers({28: eval(code, test_env)test_that("pcNet matches per-gene SVD principal component regression", new_expectations <- the$test_expectations > starting_expectations { if (snapshot_skipped) { nCells <- 200 skip("On CRAN") nGenes <- 100 } nComp <- 3 else if (!new_expectations && skip_on_empty) { set.seed(42) skip_empty() X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), } nrow = nGenes, ncol = nCells)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { rownames(X) <- paste0("Gene", seq_len(nGenes)) skip(paste0("{", e$package, "} is not installed.")) X_std <- scale(Matrix::t(X)) } reference <- matrix(0, nGenes, nGenes)}, snapshot_on_cran = function(cnd) { for (K in seq_len(nGenes)) { snapshot_skipped <<- TRUE design_matrix <- X_std[, -K] invokeRestart("muffle_cran_snapshot") principal_components <- svd(design_matrix, nu = 0, }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) nv = nComp)$v 32: pc_scores <- design_matrix %*% principal_components pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)doTryCatch(return(expr), name, parentenv, handler) reference[K, -K] <- principal_components %*% pc_coefficients }33: xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, tryCatchOne(expr, names, parentenv, handlers[[1L]]) verbose = FALSE) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)34: expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, tryCatchList(expr, classes, parentenv, handlers) nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) })35: tryCatch(withCallingHandlers({29: eval(code, test_env) eval(code, test_env) 30: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) { skip("On CRAN")31: }withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip(paste0("{", e$package, "} is not installed.")) }36: }, snapshot_on_cran = function(cnd) {doWithOneRestart(return(expr), restart) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")37: }, skip = handle_skip, warning = handle_warning, message = handle_message, withOneRestart(expr, restarts[[1L]]) error = handle_error, interrupt = handle_interrupt)38: withRestarts(tryCatch(withCallingHandlers({32: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN")33: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) { skip_empty()34: }tryCatchList(expr, classes, parentenv, handlers)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }35: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUEtryCatch(withCallingHandlers({ eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { skip("On CRAN") error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() { else if (!new_expectations && skip_on_empty) { }) skip_empty() } 39: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_code(code = exprs, env = env, reporter = get_reporter() %||% if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } StopReporter$new()) }, snapshot_on_cran = function(cnd) {40: snapshot_skipped <<- TRUEsource_file(path, env = env(env), desc = desc, shuffle = shuffle, invokeRestart("muffle_cran_snapshot") error_call = error_call)}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)41: FUN(X[[i]], ...) 36: 42: doWithOneRestart(return(expr), restart)lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) 37: 43: withOneRestart(expr, restarts[[1L]])doTryCatch(return(expr), name, parentenv, handler) 38: 44: withRestarts(tryCatch(withCallingHandlers({tryCatchOne(expr, names, parentenv, handlers[[1L]]) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN")45: }tryCatchList(expr, classes, parentenv, handlers) else if (!new_expectations && skip_on_empty) { skip_empty()46: }}, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatch(code, testthat_abort_reporter = function(cnd) { if (on_cran()) { cat(conditionMessage(cnd), "\n") skip(paste0("{", e$package, "} is not installed.")) NULL }}, snapshot_on_cran = function(cnd) {}) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 47: end_test = function() {with_reporter(reporters$multi, lapply(test_paths, test_one_file, }) env = env, desc = desc, shuffle = shuffle, error_call = error_call)) 39: 48: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 40: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, source_file(path, env = env(env), desc = desc, shuffle = shuffle, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) error_call = error_call) 41: FUN(X[[i]], ...)49: test_files(test_dir = path, test_paths = test_paths, test_package = package, 42: reporter = reporter, load_helpers = load_helpers, env = env, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, error_call = error_call) load_package = load_package, parallel = parallel, shuffle = shuffle) 43: 50: doTryCatch(return(expr), name, parentenv, handler)test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")44: tryCatchOne(expr, names, parentenv, handlers[[1L]])51: test_check("scTenifoldNet") 45: tryCatchList(expr, classes, parentenv, handlers)An irrecoverable exception occurred. R is aborting now ... 46: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 47: with_reporter(reporters$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