• using R version 4.5.2 Patched (2026-01-31 r89382)
• using platform: aarch64-apple-darwin20
• R was compiled by     Apple clang version 16.0.0 (clang-1600.0.26.6)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.7.8
• using session charset: UTF-8
• checking for file ‘scTenifoldNet/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘scTenifoldNet’ version ‘1.4.3’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘scTenifoldNet’ can be installed ... [3s/3s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [3s/3s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking examples ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [3s/2s] 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:   Traceback:   lapply(seq_len(cores), inner.do)    1: 11: FUN(X[[i]], ...)parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d,       nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, 2: mc.preschedule = TRUE)lapply(X = S, FUN = FUN, ...)      12: 3: .pcNetCoefficients(basis$Z, basis$d, nComp, nCores)doTryCatch(return(expr), name, parentenv, handler)      13: pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) 4:   tryCatchOne(expr, names, parentenv, handlers[[1L]])   14: 5: eval_bare(expr, quo_get_env(quo))   tryCatchList(expr, classes, parentenv, handlers)15:   quasi_label(enquo(object), label) 6:   tryCatch(expr, error = function(e) {16: call <- conditionCall(e)expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), if (!is.null(call)) { pcNet(X, nComp = nComp, verbose = FALSE)) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)           dcall <- deparse(call, nlines = 1L)17: prefix <- paste("Error in", dcall, ": ")eval(code, test_env) LONG <- 75L           sm <- strsplit(conditionMessage(e), "\n")[[1L]]18: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")eval(code, test_env) if (is.na(w))               w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 19: type = "b")withCallingHandlers({ if (w > LONG) eval(code, test_env) prefix <- paste0(prefix, "\n ") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else prefix <- "Error : " skip("On CRAN") msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) else if (!new_expectations && skip_on_empty) { if (!silent && isTRUE(getOption("show.error.messages"))) { skip_empty() cat(msg, file = outFile) }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { .Internal(printDeferredWarnings()) skip(paste0("{", e$package, "} is not installed.")) } } invisible(structure(msg, class = "try-error", condition = e))}, snapshot_on_cran = function(cnd) {}) snapshot_skipped <<- TRUE       invokeRestart("muffle_cran_snapshot") 7: }, skip = handle_skip, warning = handle_warning, message = handle_message, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) error = handle_error, interrupt = handle_interrupt)       8: 20: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))doTryCatch(return(expr), name, parentenv, handler)       9: 21: FUN(X[[i]], ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])      10: 22: tryCatchList(expr, classes, parentenv, handlers)lapply(seq_len(cores), inner.do)      23: 11: tryCatch(withCallingHandlers({parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, eval(code, test_env) nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, new_expectations <- the$test_expectations > starting_expectations mc.preschedule = TRUE) if (snapshot_skipped) {           skip("On CRAN")12: }.pcNetCoefficients(basis$Z, basis$d, nComp, nCores) else if (!new_expectations && skip_on_empty) {           skip_empty()13: }pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)   }, expectation = handle_expectation, packageNotFoundError = function(e) {14: if (on_cran()) {eval_bare(expr, quo_get_env(quo)) skip(paste0("{", e$package, "} is not installed."))       }}, snapshot_on_cran = function(cnd) {15: quasi_label(enquo(object), label) snapshot_skipped <<- TRUE       invokeRestart("muffle_cran_snapshot")16: }, skip = handle_skip, warning = handle_warning, message = handle_message, expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), error = handle_error, interrupt = handle_interrupt), error = handle_fatal) pcNet(X, nComp = nComp, verbose = FALSE))      24: 17: doWithOneRestart(return(expr), restart)eval(code, test_env)   25:   withOneRestart(expr, restarts[[1L]])18:   eval(code, test_env)26:   withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env)19: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {withCallingHandlers({ skip("On CRAN") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { if (snapshot_skipped) { skip_empty() } skip("On CRAN")}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) { else if (!new_expectations && skip_on_empty) { skip(paste0("{", e$package, "} is not installed.")) } skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip(paste0("{", e$package, "} is not installed.")) end_test = function() { }}, snapshot_on_cran = function(cnd) { }) snapshot_skipped <<- TRUE       invokeRestart("muffle_cran_snapshot")27: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_code(code, parent.frame()) error = handle_error, interrupt = handle_interrupt)   28:   test_that("pcNet matches per-gene SVD principal component regression", 20: {doTryCatch(return(expr), name, parentenv, handler) nCells <- 200 nGenes <- 100           nComp <- 321: set.seed(42)tryCatchOne(expr, names, parentenv, handlers[[1L]]) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98),               nrow = nGenes, ncol = nCells)22: rownames(X) <- paste0("Gene", seq_len(nGenes))tryCatchList(expr, classes, parentenv, handlers)           X_std <- scale(Matrix::t(X)) reference <- matrix(0, nGenes, nGenes)23: tryCatch(withCallingHandlers({ for (K in seq_len(nGenes)) { eval(code, test_env) design_matrix <- X_std[, -K] new_expectations <- the$test_expectations > starting_expectations principal_components <- svd(design_matrix, nu = 0, nv = nComp)$v if (snapshot_skipped) { pc_scores <- design_matrix %*% principal_components skip("On CRAN") pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) } reference[K, -K] <- principal_components %*% pc_coefficients } else if (!new_expectations && skip_on_empty) { xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, skip_empty() verbose = FALSE) } expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)}, expectation = handle_expectation, packageNotFoundError = function(e) { expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, if (on_cran()) { nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) skip(paste0("{", e$package, "} is not installed.")) }) }   }, snapshot_on_cran = function(cnd) {29: snapshot_skipped <<- TRUEeval(code, test_env)   30: invokeRestart("muffle_cran_snapshot")eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message,       error = handle_error, interrupt = handle_interrupt), error = handle_fatal)31:   withCallingHandlers({24: eval(code, test_env)doWithOneRestart(return(expr), restart) new_expectations <- the$test_expectations > starting_expectations       if (snapshot_skipped) {25: skip("On CRAN")withOneRestart(expr, restarts[[1L]]) }       else if (!new_expectations && skip_on_empty) {26: skip_empty()withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) { new_expectations <- the$test_expectations > starting_expectations if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { skip_empty() snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt) if (on_cran()) {           skip(paste0("{", e$package, "} is not installed."))32: }doTryCatch(return(expr), name, parentenv, handler)}, snapshot_on_cran = function(cnd) {       snapshot_skipped <<- TRUE33: invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,   34: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() {tryCatchList(expr, classes, parentenv, handlers) })   35:   tryCatch(withCallingHandlers({27: eval(code, test_env)test_code(code, parent.frame()) new_expectations <- the$test_expectations > starting_expectations       if (snapshot_skipped) {28: skip("On CRAN")test_that("pcNet matches per-gene SVD principal component regression", { } nCells <- 200 else if (!new_expectations && skip_on_empty) { nGenes <- 100 skip_empty() nComp <- 3 }}, expectation = handle_expectation, packageNotFoundError = function(e) { set.seed(42) if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), } nrow = nGenes, ncol = nCells)}, snapshot_on_cran = function(cnd) { rownames(X) <- paste0("Gene", seq_len(nGenes)) snapshot_skipped <<- TRUE X_std <- scale(Matrix::t(X)) invokeRestart("muffle_cran_snapshot") reference <- matrix(0, nGenes, nGenes)}, skip = handle_skip, warning = handle_warning, message = handle_message, for (K in seq_len(nGenes)) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) design_matrix <- X_std[, -K]   36: doWithOneRestart(return(expr), restart) principal_components <- svd(design_matrix, nu = 0,                   nv = nComp)$v37: withOneRestart(expr, restarts[[1L]]) pc_scores <- design_matrix %*% principal_components   38: pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)withRestarts(tryCatch(withCallingHandlers({ reference[K, -K] <- principal_components %*% pc_coefficients eval(code, test_env) } xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, verbose = FALSE) new_expectations <- the$test_expectations > starting_expectations expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) if (snapshot_skipped) { }) skip("On CRAN")   29: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {           skip_empty()30: }}, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env) if (on_cran()) {           skip(paste0("{", e$package, "} is not installed.")) }31: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUEwithCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip("On CRAN") end_test = function() { } }) else if (!new_expectations && skip_on_empty) {           skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) {39: if (on_cran()) {test_code(code = exprs, env = env, reporter = get_reporter() %||% skip(paste0("{", e$package, "} is not installed.")) StopReporter$new()) }   }, snapshot_on_cran = function(cnd) {40: source_file(path, env = env(env), desc = desc, shuffle = shuffle, snapshot_skipped <<- TRUE error_call = error_call) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)      41: 32: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)      42: 33: tryCatchOne(expr, names, parentenv, handlers[[1L]])   34: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, tryCatchList(expr, classes, parentenv, handlers)   35: error_call = error_call)tryCatch(withCallingHandlers({       eval(code, test_env)43: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN")doTryCatch(return(expr), name, parentenv, handler) } else if (!new_expectations && skip_on_empty) { skip_empty()       }44: }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {       snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")45: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)      36: 46: doWithOneRestart(return(expr), restart)tryCatch(code, testthat_abort_reporter = function(cnd) {   37: withOneRestart(expr, restarts[[1L]])   38: cat(conditionMessage(cnd), "\n")withRestarts(tryCatch(withCallingHandlers({ NULL eval(code, test_env)}) new_expectations <- the$test_expectations > starting_expectations       if (snapshot_skipped) {47: skip("On CRAN") }with_reporter(reporters$multi, lapply(test_paths, test_one_file, else if (!new_expectations && skip_on_empty) { env = env, desc = desc, shuffle = shuffle, error_call = error_call)) skip_empty()       }48: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_files_serial(test_dir = test_dir, test_package = test_package, if (on_cran()) { test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, skip(paste0("{", e$package, "} is not installed.")) error_call = error_call)       }49: }, snapshot_on_cran = function(cnd) {test_files(test_dir = path, test_paths = test_paths, test_package = package, snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, reporter = reporter, load_helpers = load_helpers, env = env, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, end_test = function() { load_package = load_package, parallel = parallel, shuffle = shuffle) })      39: 50: test_code(code = exprs, env = env, reporter = get_reporter() %||% test_dir("testthat", package = package, reporter = reporter, StopReporter$new()) ..., load_package = "installed")   40:   source_file(path, env = env(env), desc = desc, shuffle = shuffle, 51: error_call = error_call)test_check("scTenifoldNet")      41: An irrecoverable exception occurred. R is aborting now ...   FUN(X[[i]], ...)   42: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)   43: doTryCatch(return(expr), name, parentenv, handler)   44: tryCatchOne(expr, names, parentenv, handlers[[1L]])   45: tryCatchList(expr, classes, parentenv, handlers)   46: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})   47: with_reporter(reporters$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
• checking PDF version of manual ... [4s/4s] OK
• DONE

Status: 1 ERROR