Last updated on 2026-11-01 10:54:42 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 ***
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$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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() { })
27: test_code(code, parent.frame())
28: test_that("pcNet matches per-gene SVD principal component regression", { nCells <- 200 nGenes <- 100 nComp <- 3 set.seed(42) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), nrow = nGenes, ncol = nCells) rownames(X) <- paste0("Gene", seq_len(nGenes)) X_std <- scale(Matrix::t(X)) 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)$v pc_scores <- design_matrix %*% principal_components pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) reference[K, -K] <- principal_components %*% pc_coefficients } xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, verbose = FALSE) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) })
29: eval(code, test_env)
30: eval(code, test_env)
31: withCallingHandlers({
Traceback:
eval(code, test_env) 1: new_expectations <- the$test_expectations > starting_expectationsFUN(X[[i]], ...) if (snapshot_skipped) {
skip("On CRAN") 2: } else if (!new_expectations && skip_on_empty) {lapply(X = S, FUN = FUN, ...) skip_empty() }
}, expectation = handle_expectation, packageNotFoundError = function(e) { 3: doTryCatch(return(expr), name, parentenv, handler) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
} 4: }, snapshot_on_cran = function(cnd) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 5: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatchList(expr, classes, parentenv, handlers)
error = handle_error, interrupt = handle_interrupt) 6:
tryCatch(expr, error = function(e) {32: call <- conditionCall(e)doTryCatch(return(expr), name, parentenv, handler) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)33: dcall <- deparse(call, nlines = 1L)tryCatchOne(expr, names, parentenv, handlers[[1L]])
prefix <- paste("Error in", dcall, ": ")34: tryCatchList(expr, classes, parentenv, handlers) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]35: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatch(withCallingHandlers({ if (is.na(w)) eval(code, test_env) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], new_expectations <- the$test_expectations > starting_expectations type = "b") if (snapshot_skipped) { skip("On CRAN") if (w > LONG) } prefix <- paste0(prefix, "\n ") else if (!new_expectations && skip_on_empty) { skip_empty() } } else prefix <- "Error : "}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { msg <- paste0(prefix, conditionMessage(e), "\n") skip(paste0("{", e$package, "} is not installed.")) .Internal(seterrmessage(msg[1L])) } if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)}, snapshot_on_cran = function(cnd) { .Internal(printDeferredWarnings()) snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") invisible(structure(msg, class = "try-error", condition = e))}, skip = handle_skip, warning = handle_warning, message = handle_message, }) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
7: 36: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)doWithOneRestart(return(expr), restart)
8: 37: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
withOneRestart(expr, restarts[[1L]]) 9:
38: FUN(X[[i]], ...)withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)10: new_expectations <- the$test_expectations > starting_expectationslapply(seq_len(cores), inner.do)
if (snapshot_skipped) {11: skip("On CRAN")parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, } nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, else if (!new_expectations && skip_on_empty) { mc.preschedule = TRUE) skip_empty()
}12: }, expectation = handle_expectation, packageNotFoundError = function(e) {.pcNetCoefficients(basis$Z, basis$d, nComp, nCores) if (on_cran()) {
13: pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)
skip(paste0("{", e$package, "} is not installed."))14: }eval_bare(expr, quo_get_env(quo))}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE15: invokeRestart("muffle_cran_snapshot")quasi_label(enquo(object), label)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 16: end_test = function() {expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), }) pcNet(X, nComp = nComp, verbose = FALSE))
17: 39: eval(code, test_env)test_code(code = exprs, env = env, reporter = get_reporter() %||%
18: StopReporter$new())
eval(code, test_env)40: source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)
19: 41: withCallingHandlers({FUN(X[[i]], ...) eval(code, test_env)
42: new_expectations <- the$test_expectations > starting_expectationslapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, if (snapshot_skipped) { error_call = error_call) skip("On CRAN")
}43: else if (!new_expectations && skip_on_empty) {doTryCatch(return(expr), name, parentenv, handler) skip_empty()
}}, expectation = handle_expectation, packageNotFoundError = function(e) {44: if (on_cran()) { skip(paste0("{", e$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, error = handle_error, interrupt = handle_interrupt)tryCatchList(expr, classes, parentenv, handlers)
46: 20: tryCatch(code, testthat_abort_reporter = function(cnd) {doTryCatch(return(expr), name, parentenv, handler) cat(conditionMessage(cnd), "\n")
NULL21: tryCatchOne(expr, names, parentenv, handlers[[1L]])})
47: 22: with_reporter(reporters$multi, lapply(test_paths, test_one_file, tryCatchList(expr, classes, parentenv, handlers) env = env, desc = desc, shuffle = shuffle, error_call = error_call))
23: 48: tryCatch(withCallingHandlers({test_files_serial(test_dir = test_dir, test_package = test_package, eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, if (snapshot_skipped) { env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, skip("On CRAN") desc = desc, load_package = load_package, shuffle = shuffle, } error_call = error_call) else if (!new_expectations && skip_on_empty) { skip_empty()
}49: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_files(test_dir = path, test_paths = test_paths, test_package = package, if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) reporter = reporter, load_helpers = load_helpers, env = env, } stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }, snapshot_on_cran = function(cnd) { load_package = load_package, parallel = parallel, shuffle = shuffle) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")50: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_dir("testthat", package = package, reporter = reporter, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) ..., load_package = "installed")
51: 24: test_check("scTenifoldNet")doWithOneRestart(return(expr), restart)
An irrecoverable exception occurred. R is aborting now ...
25: withOneRestart(expr, restarts[[1L]])
26: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
27: test_code(code, parent.frame())
28: test_that("pcNet matches per-gene SVD principal component regression", { nCells <- 200 nGenes <- 100 nComp <- 3 set.seed(42) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), nrow = nGenes, ncol = nCells) rownames(X) <- paste0("Gene", seq_len(nGenes)) X_std <- scale(Matrix::t(X)) reference <- matrix(0, nGenes, nGenes) for (K in seq_len(nGenes)) { design_matrix <- X_std[, -K] principal_components <- svd(design_matrix, nu = 0, nv = nComp)$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