Last updated on 2026-11-07 02:58:19 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4.3 | 8.08 | 72.55 | 80.63 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4.3 | 5.05 | 54.69 | 59.74 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.4.3 | OK | ||||
| r-devel-linux-x86_64-fedora-gcc | 1.4.3 | 53.80 | OK | |||
| r-devel-windows-x86_64 | 1.4.3 | 9.00 | 87.00 | 96.00 | OK | |
| r-patched-linux-x86_64 | 1.4.3 | 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 | 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 | 102.00 | 113.00 | OK |
Version: 1.4.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/4s]
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
Traceback:
sm <- strsplit(conditionMessage(e), "\n")[[1L]] 1: 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: 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))
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)15:
8: quasi_label(enquo(object), label)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
16: 9: expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))
17: eval(code, test_env)FUN(X[[i]], ...)
10: lapply(seq_len(cores), inner.do)18:
eval(code, test_env)
19: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty()11: }parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, }, expectation = handle_expectation, packageNotFoundError = function(e) { nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) mc.preschedule = TRUE) }
12: }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot").pcNetCoefficients(basis$Z, basis$d, nComp, nCores)
}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
20: doTryCatch(return(expr), name, parentenv, handler)13:
pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14:
eval_bare(expr, quo_get_env(quo))22: tryCatchList(expr, classes, parentenv, handlers)
23: 15: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectationsquasi_label(enquo(object), label) if (snapshot_skipped) {
skip("On CRAN")16: }expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) pcNet(X, nComp = nComp, verbose = FALSE)) }
}, snapshot_on_cran = function(cnd) {17: snapshot_skipped <<- TRUEeval(code, test_env) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
18: 24: eval(code, test_env)doWithOneRestart(return(expr), restart)
25: 19: withOneRestart(expr, restarts[[1L]])
26: withCallingHandlers({withRestarts(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") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, 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")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
20: doTryCatch(return(expr), name, parentenv, handler)
end_test = function() { })
27: 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])test_code(code, parent.frame())
28: test_that("pcNet matches per-gene SVD principal component regression", 22: {tryCatchList(expr, classes, parentenv, handlers)
23: nCells <- 200 nGenes <- 100 nComp <- 3tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations set.seed(42) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), if (snapshot_skipped) { skip("On CRAN") nrow = nGenes, ncol = nCells) } else if (!new_expectations && skip_on_empty) { rownames(X) <- paste0("Gene", seq_len(nGenes)) X_std <- scale(Matrix::t(X)) reference <- matrix(0, nGenes, nGenes) skip_empty() for (K in seq_len(nGenes)) { } design_matrix <- X_std[, -K] principal_components <- svd(design_matrix, nu = 0, }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { nv = nComp)$v skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { pc_scores <- design_matrix %*% principal_components pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) snapshot_skipped <<- TRUE reference[K, -K] <- principal_components %*% pc_coefficients invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
24: xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, doWithOneRestart(return(expr), restart) verbose = FALSE)
expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) })
29: eval(code, test_env)25: withOneRestart(expr, restarts[[1L]])
26:
withRestarts(tryCatch(withCallingHandlers({30: eval(code, test_env)eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) { skip("On CRAN")31: }withCallingHandlers({ else if (!new_expectations && skip_on_empty) { skip_empty() } eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip("On CRAN") skip(paste0("{", e$package, "} is not installed.")) } } else if (!new_expectations && skip_on_empty) { skip_empty() }}, snapshot_on_cran = function(cnd) {}, expectation = handle_expectation, packageNotFoundError = function(e) { snapshot_skipped <<- TRUE if (on_cran()) { invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), } end_test = function() {}, snapshot_on_cran = function(cnd) { }) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
32: doTryCatch(return(expr), name, parentenv, handler)
33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: 27: tryCatchList(expr, classes, parentenv, handlers)
test_code(code, parent.frame())35: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty()
28: test_that("pcNet matches per-gene SVD principal component regression", { }}, expectation = handle_expectation, packageNotFoundError = function(e) { nCells <- 200 if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } nGenes <- 100 nComp <- 3 set.seed(42)}, snapshot_on_cran = function(cnd) { X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), snapshot_skipped <<- TRUE nrow = nGenes, ncol = nCells) invokeRestart("muffle_cran_snapshot") rownames(X) <- paste0("Gene", seq_len(nGenes)) X_std <- scale(Matrix::t(X)) reference <- matrix(0, nGenes, nGenes) for (K in seq_len(nGenes)) { design_matrix <- X_std[, -K]}, skip = handle_skip, warning = handle_warning, message = handle_message, principal_components <- svd(design_matrix, nu = 0, nv = nComp)$v error = handle_error, interrupt = handle_interrupt), error = handle_fatal) pc_scores <- design_matrix %*% principal_components
pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) reference[K, -K] <- principal_components %*% pc_coefficients36: } xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, doWithOneRestart(return(expr), restart) verbose = FALSE)
expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, 37: nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))withOneRestart(expr, restarts[[1L]]) })
38: 29: withRestarts(tryCatch(withCallingHandlers({eval(code, test_env) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations30: if (snapshot_skipped) {eval(code, test_env) skip("On CRAN")
} else if (!new_expectations && skip_on_empty) {31: skip_empty() }withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } eval(code, test_env)}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip("On CRAN") } end_test = function() { else if (!new_expectations && skip_on_empty) { }) skip_empty()
39: }}, expectation = handle_expectation, packageNotFoundError = function(e) {test_code(code = exprs, env = env, reporter = get_reporter() %||% if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) StopReporter$new()) }
}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE40: source_file(path, env = env(env), desc = desc, shuffle = shuffle, invokeRestart("muffle_cran_snapshot") error_call = error_call)
41: }, skip = handle_skip, warning = handle_warning, message = handle_message, FUN(X[[i]], ...)
42: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error = handle_error, interrupt = handle_interrupt) error_call = error_call)
32: 43: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
44: tryCatchOne(expr, names, parentenv, handlers[[1L]])
45:
33: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
34: 46: tryCatchList(expr, classes, parentenv, handlers)tryCatch(code, testthat_abort_reporter = function(cnd) {
35: cat(conditionMessage(cnd), "\n")tryCatch(withCallingHandlers({ NULL eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations})
if (snapshot_skipped) { skip("On CRAN")47: } else if (!new_expectations && skip_on_empty) {with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) skip_empty()
}}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))48: }test_files_serial(test_dir = test_dir, test_package = test_package, }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, invokeRestart("muffle_cran_snapshot") env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, }, skip = handle_skip, warning = handle_warning, message = handle_message, 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)
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)50:
test_dir("testthat", package = package, reporter = reporter, 36: ..., load_package = "installed")doWithOneRestart(return(expr), restart)
51: test_check("scTenifoldNet")
An irrecoverable exception occurred. R is aborting now ...
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