Last updated on 2026-10-19 21:53:56 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4.3 | 8.08 | 71.52 | 79.60 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4.3 | 6.26 | 55.44 | 61.70 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.4.3 | 54.38 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.4.3 | 53.30 | OK | |||
| r-devel-windows-x86_64 | 1.4.3 | 10.00 | 88.00 | 98.00 | OK | |
| r-patched-linux-x86_64 | 1.4.3 | 7.72 | 65.60 | 73.32 | OK | |
| r-release-linux-x86_64 | 1.4.3 | 6.78 | 66.27 | 73.05 | 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 | 10.00 | 84.00 | 94.00 | 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 | 94.00 | 105.00 | 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))
Traceback:
9: 1: FUN(X[[i]], ...)FUN(X[[i]], ...)
10: 2: lapply(X = S, FUN = FUN, ...)lapply(seq_len(cores), inner.do)
3: 11: doTryCatch(return(expr), name, parentenv, handler)parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d,
nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, 4: mc.preschedule = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: 5: .pcNetCoefficients(basis$Z, basis$d, nComp, nCores)tryCatchList(expr, classes, parentenv, handlers)
13: 6: pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)tryCatch(expr, error = function(e) {
call <- conditionCall(e)14: if (!is.null(call)) {eval_bare(expr, quo_get_env(quo)) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)
15: dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")quasi_label(enquo(object), label) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]16: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), if (is.na(w)) pcNet(X, nComp = nComp, verbose = FALSE)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")17: if (w > LONG) eval(code, test_env)
prefix <- paste0(prefix, "\n ")18: }eval(code, test_env) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")19: .Internal(seterrmessage(msg[1L]))withCallingHandlers({ if (!silent && isTRUE(getOption("show.error.messages"))) { eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations cat(msg, file = outFile) if (snapshot_skipped) { skip("On CRAN") .Internal(printDeferredWarnings()) } } else if (!new_expectations && skip_on_empty) { invisible(structure(msg, class = "try-error", condition = e))}) skip_empty()
} 7: }, expectation = handle_expectation, packageNotFoundError = function(e) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed.")) 8: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE 9: invokeRestart("muffle_cran_snapshot")FUN(X[[i]], ...)}, skip = handle_skip, warning = handle_warning, message = handle_message,
10: error = handle_error, interrupt = handle_interrupt)lapply(seq_len(cores), inner.do)
20: 11: doTryCatch(return(expr), name, parentenv, handler)parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d,
nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, 21: mc.preschedule = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: 22: .pcNetCoefficients(basis$Z, basis$d, nComp, nCores)tryCatchList(expr, classes, parentenv, handlers)
13:
pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2)23:
tryCatch(withCallingHandlers({14: eval_bare(expr, quo_get_env(quo)) eval(code, test_env)
15: new_expectations <- the$test_expectations > starting_expectationsquasi_label(enquo(object), label) if (snapshot_skipped) {
skip("On CRAN")16: expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), } pcNet(X, nComp = nComp, verbose = FALSE)) else if (!new_expectations && skip_on_empty) {
17: skip_empty()eval(code, test_env) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {18: eval(code, test_env) if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
}19: }, snapshot_on_cran = function(cnd) {withCallingHandlers({ snapshot_skipped <<- TRUE eval(code, test_env) invokeRestart("muffle_cran_snapshot") new_expectations <- the$test_expectations > starting_expectations}, skip = handle_skip, warning = handle_warning, message = handle_message, if (snapshot_skipped) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
skip("On CRAN")24: }doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]]) else if (!new_expectations && skip_on_empty) {
26: skip_empty() }withRestarts(tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) if (on_cran()) { new_expectations <- the$test_expectations > starting_expectations skip(paste0("{", e$package, "} is not installed.")) if (snapshot_skipped) { } skip("On CRAN")}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {20: skip(paste0("{", e$package, "} is not installed."))doTryCatch(return(expr), name, parentenv, handler) }
}, snapshot_on_cran = function(cnd) {21: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")tryCatchOne(expr, names, parentenv, handlers[[1L]])}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal), 22: tryCatchList(expr, classes, parentenv, handlers) end_test = function() {
})23:
tryCatch(withCallingHandlers({27: test_code(code, parent.frame()) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {28: skip("On CRAN")test_that("pcNet matches per-gene SVD principal component regression", } { else if (!new_expectations && skip_on_empty) { skip_empty() nCells <- 200 } nGenes <- 100}, expectation = handle_expectation, packageNotFoundError = function(e) { nComp <- 3 if (on_cran()) { set.seed(42) skip(paste0("{", e$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]24: principal_components <- svd(design_matrix, nu = 0, doWithOneRestart(return(expr), restart) nv = nComp)$v
pc_scores <- design_matrix %*% principal_components25: pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)withOneRestart(expr, restarts[[1L]]) reference[K, -K] <- principal_components %*% pc_coefficients
}26: xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, withRestarts(tryCatch(withCallingHandlers({ verbose = FALSE) eval(code, test_env) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) new_expectations <- the$test_expectations > starting_expectations expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, if (snapshot_skipped) { nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) skip("On CRAN") } }) else if (!new_expectations && skip_on_empty) { skip_empty()
}29: }, expectation = handle_expectation, packageNotFoundError = function(e) {eval(code, test_env) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))30: }eval(code, test_env)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE31: invokeRestart("muffle_cran_snapshot")withCallingHandlers({}, skip = handle_skip, warning = handle_warning, message = handle_message, eval(code, test_env) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), new_expectations <- the$test_expectations > starting_expectations end_test = function() { if (snapshot_skipped) { }) skip("On CRAN")
}27: else if (!new_expectations && skip_on_empty) {test_code(code, parent.frame()) skip_empty()
}28: }, expectation = handle_expectation, packageNotFoundError = function(e) {test_that("pcNet matches per-gene SVD principal component regression", if (on_cran()) { { skip(paste0("{", e$package, "} is not installed.")) nCells <- 200 } nGenes <- 100}, snapshot_on_cran = function(cnd) { nComp <- 3 snapshot_skipped <<- TRUE set.seed(42) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), error = handle_error, interrupt = handle_interrupt) nrow = nGenes, ncol = nCells)
rownames(X) <- paste0("Gene", seq_len(nGenes))32: X_std <- scale(Matrix::t(X))doTryCatch(return(expr), name, parentenv, handler) reference <- matrix(0, nGenes, nGenes)
for (K in seq_len(nGenes)) {33: design_matrix <- X_std[, -K]tryCatchOne(expr, names, parentenv, handlers[[1L]]) principal_components <- svd(design_matrix, nu = 0,
nv = nComp)$v34: pc_scores <- design_matrix %*% principal_componentstryCatchList(expr, classes, parentenv, handlers) pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)
reference[K, -K] <- principal_components %*% pc_coefficients35: }tryCatch(withCallingHandlers({ xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, eval(code, test_env) verbose = FALSE) new_expectations <- the$test_expectations > starting_expectations expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) if (snapshot_skipped) { expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, skip("On CRAN") nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) } }) else if (!new_expectations && skip_on_empty) {
skip_empty()29: }eval(code, test_env)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {30: skip(paste0("{", e$package, "} is not installed."))eval(code, test_env) }
}, snapshot_on_cran = function(cnd) {31: snapshot_skipped <<- TRUEwithCallingHandlers({ invokeRestart("muffle_cran_snapshot") eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message, new_expectations <- the$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt), error = handle_fatal) if (snapshot_skipped) {
skip("On CRAN")36: }doWithOneRestart(return(expr), restart) else if (!new_expectations && skip_on_empty) {
skip_empty()37: }withOneRestart(expr, restarts[[1L]])}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {38: skip(paste0("{", e$package, "} is not installed."))withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE new_expectations <- the$test_expectations > starting_expectations invokeRestart("muffle_cran_snapshot") if (snapshot_skipped) { skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt) else if (!new_expectations && skip_on_empty) {
skip_empty()32: }doTryCatch(return(expr), name, parentenv, handler)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {33: skip(paste0("{", e$package, "} is not installed."))tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, snapshot_on_cran = function(cnd) {34: snapshot_skipped <<- TRUEtryCatchList(expr, classes, parentenv, handlers) invokeRestart("muffle_cran_snapshot")
35: }, skip = handle_skip, warning = handle_warning, message = handle_message, tryCatch(withCallingHandlers({ error = handle_error, interrupt = handle_interrupt), error = handle_fatal), eval(code, test_env) end_test = function() { new_expectations <- the$test_expectations > starting_expectations })
if (snapshot_skipped) {39: skip("On CRAN")test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) }
else if (!new_expectations && skip_on_empty) {40: skip_empty()source_file(path, env = env(env), desc = desc, shuffle = shuffle, } error_call = error_call)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {41: skip(paste0("{", e$package, "} is not installed."))FUN(X[[i]], ...) }
}, snapshot_on_cran = function(cnd) {42: snapshot_skipped <<- TRUElapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, invokeRestart("muffle_cran_snapshot") error_call = error_call)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)43:
doTryCatch(return(expr), name, parentenv, handler)36:
doWithOneRestart(return(expr), restart)44:
tryCatchOne(expr, names, parentenv, handlers[[1L]])37:
withOneRestart(expr, restarts[[1L]])45:
tryCatchList(expr, classes, parentenv, handlers)38:
withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env)46: new_expectations <- the$test_expectations > starting_expectationstryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") if (snapshot_skipped) { NULL skip("On CRAN")}) }
else if (!new_expectations && skip_on_empty) {47: skip_empty()with_reporter(reporters$multi, lapply(test_paths, test_one_file, } env = env, desc = desc, shuffle = shuffle, error_call = error_call))
48: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, }, expectation = handle_expectation, packageNotFoundError = function(e) { error_call = error_call) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))49: }test_files(test_dir = path, test_paths = test_paths, test_package = package, }, snapshot_on_cran = function(cnd) { reporter = reporter, load_helpers = load_helpers, env = env, snapshot_skipped <<- TRUE stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, invokeRestart("muffle_cran_snapshot") load_package = load_package, parallel = parallel, shuffle = shuffle)}, skip = handle_skip, warning = handle_warning, message = handle_message,
50: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_dir("testthat", package = package, reporter = reporter, end_test = function() { ..., load_package = "installed") })
51: 39: test_check("scTenifoldNet")test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())An irrecoverable exception occurred. R is aborting now ...
40: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
41: FUN(X[[i]], ...)
42: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
43: doTryCatch(return(expr), name, parentenv, handler)
44: tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
47: with_reporter(reporters$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