Last updated on 2026-10-23 04:55:25 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4.3 | 8.11 | 72.43 | 80.54 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4.3 | 5.93 | 54.82 | 60.75 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.4.3 | 78.47 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.4.3 | 53.30 | OK | |||
| r-devel-windows-x86_64 | 1.4.3 | 10.00 | 88.00 | 98.00 | OK | |
| r-patched-linux-x86_64 | 1.4.3 | 6.88 | 66.12 | 73.00 | 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 | 3.00 | 30.00 | 33.00 | 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 | 97.00 | 109.00 | 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
Traceback:
sm <- strsplit(conditionMessage(e), "\n")[[1L]] 1: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")FUN(X[[i]], ...) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") 2: if (w > LONG) lapply(X = S, FUN = FUN, ...) prefix <- paste0(prefix, "\n ")
} 3: else prefix <- "Error : "doTryCatch(return(expr), name, parentenv, handler) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) 4: if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) cat(msg, file = outFile)
.Internal(printDeferredWarnings()) 5: }tryCatchList(expr, classes, parentenv, handlers) invisible(structure(msg, class = "try-error", condition = e))
}) 6:
tryCatch(expr, error = function(e) { 7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) call <- conditionCall(e)
if (!is.null(call)) { 8: if (identical(call[[1L]], quote(doTryCatch))) sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) 9: prefix <- paste("Error in", dcall, ": ")FUN(X[[i]], ...) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]10: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")lapply(seq_len(cores), inner.do) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
11: type = "b")parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, if (w > LONG) nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, prefix <- paste0(prefix, "\n ") mc.preschedule = TRUE) }
else prefix <- "Error : "12: msg <- paste0(prefix, conditionMessage(e), "\n").pcNetCoefficients(basis$Z, basis$d, nComp, nCores) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {13: cat(msg, file = outFile)pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) .Internal(printDeferredWarnings())
}14: invisible(structure(msg, class = "try-error", condition = e))eval_bare(expr, quo_get_env(quo))})
15:
quasi_label(enquo(object), label) 7:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)16:
expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), 8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: FUN(X[[i]], ...) pcNet(X, nComp = nComp, verbose = FALSE))
17:
eval(code, test_env)10: lapply(seq_len(cores), inner.do)
18: 11: eval(code, test_env)
parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, 19: nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, withCallingHandlers({ mc.preschedule = TRUE) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations12: if (snapshot_skipped) {.pcNetCoefficients(basis$Z, basis$d, nComp, nCores) skip("On CRAN")
}13: else if (!new_expectations && skip_on_empty) {pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) skip_empty()
}14: }, expectation = handle_expectation, packageNotFoundError = function(e) {eval_bare(expr, quo_get_env(quo)) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))15: }quasi_label(enquo(object), label)}, snapshot_on_cran = function(cnd) {
16: snapshot_skipped <<- TRUEexpect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), invokeRestart("muffle_cran_snapshot") pcNet(X, nComp = nComp, verbose = FALSE))}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)17:
eval(code, test_env)20:
doTryCatch(return(expr), name, parentenv, handler)18:
eval(code, test_env)21:
tryCatchOne(expr, names, parentenv, handlers[[1L]])19:
withCallingHandlers({22: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {23: skip("On CRAN") }tryCatch(withCallingHandlers({ else if (!new_expectations && skip_on_empty) { skip_empty() eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") skip_empty()}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) {
20: if (on_cran()) {doTryCatch(return(expr), name, parentenv, handler) skip(paste0("{", e$package, "} is not installed."))
}21: tryCatchOne(expr, names, parentenv, handlers[[1L]])}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE22: tryCatchList(expr, classes, parentenv, handlers) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 23: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)tryCatch(withCallingHandlers({
eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations24: if (snapshot_skipped) {doWithOneRestart(return(expr), restart) skip("On CRAN")
}25: else if (!new_expectations && skip_on_empty) {withOneRestart(expr, restarts[[1L]]) skip_empty()
}26: }, expectation = handle_expectation, packageNotFoundError = function(e) {withRestarts(tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {24: if (on_cran()) {doWithOneRestart(return(expr), restart) skip(paste0("{", e$package, "} is not installed."))
}25: }, snapshot_on_cran = function(cnd) {withOneRestart(expr, restarts[[1L]]) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 26: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), withRestarts(tryCatch(withCallingHandlers({ end_test = function() { }) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations27: if (snapshot_skipped) {test_code(code, parent.frame()) skip("On CRAN")
}28: else if (!new_expectations && skip_on_empty) {test_that("pcNet matches per-gene SVD principal component regression", skip_empty() { } nCells <- 200}, expectation = handle_expectation, packageNotFoundError = function(e) { nGenes <- 100 if (on_cran()) { nComp <- 3 skip(paste0("{", e$package, "} is not installed.")) set.seed(42) } X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), }, snapshot_on_cran = function(cnd) { nrow = nGenes, ncol = nCells) snapshot_skipped <<- TRUE rownames(X) <- paste0("Gene", seq_len(nGenes)) invokeRestart("muffle_cran_snapshot") X_std <- scale(Matrix::t(X))}, skip = handle_skip, warning = handle_warning, message = handle_message, reference <- matrix(0, nGenes, nGenes) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), for (K in seq_len(nGenes)) { design_matrix <- X_std[, -K] end_test = function() { principal_components <- svd(design_matrix, nu = 0, }) nv = nComp)$v
pc_scores <- design_matrix %*% principal_components27: pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)test_code(code, parent.frame()) reference[K, -K] <- principal_components %*% pc_coefficients
}28: xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, test_that("pcNet matches per-gene SVD principal component regression", verbose = FALSE) { expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) nCells <- 200 expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nGenes <- 100 nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) nComp <- 3 }) set.seed(42)
X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), 29: nrow = nGenes, ncol = nCells)eval(code, test_env) rownames(X) <- paste0("Gene", seq_len(nGenes))
X_std <- scale(Matrix::t(X))30: eval(code, test_env) reference <- matrix(0, nGenes, nGenes)
for (K in seq_len(nGenes)) {31: design_matrix <- X_std[, -K]withCallingHandlers({ principal_components <- svd(design_matrix, nu = 0, eval(code, test_env) nv = nComp)$v new_expectations <- the$test_expectations > starting_expectations pc_scores <- design_matrix %*% principal_components if (snapshot_skipped) { pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) reference[K, -K] <- principal_components %*% pc_coefficients skip("On CRAN") } xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, } verbose = FALSE) else if (!new_expectations && skip_on_empty) { expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) skip_empty() expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, }}, expectation = handle_expectation, packageNotFoundError = function(e) { nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) if (on_cran()) { })
skip(paste0("{", e$package, "} is not installed."))29: }eval(code, test_env)
}, snapshot_on_cran = function(cnd) {30: snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")eval(code, test_env)}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)31:
withCallingHandlers({32: doTryCatch(return(expr), name, parentenv, handler) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations33: if (snapshot_skipped) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip("On CRAN")
}34: else if (!new_expectations && skip_on_empty) {tryCatchList(expr, classes, parentenv, handlers)
skip_empty()35: }tryCatch(withCallingHandlers({}, expectation = handle_expectation, packageNotFoundError = function(e) { eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (on_cran()) { if (snapshot_skipped) { skip(paste0("{", e$package, "} is not installed.")) skip("On CRAN") } } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { skip_empty() snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt)
skip(paste0("{", e$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,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)34:
tryCatchList(expr, classes, parentenv, handlers)36:
doWithOneRestart(return(expr), restart)35:
tryCatch(withCallingHandlers({37: eval(code, test_env)withOneRestart(expr, restarts[[1L]]) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {38: skip("On CRAN")withRestarts(tryCatch(withCallingHandlers({ } else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, expectation = handle_expectation, packageNotFoundError = function(e) {}, skip = handle_skip, warning = handle_warning, message = handle_message, if (on_cran()) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal) skip(paste0("{", e$package, "} is not installed."))
}}, snapshot_on_cran = function(cnd) {36: snapshot_skipped <<- TRUEdoWithOneRestart(return(expr), restart) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 37: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), withOneRestart(expr, restarts[[1L]]) end_test = function() {
})38:
withRestarts(tryCatch(withCallingHandlers({39: test_code(code = exprs, env = env, reporter = get_reporter() %||% eval(code, test_env) StopReporter$new()) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {40: skip("On CRAN")source_file(path, env = env(env), desc = desc, shuffle = shuffle, } error_call = error_call) else if (!new_expectations && skip_on_empty) {
skip_empty()41: }FUN(X[[i]], ...)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {42: skip(paste0("{", e$package, "} is not installed."))lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } error_call = error_call)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE43: invokeRestart("muffle_cran_snapshot")doTryCatch(return(expr), name, parentenv, handler)
}, skip = handle_skip, warning = handle_warning, message = handle_message, 44: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), tryCatchOne(expr, names, parentenv, handlers[[1L]]) end_test = function() {
})45:
tryCatchList(expr, classes, parentenv, handlers)39:
test_code(code = exprs, env = env, reporter = get_reporter() %||% 46: tryCatch(code, testthat_abort_reporter = function(cnd) { StopReporter$new()) cat(conditionMessage(cnd), "\n")
NULL40: })source_file(path, env = env(env), desc = desc, shuffle = shuffle,
error_call = error_call)47:
with_reporter(reporters$multi, lapply(test_paths, test_one_file, 41: env = env, desc = desc, shuffle = shuffle, error_call = error_call))FUN(X[[i]], ...)
48: test_files_serial(test_dir = test_dir, test_package = test_package, 42: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) error_call = error_call)
43: 49: doTryCatch(return(expr), name, parentenv, handler)test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env, 44: stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, tryCatchOne(expr, names, parentenv, handlers[[1L]]) load_package = load_package, parallel = parallel, shuffle = shuffle)
45:
50: tryCatchList(expr, classes, parentenv, handlers)test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")46:
51: tryCatch(code, testthat_abort_reporter = function(cnd) {test_check("scTenifoldNet") cat(conditionMessage(cnd), "\n")
NULLAn irrecoverable exception occurred. R is aborting now ...
})
47: with_reporter(reporters$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