Last updated on 2026-10-09 07:55:58 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4 | 27.67 | 105.88 | 133.55 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4 | 19.23 | 86.86 | 106.09 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.4.3 | 6.00 | 51.02 | 57.02 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.4.3 | 6.00 | 51.43 | 57.43 | OK | |
| r-devel-windows-x86_64 | 1.4 | 39.00 | 204.00 | 243.00 | ERROR | |
| r-patched-linux-x86_64 | 1.4 | 24.94 | 98.66 | 123.60 | OK | |
| r-release-linux-x86_64 | 1.4 | 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 | 36.00 | 129.00 | 165.00 | 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 | 48.00 | 186.00 | 234.00 | OK |
Version: 1.4
Check: tests
Result: ERROR
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(scTenifoldNet)
>
> test_check("scTenifoldNet")
Computing regression coefficients...
Saving _problems/test-scQC-24.R
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 44 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-scQC.R:24:3'): scQC works ──────────────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'i' in selecting a method for function '[<-': lazy-load database 'D:/temp/2026_09_24_01_50_00_23554/RtmpG4bMOM/RLIBS_25d0445e43a99/Matrix/R/Matrix.rdb' is corrupt
Backtrace:
▆
1. ├─scTenifoldNet::scQC(...) at test-scQC.R:24:3
2. │ ├─methods (local) `[<-`(`*tmp*`, X < 0, value = `<dbl>`)
3. │ ├─X < 0
4. │ └─X < 0
5. └─base::.handleSimpleError(...)
6. └─base (local) h(simpleError(msg, call))
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 44 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
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]], ...)
Traceback:
10: lapply(seq_len(cores), inner.do) 1:
FUN(X[[i]], ...)11:
parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, 2: lapply(X = S, FUN = FUN, ...) nComp = nComp, secular_weights = secular_weights, mc.cores = nCores,
3: mc.preschedule = TRUE)doTryCatch(return(expr), name, parentenv, handler)
12:
.pcNetCoefficients(basis$Z, basis$d, nComp, nCores) 4:
tryCatchOne(expr, names, parentenv, handlers[[1L]])13:
pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) 5:
tryCatchList(expr, classes, parentenv, handlers)14:
eval_bare(expr, quo_get_env(quo)) 6:
tryCatch(expr, error = function(e) {15: quasi_label(enquo(object), label) call <- conditionCall(e)
if (!is.null(call)) {16: if (identical(call[[1L]], quote(doTryCatch))) expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), call <- sys.call(-4L) pcNet(X, nComp = nComp, verbose = FALSE)) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")17: LONG <- 75Leval(code, test_env) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")18: if (is.na(w)) eval(code, test_env) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")19: if (w > LONG) withCallingHandlers({ prefix <- paste0(prefix, "\n ") eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations else prefix <- "Error : " if (snapshot_skipped) { msg <- paste0(prefix, conditionMessage(e), "\n") skip("On CRAN") .Internal(seterrmessage(msg[1L])) } if (!silent && isTRUE(getOption("show.error.messages"))) { else if (!new_expectations && skip_on_empty) { cat(msg, file = outFile) skip_empty() .Internal(printDeferredWarnings()) } }}, expectation = handle_expectation, packageNotFoundError = function(e) { invisible(structure(msg, class = "try-error", condition = e)) if (on_cran()) {}) skip(paste0("{", e$package, "} is not installed."))
} 7: }, snapshot_on_cran = function(cnd) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot") 8: }, skip = handle_skip, warning = handle_warning, message = handle_message, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) error = handle_error, interrupt = handle_interrupt)
9: 20: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)
10: 21: lapply(seq_len(cores), inner.do)tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: 22: parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, tryCatchList(expr, classes, parentenv, handlers) nComp = nComp, secular_weights = secular_weights, mc.cores = nCores,
mc.preschedule = TRUE)23:
tryCatch(withCallingHandlers({12: eval(code, test_env).pcNetCoefficients(basis$Z, basis$d, nComp, nCores) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {13: skip("On CRAN")pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) }
else if (!new_expectations && skip_on_empty) {14: skip_empty()eval_bare(expr, quo_get_env(quo)) }
}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {15: skip(paste0("{", e$package, "} is not installed."))quasi_label(enquo(object), label) }
16: }, snapshot_on_cran = function(cnd) {expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), snapshot_skipped <<- TRUE pcNet(X, nComp = nComp, verbose = FALSE))
invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, 17: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)eval(code, test_env)
24: 18: doWithOneRestart(return(expr), restart)eval(code, test_env)
25: 19: withOneRestart(expr, restarts[[1L]])withCallingHandlers({
eval(code, test_env)26: new_expectations <- the$test_expectations > starting_expectationswithRestarts(tryCatch(withCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") } new_expectations <- the$test_expectations > starting_expectations else if (!new_expectations && skip_on_empty) { skip_empty() if (snapshot_skipped) { } skip("On CRAN") }}, expectation = handle_expectation, packageNotFoundError = function(e) { else if (!new_expectations && skip_on_empty) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) skip_empty() } }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) } error = handle_error, interrupt = handle_interrupt)
}, snapshot_on_cran = function(cnd) {20: snapshot_skipped <<- TRUEdoTryCatch(return(expr), name, parentenv, handler) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 21: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), tryCatchOne(expr, names, parentenv, handlers[[1L]]) end_test = function() {
})22:
tryCatchList(expr, classes, parentenv, handlers)27:
23: test_code(code, parent.frame())tryCatch(withCallingHandlers({
eval(code, test_env)28: new_expectations <- the$test_expectations > starting_expectationstest_that("pcNet matches per-gene SVD principal component regression", if (snapshot_skipped) { { skip("On CRAN") nCells <- 200 } nGenes <- 100 else if (!new_expectations && skip_on_empty) { nComp <- 3 skip_empty() set.seed(42) } X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), }, expectation = handle_expectation, packageNotFoundError = function(e) { nrow = nGenes, ncol = nCells) if (on_cran()) { rownames(X) <- paste0("Gene", seq_len(nGenes)) skip(paste0("{", e$package, "} is not installed.")) X_std <- scale(Matrix::t(X)) } reference <- matrix(0, nGenes, nGenes)}, snapshot_on_cran = function(cnd) { for (K in seq_len(nGenes)) { snapshot_skipped <<- TRUE design_matrix <- X_std[, -K] invokeRestart("muffle_cran_snapshot") principal_components <- svd(design_matrix, nu = 0, }, skip = handle_skip, warning = handle_warning, message = handle_message, nv = nComp)$v error = handle_error, interrupt = handle_interrupt), error = handle_fatal) pc_scores <- design_matrix %*% principal_components
pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2)24: reference[K, -K] <- principal_components %*% pc_coefficientsdoWithOneRestart(return(expr), restart) }
xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, 25: verbose = FALSE)withOneRestart(expr, restarts[[1L]]) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)
expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, 26: nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))withRestarts(tryCatch(withCallingHandlers({ }) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations29: if (snapshot_skipped) {eval(code, test_env) skip("On CRAN")
}30: else if (!new_expectations && skip_on_empty) { skip_empty()eval(code, test_env) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {31: withCallingHandlers({ if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) eval(code, test_env) } new_expectations <- the$test_expectations > starting_expectations}, snapshot_on_cran = function(cnd) { if (snapshot_skipped) { snapshot_skipped <<- TRUE skip("On CRAN") invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, else if (!new_expectations && skip_on_empty) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip_empty() end_test = function() { } })}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {27: skip(paste0("{", e$package, "} is not installed."))test_code(code, parent.frame()) }
}, snapshot_on_cran = function(cnd) {28: test_that("pcNet matches per-gene SVD principal component regression", snapshot_skipped <<- TRUE { invokeRestart("muffle_cran_snapshot") nCells <- 200}, skip = handle_skip, warning = handle_warning, message = handle_message, nGenes <- 100 error = handle_error, interrupt = handle_interrupt) nComp <- 3
set.seed(42)32: X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), doTryCatch(return(expr), name, parentenv, handler) nrow = nGenes, ncol = nCells)
rownames(X) <- paste0("Gene", seq_len(nGenes))33: X_std <- scale(Matrix::t(X))tryCatchOne(expr, names, parentenv, handlers[[1L]]) reference <- matrix(0, nGenes, nGenes)
for (K in seq_len(nGenes)) {34: design_matrix <- X_std[, -K] principal_components <- svd(design_matrix, nu = 0, tryCatchList(expr, classes, parentenv, handlers) nv = nComp)$v
pc_scores <- design_matrix %*% principal_components35: tryCatch(withCallingHandlers({ pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) eval(code, test_env) reference[K, -K] <- principal_components %*% pc_coefficients new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, skip("On CRAN") verbose = FALSE) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) } expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, else if (!new_expectations && skip_on_empty) { nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) skip_empty() }) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {29: eval(code, test_env) if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))30: }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$test_expectations > starting_expectations error = handle_error, interrupt = handle_interrupt), error = handle_fatal) if (snapshot_skipped) {
skip("On CRAN")36: }doWithOneRestart(return(expr), restart) else if (!new_expectations && skip_on_empty) {
skip_empty()37: }withOneRestart(expr, restarts[[1L]])}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))38: withRestarts(tryCatch(withCallingHandlers({ } eval(code, test_env)}, snapshot_on_cran = function(cnd) { new_expectations <- the$test_expectations > starting_expectations snapshot_skipped <<- TRUE if (snapshot_skipped) { invokeRestart("muffle_cran_snapshot") skip("On CRAN")}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt)
else if (!new_expectations && skip_on_empty) {32: skip_empty()doTryCatch(return(expr), name, parentenv, handler) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {33: if (on_cran()) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip(paste0("{", e$package, "} is not installed."))
}34: }, snapshot_on_cran = function(cnd) {tryCatchList(expr, classes, parentenv, handlers) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, 35: error = handle_error, interrupt = handle_interrupt), error = handle_fatal), tryCatch(withCallingHandlers({ end_test = function() { eval(code, test_env) }) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {39: skip("On CRAN") }test_code(code = exprs, env = env, reporter = get_reporter() %||% else if (!new_expectations && skip_on_empty) { StopReporter$new()) skip_empty() }
}, expectation = handle_expectation, packageNotFoundError = function(e) {40: if (on_cran()) {source_file(path, env = env(env), desc = desc, shuffle = shuffle, skip(paste0("{", e$package, "} is not installed.")) error_call = error_call) }}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE41: invokeRestart("muffle_cran_snapshot")FUN(X[[i]], ...)
}, skip = handle_skip, warning = handle_warning, message = handle_message, 42: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, 36: error_call = error_call)
doWithOneRestart(return(expr), restart)43:
doTryCatch(return(expr), name, parentenv, handler)37:
withOneRestart(expr, restarts[[1L]])44:
tryCatchOne(expr, names, parentenv, handlers[[1L]])38:
withRestarts(tryCatch(withCallingHandlers({45: eval(code, test_env)tryCatchList(expr, classes, parentenv, handlers) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {46: skip("On CRAN")tryCatch(code, testthat_abort_reporter = function(cnd) { } cat(conditionMessage(cnd), "\n") else if (!new_expectations && skip_on_empty) { NULL skip_empty()}) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {47: if (on_cran()) {with_reporter(reporters$multi, lapply(test_paths, test_one_file, skip(paste0("{", e$package, "} is not installed.")) } env = env, desc = desc, shuffle = shuffle, error_call = error_call))}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")48: }, skip = handle_skip, warning = handle_warning, message = handle_message, test_files_serial(test_dir = test_dir, test_package = test_package, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, end_test = function() { }) env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
desc = desc, load_package = load_package, shuffle = shuffle, 39: error_call = error_call)test_code(code = exprs, env = env, reporter = get_reporter() %||%
StopReporter$new())49:
test_files(test_dir = path, test_paths = test_paths, test_package = package, 40: reporter = reporter, load_helpers = load_helpers, env = env, source_file(path, env = env(env), desc = desc, shuffle = shuffle, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, error_call = error_call) load_package = load_package, parallel = parallel, shuffle = shuffle)
41: 50: FUN(X[[i]], ...)
test_dir("testthat", package = package, reporter = reporter, 42: ..., load_package = "installed")lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)
51: 43: test_check("scTenifoldNet")doTryCatch(return(expr), name, parentenv, handler)
44: An irrecoverable exception occurred. R is aborting now ...
tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
47: with_reporter(reporters$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