Last updated on 2026-10-14 03:11:02 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4.3 | 7.52 | 72.87 | 80.39 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4.3 | 5.33 | 55.46 | 60.79 | 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 | 53.33 | 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 | 1.4.3 | 7.10 | 66.43 | 73.53 | 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 | 3.00 | 29.00 | 32.00 | 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 | 94.00 | 106.00 | 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]], ...)
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)) {
Traceback:
design_matrix <- X_std[, -K] principal_components <- svd(design_matrix, nu = 0, 1: nv = nComp)$vFUN(X[[i]], ...) pc_scores <- design_matrix %*% principal_components
pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) 2: reference[K, -K] <- principal_components %*% pc_coefficientslapply(X = S, FUN = FUN, ...) }
xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, 3: verbose = FALSE)doTryCatch(return(expr), name, parentenv, handler) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)
expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, 4: nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))tryCatchOne(expr, names, parentenv, handlers[[1L]]) })
5: 29: tryCatchList(expr, classes, parentenv, handlers)eval(code, test_env)
6: 30: tryCatch(expr, error = function(e) {eval(code, test_env) call <- conditionCall(e)
if (!is.null(call)) {31: if (identical(call[[1L]], quote(doTryCatch))) withCallingHandlers({ call <- sys.call(-4L) eval(code, test_env) dcall <- deparse(call, nlines = 1L) new_expectations <- the$test_expectations > starting_expectations prefix <- paste("Error in", dcall, ": ") if (snapshot_skipped) { LONG <- 75L skip("On CRAN") sm <- strsplit(conditionMessage(e), "\n")[[1L]] } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") else if (!new_expectations && skip_on_empty) { if (is.na(w)) skip_empty() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b")}, expectation = handle_expectation, packageNotFoundError = function(e) { if (w > LONG) if (on_cran()) { prefix <- paste0(prefix, "\n ") skip(paste0("{", e$package, "} is not installed.")) } } else prefix <- "Error : "}, snapshot_on_cran = function(cnd) { msg <- paste0(prefix, conditionMessage(e), "\n") snapshot_skipped <<- TRUE .Internal(seterrmessage(msg[1L])) invokeRestart("muffle_cran_snapshot") if (!silent && isTRUE(getOption("show.error.messages"))) {}, skip = handle_skip, warning = handle_warning, message = handle_message, cat(msg, file = outFile) error = handle_error, interrupt = handle_interrupt) .Internal(printDeferredWarnings())
}32: invisible(structure(msg, class = "try-error", condition = e))doTryCatch(return(expr), name, parentenv, handler)})
33: 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)34:
tryCatchList(expr, classes, parentenv, handlers) 8:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))35:
tryCatch(withCallingHandlers({ 9: eval(code, test_env)FUN(X[[i]], ...) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {10: skip("On CRAN")lapply(seq_len(cores), inner.do)
}11: else if (!new_expectations && skip_on_empty) {parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, skip_empty() nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, } mc.preschedule = TRUE)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {12: skip(paste0("{", e$package, "} is not installed.")).pcNetCoefficients(basis$Z, basis$d, nComp, nCores) }
}, snapshot_on_cran = function(cnd) {13: snapshot_skipped <<- TRUEpcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt), error = handle_fatal)14:
eval_bare(expr, quo_get_env(quo))36:
doWithOneRestart(return(expr), restart)15:
quasi_label(enquo(object), label)37:
withOneRestart(expr, restarts[[1L]])16:
expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), 38: pcNet(X, nComp = nComp, verbose = FALSE))withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)17: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
skip("On CRAN")18: }eval(code, test_env) else if (!new_expectations && skip_on_empty) {
skip_empty()19: }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) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, }, expectation = handle_expectation, packageNotFoundError = function(e) { error = handle_error, interrupt = handle_interrupt), error = handle_fatal), if (on_cran()) { end_test = function() { skip(paste0("{", e$package, "} is not installed.")) }) }
}, snapshot_on_cran = function(cnd) {39: snapshot_skipped <<- TRUEtest_code(code = exprs, env = env, reporter = get_reporter() %||% invokeRestart("muffle_cran_snapshot") StopReporter$new())}, skip = handle_skip, warning = handle_warning, message = handle_message,
error = handle_error, interrupt = handle_interrupt)40:
source_file(path, env = env(env), desc = desc, shuffle = shuffle, 20: error_call = error_call)doTryCatch(return(expr), name, parentenv, handler)
41: 21: FUN(X[[i]], ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: 22: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, tryCatchList(expr, classes, parentenv, handlers) error_call = error_call)
23: 43: tryCatch(withCallingHandlers({doTryCatch(return(expr), name, parentenv, handler) eval(code, test_env)
new_expectations <- the$test_expectations > starting_expectations44: if (snapshot_skipped) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip("On CRAN")
}45: else if (!new_expectations && skip_on_empty) {tryCatchList(expr, classes, parentenv, handlers) skip_empty()
}46: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatch(code, testthat_abort_reporter = function(cnd) { if (on_cran()) { cat(conditionMessage(cnd), "\n") skip(paste0("{", e$package, "} is not installed.")) NULL }})}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE47: invokeRestart("muffle_cran_snapshot")with_reporter(reporters$multi, lapply(test_paths, test_one_file, }, skip = handle_skip, warning = handle_warning, message = handle_message, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
48: 24: test_files_serial(test_dir = test_dir, test_package = test_package, doWithOneRestart(return(expr), restart) test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 25: desc = desc, load_package = load_package, shuffle = shuffle, withOneRestart(expr, restarts[[1L]]) error_call = error_call)
26: 49: withRestarts(tryCatch(withCallingHandlers({test_files(test_dir = path, test_paths = test_paths, test_package = package, eval(code, test_env) reporter = reporter, load_helpers = load_helpers, env = env, new_expectations <- the$test_expectations > starting_expectations stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, if (snapshot_skipped) { load_package = load_package, parallel = parallel, shuffle = shuffle) skip("On CRAN")
}50: else if (!new_expectations && skip_on_empty) {test_dir("testthat", package = package, reporter = reporter, skip_empty() ..., load_package = "installed") }
}, expectation = handle_expectation, packageNotFoundError = function(e) {51: if (on_cran()) {test_check("scTenifoldNet")
skip(paste0("{", e$package, "} is not installed."))An irrecoverable exception occurred. R is aborting now ...
}}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
27: test_code(code, parent.frame())
28: test_that("pcNet matches per-gene SVD principal component regression", { nCells <- 200 nGenes <- 100 nComp <- 3 set.seed(42) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), nrow = nGenes, ncol = nCells) rownames(X) <- paste0("Gene", seq_len(nGenes)) X_std <- scale(Matrix::t(X)) reference <- matrix(0, nGenes, nGenes) for (K in seq_len(nGenes)) { design_matrix <- X_std[, -K] principal_components <- svd(design_matrix, nu = 0, nv = nComp)$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