Last updated on 2026-10-13 20:54:51 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 | 5.45 | 54.15 | 59.60 | 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)
Traceback:
prefix <- paste0(prefix, "\n ") 1: FUN(X[[i]], ...) }
else prefix <- "Error : " 2: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))lapply(X = S, FUN = FUN, ...) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile) 3: .Internal(printDeferredWarnings())doTryCatch(return(expr), name, parentenv, handler) }
invisible(structure(msg, class = "try-error", condition = e))}) 4:
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
5: 8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchList(expr, classes, parentenv, handlers)
9: 6: FUN(X[[i]], ...)tryCatch(expr, error = function(e) { call <- conditionCall(e)
if (!is.null(call)) {10: if (identical(call[[1L]], quote(doTryCatch))) lapply(seq_len(cores), inner.do)
call <- sys.call(-4L)11: dcall <- deparse(call, nlines = 1L)parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, prefix <- paste("Error in", dcall, ": ") nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, LONG <- 75L mc.preschedule = TRUE) 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], 12: type = "b").pcNetCoefficients(basis$Z, basis$d, nComp, nCores) if (w > LONG)
prefix <- paste0(prefix, "\n ")13: pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) }
else prefix <- "Error : "14: eval_bare(expr, quo_get_env(quo)) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))15: if (!silent && isTRUE(getOption("show.error.messages"))) {quasi_label(enquo(object), label) cat(msg, file = outFile)
.Internal(printDeferredWarnings()) }16: invisible(structure(msg, class = "try-error", condition = e))expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), }) pcNet(X, nComp = nComp, verbose = FALSE))
7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)17:
eval(code, test_env) 8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: 18: FUN(X[[i]], ...)eval(code, test_env)
19: 10: withCallingHandlers({lapply(seq_len(cores), inner.do) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations
if (snapshot_skipped) {11: skip("On CRAN")parallel::mclapply(gene_blocks, coefficient_rows, Z = Z, d = d, nComp = nComp, secular_weights = secular_weights, mc.cores = nCores, } mc.preschedule = TRUE) else if (!new_expectations && skip_on_empty) {
skip_empty()12: }.pcNetCoefficients(basis$Z, basis$d, nComp, nCores)}, expectation = handle_expectation, packageNotFoundError = function(e) {
if (on_cran()) {13: skip(paste0("{", e$package, "} is not installed."))pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2) }
14: }, snapshot_on_cran = function(cnd) {eval_bare(expr, quo_get_env(quo)) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")15: }, skip = handle_skip, warning = handle_warning, message = handle_message, quasi_label(enquo(object), label) error = handle_error, interrupt = handle_interrupt)
16:
expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, nCores = 2), 20: doTryCatch(return(expr), name, parentenv, handler) pcNet(X, nComp = nComp, verbose = FALSE))
21: 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(code, test_env)
22: tryCatchList(expr, classes, parentenv, handlers)18:
eval(code, test_env)23: tryCatch(withCallingHandlers({
eval(code, test_env)19: new_expectations <- the$test_expectations > starting_expectationswithCallingHandlers({ if (snapshot_skipped) { eval(code, test_env) skip("On CRAN") new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) { else if (!new_expectations && skip_on_empty) { skip("On CRAN") skip_empty() } } else if (!new_expectations && skip_on_empty) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip_empty() if (on_cran()) { } skip(paste0("{", e$package, "} is not installed."))}, expectation = handle_expectation, packageNotFoundError = function(e) { } if (on_cran()) {}, snapshot_on_cran = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot")}, 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, 24: error = handle_error, interrupt = handle_interrupt)doWithOneRestart(return(expr), restart)
20: 25: doTryCatch(return(expr), name, parentenv, handler)withOneRestart(expr, restarts[[1L]])
21: 26: tryCatchOne(expr, names, parentenv, handlers[[1L]])withRestarts(tryCatch(withCallingHandlers({
eval(code, test_env)22: new_expectations <- the$test_expectations > starting_expectationstryCatchList(expr, classes, parentenv, handlers) if (snapshot_skipped) {
skip("On CRAN") }23: tryCatch(withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, expectation = handle_expectation, packageNotFoundError = function(e) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) else if (!new_expectations && skip_on_empty) { } skip_empty()}, snapshot_on_cran = function(cnd) { } snapshot_skipped <<- TRUE}, expectation = handle_expectation, packageNotFoundError = function(e) { invokeRestart("muffle_cran_snapshot") if (on_cran()) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip(paste0("{", e$package, "} is not installed.")) error = handle_error, interrupt = handle_interrupt), 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, 27: error = handle_error, interrupt = handle_interrupt), error = handle_fatal)test_code(code, parent.frame())
24: 28: doWithOneRestart(return(expr), restart)test_that("pcNet matches per-gene SVD principal component regression",
{25: nCells <- 200withOneRestart(expr, restarts[[1L]])
nGenes <- 10026: nComp <- 3withRestarts(tryCatch(withCallingHandlers({ set.seed(42) eval(code, test_env) X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), new_expectations <- the$test_expectations > starting_expectations nrow = nGenes, ncol = nCells) if (snapshot_skipped) { rownames(X) <- paste0("Gene", seq_len(nGenes)) skip("On CRAN") X_std <- scale(Matrix::t(X)) reference <- matrix(0, nGenes, nGenes) } for (K in seq_len(nGenes)) { else if (!new_expectations && skip_on_empty) { design_matrix <- X_std[, -K] skip_empty() principal_components <- svd(design_matrix, nu = 0, } nv = nComp)$v}, expectation = handle_expectation, packageNotFoundError = function(e) { pc_scores <- design_matrix %*% principal_components if (on_cran()) { pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) skip(paste0("{", e$package, "} is not installed.")) reference[K, -K] <- principal_components %*% pc_coefficients } } xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE, }, snapshot_on_cran = function(cnd) { verbose = FALSE) snapshot_skipped <<- TRUE expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08) invokeRestart("muffle_cran_snapshot") expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, }, skip = handle_skip, warning = handle_warning, message = handle_message, nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE)) error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }) end_test = function() {
})29:
eval(code, test_env)27:
test_code(code, parent.frame())30:
eval(code, test_env)
28: 31: test_that("pcNet matches per-gene SVD principal component regression", withCallingHandlers({ { eval(code, test_env) nCells <- 200 new_expectations <- the$test_expectations > starting_expectations nGenes <- 100 if (snapshot_skipped) { nComp <- 3 skip("On CRAN") set.seed(42) } X <- matrix(rnbinom(n = nGenes * nCells, size = 20, prob = 0.98), else if (!new_expectations && skip_on_empty) { nrow = nGenes, ncol = nCells) skip_empty() rownames(X) <- paste0("Gene", seq_len(nGenes)) } X_std <- scale(Matrix::t(X))}, expectation = handle_expectation, packageNotFoundError = function(e) { reference <- matrix(0, nGenes, nGenes) if (on_cran()) { for (K in seq_len(nGenes)) { skip(paste0("{", e$package, "} is not installed.")) design_matrix <- X_std[, -K] } principal_components <- svd(design_matrix, nu = 0, }, snapshot_on_cran = function(cnd) { nv = nComp)$v snapshot_skipped <<- TRUE pc_scores <- design_matrix %*% principal_components pc_coefficients <- colSums(X_std[, K] * pc_scores)/colSums(pc_scores^2) invokeRestart("muffle_cran_snapshot") reference[K, -K] <- principal_components %*% pc_coefficients}, skip = handle_skip, warning = handle_warning, message = handle_message, } error = handle_error, interrupt = handle_interrupt) xNet <- pcNet(X, nComp = nComp, scaleScores = FALSE,
verbose = FALSE)32: doTryCatch(return(expr), name, parentenv, handler) expect_equal(unname(as.matrix(xNet)), reference, tolerance = 1e-08)
33: expect_equal(pcNet(X, nComp = nComp, verbose = FALSE, tryCatchOne(expr, names, parentenv, handlers[[1L]])
nCores = 2), pcNet(X, nComp = nComp, verbose = FALSE))34: })tryCatchList(expr, classes, parentenv, handlers)
29: 35: eval(code, test_env)tryCatch(withCallingHandlers({
eval(code, test_env)30: new_expectations <- the$test_expectations > starting_expectationseval(code, test_env) if (snapshot_skipped) {
skip("On CRAN")31: }withCallingHandlers({ else if (!new_expectations && skip_on_empty) { eval(code, test_env) skip_empty() new_expectations <- the$test_expectations > starting_expectations }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (snapshot_skipped) { skip("On CRAN") if (on_cran()) { } skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { else if (!new_expectations && skip_on_empty) { snapshot_skipped <<- TRUE skip_empty() invokeRestart("muffle_cran_snapshot") }}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
skip(paste0("{", e$package, "} is not installed."))36: }doWithOneRestart(return(expr), restart)}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE37: withOneRestart(expr, restarts[[1L]]) invokeRestart("muffle_cran_snapshot")
}, skip = handle_skip, warning = handle_warning, message = handle_message, 38: error = handle_error, interrupt = handle_interrupt)
withRestarts(tryCatch(withCallingHandlers({32: eval(code, test_env)doTryCatch(return(expr), name, parentenv, handler) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {
skip("On CRAN")33: } else if (!new_expectations && skip_on_empty) {tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: skip_empty()tryCatchList(expr, classes, parentenv, handlers)
}35: }, expectation = handle_expectation, packageNotFoundError = function(e) {tryCatch(withCallingHandlers({ if (on_cran()) { eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) new_expectations <- the$test_expectations > starting_expectations } if (snapshot_skipped) {}, snapshot_on_cran = function(cnd) { skip("On CRAN") snapshot_skipped <<- TRUE } invokeRestart("muffle_cran_snapshot") else if (!new_expectations && skip_on_empty) {}, skip = handle_skip, warning = handle_warning, message = handle_message, skip_empty() error = handle_error, interrupt = handle_interrupt), error = handle_fatal), }}, expectation = handle_expectation, packageNotFoundError = function(e) { end_test = function() { if (on_cran()) { }) skip(paste0("{", e$package, "} is not installed."))
}39: }, snapshot_on_cran = function(cnd) {test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) snapshot_skipped <<- TRUE
invokeRestart("muffle_cran_snapshot")40: }, skip = handle_skip, warning = handle_warning, message = handle_message, source_file(path, env = env(env), desc = desc, shuffle = shuffle, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) error_call = error_call)
36: 41: doWithOneRestart(return(expr), restart)
FUN(X[[i]], ...)37:
42: withOneRestart(expr, restarts[[1L]])lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,
error_call = error_call)38:
withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env)43: new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler) if (snapshot_skipped) {
skip("On CRAN")44: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) else if (!new_expectations && skip_on_empty) {
45: skip_empty()tryCatchList(expr, classes, parentenv, handlers) }
}, expectation = handle_expectation, packageNotFoundError = function(e) {46: if (on_cran()) {tryCatch(code, testthat_abort_reporter = function(cnd) { skip(paste0("{", e$package, "} is not installed.")) cat(conditionMessage(cnd), "\n") NULL }})}, snapshot_on_cran = function(cnd) {
snapshot_skipped <<- TRUE47: invokeRestart("muffle_cran_snapshot")with_reporter(reporters$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),
end_test = function() {48: })test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 39: env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, test_code(code = exprs, env = env, reporter = get_reporter() %||% desc = desc, load_package = load_package, shuffle = shuffle, StopReporter$new()) error_call = error_call)
40: 49: source_file(path, env = env(env), desc = desc, shuffle = shuffle, test_files(test_dir = path, test_paths = test_paths, test_package = package, error_call = error_call) reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 41: load_package = load_package, parallel = parallel, shuffle = shuffle)FUN(X[[i]], ...)
50: 42: test_dir("testthat", package = package, reporter = reporter, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, ..., load_package = "installed") error_call = error_call)
51: 43: test_check("scTenifoldNet")doTryCatch(return(expr), name, parentenv, handler)
44: An irrecoverable exception occurred. R is aborting now ...
tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
47: with_reporter(reporters$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