Last updated on 2026-04-21 02:55:26 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| teal | 1 | 13 | |
| teal.code | 14 | ||
| teal.data | 14 | ||
| teal.logger | 14 | ||
| teal.modules.clinical | 14 | ||
| teal.modules.general | 14 | ||
| teal.reporter | 14 | ||
| teal.slice | 1 | 13 | |
| teal.transform | 14 | ||
| teal.widgets | 14 |
Current CRAN status: NOTE: 1, OK: 13
Version: 1.1.0
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘.renv’ ‘BiocManager’
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: ERROR: 1, OK: 13
Version: 0.7.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [149s/157s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> pkg_name <- "teal.slice"
> library(pkg_name, character.only = TRUE)
> testthat::test_check(pkg_name)
Saving _problems/test-MAEFilteredDataset-182.R
{
"dataname" : "data",
"varname" : "var",
"id" : "data var",
"fixed" : false,
"anchored" : false,
"multiple" : true
}{
"slices": [
{
"dataname" : "data",
"varname" : "var1",
"id" : "data var1",
"fixed" : false,
"anchored" : false,
"multiple" : true
},
{
"dataname" : "data",
"varname" : "var2",
"id" : "data var2",
"fixed" : false,
"anchored" : false,
"multiple" : true
}
],
"attributes": {
"allow_add" : true
}
}
[ FAIL 1 | WARN 0 | SKIP 15 | PASS 851 ]
══ Skipped tests (15) ══════════════════════════════════════════════════════════
• testing depth 3 is below current testing specification 5 (15):
'test-shinytest2_DataframeFilteredDataset.R:71:5',
'test-shinytest2_DataframeFilteredDataset.R:78:5',
'test-shinytest2_DataframeFilteredDataset.R:88:5',
'test-shinytest2_DataframeFilteredDataset.R:95:5',
'test-shinytest2_DataframeFilteredDataset.R:105:5',
'test-shinytest2_DataframeFilteredDataset.R:116:5',
'test-shinytest2_DataframeFilteredDataset.R:127:3',
'test-shinytest2_DataframeFilteredDataset.R:136:3',
'test-shinytest2_DataframeFilteredDataset.R:155:3',
'test-shinytest2_DataframeFilteredDataset.R:170:3',
'test-shinytest2_DataframeFilteredDataset.R:184:3',
'test-shinytest2_DataframeFilteredDataset.R:200:3',
'test-shinytest2_DataframeFilteredDataset.R:216:3',
'test-shinytest2_DataframeFilteredDataset.R:230:3',
'test-shinytest2_MAEFilteredDataset.R:66:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-MAEFilteredDataset.R:173:3'): get_filter_overview returns overview matrix for MAEFilteredDataset with filtering ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "Filter call execution failed:\n - call:\n miniacc <- MultiAssayExperiment::subsetByColData(miniacc, miniacc$years_to_birth >= 30 & miniacc$years_to_birth <= 50 & miniacc$vital_status == 1 & miniacc$gender == \"female\")\n - message:\n Error in loadNamespace(x): there is no package called 'BiocBaseUtils'\n ", call = value[[3L]](cond)), class = c("simpleError", "error", "condition"), stack.trace = structure(pairlist(testthat::test_check(pkg_name), test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed"), 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), 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), with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)), tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL }), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr), name, parentenv, handler), lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call), FUN(X[[i]], ...), source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call), test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()), 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() { }), withOneRestart(expr, restarts[[1L]]), doWithOneRestart(return(expr), restart), 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), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr), name, parentenv, handler), 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), eval(code, test_env), eval(code, test_env), testthat::test_that("get_filter_overview returns overview matrix for MAEFilteredDataset with filtering", { testthat::skip_if_not_installed("MultiAssayExperiment") utils::data(miniACC, package = "MultiAssayExperiment") filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc") fs <- teal_slices(teal_slice(dataname = "miniacc", varname = "years_to_birth", selected = c(30, 50), keep_na = TRUE, keep_inf = FALSE), teal_slice(dataname = "miniacc", varname = "vital_status", selected = "1", keep_na = FALSE), teal_slice(dataname = "miniacc", varname = "gender", selected = "female", keep_na = TRUE), teal_slice(dataname = "miniacc", varname = "ARRAY_TYPE", selected = "", keep_na = TRUE, experiment = "RPPAArray", arg = "subset")) filtered_dataset$set_filter_state(fs) testthat::expect_equal(shiny::isolate(filtered_dataset$get_filter_overview()), data.frame(dataname = c("miniacc", sprintf("- %s", names(miniACC))), subjects = c(92, 79, 90, 46, 90, 80), subjects_filtered = c(6, 5, 6, 4, 5, 5), obs = c(NA_real_, 198, 198, 33, 97, 471), obs_filtered = c(NA_real_, 198, 198, 26, 97, 471))) }), test_code(code, parent.frame()), withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) } }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }), withOneRestart(expr, restarts[[1L]]), doWithOneRestart(return(expr), restart), tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) } }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr), name, parentenv, handler), withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) } }, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), eval(code, test_env), eval(code, test_env), testthat::expect_equal(shiny::isolate(filtered_dataset$get_filter_overview()), data.frame(dataname = c("miniacc", sprintf("- %s", names(miniACC))), subjects = c(92, 79, 90, 46, 90, 80), subjects_filtered = c(6, 5, 6, 4, 5, 5), obs = c(NA_real_, 198, 198, 33, 97, 471), obs_filtered = c(NA_real_, 198, 198, 26, 97, 471))), quasi_label(enquo(object), label), eval_bare(expr, quo_get_env(quo)), shiny::isolate(filtered_dataset$get_filter_overview()), ..stacktraceoff..(ctx$run(function() { ..stacktraceon..(expr) })), ctx$run(function() { ..stacktraceon..(expr) }), promises::with_promise_domain(reactivePromiseDomain(), { withReactiveDomain(.domain, { with_otel_span_context(.otel_info, domain = .domain, { captureStackTraces({ env <- .getReactiveEnvironment() rLog$enter(.reactId, id, .reactType, .domain) on.exit(rLog$exit(.reactId, id, .reactType, .domain), add = TRUE) env$runWith(self, func) }) }) }) }), domain$wrapSync(expr), withReactiveDomain(.domain, { with_otel_span_context(.otel_info, domain = .domain, { captureStackTraces({ env <- .getReactiveEnvironment() rLog$enter(.reactId, id, .reactType, .domain) on.exit(rLog$exit(.reactId, id, .reactType, .domain), add = TRUE) env$runWith(self, func) }) }) }), promises::with_promise_domain(createVarPromiseDomain(.globals, "domain", domain), expr), domain$wrapSync(expr), force(expr), with_otel_span_context(.otel_info, domain = .domain, { captureStackTraces({ env <- .getReactiveEnvironment() rLog$enter(.reactId, id, .reactType, .domain) on.exit(rLog$exit(.reactId, id, .reactType, .domain), add = TRUE) env$runWith(self, func) }) }), force(expr), captureStackTraces({ env <- .getReactiveEnvironment() rLog$enter(.reactId, id, .reactType, .domain) on.exit(rLog$exit(.reactId, id, .reactType, .domain), add = TRUE) env$runWith(self, func) }), promises::with_promise_domain(createStackTracePromiseDomain(), expr), domain$wrapSync(expr), withCallingHandlers(expr, error = doCaptureStack), env$runWith(self, func), contextFunc(), ..stacktraceon..(expr), filtered_dataset$get_filter_overview(), data.frame(dataname = private$dataname, subjects = nrow(SummarizedExperiment::colData(data)), subjects_filtered = nrow(SummarizedExperiment::colData(data_filtered()))), nrow(SummarizedExperiment::colData(data_filtered())), SummarizedExperiment::colData(data_filtered()), data_filtered(), ..stacktraceoff..(self$.updateValue()), self$.updateValue(), ctx$run(function() { result <- withCallingHandlers({ .error <<- FALSE withVisible(.func()) }, error = function(cond) { if (.isRecordingOtel) { cond <- mark_otel_exception_as_seen(cond) } .value <<- cond .error <<- TRUE .visible <<- FALSE }) .value <<- result$value .visible <<- result$visible }), promises::with_promise_domain(reactivePromiseDomain(), { withReactiveDomain(.domain, { with_otel_span_context(.otel_info, domain = .domain, { captureStackTraces({ env <- .getReactiveEnvironment() rLog$enter(.reactId, id, .reactType, .domain) on.exit(rLog$exit(.reactId, id, .reactType, .domain), add = TRUE) env$runWith(self, func) }) }) }) }), domain$wrapSync(expr), withReactiveDomain(.domain, { with_otel_span_context(.otel_info, domain = .domain, { captureStackTraces({ env <- .getReactiveEnvironment() rLog$enter(.reactId, id, .reactType, .domain) on.exit(rLog$exit(.reactId, id, .reactType, .domain), add = TRUE) env$runWith(self, func) }) }) }), promises::with_promise_domain(createVarPromiseDomain(.globals, "domain", domain), expr), domain$wrapSync(expr), force(expr), with_otel_span_context(.otel_info, domain = .domain, { captureStackTraces({ env <- .getReactiveEnvironment() rLog$enter(.reactId, id, .reactType, .domain) on.exit(rLog$exit(.reactId, id, .reactType, .domain), add = TRUE) env$runWith(self, func) }) }), force(expr), captureStackTraces({ env <- .getReactiveEnvironment() rLog$enter(.reactId, id, .reactType, .domain) on.exit(rLog$exit(.reactId, id, .reactType, .domain), add = TRUE) env$runWith(self, func) }), promises::with_promise_domain(createStackTracePromiseDomain(), expr), domain$wrapSync(expr), withCallingHandlers(expr, error = doCaptureStack), env$runWith(self, func), contextFunc(), withCallingHandlers({ .error <<- FALSE withVisible(.func()) }, error = function(cond) { if (.isRecordingOtel) { cond <- mark_otel_exception_as_seen(cond) } .value <<- cond .error <<- TRUE .visible <<- FALSE }), withVisible(.func()), .func(), ..stacktraceon..(`<reactive>`(...)), `<reactive>`(...), private$data_filtered_fun(), eval_expr_with_msg(filter_call, env), lapply(expr, function(x) { tryCatch(eval(x, envir = env), error = function(e) { stop(sprintf("Filter call execution failed:\n - call:\n %s\n - message:\n %s ", deparse1(x, collapse = "\n"), e)) }) }), FUN(X[[i]], ...), tryCatch(eval(x, envir = env), error = function(e) { stop(sprintf("Filter call execution failed:\n - call:\n %s\n - message:\n %s ", deparse1(x, collapse = "\n"), e)) }), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(expr, names, parentenv, handlers[[1L]]), value[[3L]](cond), stop(sprintf("Filter call execution failed:\n - call:\n %s\n - message:\n %s ", deparse1(x, collapse = "\n"), e)), .handleSimpleError(function (e) { if (is.null(attr(e, "stack.trace", exact = TRUE))) { calls <- sys.calls() parents <- sys.parents() attr(calls, "parents") <- parents calls <- saveCallStackDigest(calls) attr(e, "stack.trace") <- calls } if (deepStacksEnabled()) { if (is.null(attr(e, "deep.stack.trace", exact = TRUE)) && !is.null(.globals$deepStack)) { attr(e, "deep.stack.trace") <- .globals$deepStack } } stop(e) }, "Filter call execution failed:\n - call:\n miniacc <- MultiAssayExperiment::subsetByColData(miniacc, miniacc$years_to_birth >= 30 & miniacc$years_to_birth <= 50 & miniacc$vital_status == 1 & miniacc$gender == \"female\")\n - message:\n Error in loadNamespace(x): there is no package called 'BiocBaseUtils'\n ", base::quote(value[[3L]](cond))), h(simpleError(msg, call))), parents = c(0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 4L, 10L, 11L, 12L, 13L, 14L, 15L, 13L, 17L, 18L, 19L, 13L, 13L, 22L, 23L, 24L, 25L, 26L, 27L, 25L, 29L, 30L, 31L, 25L, 25L, 34L, 35L, 36L, 37L, 35L, 39L, 39L, 41L, 42L, 41L, 44L, 45L, 46L, 41L, 48L, 41L, 50L, 51L, 52L, 41L, 54L, 55L, 35L, 57L, 57L, 57L, 57L, 61L, 61L, 63L, 64L, 65L, 64L, 67L, 68L, 69L, 64L, 71L, 64L, 73L, 74L, 75L, 64L, 77L, 78L, 78L, 78L, 81L, 81L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 93L, 93L), shiny.stack.digest = "05061b97d53c9b294f0d091b83b61690")))`: error in evaluating the argument 'x' in selecting a method for function 'colData': Filter call execution failed:
- call:
miniacc <- MultiAssayExperiment::subsetByColData(miniacc, miniacc$years_to_birth >= 30 & miniacc$years_to_birth <= 50 & miniacc$vital_status == 1 & miniacc$gender == "female")
- message:
Error in loadNamespace(x): there is no package called 'BiocBaseUtils'
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-MAEFilteredDataset.R:173:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─shiny::isolate(filtered_dataset$get_filter_overview())
5. │ ├─shiny::..stacktraceoff..(...)
6. │ └─ctx$run(...)
7. │ ├─promises::with_promise_domain(...)
8. │ │ └─domain$wrapSync(expr)
9. │ ├─shiny::withReactiveDomain(...)
10. │ │ └─promises::with_promise_domain(...)
11. │ │ └─domain$wrapSync(expr)
12. │ │ └─base::force(expr)
13. │ ├─shiny:::with_otel_span_context(...)
14. │ │ └─base::force(expr)
15. │ ├─shiny::captureStackTraces(...)
16. │ │ └─promises::with_promise_domain(...)
17. │ │ └─domain$wrapSync(expr)
18. │ │ └─base::withCallingHandlers(expr, error = doCaptureStack)
19. │ └─env$runWith(self, func)
20. │ └─shiny (local) contextFunc()
21. │ └─shiny::..stacktraceon..(expr)
22. ├─filtered_dataset$get_filter_overview()
23. │ ├─base::data.frame(...)
24. │ ├─base::nrow(SummarizedExperiment::colData(data_filtered()))
25. │ ├─SummarizedExperiment::colData(data_filtered())
26. │ └─shiny (local) data_filtered()
27. │ ├─shiny::..stacktraceoff..(self$.updateValue())
28. │ └─self$.updateValue()
29. │ └─ctx$run(...)
30. │ ├─promises::with_promise_domain(...)
31. │ │ └─domain$wrapSync(expr)
32. │ ├─shiny::withReactiveDomain(...)
33. │ │ └─promises::with_promise_domain(...)
34. │ │ └─domain$wrapSync(expr)
35. │ │ └─base::force(expr)
36. │ ├─shiny:::with_otel_span_context(...)
37. │ │ └─base::force(expr)
38. │ ├─shiny::captureStackTraces(...)
39. │ │ └─promises::with_promise_domain(...)
40. │ │ └─domain$wrapSync(expr)
41. │ │ └─base::withCallingHandlers(expr, error = doCaptureStack)
42. │ └─env$runWith(self, func)
43. │ └─shiny (local) contextFunc()
44. │ ├─base::withCallingHandlers(...)
45. │ ├─base::withVisible(.func())
46. │ └─shiny (local) .func()
47. │ ├─shiny::..stacktraceon..(`<reactive>`(...))
48. │ └─teal.slice (local) `<reactive>`(...)
49. │ └─private$data_filtered_fun()
50. │ └─teal.slice:::eval_expr_with_msg(filter_call, env)
51. │ └─base::lapply(...)
52. │ └─teal.slice (local) FUN(X[[i]], ...)
53. │ └─base::tryCatch(...)
54. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
55. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
56. │ └─value[[3L]](cond)
57. │ └─base::stop(...)
58. ├─base::.handleSimpleError(...)
59. │ └─shiny (local) h(simpleError(msg, call))
60. │ └─base::stop(e)
61. ├─base (local) `<fn>`(`<smplErrr>`)
62. └─base::.handleSimpleError(...)
63. └─shiny (local) h(simpleError(msg, call))
[ FAIL 1 | WARN 0 | SKIP 15 | PASS 851 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 14
Current CRAN status: OK: 14