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