Package: bupaR
Check: for code/documentation mismatches
New result: WARNING
  Codoc mismatches from Rd file 'fill.Rd':
  fill
    Code: function(data, ..., .by = NULL, .direction = c("down", "up",
                   "downup", "updown"))
    Docs: function(data, ..., .direction = c("down", "up", "downup",
                   "updown"))
    Argument names in code not in docs:
      .by
    Mismatches in argument names:
      Position: 3 Code: .by Docs: .direction

Package: matrixset
Check: tests
New result: ERROR
    Running ‘testthat.R’ [62s/62s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(matrixset)
    > 
    > test_check("matrixset")
    'as(<dgCMatrix>, "dgeMatrix")' is deprecated.
    Use 'as(., "unpackedMatrix")' instead.
    See help("Deprecated") and help("Matrix-deprecated").
    Saving _problems/test-fn-Matrix-773.R
    Saving _problems/test-fn-Matrix-798.R
    Saving _problems/test-fn-Matrix-823.R
    Saving _problems/test-fn-Matrix-848.R
    Saving _problems/test-fn-Matrix-873.R
    Saving _problems/test-fn-Matrix-898.R
    Saving _problems/test-fn-Matrix-1116.R
    Saving _problems/test-fn-Matrix-1141.R
    Saving _problems/test-fn-Matrix-1166.R
    Saving _problems/test-fn-Matrix-1191.R
    Saving _problems/test-fn-999.R
    Saving _problems/test-fn-1024.R
    Saving _problems/test-fn-1049.R
    Saving _problems/test-fn-1074.R
    Saving _problems/test-fn-1099.R
    Saving _problems/test-fn-1124.R
    Saving _problems/test-fn-1361.R
    Saving _problems/test-fn-1386.R
    Saving _problems/test-fn-1411.R
    Saving _problems/test-fn-1436.R
    [ FAIL 20 | WARN 0 | SKIP 0 | PASS 1359 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-fn-Matrix.R:773:3'): matrixset 'long' loop works ─────────────
    Expected `grmn` to be identical to `mn_ref`.
    Differences:
    `names(actual$failure)`:   "program" ".rowname" "mean"     "median"
    `names(expected$failure)`: "program" ".rowname" ".rows_id" "mean"  
    
    `actual$failure$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$failure$.rowname` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    
    `actual$failure$median` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    `expected$failure$median` is absent
    
    `actual$failure$.rows_id` is absent
    `expected$failure$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    `names(actual$remedial)`:   "program" ".rowname" "mean"     "median"
    `names(expected$remedial)`: "program" ".rowname" ".rows_id" "mean"  
    
    `actual$remedial$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$remedial$.rowname` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    
    `actual$remedial$median` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    `expected$remedial$median` is absent
    
    `actual$remedial$.rows_id` is absent
    `expected$remedial$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    ── Failure ('test-fn-Matrix.R:798:3'): matrixset 'long' loop works ─────────────
    Expected `grmn` to be identical to `grmn_ref`.
    Differences:
    `names(actual$failure)`:   "teacher" "class" ".colname" "mean"        "median"
    `names(expected$failure)`: "teacher" "class" ".colname" ".columns_id" "mean"  
    
    `actual$failure$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$failure$.colname` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    
    `actual$failure$median` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    `expected$failure$median` is absent
    
    `actual$failure$.columns_id` is absent
    `expected$failure$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    `names(actual$remedial)`:   "teacher" "class" ".colname" "mean"        "median"
    `names(expected$remedial)`: "teacher" "class" ".colname" ".columns_id" "mean"  
    
    `actual$remedial$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$remedial$.colname` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    
    `actual$remedial$median` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    `expected$remedial$median` is absent
    
    `actual$remedial$.columns_id` is absent
    `expected$remedial$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    ── Failure ('test-fn-Matrix.R:823:3'): matrixset 'long' loop works ─────────────
    Expected `grmn` to be identical to `mn_ref`.
    Differences:
    `names(actual$failure)`:   "program" ".rowname" "mn"       "md"
    `names(expected$failure)`: "program" ".rowname" ".rows_id" "mn"
    
    `actual$failure$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$failure$.rowname` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    
    `actual$failure$md` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    `expected$failure$md` is absent
    
    `actual$failure$.rows_id` is absent
    `expected$failure$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    `names(actual$remedial)`:   "program" ".rowname" "mn"       "md"
    `names(expected$remedial)`: "program" ".rowname" ".rows_id" "mn"
    
    `actual$remedial$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$remedial$.rowname` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    
    `actual$remedial$md` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    `expected$remedial$md` is absent
    
    `actual$remedial$.rows_id` is absent
    `expected$remedial$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    ── Failure ('test-fn-Matrix.R:848:3'): matrixset 'long' loop works ─────────────
    Expected `grmn` to be identical to `grmn_ref`.
    Differences:
    `names(actual$failure)`:   "teacher" "class" ".colname" "mn"          "md"
    `names(expected$failure)`: "teacher" "class" ".colname" ".columns_id" "mn"
    
    `actual$failure$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$failure$.colname` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    
    `actual$failure$md` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    `expected$failure$md` is absent
    
    `actual$failure$.columns_id` is absent
    `expected$failure$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    `names(actual$remedial)`:   "teacher" "class" ".colname" "mn"          "md"
    `names(expected$remedial)`: "teacher" "class" ".colname" ".columns_id" "mn"
    
    `actual$remedial$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$remedial$.colname` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    
    `actual$remedial$md` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    `expected$remedial$md` is absent
    
    `actual$remedial$.columns_id` is absent
    `expected$remedial$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    ── Failure ('test-fn-Matrix.R:873:3'): matrixset 'long' loop works ─────────────
    Expected `grmn` to be identical to `mn_ref`.
    Differences:
    `names(actual$failure)`:   "program" ".rowname" "ct.name"  "ct"     
    `names(expected$failure)`: "program" ".rowname" ".rows_id" "ct.name"
    
    `actual$failure$.rowname` is a character vector ('student 1', 'student 1', 'student 2', 'student 2', 'student 3', ...)
    `expected$failure$.rowname` is a double vector (0.270800364844035, 0.270800364844035, 0.208336764364503, 0.208336764364503, 0.28514515561983, ...)
    
    `actual$failure$ct` is a double vector (0.270800364844035, 0.270800364844035, 0.208336764364503, 0.208336764364503, 0.28514515561983, ...)
    `expected$failure$ct` is absent
    
    `actual$failure$.rows_id` is absent
    `expected$failure$.rows_id` is a character vector ('student 1', 'student 1', 'student 2', 'student 2', 'student 3', ...)
    
    `names(actual$remedial)`:   "program" ".rowname" "ct.name"  "ct"     
    `names(expected$remedial)`: "program" ".rowname" ".rows_id" "ct.name"
    
    `actual$remedial$.rowname` is a character vector ('student 1', 'student 1', 'student 2', 'student 2', 'student 3', ...)
    `expected$remedial$.rowname` is a double vector (0.688091438869014, 0.688091438869014, 0.701310815196484, 0.701310815196484, 0.60816297729034, ...)
    
    `actual$remedial$ct` is a double vector (0.688091438869014, 0.688091438869014, 0.701310815196484, 0.701310815196484, 0.60816297729034, ...)
    `expected$remedial$ct` is absent
    
    `actual$remedial$.rows_id` is absent
    `expected$remedial$.rows_id` is a character vector ('student 1', 'student 1', 'student 2', 'student 2', 'student 3', ...)
    
    ── Failure ('test-fn-Matrix.R:898:3'): matrixset 'long' loop works ─────────────
    Expected `grmn` to be identical to `grmn_ref`.
    Differences:
    `names(actual$failure)`:   "teacher" "class" ".colname" "ct.name"     "ct"     
    `names(expected$failure)`: "teacher" "class" ".colname" ".columns_id" "ct.name"
    
    `actual$failure$.colname` is a character vector ('Mathematics', 'Mathematics', 'English', 'English', 'Science', ...)
    `expected$failure$.colname` is a double vector (0.238355657621287, 0.278814054443501, 0.275448489934206, 0.27191398316063, 0.238362765847705, ...)
    
    `actual$failure$ct` is a double vector (0.238355657621287, 0.278814054443501, 0.275448489934206, 0.27191398316063, 0.238362765847705, ...)
    `expected$failure$ct` is absent
    
    `actual$failure$.columns_id` is absent
    `expected$failure$.columns_id` is a character vector ('Mathematics', 'Mathematics', 'English', 'English', 'Science', ...)
    
    `names(actual$remedial)`:   "teacher" "class" ".colname" "ct.name"     "ct"     
    `names(expected$remedial)`: "teacher" "class" ".colname" ".columns_id" "ct.name"
    
    `actual$remedial$.colname` is a character vector ('Mathematics', 'Mathematics', 'English', 'English', 'Science', ...)
    `expected$remedial$.colname` is a double vector (0.584936223207042, 0.570959241595119, 0.73719495611731, 0.673024803260341, 0.739771230975166, ...)
    
    `actual$remedial$ct` is a double vector (0.584936223207042, 0.570959241595119, 0.73719495611731, 0.673024803260341, 0.739771230975166, ...)
    `expected$remedial$ct` is absent
    
    `actual$remedial$.columns_id` is absent
    `expected$remedial$.columns_id` is a character vector ('Mathematics', 'Mathematics', 'English', 'English', 'Science', ...)
    
    ── Failure ('test-fn-Matrix.R:1116:3'): matrixset 'wide' loop works ────────────
    Expected `grmn` to be identical to `mn_ref`.
    Differences:
    `names(actual$failure)`:   "program" ".rowname" "mean"     "median"
    `names(expected$failure)`: "program" ".rowname" ".rows_id" "mean"  
    
    `actual$failure$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$failure$.rowname` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    
    `actual$failure$median` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    `expected$failure$median` is absent
    
    `actual$failure$.rows_id` is absent
    `expected$failure$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    `names(actual$remedial)`:   "program" ".rowname" "mean"     "median"
    `names(expected$remedial)`: "program" ".rowname" ".rows_id" "mean"  
    
    `actual$remedial$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$remedial$.rowname` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    
    `actual$remedial$median` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    `expected$remedial$median` is absent
    
    `actual$remedial$.rows_id` is absent
    `expected$remedial$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    ── Failure ('test-fn-Matrix.R:1141:3'): matrixset 'wide' loop works ────────────
    Expected `grmn` to be identical to `grmn_ref`.
    Differences:
    `names(actual$failure)`:   "teacher" "class" ".colname" "mean"        "median"
    `names(expected$failure)`: "teacher" "class" ".colname" ".columns_id" "mean"  
    
    `actual$failure$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$failure$.colname` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    
    `actual$failure$median` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    `expected$failure$median` is absent
    
    `actual$failure$.columns_id` is absent
    `expected$failure$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    `names(actual$remedial)`:   "teacher" "class" ".colname" "mean"        "median"
    `names(expected$remedial)`: "teacher" "class" ".colname" ".columns_id" "mean"  
    
    `actual$remedial$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$remedial$.colname` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    
    `actual$remedial$median` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    `expected$remedial$median` is absent
    
    `actual$remedial$.columns_id` is absent
    `expected$remedial$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    ── Failure ('test-fn-Matrix.R:1166:3'): matrixset 'wide' loop works ────────────
    Expected `grmn` to be identical to `mn_ref`.
    Differences:
    `names(actual$failure)`:   "program" ".rowname" "mn"       "md"
    `names(expected$failure)`: "program" ".rowname" ".rows_id" "mn"
    
    `actual$failure$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$failure$.rowname` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    
    `actual$failure$md` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    `expected$failure$md` is absent
    
    `actual$failure$.rows_id` is absent
    `expected$failure$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    `names(actual$remedial)`:   "program" ".rowname" "mn"       "md"
    `names(expected$remedial)`: "program" ".rowname" ".rows_id" "mn"
    
    `actual$remedial$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$remedial$.rowname` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    
    `actual$remedial$md` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    `expected$remedial$md` is absent
    
    `actual$remedial$.rows_id` is absent
    `expected$remedial$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    ── Failure ('test-fn-Matrix.R:1191:3'): matrixset 'wide' loop works ────────────
    Expected `grmn` to be identical to `grmn_ref`.
    Differences:
    `names(actual$failure)`:   "teacher" "class" ".colname" "mn"          "md"
    `names(expected$failure)`: "teacher" "class" ".colname" ".columns_id" "mn"
    
    `actual$failure$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$failure$.colname` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    
    `actual$failure$md` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    `expected$failure$md` is absent
    
    `actual$failure$.columns_id` is absent
    `expected$failure$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    `names(actual$remedial)`:   "teacher" "class" ".colname" "mn"          "md"
    `names(expected$remedial)`: "teacher" "class" ".colname" ".columns_id" "mn"
    
    `actual$remedial$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$remedial$.colname` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    
    `actual$remedial$md` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    `expected$remedial$md` is absent
    
    `actual$remedial$.columns_id` is absent
    `expected$remedial$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    ── Failure ('test-fn.R:999:3'): matrixset 'long' loop works ────────────────────
    Expected `grmn` to be identical to `mn_ref`.
    Differences:
    `names(actual$failure)`:   "program" ".rowname" "mean"     "median"
    `names(expected$failure)`: "program" ".rowname" ".rows_id" "mean"  
    
    `actual$failure$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$failure$.rowname` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    
    `actual$failure$median` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    `expected$failure$median` is absent
    
    `actual$failure$.rows_id` is absent
    `expected$failure$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    `names(actual$remedial)`:   "program" ".rowname" "mean"     "median"
    `names(expected$remedial)`: "program" ".rowname" ".rows_id" "mean"  
    
    `actual$remedial$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$remedial$.rowname` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    
    `actual$remedial$median` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    `expected$remedial$median` is absent
    
    `actual$remedial$.rows_id` is absent
    `expected$remedial$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    ── Failure ('test-fn.R:1024:3'): matrixset 'long' loop works ───────────────────
    Expected `grmn` to be identical to `grmn_ref`.
    Differences:
    `names(actual$failure)`:   "teacher" "class" ".colname" "mean"        "median"
    `names(expected$failure)`: "teacher" "class" ".colname" ".columns_id" "mean"  
    
    `actual$failure$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$failure$.colname` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    
    `actual$failure$median` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    `expected$failure$median` is absent
    
    `actual$failure$.columns_id` is absent
    `expected$failure$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    `names(actual$remedial)`:   "teacher" "class" ".colname" "mean"        "median"
    `names(expected$remedial)`: "teacher" "class" ".colname" ".columns_id" "mean"  
    
    `actual$remedial$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$remedial$.colname` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    
    `actual$remedial$median` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    `expected$remedial$median` is absent
    
    `actual$remedial$.columns_id` is absent
    `expected$remedial$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    ── Failure ('test-fn.R:1049:3'): matrixset 'long' loop works ───────────────────
    Expected `grmn` to be identical to `mn_ref`.
    Differences:
    `names(actual$failure)`:   "program" ".rowname" "mn"       "md"
    `names(expected$failure)`: "program" ".rowname" ".rows_id" "mn"
    
    `actual$failure$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$failure$.rowname` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    
    `actual$failure$md` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    `expected$failure$md` is absent
    
    `actual$failure$.rows_id` is absent
    `expected$failure$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    `names(actual$remedial)`:   "program" ".rowname" "mn"       "md"
    `names(expected$remedial)`: "program" ".rowname" ".rows_id" "mn"
    
    `actual$remedial$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$remedial$.rowname` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    
    `actual$remedial$md` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    `expected$remedial$md` is absent
    
    `actual$remedial$.rows_id` is absent
    `expected$remedial$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    ── Failure ('test-fn.R:1074:3'): matrixset 'long' loop works ───────────────────
    Expected `grmn` to be identical to `grmn_ref`.
    Differences:
    `names(actual$failure)`:   "teacher" "class" ".colname" "mn"          "md"
    `names(expected$failure)`: "teacher" "class" ".colname" ".columns_id" "mn"
    
    `actual$failure$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$failure$.colname` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    
    `actual$failure$md` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    `expected$failure$md` is absent
    
    `actual$failure$.columns_id` is absent
    `expected$failure$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    `names(actual$remedial)`:   "teacher" "class" ".colname" "mn"          "md"
    `names(expected$remedial)`: "teacher" "class" ".colname" ".columns_id" "mn"
    
    `actual$remedial$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$remedial$.colname` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    
    `actual$remedial$md` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    `expected$remedial$md` is absent
    
    `actual$remedial$.columns_id` is absent
    `expected$remedial$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    ── Failure ('test-fn.R:1099:3'): matrixset 'long' loop works ───────────────────
    Expected `grmn` to be identical to `mn_ref`.
    Differences:
    `names(actual$failure)`:   "program" ".rowname" "ct.name"  "ct"     
    `names(expected$failure)`: "program" ".rowname" ".rows_id" "ct.name"
    
    `actual$failure$.rowname` is a character vector ('student 1', 'student 1', 'student 2', 'student 2', 'student 3', ...)
    `expected$failure$.rowname` is a double vector (0.270800364844035, 0.270800364844035, 0.208336764364503, 0.208336764364503, 0.28514515561983, ...)
    
    `actual$failure$ct` is a double vector (0.270800364844035, 0.270800364844035, 0.208336764364503, 0.208336764364503, 0.28514515561983, ...)
    `expected$failure$ct` is absent
    
    `actual$failure$.rows_id` is absent
    `expected$failure$.rows_id` is a character vector ('student 1', 'student 1', 'student 2', 'student 2', 'student 3', ...)
    
    `names(actual$remedial)`:   "program" ".rowname" "ct.name"  "ct"     
    `names(expected$remedial)`: "program" ".rowname" ".rows_id" "ct.name"
    
    `actual$remedial$.rowname` is a character vector ('student 1', 'student 1', 'student 2', 'student 2', 'student 3', ...)
    `expected$remedial$.rowname` is a double vector (0.688091438869014, 0.688091438869014, 0.701310815196484, 0.701310815196484, 0.60816297729034, ...)
    
    `actual$remedial$ct` is a double vector (0.688091438869014, 0.688091438869014, 0.701310815196484, 0.701310815196484, 0.60816297729034, ...)
    `expected$remedial$ct` is absent
    
    `actual$remedial$.rows_id` is absent
    `expected$remedial$.rows_id` is a character vector ('student 1', 'student 1', 'student 2', 'student 2', 'student 3', ...)
    
    ── Failure ('test-fn.R:1124:3'): matrixset 'long' loop works ───────────────────
    Expected `grmn` to be identical to `grmn_ref`.
    Differences:
    `names(actual$failure)`:   "teacher" "class" ".colname" "ct.name"     "ct"     
    `names(expected$failure)`: "teacher" "class" ".colname" ".columns_id" "ct.name"
    
    `actual$failure$.colname` is a character vector ('Mathematics', 'Mathematics', 'English', 'English', 'Science', ...)
    `expected$failure$.colname` is a double vector (0.238355657621287, 0.278814054443501, 0.275448489934206, 0.27191398316063, 0.238362765847705, ...)
    
    `actual$failure$ct` is a double vector (0.238355657621287, 0.278814054443501, 0.275448489934206, 0.27191398316063, 0.238362765847705, ...)
    `expected$failure$ct` is absent
    
    `actual$failure$.columns_id` is absent
    `expected$failure$.columns_id` is a character vector ('Mathematics', 'Mathematics', 'English', 'English', 'Science', ...)
    
    `names(actual$remedial)`:   "teacher" "class" ".colname" "ct.name"     "ct"     
    `names(expected$remedial)`: "teacher" "class" ".colname" ".columns_id" "ct.name"
    
    `actual$remedial$.colname` is a character vector ('Mathematics', 'Mathematics', 'English', 'English', 'Science', ...)
    `expected$remedial$.colname` is a double vector (0.584936223207042, 0.570959241595119, 0.73719495611731, 0.673024803260341, 0.739771230975166, ...)
    
    `actual$remedial$ct` is a double vector (0.584936223207042, 0.570959241595119, 0.73719495611731, 0.673024803260341, 0.739771230975166, ...)
    `expected$remedial$ct` is absent
    
    `actual$remedial$.columns_id` is absent
    `expected$remedial$.columns_id` is a character vector ('Mathematics', 'Mathematics', 'English', 'English', 'Science', ...)
    
    ── Failure ('test-fn.R:1361:3'): matrixset 'wide' loop works ───────────────────
    Expected `grmn` to be identical to `mn_ref`.
    Differences:
    `names(actual$failure)`:   "program" ".rowname" "mean"     "median"
    `names(expected$failure)`: "program" ".rowname" ".rows_id" "mean"  
    
    `actual$failure$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$failure$.rowname` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    
    `actual$failure$median` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    `expected$failure$median` is absent
    
    `actual$failure$.rows_id` is absent
    `expected$failure$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    `names(actual$remedial)`:   "program" ".rowname" "mean"     "median"
    `names(expected$remedial)`: "program" ".rowname" ".rows_id" "mean"  
    
    `actual$remedial$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$remedial$.rowname` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    
    `actual$remedial$median` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    `expected$remedial$median` is absent
    
    `actual$remedial$.rows_id` is absent
    `expected$remedial$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    ── Failure ('test-fn.R:1386:3'): matrixset 'wide' loop works ───────────────────
    Expected `grmn` to be identical to `grmn_ref`.
    Differences:
    `names(actual$failure)`:   "teacher" "class" ".colname" "mean"        "median"
    `names(expected$failure)`: "teacher" "class" ".colname" ".columns_id" "mean"  
    
    `actual$failure$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$failure$.colname` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    
    `actual$failure$median` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    `expected$failure$median` is absent
    
    `actual$failure$.columns_id` is absent
    `expected$failure$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    `names(actual$remedial)`:   "teacher" "class" ".colname" "mean"        "median"
    `names(expected$remedial)`: "teacher" "class" ".colname" ".columns_id" "mean"  
    
    `actual$remedial$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$remedial$.colname` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    
    `actual$remedial$median` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    `expected$remedial$median` is absent
    
    `actual$remedial$.columns_id` is absent
    `expected$remedial$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    ── Failure ('test-fn.R:1411:3'): matrixset 'wide' loop works ───────────────────
    Expected `grmn` to be identical to `mn_ref`.
    Differences:
    `names(actual$failure)`:   "program" ".rowname" "mn"       "md"
    `names(expected$failure)`: "program" ".rowname" ".rows_id" "mn"
    
    `actual$failure$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$failure$.rowname` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    
    `actual$failure$md` is a double vector (0.270800364844035, 0.208336764364503, 0.28514515561983, 0.153522788372356, 0.273990985471755, ...)
    `expected$failure$md` is absent
    
    `actual$failure$.rows_id` is absent
    `expected$failure$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    `names(actual$remedial)`:   "program" ".rowname" "mn"       "md"
    `names(expected$remedial)`: "program" ".rowname" ".rows_id" "mn"
    
    `actual$remedial$.rowname` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    `expected$remedial$.rowname` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    
    `actual$remedial$md` is a double vector (0.688091438869014, 0.701310815196484, 0.60816297729034, 0.672235043649562, 0.641968360450119, ...)
    `expected$remedial$md` is absent
    
    `actual$remedial$.rows_id` is absent
    `expected$remedial$.rows_id` is a character vector ('student 1', 'student 2', 'student 3', 'student 4', 'student 5', ...)
    
    ── Failure ('test-fn.R:1436:3'): matrixset 'wide' loop works ───────────────────
    Expected `grmn` to be identical to `grmn_ref`.
    Differences:
    `names(actual$failure)`:   "teacher" "class" ".colname" "mn"          "md"
    `names(expected$failure)`: "teacher" "class" ".colname" ".columns_id" "mn"
    
    `actual$failure$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$failure$.colname` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    
    `actual$failure$md` is a double vector (0.278814054443501, 0.27191398316063, 0.26278667524457, 0.430513228056952, 0.185918002622202, ...)
    `expected$failure$md` is absent
    
    `actual$failure$.columns_id` is absent
    `expected$failure$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    `names(actual$remedial)`:   "teacher" "class" ".colname" "mn"          "md"
    `names(expected$remedial)`: "teacher" "class" ".colname" ".columns_id" "mn"
    
    `actual$remedial$.colname` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    `expected$remedial$.colname` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    
    `actual$remedial$md` is a double vector (0.570959241595119, 0.673024803260341, 0.75271222749725, 0.653165368549526, 0.706115457962733, ...)
    `expected$remedial$md` is absent
    
    `actual$remedial$.columns_id` is absent
    `expected$remedial$.columns_id` is a character vector ('Mathematics', 'English', 'Science', 'Mathematics', 'English', ...)
    
    
    [ FAIL 20 | WARN 0 | SKIP 0 | PASS 1359 ]
    Error:
    ! Test failures.
    Execution halted

Package: PhenotypeR
Check: dependencies in R code
New result: WARNING
  Missing or unexported object: ‘CodelistGenerator::buildAchillesTables’

Package: PhenotypeR
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘CodelistDiagnostics.Rmd’ using rmarkdown
  trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
  Content type 'application/zip' length 593048982 bytes (565.6 MB)
  ==================================================
  downloaded 565.6 MB
  
  
  Quitting from CodelistDiagnostics.Rmd:60-62 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'CodelistDiagnostics.Rmd' failed with diagnostics:
  ✖ `checks` a choice between: measurement_summary,
    measurement_value_as_number, and measurement_value_as_concept.
  ! `checks` must be a choice between: measurement_summary,
    measurement_value_as_number, and measurement_value_as_concept; it can not
    contain NA; it can not be NULL.
  --- failed re-building ‘CodelistDiagnostics.Rmd’
  
  --- re-building ‘CohortDiagnostics.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘CohortDiagnostics.Rmd’
  
  --- re-building ‘DatabaseDiagnostics.Rmd’ using rmarkdown
  trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
  Content type 'application/zip' length 593048982 bytes (565.6 MB)
  ==================================================
  downloaded 565.6 MB
  
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘DatabaseDiagnostics.Rmd’
  
  --- re-building ‘PhenotypeDiagnostics.Rmd’ using rmarkdown
  trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
  Content type 'application/zip' length 593048982 bytes (565.6 MB)
  ==================================================
  downloaded 565.6 MB
  
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘PhenotypeDiagnostics.Rmd’
  
  --- re-building ‘PhenotypeExpectations.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘PhenotypeExpectations.Rmd’
  
  --- re-building ‘PopulationDiagnostics.Rmd’ using rmarkdown
  trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
  Content type 'application/zip' length 593048982 bytes (565.6 MB)
  ==================================================
  downloaded 565.6 MB
  
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘PopulationDiagnostics.Rmd’
  
  --- re-building ‘ShinyDiagnostics.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘ShinyDiagnostics.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘CodelistDiagnostics.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: PhenotypeR
Check: tests
New result: ERROR
    Running ‘testthat.R’ [19s/19s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # This file is part of the standard setup for testthat.
    > # It is recommended that you do not modify it.
    > #
    > # Where should you do additional test configuration?
    > # Learn more about the roles of various files in:
    > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
    > # * https://testthat.r-lib.org/articles/special-files.html
    > 
    > library(testthat)
    > library(PhenotypeR)
    > 
    > test_check("PhenotypeR")
    * Getting codelists from cohorts
    * Getting index event breakdown
    Getting counts of b codes for cohort cohort_1
    * Getting diagnostics for measurement concepts
    Saving _problems/test-codelistDiagnostics-90.R
    [ FAIL 1 | WARN 4 | SKIP 21 | PASS 0 ]
    
    ══ Skipped tests (21) ══════════════════════════════════════════════════════════
    • On CRAN (17): 'test-addCodelistAttribute.R:2:3',
      'test-addCodelistAttribute.R:70:3', 'test-addCodelistAttribute.R:118:3',
      'test-codelistDiagnostics.R:2:3', 'test-codelistDiagnostics.R:48:3',
      'test-cohortDiagnostics.R:2:3', 'test-cohortDiagnostics.R:51:3',
      'test-databaseDiagnostics.R:2:3', 'test-dbms.R:3:3', 'test-dbms.R:25:3',
      'test-getCohortExpectations.R:3:3', 'test-getCohortExpectations.R:26:3',
      'test-getCohortExpectations.R:61:3', 'test-phenotypeDiagnostics.R:3:3',
      'test-populationDiagnostics.R:2:3', 'test-shinyDiagnostics.R:3:3',
      'test-shinyDiagnostics.R:53:3'
    • empty test (4): 'test-cohortDiagnostics.R:144:1',
      'test-cohortDiagnostics.R:148:1', 'test-cohortDiagnostics.R:152:1',
      'test-cohortDiagnostics.R:158:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-codelistDiagnostics.R:90:3'): measurementDiagnostics working ───
    Error in `summariseMeasurementUseInternal(cdm = cdm, codes = codes, cohort = cohort, timing = timing, timingName = timing, byConcept = byConcept, byYear = byYear, bySex = bySex, ageGroup = ageGroup, dateRange = dateRange, estimates = estimates, histogram = histogram, checks = checks)`: x `checks` a choice between: measurement_summary, measurement_value_as_number, and measurement_value_as_concept.
    ! `checks` must be a choice between: measurement_summary, measurement_value_as_number, and measurement_value_as_concept; it can not contain NA; it can not be NULL.
    Backtrace:
        ▆
     1. └─PhenotypeR::codelistDiagnostics(cdm$my_cohort) at test-codelistDiagnostics.R:90:3
     2.   └─MeasurementDiagnostics::summariseCohortMeasurementUse(...)
     3.     └─MeasurementDiagnostics:::summariseMeasurementUseInternal(...)
     4.       └─omopgenerics::assertChoice(checks, choices = allowedChecks)
     5.         └─omopgenerics:::errorMessage(...)
     6.           └─cli::cli_abort(message = message, call = call)
     7.             └─rlang::abort(...)
    
    [ FAIL 1 | WARN 4 | SKIP 21 | PASS 0 ]
    Error:
    ! Test failures.
    Execution halted

Package: readabs
Check: tests
New result: ERROR
    Running ‘testthat.R’ [51s/160s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(readabs)
    Environment variable 'R_READABS_PATH' is unset. Downloaded files will be saved in a temporary directory.
    You can set 'R_READABS_PATH' at any time. To set it for the rest of this session, use
    	Sys.setenv(R_READABS_PATH = <path>)
    > 
    > test_check("readabs")
    Saving _problems/test-download_data_cube-5.R
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101059.xlsx'
    downloaded 197 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101051.xlsx'
    downloaded 192 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101052.xlsx'
    downloaded 191 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101053.xlsx'
    downloaded 188 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101054.xlsx'
    downloaded 185 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101055.xlsx'
    downloaded 185 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101056.xlsx'
    downloaded 179 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101057.xlsx'
    downloaded 171 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101058.xlsx'
    downloaded 175 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/310101.xlsx'
    downloaded 69 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/310102.xlsx'
    Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 93563 bytes (91 KB)
    ==================================================
    downloaded 91 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/310104.xlsx'
    Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 90556 bytes (88 KB)
    ==================================================
    downloaded 88 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101016a.xlsx'
    Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 60844 bytes (59 KB)
    ==================================================
    downloaded 59 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101016b.xlsx'
    downloaded 59 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101051.xlsx'
    downloaded 192 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101052.xlsx'
    downloaded 191 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101053.xlsx'
    downloaded 188 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101054.xlsx'
    downloaded 185 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101055.xlsx'
    downloaded 185 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101056.xlsx'
    downloaded 179 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101057.xlsx'
    downloaded 171 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101058.xlsx'
    downloaded 175 KB
    
    trying URL 'https://www.abs.gov.au/statistics/people/population/national-state-and-territory-population/latest-release/3101059.xlsx'
    downloaded 197 KB
    
    [ FAIL 1 | WARN 0 | SKIP 34 | PASS 99 ]
    
    ══ Skipped tests (34) ══════════════════════════════════════════════════════════
    • On CRAN (34): 'test-abs_api.R:2:3', 'test-abs_api.R:16:3',
      'test-abs_api.R:46:3', 'test-abs_api.R:55:3', 'test-check_latest_date.R:2:3',
      'test-data-uptodate.R:2:3', 'test-data-uptodate.R:15:3',
      'test-download-data-cube.r:4:3', 'test-download_abs.R:2:3', 'test-fst.R:2:3',
      'test-get_available_files.r:2:3', 'test-individual-readabs-steps.R:2:3',
      'test-match_tables.R:9:3', 'test-read_abs_url.R:2:3', 'test-read_awe.R:19:3',
      'test-read_job_mobility.R:2:3', 'test-read_lfs_grossflows.R:2:3',
      'test-read_payrolls.R:2:3', 'test-readabs.R:6:3', 'test-readabs.R:19:3',
      'test-readabs.R:38:3', 'test-readabs.R:50:3', 'test-readabs.R:63:3',
      'test-readabs.R:83:3', 'test-readabs.R:96:3', 'test-readabs.R:109:3',
      'test-readabs.R:118:3', 'test-readabs.R:152:3', 'test-readabs.R:162:3',
      'test-readabs.R:169:3', 'test-search_catalogues.R:19:3',
      'test-separate_series.R:7:3', 'test-separate_series.R:54:3',
      'test-show_available_catalogues.r:15:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-download_data_cube.R:5:3'): read_lfs_datacube ────────────────
    Expected `nrow(avail_cubes)` > 50.
    Actual comparison: 48.0 <= 50.0
    Difference: -2.0 <= 0
    
    [ FAIL 1 | WARN 0 | SKIP 34 | PASS 99 ]
    Error:
    ! Test failures.
    Execution halted

Package: reptiledbr
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘format_all.Rmd’ using rmarkdown
  
  Quitting from format_all.Rmd:125-134 [unnamed-chunk-4]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'format_all.Rmd' failed with diagnostics:
  ℹ In argument: `stringr::str_detect(comment_detail, "Venomous")`.
  Caused by error:
  ! object 'comment_detail' not found
  --- failed re-building ‘format_all.Rmd’
  
  --- re-building ‘introduction.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘introduction.Rmd’
  
  --- re-building ‘local_search.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘local_search.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘format_all.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: retroharmonize
Check: examples
New result: ERROR
  Running examples in ‘retroharmonize-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: create_codebook
  > ### Title: Create a codebook
  > ### Aliases: create_codebook codebook_waves_create
  > 
  > ### ** Examples
  > 
  > create_codebook (
  +  survey = read_rds (
  +           system.file("examples", "ZA7576.rds",
  +                       package = "retroharmonize")
  +           )
  + )
  Error in `bind_rows()`:
  ! Can't combine `..1$val_label_orig` <double> and `..2$val_label_orig` <character>.
  Backtrace:
       ▆
    1. ├─retroharmonize::create_codebook(...)
    2. │ └─num_labels %>% bind_rows(char_labels) %>% ...
    3. ├─dplyr::arrange(., .data$entry)
    4. ├─dplyr::bind_rows(., char_labels)
    5. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env())
    6. └─vctrs (local) `<fn>`()
    7.   └─vctrs::vec_default_ptype2(...)
    8.     ├─base::withRestarts(...)
    9.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
   10.     │   └─base (local) doWithOneRestart(return(expr), restart)
   11.     └─vctrs::stop_incompatible_type(...)
   12.       └─vctrs:::stop_incompatible(...)
   13.         └─vctrs:::stop_vctrs(...)
   14.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
  Execution halted

Package: retroharmonize
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [9s/9s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(retroharmonize)
    > 
    > test_check("retroharmonize")
    Saving _problems/test-codebook_create-12.R
     dbl+lbl [1:7] 1, 0, 1, 1, 0, 8, 9
     @ labels   : Named num [1:4] 1 0 8 9
      ..- attr(*, "names")= chr [1:4] "TRUST" "NOT TRUST" "DON'T KNOW" "INAP. HERE"
     @ na_values: num [1:2] 8 9
    Loading required package: dplyr
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    
    Attaching package: 'vctrs'
    
    The following object is masked from 'package:dplyr':
    
        data_frame
    
    
    Attaching package: 'rlang'
    
    The following object is masked from 'package:retroharmonize':
    
        as_character
    
    Survey ID: test
    Survey ID: test2
    Survey ID: test2
    Survey ID: test2
    Survey ID: test
    [ FAIL 1 | WARN 23 | SKIP 3 | PASS 99 ]
    
    ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
    • On CRAN (3): 'test-harmonize_na_values.R:18:3',
      'test-labelled_spss_survey.R:136:1', 'test-subset_save_surveys.R:32:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-codebook_create.R:12:1'): (code run outside of `test_that()`) ──
    <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
    Error in `bind_rows(., char_labels)`: Can't combine `..1$val_label_orig` <double> and `..2$val_label_orig` <character>.
    Backtrace:
         ▆
      1. ├─retroharmonize::create_codebook(metadata) at test-codebook_create.R:12:1
      2. │ └─num_labels %>% bind_rows(char_labels) %>% ...
      3. ├─dplyr::arrange(., .data$entry)
      4. ├─dplyr::bind_rows(., char_labels)
      5. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env())
      6. └─vctrs (local) `<fn>`()
      7.   └─vctrs::vec_default_ptype2(...)
      8.     ├─base::withRestarts(...)
      9.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
     10.     │   └─base (local) doWithOneRestart(return(expr), restart)
     11.     └─vctrs::stop_incompatible_type(...)
     12.       └─vctrs:::stop_incompatible(...)
     13.         └─vctrs:::stop_vctrs(...)
     14.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
    
    [ FAIL 1 | WARN 23 | SKIP 3 | PASS 99 ]
    Error:
    ! Test failures.
    Execution halted