Running ‘testthat.R’ [6s/86s]
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(portalr)
  > 
  > test_check("portalr")
  Saving _problems/test-02-data-processing-8.R
  Saving _problems/test-04-weather-4.R
  Saving _problems/test-05-individual-stake-data-6.R
  Saving _problems/test-06-summarize-plants-12.R
  Saving _problems/test-06-summarize-plants-33.R
  Saving _problems/test-07-seasons-8.R
  Saving _problems/test-08-NDVI-4.R
  Saving _problems/test-09-get-future-moons-6.R
  Saving _problems/test-10-summarize_ants-7.R
  Saving _problems/test-10-summarize_ants-21.R
  Saving _problems/test-10-summarize_ants-35.R
  Saving _problems/test-10-summarize_ants-49.R
  Downloading version `6.33.0` of the data...
  [ FAIL 12 | WARN 42 | SKIP 44 | PASS 14 ]
  
  ══ Skipped tests (44) ══════════════════════════════════════════════════════════
  • On CRAN (44): 'test-01-data-retrieval.R:5:5',
    'test-01-data-retrieval.R:41:5', 'test-01-data-retrieval.R:48:5',
    'test-01-data-retrieval.R:63:5', 'test-01-data-retrieval.R:78:5',
    'test-01-data-retrieval.R:92:1', 'test-03-summarize-rodents.R:6:3',
    'test-03-summarize-rodents.R:32:3', 'test-03-summarize-rodents.R:38:3',
    'test-03-summarize-rodents.R:60:3', 'test-03-summarize-rodents.R:85:3',
    'test-03-summarize-rodents.R:110:3', 'test-03-summarize-rodents.R:129:3',
    'test-03-summarize-rodents.R:195:3', 'test-99-regression.R:8:3',
    'test-99-regression.R:18:3', 'test-99-regression.R:32:3',
    'test-99-regression.R:50:3', 'test-99-regression.R:74:3',
    'test-99-regression.R:84:3', 'test-99-regression.R:93:3',
    'test-99-regression.R:106:3', 'test-99-regression.R:115:3',
    'test-99-regression.R:124:3', 'test-99-regression.R:136:3',
    'test-99-regression.R:147:3', 'test-99-regression.R:159:3',
    'test-99-regression.R:168:3', 'test-99-regression.R:177:3',
    'test-99-regression.R:187:3', 'test-99-regression.R:201:3',
    'test-99-regression.R:213:3', 'test-99-regression.R:221:3',
    'test-99-regression.R:233:3', 'test-99-regression.R:241:3',
    'test-99-regression.R:253:3', 'test-99-regression.R:261:3',
    'test-99-regression.R:273:3', 'test-99-regression.R:286:3',
    'test-99-regression.R:296:3', 'test-99-regression.R:306:5',
    'test-99-regression.R:323:3', 'test-99-regression.R:341:3',
    'test-99-regression.R:353:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-02-data-processing.R:8:1'): (code run outside of `test_that()`) ──
  Error in `UseMethod("rename")`: no applicable method for 'rename' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. └─portalr::load_rodent_data(portal_data_path) at test-02-data-processing.R:8:1
   2.   └─dplyr::rename(species_table, species = "speciescode")
  ── Error ('test-04-weather.R:4:1'): (code run outside of `test_that()`) ────────
  Error in `UseMethod("select")`: no applicable method for 'select' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. ├─portalr::weather("daily", path = portal_data_path) at test-04-weather.R:4:1
   2. │ └─... %>% ...
   3. └─dplyr::select(...)
  ── Error ('test-05-individual-stake-data.R:6:3'): summarize_individual_rodents returns expected columns ──
  Error in `UseMethod("rename")`: no applicable method for 'rename' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. └─portalr::summarize_individual_rodents(path = portal_data_path) at test-05-individual-stake-data.R:6:3
   2.   └─portalr::load_rodent_data(...)
   3.     └─dplyr::rename(species_table, species = "speciescode")
  ── Error ('test-06-summarize-plants.R:10:3'): plant_abundance returns expected results ──
  Error in `UseMethod("rename")`: no applicable method for 'rename' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. ├─portalr::plant_abundance(...) at test-06-summarize-plants.R:10:3
   2. │ ├─... %>% dplyr::filter(.data$abundance > 0)
   3. │ └─portalr::summarize_plant_data(..., shape = "flat", output = "abundance")
   4. │   └─portalr::load_plant_data(...)
   5. │     └─portalr:::reformat_species_table(species_table)
   6. │       └─dplyr::rename(species_table, sp = "species", species = "speciescode")
   7. └─dplyr::filter(., .data$abundance > 0)
  ── Error ('test-06-summarize-plants.R:31:3'): shrub_cover returns expected results ──
  Error in `UseMethod("rename")`: no applicable method for 'rename' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. └─portalr::shrub_cover(...) at test-06-summarize-plants.R:31:3
   2.   └─portalr::load_plant_data(...)
   3.     └─portalr:::reformat_species_table(species_table)
   4.       └─dplyr::rename(species_table, sp = "species", species = "speciescode")
  ── Error ('test-07-seasons.R:8:1'): (code run outside of `test_that()`) ────────
  Error in `UseMethod("rename")`: no applicable method for 'rename' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. └─portalr::abundance(path = portal_data_path, level = "plot", shape = "flat") at test-07-seasons.R:8:1
   2.   └─portalr::summarize_rodent_data(..., output = "abundance")
   3.     └─portalr::load_rodent_data(...)
   4.       └─dplyr::rename(species_table, species = "speciescode")
  ── Error ('test-08-NDVI.R:4:1'): (code run outside of `test_that()`) ───────────
  Error in `UseMethod("filter")`: no applicable method for 'filter' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. ├─portalr::ndvi("monthly", path = portal_data_path) at test-08-NDVI.R:4:1
   2. │ └─... %>% dplyr::filter(.data$sensor %in% filtering)
   3. └─dplyr::filter(., .data$sensor %in% filtering)
  ── Error ('test-09-get-future-moons.R:6:3'): get_future_newmoons returns expected results using current newmoons_table ──
  Error in `UseMethod("left_join")`: no applicable method for 'left_join' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. ├─portalr::load_trapping_data(portal_data_path) at test-09-get-future-moons.R:6:3
   2. │ └─portalr:::clean_data(newmoons_table, trapping_table, by = "period")
   3. │   └─... %>% unique()
   4. ├─base::unique(.)
   5. ├─dplyr::select(., dplyr::all_of(columns_to_keep))
   6. ├─dplyr::filter(., .data$qcflag == 1)
   7. └─dplyr::left_join(., trapping_table, ...)
  ── Error ('test-10-summarize_ants.R:6:3'): colony_presence_absence returns expected results ──
  Error in `UseMethod("rename")`: no applicable method for 'rename' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. └─portalr::colony_presence_absence(...) at test-10-summarize_ants.R:6:3
   2.   └─portalr:::reformat_species_table(antsp)
   3.     └─dplyr::rename(species_table, sp = "species", species = "speciescode")
  ── Error ('test-10-summarize_ants.R:21:3'): bait_presence_absence returns expected results ──
  Error in `UseMethod("select")`: no applicable method for 'select' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. ├─portalr::bait_presence_absence(path = portal_data_path, level = "Stake") at test-10-summarize_ants.R:21:3
   2. │ ├─compute_presence(bait, level) %>% as.data.frame()
   3. │ └─portalr:::compute_presence(bait, level)
   4. │   └─... %>% ...
   5. ├─base::as.data.frame(.)
   6. ├─tidyr::complete(., !!!grouping, fill = list(presence = 0))
   7. ├─dplyr::mutate(., presence = 1)
   8. ├─dplyr::distinct(.)
   9. └─dplyr::select(., dplyr::all_of(vars_to_keep))
  ── Error ('test-10-summarize_ants.R:34:3'): colony_presence_absence returns expected results ──
  Error in `UseMethod("rename")`: no applicable method for 'rename' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. └─portalr::colony_presence_absence(...) at test-10-summarize_ants.R:34:3
   2.   └─portalr:::reformat_species_table(antsp)
   3.     └─dplyr::rename(species_table, sp = "species", species = "speciescode")
  ── Error ('test-10-summarize_ants.R:49:3'): bait_presence_absence returns expected results ──
  Error in `UseMethod("select")`: no applicable method for 'select' applied to an object of class "c('simpleWarning', 'warning', 'condition')"
  Backtrace:
      ▆
   1. ├─portalr::bait_presence_absence(path = portal_data_path, level = "plot") at test-10-summarize_ants.R:49:3
   2. │ ├─compute_presence(bait, level) %>% as.data.frame()
   3. │ └─portalr:::compute_presence(bait, level)
   4. │   └─... %>% ...
   5. ├─base::as.data.frame(.)
   6. ├─tidyr::complete(., !!!grouping, fill = list(presence = 0))
   7. ├─dplyr::mutate(., presence = 1)
   8. ├─dplyr::distinct(.)
   9. └─dplyr::select(., dplyr::all_of(vars_to_keep))
  
  [ FAIL 12 | WARN 42 | SKIP 44 | PASS 14 ]
  Error:
  ! Test failures.
  Execution halted