Running 'testthat.R' [44s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(portalr)
  > 
  > test_check("portalr")
  [ FAIL 12 | WARN 45 | SKIP 44 | PASS 13 ]
  
  == Skipped tests ===============================================================
  * On CRAN (41)
  * is.null(daily_pheno) is TRUE (1)
  * is.null(monthly_pheno) is TRUE (1)
  * is.null(newmoon_pheno) is TRUE (1)
  
  == Failed tests ================================================================
  -- Error ('test-02-data-processing.R:8'): (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:
      x
   1. \-portalr::load_rodent_data(portal_data_path) at test-02-data-processing.R:8:0
   2.   \-dplyr::rename(species_table, species = "speciescode")
  -- Error ('test-04-weather.R:4'): (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:
      x
   1. +-portalr::weather("daily", path = portal_data_path) at test-04-weather.R:4:0
   2. | \-... %>% ...
   3. \-dplyr::select(...)
  -- Error ('test-05-individual-stake-data.R:6'): 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:
      x
   1. \-portalr::summarize_individual_rodents(path = portal_data_path) at test-05-individual-stake-data.R:6:2
   2.   \-portalr::load_rodent_data(...)
   3.     \-dplyr::rename(species_table, species = "speciescode")
  -- Error ('test-06-summarize-plants.R:10'): 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:
      x
   1. +-portalr::plant_abundance(...) at test-06-summarize-plants.R:10:2
   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'): 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:
      x
   1. \-portalr::shrub_cover(...) at test-06-summarize-plants.R:31:2
   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'): (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:
      x
   1. \-portalr::abundance(path = portal_data_path, level = "plot", shape = "flat") at test-07-seasons.R:8:0
   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'): (code run outside of `test_that()`) -------------
  Error in `as.POSIXlt.character(x, tz = tz(x))`: character string is not in a standard unambiguous format
  Backtrace:
      x
   1. \-portalr::ndvi("monthly", path = portal_data_path) at test-08-NDVI.R:4:0
   2.   +-lubridate::month(paste0(NDVI$date, "-01"))
   3.   \-lubridate:::month.default(paste0(NDVI$date, "-01"))
   4.     +-lubridate::month(...)
   5.     +-base::as.POSIXlt(x, tz = tz(x))
   6.     \-base::as.POSIXlt.character(x, tz = tz(x))
  -- Error ('test-09-get-future-moons.R:6'): get_future_moons 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:
      x
   1. +-portalr::load_trapping_data(portal_data_path) at test-09-get-future-moons.R:6:2
   2. | \-portalr:::clean_data(newmoons_table, trapping_table, by = "period")
   3. |   \-... %>% unique()
   4. +-base::unique(.)
   5. +-dplyr::select(., columns_to_keep)
   6. +-dplyr::filter(., .data$qcflag == 1)
   7. \-dplyr::left_join(., trapping_table, ...)
  -- Error ('test-10-summarize_ants.R:6'): 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:
      x
   1. \-portalr::colony_presence_absence(...) at test-10-summarize_ants.R:6:2
   2.   \-portalr:::reformat_species_table(antsp)
   3.     \-dplyr::rename(species_table, sp = "species", species = "speciescode")
  -- Error ('test-10-summarize_ants.R:21'): 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:
      x
   1. +-portalr::bait_presence_absence(path = portal_data_path, level = "Stake") at test-10-summarize_ants.R:21:2
   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(., !!!grouping)
  -- Error ('test-10-summarize_ants.R:34'): 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:
      x
   1. \-portalr::colony_presence_absence(...) at test-10-summarize_ants.R:34:2
   2.   \-portalr:::reformat_species_table(antsp)
   3.     \-dplyr::rename(species_table, sp = "species", species = "speciescode")
  -- Error ('test-10-summarize_ants.R:49'): 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:
      x
   1. +-portalr::bait_presence_absence(path = portal_data_path, level = "plot") at test-10-summarize_ants.R:49:2
   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(., !!!grouping)
  
  [ FAIL 12 | WARN 45 | SKIP 44 | PASS 13 ]
  Error: Test failures
  Execution halted