R Under development (unstable) (2024-11-27 r87386 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
> library(bdc)
> 
> test_check("bdc")

bdc_basisOfRecords_notStandard:
Flagged 4 of the following specific nature:
 c("FOSSIL_SPECIMEN", NA, "Specimen", "PRESERVED_SPECIMEN") 
One column was added to the database.


bdc_basisOfRecords_notStandard:
Flagged 2 of the following specific nature:
 c("FOSSIL_SPECIMEN", "RON") 
One column was added to the database.

Loading required package: rnaturalearth
Spherical geometry (s2) switched off
The rnaturalearthhires package needs to be installed.
Installing the rnaturalearthhires package.

bdc_coordinates_empty:
Flagged 4 records.
One column was added to the database.


bdc_coordinates_empty:
Flagged 4 records.
One column was added to the database.


bdc_coordinates_empty:
Flagged 4 records.
One column was added to the database.


bdc_coordinates_from_locality 
Found 3 records missing or with invalid coordinates but with potentially useful information on locality.


bdc_coordinates_outOfRange:
Flagged 2 records.
One column was added to the database.

bdc_coordinates_precision:
Flagged 4 records
One column was added to the database.

bdc_coordinates_precision:
Flagged 0 records
One column was added to the database.

Loading required package: readr

Attaching package: 'readr'

The following objects are masked from 'package:testthat':

    edition_get, local_edition

Loading required package: rnaturalearthdata

Attaching package: 'rnaturalearthdata'

The following object is masked from 'package:rnaturalearth':

    countries110

The rnaturalearthhires package needs to be installed.
Installing the rnaturalearthhires package.

bdc_scientificName_empty:
Flagged 5 records.
One column was added to the database.


bdc_coordinates_empty:
Flagged 44 records.
One column was added to the database.


bdc_coordinates_outOfRange:
Flagged 1 records.
One column was added to the database.


bdc_basisOfRecords_notStandard:
Flagged 0 of the following specific nature:
 character(0) 
One column was added to the database.

The rnaturalearthhires package needs to be installed.
Installing the rnaturalearthhires package.
Loading auxiliary data: country names

Standardizing country names

country found: Bolivia
country found: Brazil

bdc_country_standardized:
The country names of 3 records were standardized.
Two columns ('country_suggested' and 'countryCode') were added to the database.

The rnaturalearthhires package needs to be installed.
Installing the rnaturalearthhires package.
The rnaturalearthhires package needs to be installed.
Installing the rnaturalearthhires package.
The rnaturalearthhires package needs to be installed.
Installing the rnaturalearthhires package.
The rnaturalearthhires package needs to be installed.
Installing the rnaturalearthhires package.
The rnaturalearthhires package needs to be installed.
Installing the rnaturalearthhires package.
Loading required package: cowplot
Loading required package: DT

bdc_eventDate_empty:
Flagged 3 records.
One column was added to the database.


bdc_fiter_out_flags:
The following columns were removed from the database:
.bdc_scientificName_empty, .bdc_coordinates_empty, .bdc_coordinates_outOfRange, .summary

bdc_fiter_out_flags:
The following columns were removed from the database:
.summary
The rnaturalearthhires package needs to be installed.
Installing the rnaturalearthhires package.

bdc_coordinates_empty:
Flagged 0 records.
One column was added to the database.

Loading required package: ggplot2

bdc_scientificName_empty:
Flagged 2 records.
One column was added to the database.


bdc_scientificName_empty:
Flagged 2 records.
One column was added to the database.

The rnaturalearthhires package needs to be installed.
Installing the rnaturalearthhires package.
Standardizing datafake1 file
Standardizing datafake2 file
Standardizing datafake3 file
Standardizing datafake1 file
Standardizing datafake2 file
Standardizing datafake3 file
[ERROR]: Column names defined in the metadata do not match column names in the datafake4 file
[INFO]: Column(s) `y` and `notes` defined in the metadata not present in the datafake4

bdc_summary_col:
Flagged 4 records.
One column was added to the database.


bdc_year_from_eventDate:
Four-digit year were extracted from 5 records.


bdc_year_outOfRange:
Flagged 1 records.
One column was added to the database.

[ FAIL 12 | WARN 0 | SKIP 5 | PASS 63 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (5): 'test-bdc_clean_names.R:2:1', 'test-bdc_filter_name.R:2:1',
  'test-bdc_query_names_taxadb.R:2:1', 'test-bdc_standardize_datasets.R:180:1',
  'test-bdc_suggest_names_taxadb.R:2:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bdc_coordinates_country_inconsistent.R:5:1'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: Failed to install the rnaturalearthhires package.
  Please try installing the package for yourself using the following command: 
     devtools::install_github("ropensci/rnaturalearthhires")
Backtrace:
     ▆
  1. ├─bdc::bdc_coordinates_country_inconsistent(...) at test-bdc_coordinates_country_inconsistent.R:5:1
  2. │ ├─... %>% bdc_reword_countries()
  3. │ └─rnaturalearth::ne_countries(...)
  4. │   └─rnaturalearth:::get_data(scale = scale, type = type)
  5. │     └─rnaturalearth::check_rnaturalearthhires()
  6. │       └─rnaturalearth::install_rnaturalearthhires()
  7. │         └─base::tryCatch(...)
  8. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │             ├─base (local) tryCatchOne(...)
 10. │             │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11. │             └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 12. │               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13. │                 └─value[[3L]](cond)
 14. ├─bdc:::bdc_reword_countries(.)
 15. │ └─data %>% ...
 16. └─dplyr::mutate(., name_long = dplyr::recode(name_long, !!!vec_reword))
── Error ('test-bdc_coordinates_transposed.R:21:3'): test based on function example dataset ──
Error in `value[[3L]](cond)`: Failed to install the rnaturalearthhires package.
  Please try installing the package for yourself using the following command: 
     devtools::install_github("ropensci/rnaturalearthhires")
Backtrace:
     ▆
  1. ├─bdc::bdc_coordinates_transposed(...) at test-bdc_coordinates_transposed.R:21:3
  2. │ └─bdc:::bdc_get_world_map()
  3. │   ├─base::suppressWarnings(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   ├─... %>% sf::as_Spatial()
  6. │   └─rnaturalearth::ne_countries(scale = "large", returnclass = "sf")
  7. │     └─rnaturalearth:::get_data(scale = scale, type = type)
  8. │       └─rnaturalearth::check_rnaturalearthhires()
  9. │         └─rnaturalearth::install_rnaturalearthhires()
 10. │           └─base::tryCatch(...)
 11. │             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12. │               ├─base (local) tryCatchOne(...)
 13. │               │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 14. │               └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 15. │                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16. │                   └─value[[3L]](cond)
 17. ├─sf::as_Spatial(.)
 18. ├─dplyr::select(., name_long, iso2c, geometry)
 19. ├─dplyr::mutate(...)
 20. ├─dplyr::left_join(., cntr_names, by = c(name_long = "english_name"))
 21. ├─bdc:::bdc_reword_countries(.)
 22. │ └─data %>% ...
 23. └─dplyr::mutate(., name_long = dplyr::recode(name_long, !!!vec_reword))
── Error ('test-bdc_coordinates_transposed.R:92:1'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: Failed to install the rnaturalearthhires package.
  Please try installing the package for yourself using the following command: 
     devtools::install_github("ropensci/rnaturalearthhires")
Backtrace:
     ▆
  1. ├─bdc::bdc_country_from_coordinates(...) at test-bdc_coordinates_transposed.R:92:1
  2. │ ├─... %>% bdc_reword_countries()
  3. │ └─rnaturalearth::ne_countries(scale = "large", returnclass = "sf")
  4. │   └─rnaturalearth:::get_data(scale = scale, type = type)
  5. │     └─rnaturalearth::check_rnaturalearthhires()
  6. │       └─rnaturalearth::install_rnaturalearthhires()
  7. │         └─base::tryCatch(...)
  8. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │             ├─base (local) tryCatchOne(...)
 10. │             │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11. │             └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 12. │               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13. │                 └─value[[3L]](cond)
 14. ├─bdc:::bdc_reword_countries(.)
 15. │ └─data %>% ...
 16. └─dplyr::mutate(., name_long = dplyr::recode(name_long, !!!vec_reword))
── Error ('test-bdc_correct_coordinates.R:25:1'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: Failed to install the rnaturalearthhires package.
  Please try installing the package for yourself using the following command: 
     devtools::install_github("ropensci/rnaturalearthhires")
Backtrace:
     ▆
  1. ├─bdc:::bdc_get_world_map() at test-bdc_correct_coordinates.R:25:1
  2. │ ├─base::suppressWarnings(...)
  3. │ │ └─base::withCallingHandlers(...)
  4. │ ├─... %>% sf::as_Spatial()
  5. │ └─rnaturalearth::ne_countries(scale = "large", returnclass = "sf")
  6. │   └─rnaturalearth:::get_data(scale = scale, type = type)
  7. │     └─rnaturalearth::check_rnaturalearthhires()
  8. │       └─rnaturalearth::install_rnaturalearthhires()
  9. │         └─base::tryCatch(...)
 10. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11. │             ├─base (local) tryCatchOne(...)
 12. │             │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 13. │             └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 14. │               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15. │                 └─value[[3L]](cond)
 16. ├─sf::as_Spatial(.)
 17. ├─dplyr::select(., name_long, iso2c, geometry)
 18. ├─dplyr::mutate(...)
 19. ├─dplyr::left_join(., cntr_names, by = c(name_long = "english_name"))
 20. ├─bdc:::bdc_reword_countries(.)
 21. │ └─data %>% ...
 22. └─dplyr::mutate(., name_long = dplyr::recode(name_long, !!!vec_reword))
── Error ('test-bdc_country_from_coordinates.R:9:3'): it can return country names ──
Error in `value[[3L]](cond)`: Failed to install the rnaturalearthhires package.
  Please try installing the package for yourself using the following command: 
     devtools::install_github("ropensci/rnaturalearthhires")
Backtrace:
     ▆
  1. ├─bdc::bdc_country_from_coordinates(...) at test-bdc_country_from_coordinates.R:9:3
  2. │ ├─... %>% bdc_reword_countries()
  3. │ └─rnaturalearth::ne_countries(scale = "large", returnclass = "sf")
  4. │   └─rnaturalearth:::get_data(scale = scale, type = type)
  5. │     └─rnaturalearth::check_rnaturalearthhires()
  6. │       └─rnaturalearth::install_rnaturalearthhires()
  7. │         └─base::tryCatch(...)
  8. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │             ├─base (local) tryCatchOne(...)
 10. │             │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11. │             └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 12. │               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13. │                 └─value[[3L]](cond)
 14. ├─bdc:::bdc_reword_countries(.)
 15. │ └─data %>% ...
 16. └─dplyr::mutate(., name_long = dplyr::recode(name_long, !!!vec_reword))
── Error ('test-bdc_country_from_coordinates.R:31:3'): return message ──────────
Error in `value[[3L]](cond)`: Failed to install the rnaturalearthhires package.
  Please try installing the package for yourself using the following command: 
     devtools::install_github("ropensci/rnaturalearthhires")
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test-bdc_country_from_coordinates.R:31:3
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. ├─bdc::bdc_country_from_coordinates(...)
  8. │ ├─... %>% bdc_reword_countries()
  9. │ └─rnaturalearth::ne_countries(scale = "large", returnclass = "sf")
 10. │   └─rnaturalearth:::get_data(scale = scale, type = type)
 11. │     └─rnaturalearth::check_rnaturalearthhires()
 12. │       └─rnaturalearth::install_rnaturalearthhires()
 13. │         └─base::tryCatch(...)
 14. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15. │             ├─base (local) tryCatchOne(...)
 16. │             │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17. │             └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 18. │               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 19. │                 └─value[[3L]](cond)
 20. ├─bdc:::bdc_reword_countries(.)
 21. │ └─data %>% ...
 22. └─dplyr::mutate(., name_long = dplyr::recode(name_long, !!!vec_reword))
── Error ('test-bdc_country_from_coordinates.R:46:3'): return country names when all contry names is missing ──
Error in `value[[3L]](cond)`: Failed to install the rnaturalearthhires package.
  Please try installing the package for yourself using the following command: 
     devtools::install_github("ropensci/rnaturalearthhires")
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test-bdc_country_from_coordinates.R:46:3
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. ├─bdc::bdc_country_from_coordinates(...)
  8. │ ├─... %>% bdc_reword_countries()
  9. │ └─rnaturalearth::ne_countries(scale = "large", returnclass = "sf")
 10. │   └─rnaturalearth:::get_data(scale = scale, type = type)
 11. │     └─rnaturalearth::check_rnaturalearthhires()
 12. │       └─rnaturalearth::install_rnaturalearthhires()
 13. │         └─base::tryCatch(...)
 14. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15. │             ├─base (local) tryCatchOne(...)
 16. │             │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17. │             └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 18. │               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 19. │                 └─value[[3L]](cond)
 20. ├─bdc:::bdc_reword_countries(.)
 21. │ └─data %>% ...
 22. └─dplyr::mutate(., name_long = dplyr::recode(name_long, !!!vec_reword))
── Error ('test-bdc_country_from_coordinates.R:69:1'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: Failed to install the rnaturalearthhires package.
  Please try installing the package for yourself using the following command: 
     devtools::install_github("ropensci/rnaturalearthhires")
Backtrace:
     ▆
  1. ├─bdc::bdc_country_from_coordinates(data) at test-bdc_country_from_coordinates.R:69:1
  2. │ ├─... %>% bdc_reword_countries()
  3. │ └─rnaturalearth::ne_countries(scale = "large", returnclass = "sf")
  4. │   └─rnaturalearth:::get_data(scale = scale, type = type)
  5. │     └─rnaturalearth::check_rnaturalearthhires()
  6. │       └─rnaturalearth::install_rnaturalearthhires()
  7. │         └─base::tryCatch(...)
  8. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │             ├─base (local) tryCatchOne(...)
 10. │             │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11. │             └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 12. │               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13. │                 └─value[[3L]](cond)
 14. ├─bdc:::bdc_reword_countries(.)
 15. │ └─data %>% ...
 16. └─dplyr::mutate(., name_long = dplyr::recode(name_long, !!!vec_reword))
── Error ('test-bdc_create_dir.R:2:1'): (code run outside of `test_that()`) ────
<ENOENT/fs_error/error/condition>
Error: [ENOENT] Failed to make directory 'D:/RCompile/Output/Check': no such file or directory
Backtrace:
    ▆
 1. └─bdc:::bdc_create_dir() at test-bdc_create_dir.R:2:1
 2.   └─fs::dir_create(here::here("Output/Check"))
── Error ('test-bdc_create_figures.R:21:1'): (code run outside of `test_that()`) ──
Error: Package `rworldmap` needed for this function to work! Please, install it with: `install.packages("rworldmap")`
Backtrace:
    ▆
 1. └─bdc::bdc_create_figures(...) at test-bdc_create_figures.R:21:1
 2.   ├─base::suppressWarnings(...)
 3.   │ └─base::withCallingHandlers(...)
 4.   └─bdc:::check_require_cran("rworldmap")
── Error ('test-bdc_get_world_map.R:3:1'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: Failed to install the rnaturalearthhires package.
  Please try installing the package for yourself using the following command: 
     devtools::install_github("ropensci/rnaturalearthhires")
Backtrace:
     ▆
  1. ├─bdc:::bdc_get_world_map() at test-bdc_get_world_map.R:3:1
  2. │ ├─base::suppressWarnings(...)
  3. │ │ └─base::withCallingHandlers(...)
  4. │ ├─... %>% sf::as_Spatial()
  5. │ └─rnaturalearth::ne_countries(scale = "large", returnclass = "sf")
  6. │   └─rnaturalearth:::get_data(scale = scale, type = type)
  7. │     └─rnaturalearth::check_rnaturalearthhires()
  8. │       └─rnaturalearth::install_rnaturalearthhires()
  9. │         └─base::tryCatch(...)
 10. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11. │             ├─base (local) tryCatchOne(...)
 12. │             │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 13. │             └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 14. │               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15. │                 └─value[[3L]](cond)
 16. ├─sf::as_Spatial(.)
 17. ├─dplyr::select(., name_long, iso2c, geometry)
 18. ├─dplyr::mutate(...)
 19. ├─dplyr::left_join(., cntr_names, by = c(name_long = "english_name"))
 20. ├─bdc:::bdc_reword_countries(.)
 21. │ └─data %>% ...
 22. └─dplyr::mutate(., name_long = dplyr::recode(name_long, !!!vec_reword))
── Error ('test-bdc_standardize_country.R:6:1'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: Failed to install the rnaturalearthhires package.
  Please try installing the package for yourself using the following command: 
     devtools::install_github("ropensci/rnaturalearthhires")
Backtrace:
     ▆
  1. ├─bdc:::bdc_get_world_map() at test-bdc_standardize_country.R:6:1
  2. │ ├─base::suppressWarnings(...)
  3. │ │ └─base::withCallingHandlers(...)
  4. │ ├─... %>% sf::as_Spatial()
  5. │ └─rnaturalearth::ne_countries(scale = "large", returnclass = "sf")
  6. │   └─rnaturalearth:::get_data(scale = scale, type = type)
  7. │     └─rnaturalearth::check_rnaturalearthhires()
  8. │       └─rnaturalearth::install_rnaturalearthhires()
  9. │         └─base::tryCatch(...)
 10. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11. │             ├─base (local) tryCatchOne(...)
 12. │             │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 13. │             └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 14. │               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15. │                 └─value[[3L]](cond)
 16. ├─sf::as_Spatial(.)
 17. ├─dplyr::select(., name_long, iso2c, geometry)
 18. ├─dplyr::mutate(...)
 19. ├─dplyr::left_join(., cntr_names, by = c(name_long = "english_name"))
 20. ├─bdc:::bdc_reword_countries(.)
 21. │ └─data %>% ...
 22. └─dplyr::mutate(., name_long = dplyr::recode(name_long, !!!vec_reword))

[ FAIL 12 | WARN 0 | SKIP 5 | PASS 63 ]
Error: Test failures
Execution halted