* using log directory 'd:/RCompile/CRANincoming/R-devel/bdc.Rcheck' * using R Under development (unstable) (2024-11-27 r87386 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'bdc/DESCRIPTION' ... OK * this is package 'bdc' version '1.1.5' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [11s] NOTE Maintainer: 'Bruno Ribeiro ' Package has a VignetteBuilder field but no prebuilt vignette index. * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'bdc' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [22s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': 'articles/integrate_datasets.Rmd' 'articles/prefilter.Rmd' 'articles/space.Rmd' 'articles/taxonomy.Rmd' 'articles/time.Rmd' 'help/installing_gnparser.Rmd' 'images/map_summary_space_vignette.png' 'images/prefilter_.coordinates_country_inconsistent_MAP.png' 'images/prefilter_summary_all_tests_BAR.png' 'images/space_.rou_BAR.png' 'images/space_.urb_MAP.png' 'images/space_summary_all_tests_BAR.png' 'images/time_.eventDate_empty_BAR.png' 'images/time_.summary_BAR.png' 'images/time_summary_all_tests_BAR.png' 'images/time_year_BAR.png' * checking examples ... [11s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ERROR Running 'testthat.R' Running the tests in 'tests/testthat.R' failed. Complete output: > 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. 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: 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 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. 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 1 | WARN 0 | SKIP 12 | PASS 60 ] ══ Skipped tests (12) ══════════════════════════════════════════════════════════ • On CRAN (12): 'test-bdc_clean_names.R:2:1', 'test-bdc_coordinates_country_inconsistent.R:2:1', 'test-bdc_coordinates_transposed.R:2:1', 'test-bdc_correct_coordinates.R:2:1', 'test-bdc_country_from_coordinates.R:2:1', 'test-bdc_create_figures.R:2:1', 'test-bdc_filter_name.R:2:1', 'test-bdc_get_world_map.R:2:1', 'test-bdc_query_names_taxadb.R:2:1', 'test-bdc_standardize_country.R:2:1', 'test-bdc_standardize_datasets.R:180:1', 'test-bdc_suggest_names_taxadb.R:2:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-bdc_create_dir.R:2:1'): (code run outside of `test_that()`) ──── 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")) [ FAIL 1 | WARN 0 | SKIP 12 | PASS 60 ] Error: Test failures Execution halted * checking package vignettes ... NOTE Package has 'vignettes' subdirectory but apparently no vignettes. Perhaps the 'VignetteBuilder' information is missing from the DESCRIPTION file? * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 2 NOTEs