* using log directory 'd:/Rcompile/CRANpkg/local/4.6/glossa.Rcheck'
* using R Under development (unstable) (2025-05-03 r88188 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'glossa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'glossa' version '1.0.0'
* package encoding: UTF-8
* 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 whether package 'glossa' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 ... [2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s] OK
* checking whether the package can be unloaded cleanly ... [2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s] OK
* checking loading without being on the library search path ... [2s] 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 ... [8s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 examples ... [2s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [10s] ERROR
  Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(glossa)
  Loading required package: bs4Dash
  
  Attaching package: 'bs4Dash'
  
  The following object is masked from 'package:graphics':
  
      box
  
  Loading required package: shiny
  
  Attaching package: 'shiny'
  
  The following objects are masked from 'package:bs4Dash':
  
      actionButton, column, insertTab, navbarMenu, tabsetPanel
  
  > library(terra)
  terra 1.8.42
  
  Attaching package: 'terra'
  
  The following objects are masked from 'package:testthat':
  
      compare, describe
  
  > library(sf)
  Linking to GEOS 3.13.1, GDAL 3.10.2, PROJ 9.5.1; sf_use_s2() is TRUE
  > 
  > test_check("glossa")
  Spherical geometry (s2) switched off
  although coordinates are longitude/latitude, st_difference assumes that they
  are planar
  although coordinates are longitude/latitude, st_difference assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  although coordinates are longitude/latitude, st_intersects assumes that they
  are planar
  [ FAIL 2 | WARN 0 | SKIP 11 | PASS 43 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (11): 'test-glossa_analysis.R:5:3', 'test-process_layers.R:5:3',
    'test-process_polygon.R:5:3', 'test-read_validate_files.R:5:3',
    'test-read_validate_files.R:18:3', 'test-read_validate_files.R:30:3',
    'test-read_validate_files.R:42:3', 'test-read_validate_files.R:54:3',
    'test-read_validate_files.R:78:3', 'test-read_validate_files.R:104:3',
    'test-utils.R:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-process_presence_absence.R:31:3'): clean_coordinates removes close points based on decimal_digits ──
  Error in `GeoThinneR::thin_points(df, long_col = coords[1], lat_col = coords[2], 
      group_col = group_col, method = "precision", trials = 1, 
      all_trials = FALSE, seed = seed, precision = decimal_digits)`: Specified longitude or latitude columns do not exist in the data.
  Backtrace:
      ▆
   1. └─glossa::clean_coordinates(toy_data, study_area, decimal_digits = 0) at test-process_presence_absence.R:31:3
   2.   └─GeoThinneR::thin_points(...)
  ── Error ('test-process_presence_absence.R:62:3'): clean_coordinates is reproducible with seed ──
  Error in `GeoThinneR::thin_points(df, long_col = coords[1], lat_col = coords[2], 
      group_col = group_col, method = "precision", trials = 1, 
      all_trials = FALSE, seed = seed, precision = decimal_digits)`: Specified longitude or latitude columns do not exist in the data.
  Backtrace:
      ▆
   1. └─glossa::clean_coordinates(...) at test-process_presence_absence.R:62:3
   2.   └─GeoThinneR::thin_points(...)
  
  [ FAIL 2 | WARN 0 | SKIP 11 | PASS 43 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [6s] OK
* DONE
Status: 1 ERROR