• using R version 4.5.0 (2025-04-11)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• 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
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• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘glossa’ can be installed ... OK See the install log for details.
• 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
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• checking dependencies in R code ... OK
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• checking R code for possible problems ... [15s/21s] OK
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• checking for missing documentation entries ... OK
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• checking for unstated dependencies in examples ... OK
• checking examples ... [2s/3s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [12s/15s] ERROR   Running ‘testthat.R’ [12s/15s] 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 3.10.3, PROJ 9.6.0; 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 ... [5s/7s] OK
• checking HTML version of manual ... [1s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR