• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘glossa/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘glossa’ version ‘1.2.4’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘flexsdm’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• 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
• checking whether the package can be loaded ... [4s/6s] OK
• checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
• checking whether the package can be unloaded cleanly ... [4s/4s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
• checking loading without being on the library search path ... [4s/5s] 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 ... [28s/35s] OK
• checking Rd files ... [1s/1s] 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 examples ... [4s/6s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [26s/31s] ERROR   Running ‘testthat.R’ [26s/31s] 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 1.8.86      Attaching package: 'terra'      The following objects are masked from 'package:testthat':          compare, describe      > library(sf)   Linking to GEOS 3.14.1, GDAL 3.12.0, PROJ 9.7.1; sf_use_s2() is TRUE   >   > test_check("glossa")        |     | | 0%     |     |= | 2%     |     |=== | 4%     |     |==== | 6%     |     |====== | 8%     |     |======= | 10%     |     |======== | 12%     |     |========== | 14%     |     |=========== | 16%     |     |============= | 18%     |     |============== | 20%     |     |=============== | 22%     |     |================= | 24%     |     |================== | 26%     |     |==================== | 28%     |     |===================== | 30%     |     |====================== | 32%     |     |======================== | 34%     |     |========================= | 36%     |     |=========================== | 38%     |     |============================ | 40%     |     |============================= | 42%     |     |=============================== | 44%     |     |================================ | 46%     |     |================================== | 48%     |     |=================================== | 50%     |     |==================================== | 52%     |     |====================================== | 54%     |     |======================================= | 56%     |     |========================================= | 58%     |     |========================================== | 60%     |     |=========================================== | 62%     | 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    |     |================================================================ | 92%     |     |================================================================== | 94%     |     |=================================================================== | 96%     |     |===================================================================== | 98%     |     |======================================================================| 100%     train_0 train_1 test_0 test_1   1 4 3 15 28   2 15 28 4 3   Spherical geometry (s2) switched off   Spherical geometry (s2) switched on        |     | | 0%     |     |= | 2%     |     |=== | 4%     |     |==== | 6%     |     |====== | 8%     |     |======= | 10%     |     |======== | 12%     |     |========== | 14%     |     |=========== | 16%     |     |============= | 18%     |     |============== | 20%     |     |=============== | 22%     |     |================= | 24%     |     |================== | 26%     |     |==================== | 28%     | 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    |================================================ | 68%     |     |================================================= | 70%     |     |================================================== | 72%     |     |==================================================== | 74%     |     |===================================================== | 76%     |     |======================================================= | 78%     |     |======================================================== | 80%     |     |========================================================= | 82%     |     |=========================================================== | 84%     |     |============================================================ | 86%     |     |============================================================== | 88%     |     |=============================================================== | 90%     |     |================================================================ | 92%     |     |================================================================== | 94%     |     |=================================================================== | 96%     |     |===================================================================== | 98%     |     |======================================================================| 100%     train_0 train_1 test_0 test_1   1 9 16 10 15   2 10 15 9 16   Spherical geometry (s2) switched off   Spherical geometry (s2) switched on   Spherical geometry (s2) switched off   Spherical geometry (s2) switched on        |     | | 0%     |     |= | 2%     |     |=== | 4%     |     |==== | 6%     |     |====== | 8%     |     |======= | 10%     |     |======== | 12%     |     |========== | 14%     |     |=========== | 16%     |     |============= | 18%     |     |============== | 20%     |     |=============== | 22%     |     |================= | 24%     |     |================== | 26%     |     |==================== | 28%     | 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    |================================================ | 68%     |     |================================================= | 70%     |     |================================================== | 72%     |     |==================================================== | 74%     |     |===================================================== | 76%     |     |======================================================= | 78%     |     |======================================================== | 80%     |     |========================================================= | 82%     |     |=========================================================== | 84%     |     |============================================================ | 86%     |     |============================================================== | 88%     |     |=============================================================== | 90%     |     |================================================================ | 92%     |     |================================================================== | 94%     |     |=================================================================== | 96%     |     |===================================================================== | 98%     |     |======================================================================| 100%     train_0 train_1 test_0 test_1   1 9 11 5 5   2 9 10 5 6   3 10 11 4 5   Spherical geometry (s2) switched off   Spherical geometry (s2) switched on   Spherical geometry (s2) switched off   Spherical geometry (s2) switched on   dist is assumed to be in decimal degrees (arc_degrees).   dist is assumed to be in decimal degrees (arc_degrees).   although coordinates are longitude/latitude, st_difference assumes that they   are planar   although coordinates are longitude/latitude, st_difference assumes that they   are planar   Running thinning with method 'precision' and thinning value 1   Running thinning with method 'precision' and thinning value 1   Running thinning with method 'distance' and thinning value 5e+05   Running thinning with method 'grid' and thinning value 0.05   Saving _problems/test-process_presence_absence-100.R   Running thinning with method 'precision' and thinning value 3   [ FAIL 1 | WARN 0 | SKIP 12 | PASS 95 ]      ══ Skipped tests (12) ══════════════════════════════════════════════════════════   • 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'   • {flexsdm} is not installed (1): 'test-generate_pseudo_absences.R:98:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-process_presence_absence.R:100:3'): Grid thinning reduces to one per cell ──   Error in ``[.data.table`(keep_points_trial, , `:=`("rank_within_cell", seq_len(.N)), by = "grid_cell")`: attempt access index 3/3 in VECTOR_ELT   Backtrace:       ▆    1. └─glossa::clean_coordinates(...) at test-process_presence_absence.R:100:3    2. └─GeoThinneR::thin_points(...)    3. └─GeoThinneR (local) perform_thinning(group_data)    4. └─GeoThinneR::grid_thinning(...)    5. ├─keep_points_trial[, `:=`("rank_within_cell", seq_len(.N)), by = "grid_cell"]    6. └─data.table:::`[.data.table`(...)      [ FAIL 1 | WARN 0 | SKIP 12 | PASS 95 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [3s/4s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR