* using log directory ‘/home/hornik/tmp/CRAN_pretest/b3gbi.Rcheck’ * using R Under development (unstable) (2026-10-09 r90656) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 23.1.0 (2) Debian flang version 23.1.0 (2) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-10-10 21:23:20 UTC * checking for file ‘b3gbi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘b3gbi’ version ‘1.1.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/9s] NOTE Maintainer: ‘Shawn Dove ’ New submission Possibly misspelled words in DESCRIPTION: EEA (22:9) EQDGC (22:69) ISEA (23:5) MGRS (22:29) Suggests or Enhances not in mainstream repositories: dubicube, rnaturalearthhires Availability using Additional_repositories specification: dubicube yes https://b-cubed-eu.r-universe.dev rnaturalearthhires yes https://ropensci.r-universe.dev * checking package namespace information ... OK * checking package dependencies ... INFO Packages suggested but not available for checking: 'dubicube', 'rnaturalearthhires' * 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 ‘b3gbi’ can be installed ... [7s/7s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [13s/13s] OK * checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [6s/6s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [73s/73s] ERROR Running ‘testthat.R’ [73s/73s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(b3gbi) > > test_check("b3gbi") ATTENTION: User-provided cell_size (0.3degrees) is smaller than the recommended minimum based on 1e+06 total cells (1degrees). This may result in a large output and long processing time. Automatically determined grid cell size of 1 km would be smaller than the grid cells of the cube. Therefore, setting cell_size to 10 km to match cube resolution. ATTENTION: User-provided cell_size (1km) is smaller than the recommended minimum based on 1e+06 total cells (32km). This may result in a large output and long processing time. Setting cell_size to match data resolution (1km). This is smaller than the recommended minimum based on 1e+06 total cells (10km). This may result in a large output and long processing time. Consider using 'auto' or manually setting a larger size. Setting cell_size to match data resolution (1km). This is smaller than the recommended minimum based on 1e+06 total cells (10km). This may result in a large output and long processing time. Consider using 'auto' or manually setting a larger size. Setting cell_size to match data resolution (1km). This is smaller than the recommended minimum based on 1e+06 total cells (10km). This may result in a large output and long processing time. Consider using 'auto' or manually setting a larger size. Setting cell_size to match data resolution (1km). This is smaller than the recommended minimum based on 1e+06 total cells (10km). This may result in a large output and long processing time. Consider using 'auto' or manually setting a larger size. Writing layer `file3f22e6b78d6f7' to data source `/tmp/RtmpqlMPzl/working_dir/RtmpNKf4Iz/file3f22e6b78d6f7.shp' using driver `ESRI Shapefile' Writing 1 features with 0 fields and geometry type Polygon. Writing layer `file3f22e1ba5d973' to data source `/tmp/RtmpqlMPzl/working_dir/RtmpNKf4Iz/file3f22e1ba5d973.shp' using driver `ESRI Shapefile' Writing 1 features with 0 fields and geometry type Polygon. Linking to GEOS 3.15.0, GDAL 3.13.3, PROJ 9.8.1; sf_use_s2() is TRUE Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Package 'dubicube' is not installed, so confidence intervals are calculated by indicator-level bootstrapping. i For cube-level bootstrapping, install 'dubicube' with install.packages("dubicube", repos = c("https://b-cubed-eu.r-universe.dev", "https://cloud.r-project.org")) This message is displayed once per session. [1] "All values of t are equal to 4 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 3 \n Cannot calculate confidence intervals" Saving _problems/test-hex-grids-304.R [1] "All values of t are equal to 2 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 2 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 3 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 2 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 2 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 2 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 4 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 3 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 2 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 2 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 5 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 4 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 3 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 5 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 15 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 10 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 20 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 5 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 15 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 10 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 20 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" [1] "All values of t are equal to 1 \n Cannot calculate confidence intervals" Retrying intersection with S2 disabled... although coordinates are longitude/latitude, st_intersects assumes that they are planar Optimized intersection failed or returned empty. Falling back to st_filter. although coordinates are longitude/latitude, st_intersects assumes that they are planar Retrying intersection with S2 disabled... although coordinates are longitude/latitude, st_intersects assumes that they are planar although coordinates are longitude/latitude, st_within assumes that they are planar although coordinates are longitude/latitude, st_intersection assumes that they are planar although coordinates are longitude/latitude, st_intersection assumes that they are planar although coordinates are longitude/latitude, st_intersection assumes that they are planar although coordinates are longitude/latitude, st_intersection assumes that they are planar although coordinates are longitude/latitude, st_intersection assumes that they are planar although coordinates are longitude/latitude, st_intersection assumes that they are planar Removed 5 rows with missing cell codes Replaced 2 NA values with zeroes. Replaced 2 NA values with zeroes. Gridded completeness returned no results. Try lowering 'cutoff_length' or using a coarser grid. [1] "All values of t are equal to 2000 \n Cannot calculate confidence intervals" although coordinates are longitude/latitude, st_intersection assumes that they are planar [ FAIL 1 | WARN 0 | SKIP 49 | PASS 1548 ] ══ Skipped tests (49) ══════════════════════════════════════════════════════════ • On CRAN (39): 'test-add_NE_layer.R:80:3', 'test-audit-ci.R:28:3', 'test-audit-ci.R:49:3', 'test-audit-ci.R:71:3', 'test-audit-occ-density-ci.R:2:3', 'test-audit-wrappers-gridded-completeness.R:2:3', 'test-audit-wrappers-gridded-completeness.R:26:3', 'test-completeness.R:14:3', 'test-completeness.R:37:3', 'test-completeness.R:59:3', 'test-completeness.R:74:3', 'test-completeness.R:86:3', 'test-completeness.R:101:3', 'test-create_grid.R:29:3', 'test-get_NE_data.R:2:3', 'test-gridded-completeness.R:5:3', 'test-hex-grids.R:310:3', 'test-indicator_wrappers.R:1088:3', 'test-indicator_wrappers.R:1102:3', 'test-indicator_wrappers.R:1110:3', 'test-integration_add_ci.R:27:3', 'test-plot_methods.R:403:3', 'test-plot_methods.R:860:3', 'test-relative_occupancy.R:11:3', 'test-relative_occupancy.R:24:3', 'test-relative_occupancy.R:37:3', 'test-relative_occupancy.R:51:3', 'test-relative_occupancy.R:68:3', 'test-relative_occupancy.R:81:3', 'test-relative_occupancy.R:96:3', 'test-relative_occupancy.R:111:3', 'test-relative_occupancy.R:126:3', 'test-relative_occupancy.R:141:3', 'test-relative_occupancy.R:155:3', 'test-tax_distinct.R:288:3', 'test-workflow-clipping.R:5:3', 'test-workflow-clipping.R:39:3', 'test-workflow-clipping.R:58:3', 'test-workflow-clipping.R:83:3' • PROJ cannot round-trip all ISEA3H cells to EPSG:3857 on this system (1): 'test-hex-grids.R:260:3' • empty test (1): 'test-coverage_boost.R:73:1' • {dubicube} is not installed (5): 'test-add_ci.R:81:3', 'test-add_ci.R:132:3', 'test-add_ci.R:198:3', 'test-add_ci_dubicube_optional.R:59:3', 'test-calc_ts_dispatch.R:7:1' • {rnaturalearthhires} is not installed (3): 'test-add_NE_layer.R:118:3', 'test-add_NE_layer.R:148:3', 'test-add_NE_layer.R:197:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-hex-grids.R:304:3'): obs_richness_map with isea3h uses native R fallback correctly ── Error in `intersect_grid_with_polygon(grid, intersection_target)`: No spatial intersection between map data and grid. Backtrace: ▆ 1. ├─base::suppressWarnings(suppressMessages(obs_richness_map(mock_cube))) at test-hex-grids.R:304:3 2. │ └─base::withCallingHandlers(...) 3. ├─base::suppressMessages(obs_richness_map(mock_cube)) 4. │ └─base::withCallingHandlers(...) 5. └─b3gbi::obs_richness_map(mock_cube) 6. └─b3gbi::compute_indicator_workflow(...) 7. └─b3gbi:::intersect_grid_with_polygon(grid, intersection_target) [ FAIL 1 | WARN 0 | SKIP 49 | PASS 1548 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [11s/11s] OK * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE