Last updated on 2025-12-03 05:50:49 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| DOYPAColors | 13 | ||
| GeoThinneR | 1 | 12 | |
| glossa | 1 | 2 | 10 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 2.1.0
Check: examples
Result: ERROR
Running examples in 'GeoThinneR-Ex.R' failed
The error most likely occurred in:
> ### Name: grid_thinning
> ### Title: Perform Grid-Based Thinning of Spatial Points
> ### Aliases: grid_thinning
>
> ### ** Examples
>
> # Example: Grid thinning using thin_dist
> coords <- matrix(c(-122.4194, 37.7749,
+ -122.4195, 37.7740,
+ -122.4196, 37.7741), ncol = 2, byrow = TRUE)
>
> result <- grid_thinning(coords, thin_dist = 10, trials = 5, all_trials = TRUE)
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 2.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [15s]
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(GeoThinneR)
>
> test_check("GeoThinneR")
Saving _problems/test-grid_thinning-8.R
Saving _problems/test-grid_thinning-15.R
terra 1.8.86
Attaching package: 'terra'
The following objects are masked from 'package:testthat':
compare, describe
Saving _problems/test-grid_thinning-32.R
Saving _problems/test-grid_thinning-39.R
Saving _problems/test-grid_thinning-56.R
Starting spatial thinning at 2025-12-02 00:31:22
Thinning using method: distance
Thinning process completed.
Total execution time: 0.07 seconds
Saving _problems/test-thin_points-46.R
[ FAIL 6 | WARN 6 | SKIP 0 | PASS 99 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-grid_thinning.R:8:3'): grid_thinning works with thin_dist ──────
Error: [rast] empty srs
Backtrace:
▆
1. └─GeoThinneR::grid_thinning(...) at test-grid_thinning.R:8:3
2. ├─terra::rast(...)
3. └─terra::rast(...)
4. └─terra (local) .local(x = x, ...)
5. └─terra:::new_rast(...)
6. └─terra:::messages(r, "rast")
7. └─terra:::error(f, x@pntr$getError())
── Error ('test-grid_thinning.R:15:3'): grid_thinning works with resolution ────
Error: [rast] empty srs
Backtrace:
▆
1. └─GeoThinneR::grid_thinning(...) at test-grid_thinning.R:15:3
2. ├─terra::rast(...)
3. └─terra::rast(...)
4. └─terra (local) .local(x = x, ...)
5. └─terra:::new_rast(...)
6. └─terra:::messages(r, "rast")
7. └─terra:::error(f, x@pntr$getError())
── Error ('test-grid_thinning.R:32:3'): grid_thinning returns multiple trials when all_trials = TRUE ──
Error: [rast] empty srs
Backtrace:
▆
1. └─GeoThinneR::grid_thinning(...) at test-grid_thinning.R:32:3
2. ├─terra::rast(...)
3. └─terra::rast(...)
4. └─terra (local) .local(x = x, ...)
5. └─terra:::new_rast(...)
6. └─terra:::messages(r, "rast")
7. └─terra:::error(f, x@pntr$getError())
── Error ('test-grid_thinning.R:39:3'): grid_thinning works with priority ──────
Error: [rast] empty srs
Backtrace:
▆
1. └─GeoThinneR::grid_thinning(...) at test-grid_thinning.R:39:3
2. ├─terra::rast(...)
3. └─terra::rast(...)
4. └─terra (local) .local(x = x, ...)
5. └─terra:::new_rast(...)
6. └─terra:::messages(r, "rast")
7. └─terra:::error(f, x@pntr$getError())
── Error ('test-grid_thinning.R:56:3'): grid_thinning invalid input ────────────
Error: [rast] empty srs
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-grid_thinning.R:56:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─GeoThinneR::grid_thinning(...)
8. ├─terra::rast(...)
9. └─terra::rast(...)
10. └─terra (local) .local(x = x, ...)
11. └─terra:::new_rast(...)
12. └─terra:::messages(r, "rast")
13. └─terra:::error(f, x@pntr$getError())
── Error ('test-thin_points.R:46:3'): thin_points works with grid thinning ─────
Error: [rast] empty srs
Backtrace:
▆
1. └─GeoThinneR::thin_points(...) at test-thin_points.R:46:3
2. └─GeoThinneR (local) perform_thinning(data)
3. └─GeoThinneR::grid_thinning(...)
4. ├─terra::rast(...)
5. └─terra::rast(...)
6. └─terra (local) .local(x = x, ...)
7. └─terra:::new_rast(...)
8. └─terra:::messages(r, "rast")
9. └─terra:::error(f, x@pntr$getError())
[ FAIL 6 | WARN 6 | SKIP 0 | PASS 99 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 2.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'GeoThinneR.Rmd' using rmarkdown
Quitting from GeoThinneR.Rmd:308-322 [unnamed-chunk-17]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! [rast] empty srs
---
Backtrace:
▆
1. ├─base::system.time(...)
2. └─GeoThinneR::thin_points(...)
3. └─GeoThinneR (local) perform_thinning(data)
4. └─GeoThinneR::grid_thinning(...)
5. ├─terra::rast(...)
6. └─terra::rast(...)
7. └─terra (local) .local(x = x, ...)
8. └─terra:::new_rast(...)
9. └─terra:::messages(r, "rast")
10. └─terra:::error(f, x@pntr$getError())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GeoThinneR.Rmd' failed with diagnostics:
[rast] empty srs
--- failed re-building 'GeoThinneR.Rmd'
SUMMARY: processing the following file failed:
'GeoThinneR.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-x86_64
Current CRAN status: ERROR: 1, NOTE: 2, OK: 10
Version: 1.2.4
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘flexsdm’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [34s]
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 3.13.0, GDAL 3.10.1, PROJ 9.5.1; sf_use_s2() is TRUE
>
> test_check("glossa")
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Saving _problems/test-process_layers-18.R
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
Saving _problems/test-read_validate_files-88.R
Saving _problems/test-read_validate_files-93.R
Saving _problems/test-read_validate_files-114.R
Saving _problems/test-utils-38.R
[ FAIL 6 | WARN 11 | SKIP 12 | PASS 84 ]
══ 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_layers.R:18:1'): (code run outside of `test_that()`) ───
Error: [rast] empty srs
Backtrace:
▆
1. ├─terra::rast(raster_data, ext = c(-123, -121, 36, 38), crs = "epsg:4326") at test-process_layers.R:18:1
2. └─terra::rast(raster_data, ext = c(-123, -121, 36, 38), crs = "epsg:4326")
3. └─terra (local) .local(x, ...)
4. ├─terra::rast(nrows = nrow(x), ncols = ncol(x), crs = crs, extent = extent)
5. └─terra::rast(nrows = nrow(x), ncols = ncol(x), crs = crs, extent = extent)
6. └─terra (local) .local(x = x, ...)
7. └─terra:::new_rast(...)
8. └─terra:::messages(r, "rast")
9. └─terra:::error(f, x@pntr$getError())
── Error ('test-process_presence_absence.R:100:3'): Grid thinning reduces to one per cell ──
Error: [rast] empty srs
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. ├─terra::rast(...)
6. └─terra::rast(...)
7. └─terra (local) .local(x = x, ...)
8. └─terra:::new_rast(...)
9. └─terra:::messages(r, "rast")
10. └─terra:::error(f, x@pntr$getError())
── Error ('test-read_validate_files.R:88:3'): read_layers_zip loads layers correctly ──
Error: [project] cannot get output boundaries for the target crs
Backtrace:
▆
1. └─glossa::read_layers_zip(fit_layers, extend = TRUE, first_layer = TRUE) at test-read_validate_files.R:88:3
2. └─base::lapply(layers, function(x) terra::project(x, "epsg:4326"))
3. └─glossa (local) FUN(X[[i]], ...)
4. ├─terra::project(x, "epsg:4326")
5. └─terra::project(x, "epsg:4326")
6. └─terra (local) .local(x, ...)
7. └─terra:::messages(x, "project")
8. └─terra:::error(f, x@pntr$getError())
── Error ('test-read_validate_files.R:93:3'): read_layers_zip loads layers correctly ──
Error: [project] cannot get output boundaries for the target crs
Backtrace:
▆
1. └─glossa::read_layers_zip(fit_layers, extend = FALSE, first_layer = FALSE) at test-read_validate_files.R:93:3
2. └─base::lapply(layers, function(x) terra::project(x, "epsg:4326"))
3. └─glossa (local) FUN(X[[i]], ...)
4. ├─terra::project(x, "epsg:4326")
5. └─terra::project(x, "epsg:4326")
6. └─terra (local) .local(x, ...)
7. └─terra:::messages(x, "project")
8. └─terra:::error(f, x@pntr$getError())
── Error ('test-read_validate_files.R:114:3'): validate_layers_zip validates layers correctly ──
Error: [project] cannot get output boundaries for the target crs
Backtrace:
▆
1. ├─base::suppressWarnings(validate_layers_zip(fit_layers)) at test-read_validate_files.R:114:3
2. │ └─base::withCallingHandlers(...)
3. └─glossa::validate_layers_zip(fit_layers)
4. └─base::lapply(layers, function(layer) terra::project(layer, "epsg:4326"))
5. └─glossa (local) FUN(X[[i]], ...)
6. ├─terra::project(layer, "epsg:4326")
7. └─terra::project(layer, "epsg:4326")
8. └─terra (local) .local(x, ...)
9. └─terra:::messages(x, "project")
10. └─terra:::error(f, x@pntr$getError())
── Error ('test-utils.R:38:3'): create_coords_layer generates correct coordinate layers ──
Error: [rast] empty srs
Backtrace:
▆
1. ├─terra::rast(...) at test-utils.R:38:3
2. └─terra::rast(...)
3. └─terra (local) .local(x = x, ...)
4. └─terra:::new_rast(...)
5. └─terra:::messages(r, "rast")
6. └─terra:::error(f, x@pntr$getError())
[ FAIL 6 | WARN 11 | SKIP 12 | PASS 84 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64