CRAN Package Check Results for Maintainer ‘Jorge Mestre <jorge.mestre.tomas at csic.es>’

Last updated on 2025-12-04 09:50:25 CET.

Package	ERROR	NOTE	OK
DOYPAColors			13
GeoThinneR	1		12
glossa	1	2	10

Package DOYPAColors

Current CRAN status: OK: 13

Package GeoThinneR

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 2025-12-03 12:53:45 Thinning using method: distance Thinning process completed. Total execution time: 0.06 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

Package glossa

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") | | | 0% | |= | 2% | |=== | 4% | |==== | 6% | |====== | 8% | |======= | 10% | |======== | 12% | |========== | 14% | |=========== | 16% | |============= | 18% | |============== | 20% | |=============== | 22% | |================= | 24% | |================== | 26% | |==================== | 28% | |===================== | 30% | |====================== | 32% | |======================== | 34% | 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Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on 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