CRAN Package Check Results for Package glossa

Last updated on 2025-12-04 09:49:54 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.2.4	17.20	149.15	166.35	OK
r-devel-linux-x86_64-debian-gcc	1.2.4	10.41	103.58	113.99	OK
r-devel-linux-x86_64-fedora-clang	1.2.4	35.00	220.80	255.80	OK
r-devel-linux-x86_64-fedora-gcc	1.2.4	82.00	190.96	272.96	OK
r-devel-windows-x86_64	1.2.4	17.00	144.00	161.00	OK
r-patched-linux-x86_64	1.2.4	16.23	142.39	158.62	OK
r-release-linux-x86_64	1.2.4	15.75	140.96	156.71	OK
r-release-macos-arm64	1.2.4				OK
r-release-macos-x86_64	1.2.4	16.00	128.00	144.00	OK
r-release-windows-x86_64	1.2.4	20.00	142.00	162.00	OK
r-oldrel-macos-arm64	1.2.4				NOTE
r-oldrel-macos-x86_64	1.2.4	15.00	126.00	141.00	NOTE
r-oldrel-windows-x86_64	1.2.4	25.00	188.00	213.00	ERROR

Check Details

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% | |========================= | 36% | |=========================== | 38% | |============================ | 40% | |============================= | 42% | |=============================== | 44% | |================================ | 46% | |================================== | 48% | |=================================== | 50% | |==================================== | 52% | |====================================== | 54% | |======================================= | 56% | |========================================= | 58% | |========================================== | 60% | |=========================================== | 62% | |============================================= | 64% | |============================================== | 66% | |================================================ | 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 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% | |===================== | 30% | |====================== | 32% | |======================== | 34% | |========================= | 36% | |=========================== | 38% | |============================ | 40% | |============================= | 42% | |=============================== | 44% | |================================ | 46% | |================================== | 48% | |=================================== | 50% | |==================================== | 52% | |====================================== | 54% | |======================================= | 56% | |========================================= | 58% | |========================================== | 60% | |=========================================== | 62% | |============================================= | 64% | |============================================== | 66% | |================================================ | 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% | |===================== | 30% | |====================== | 32% | |======================== | 34% | |========================= | 36% | |=========================== | 38% | |============================ | 40% | |============================= | 42% | |=============================== | 44% | |================================ | 46% | |================================== | 48% | |=================================== | 50% | |==================================== | 52% | |====================================== | 54% | |======================================= | 56% | |========================================= | 58% | |========================================== | 60% | |=========================================== | 62% | |============================================= | 64% | |============================================== | 66% | |================================================ | 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 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