* using log directory 'd:/Rcompile/CRANpkg/local/4.4/glossa.Rcheck' * using R version 4.4.3 (2025-02-28 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * 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 package namespace information ... OK * checking package dependencies ... NOTE 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'glossa' can be installed ... OK * checking installed package size ... OK * checking package 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 ... [5s] OK * checking whether the package can be loaded with stated dependencies ... [5s] OK * checking whether the package can be unloaded cleanly ... [4s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s] OK * checking whether the namespace can be unloaded cleanly ... [4s] OK * checking loading without being on the library search path ... [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 ... [17s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... 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 ... [5s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [34s] 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 * checking PDF version of manual ... [18s] OK * checking HTML version of manual ... [8s] OK * DONE Status: 1 ERROR, 1 NOTE