- using R Under development (unstable) (2025-02-14 r87718 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 'wallace/DESCRIPTION' ... OK
- this is package 'wallace' version '2.1.3'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- 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 'wallace' can be installed ... OK
See the install log for details.
- 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 ... [1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s] OK
- checking whether the package can be unloaded cleanly ... [1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s] OK
- checking loading without being on the library search path ... [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 ... [6s] 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 ... [6s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [164s] ERROR
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> Sys.setenv("R_TEST" = "")
> library(testthat)
> library(wallace)
Loading required package: shiny
Loading required package: leaflet
>
> test_check("wallace")
trying URL 'https://www.dropbox.com/sh/kijh17ehg8v3uv8/AADWJOs0_8zQmhc0XJxJE9a2a/bio%20%23baseline_Modern%281950-1999%29%23%20CCSM_LGM%2821ka%29.txt?dl=1'
Content type 'application/binary' length 86163749 bytes (82.2 MB)
==================================================
downloaded 82.2 MB
trying URL 'https://geodata.ucdavis.edu/climate/worldclim/2_1/base/wc2.1_10m_bio.zip'
Content type 'application/zip' length 49869449 bytes (47.6 MB)
==================================================
downloaded 47.6 MB
Reading layer `Bassaricyon_neblina' from data source
`D:\RCompile\CRANpkg\lib\4.5\wallace\extdata\shp\Bassaricyon_neblina.shp'
using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 1 field
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -79.47486 ymin: -1.15418 xmax: -74.50839 ymax: 6.83333
CRS: NA
Reading layer `Bassaricyon_neblina' from data source
`D:\RCompile\CRANpkg\lib\4.5\wallace\extdata\shp\Bassaricyon_neblina.shp'
using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 1 field
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -79.47486 ymin: -1.15418 xmax: -74.50839 ymax: 6.83333
CRS: NA
Reading layer `Bassaricyon_neblina' from data source
`D:\RCompile\CRANpkg\lib\4.5\wallace\extdata\shp\Bassaricyon_neblina.shp'
using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 1 field
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -79.47486 ymin: -1.15418 xmax: -74.50839 ymax: 6.83333
CRS: NA
Reading layer `Bassaricyon_neblina' from data source
`D:\RCompile\CRANpkg\lib\4.5\wallace\extdata\shp\Bassaricyon_neblina.shp'
using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 1 field
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -79.47486 ymin: -1.15418 xmax: -74.50839 ymax: 6.83333
CRS: NA
Reading layer `Bassaricyon_neblina' from data source
`D:\RCompile\CRANpkg\lib\4.5\wallace\extdata\shp\Bassaricyon_neblina.shp'
using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 1 field
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -79.47486 ymin: -1.15418 xmax: -74.50839 ymax: 6.83333
CRS: NA
Reading layer `Bassaricyon_neblina' from data source
`D:\RCompile\CRANpkg\lib\4.5\wallace\extdata\shp\Bassaricyon_neblina.shp'
using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 1 field
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -79.47486 ymin: -1.15418 xmax: -74.50839 ymax: 6.83333
CRS: NA
[ FAIL 4 | WARN 1 | SKIP 5 | PASS 192 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (5): 'test_envs_ecoClimate.R:23:3', 'test_envs_ecoClimate.R:46:3',
'test_envs_worldclim.R:27:3', 'test_occs_queryDb.R:85:3',
'test_occs_queryDb.R:85:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_model_bioclim.R:17:1'): (code run outside of `test_that()`) ────
Error in `ENMeval::ENMevaluate(occs = occs.xy, envs = bgMsk, bg = bg.xy,
algorithm = "bioclim", partitions = "user", user.grp = user.grp)`: From this version of ENMeval, the package will only use "terra" raster data types. Please convert from "raster" to "terra" with terra::rast(r), where r is a RasterStack.
Backtrace:
▆
1. └─wallace::model_bioclim(occs, bg, partblock, envs) at test_model_bioclim.R:17:1
2. ├─wallace::smartProgress(...)
3. └─ENMeval::ENMevaluate(...)
── Error ('test_model_maxent.R:49:3'): (code run outside of `test_that()`) ─────
Error in `ENMeval::ENMevaluate(occs = as.data.frame(occs.xy), bg = as.data.frame(bg.xy),
partitions = "user", user.grp = user.grp, envs = bgMsk, tune.args = tune.args,
doClamp = clampSel, algorithm = algMaxent, categoricals = catEnvs,
parallel = parallel, numCores = numCores, parallelType = "doSNOW",
updateProgress = updateProgress, quiet = FALSE)`: unused argument (parallelType = "doSNOW")
Backtrace:
▆
1. └─wallace::model_maxent(...) at test_model_maxent.R:49:3
── Error ('test_part_partitionOccs.R:45:1'): (code run outside of `test_that()`) ──
Error: [spatSample] not yet implemented for these strata
Backtrace:
▆
1. └─wallace::part_partitionOccs(...) at test_part_partitionOccs.R:45:1
2. ├─wallace::smartProgress(...)
3. └─ENMeval::get.checkerboard1(occs.xy, bgMask, bg.xy, aggFact)
4. └─ENMeval::get.checkerboard(...)
5. ├─terra::spatSample(...)
6. └─terra::spatSample(...)
7. └─terra (local) .local(x, ...)
8. └─terra:::error("spatSample", "not yet implemented for these strata")
── Error ('test_vis_bioclimPlot.R:19:1'): (code run outside of `test_that()`) ──
Error in `ENMeval::ENMevaluate(occs = occs.xy, envs = bgMsk, bg = bg.xy,
algorithm = "bioclim", partitions = "user", user.grp = user.grp)`: From this version of ENMeval, the package will only use "terra" raster data types. Please convert from "raster" to "terra" with terra::rast(r), where r is a RasterStack.
Backtrace:
▆
1. └─wallace::model_bioclim(occs, bg, partblock, envs) at test_vis_bioclimPlot.R:19:1
2. ├─wallace::smartProgress(...)
3. └─ENMeval::ENMevaluate(...)
[ FAIL 4 | WARN 1 | SKIP 5 | PASS 192 ]
Error: Test failures
Execution halted
- checking PDF version of manual ... [21s] OK
- checking HTML version of manual ... [8s] OK
- DONE
Status: 1 ERROR