Last updated on 2025-03-06 01:51:25 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.3 | 6.59 | 211.94 | 218.53 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.1.3 | 4.76 | 147.31 | 152.07 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.3 | 279.76 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.3 | 249.00 | ERROR | |||
| r-devel-macos-arm64 | 2.1.3 | 93.00 | ERROR | |||
| r-devel-macos-x86_64 | 2.1.3 | 265.00 | OK | |||
| r-devel-windows-x86_64 | 2.1.3 | 12.00 | 243.00 | 255.00 | ERROR | |
| r-patched-linux-x86_64 | 2.1.3 | ERROR | ||||
| r-release-linux-x86_64 | 2.1.3 | 6.75 | 196.82 | 203.57 | ERROR | |
| r-release-macos-arm64 | 2.1.3 | 87.00 | ERROR | |||
| r-release-macos-x86_64 | 2.1.3 | 313.00 | OK | |||
| r-release-windows-x86_64 | 2.1.3 | 11.00 | 244.00 | 255.00 | ERROR | |
| r-oldrel-macos-arm64 | 2.1.3 | ERROR | ||||
| r-oldrel-macos-x86_64 | 2.1.3 | 286.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.1.3 | 13.00 | 307.00 | 320.00 | ERROR |
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [150s/199s]
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
`/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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 191 ]
══ 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 191 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [104s/131s]
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
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 191 ]
══ 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 191 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [177s/208s]
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
`/data/gannet/ripley/R/packages/tests-clang/wallace.Rcheck/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
`/data/gannet/ripley/R/packages/tests-clang/wallace.Rcheck/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
`/data/gannet/ripley/R/packages/tests-clang/wallace.Rcheck/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
`/data/gannet/ripley/R/packages/tests-clang/wallace.Rcheck/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
`/data/gannet/ripley/R/packages/tests-clang/wallace.Rcheck/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
`/data/gannet/ripley/R/packages/tests-clang/wallace.Rcheck/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 191 ]
══ 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 191 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [154s/180s]
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
`/data/gannet/ripley/R/packages/tests-devel/wallace.Rcheck/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
`/data/gannet/ripley/R/packages/tests-devel/wallace.Rcheck/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
`/data/gannet/ripley/R/packages/tests-devel/wallace.Rcheck/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
`/data/gannet/ripley/R/packages/tests-devel/wallace.Rcheck/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
`/data/gannet/ripley/R/packages/tests-devel/wallace.Rcheck/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
`/data/gannet/ripley/R/packages/tests-devel/wallace.Rcheck/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 191 ]
══ 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 191 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [47s/64s]
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
|
| | 0%
|
| | 0%
|
|================== | 25%
*** caught illegal operation ***
address 0x126d82f78, cause 'illegal trap'
Traceback:
1: rJava::.jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o", dirout, "-s", pfn, args))
2: .local(x, p, ...)
3: (new("standardGeneric", .Data = function (x, p, ...) standardGeneric("maxent"), generic = "maxent", package = "dismo", group = list(), valueClass = character(0), signature = c("x", "p"), default = NULL, skeleton = (function (x, p, ...) stop(gettextf("invalid call in method dispatch to '%s' (no default method)", "maxent"), domain = NA))(x, p, ...)))(x = list(bio05 = c(316, 319, 217, 325, 323, 327, 274, 321, 322, 323, 273, 306, 339, 325, 355, 321, 316, 243, 265, 333, 335, 276, 240, 307, 274, 300, 349, 325, 269, 298, 250, 315, 312, 306, 323, 327, 333, 324, 327, 318, 334, 349, 356, 318, 319, 329, 302, 326, 338, 293, 295, 323, 316, 319, 327, 321, 332, 315, 336, 336, 269, 317, 327, 182, 322, 332, 317, 313, 316, 333, 333, 323, 327, 328, 355, 286, 340, 325, 352, 323, 319, 141, 314, 327, 335, 311, 261, 331, 324, 314, 316, 316, 319, 328, 334, 335, 330, 311, 315, 307, 320, 313, 245, 315, 326, 329, 330, 317, 338, 327, 325, 345, 317, 256, 326, 323, 316, 319, 319, 358, 342, 350, 202, 290, 329, 325, 229, 313, 354, 341, 318, 321, 314, 314, 306, 292, 312, 172, 268, 284, 318, 315, 339, 197, 315, 318, 254, 294, 342, 308, 334, 328, 327, 332, 321, 329, 312, 331, 318, 234, 320, 339, 331, 331, 318, 304, 222, 314, 319, 337, 328, 316, 285, 323, 331, 209, 337, 344, 321, 319, 321, 204, 325, 329, 151, 219, 331, 350, 327, 343, 328, 314, 322, 332, 320, 330, 280, 353, 337, 318, 332, 287, 251, 312, 330, 330, 319, 281, 265, 231, 313, 272, 342, 316, 325, 317, 322, 319, 325, 311, 307, 269, 332, 321, 342, 321, 337, 317, 311, 357, 320, 299, 319, 175, 330, 341, 352, 252, 312, 354, 313, 322, 126, 342, 335, 322, 326, 328, 322, 335, 338, 322, 329, 325, 343, 324, 142, 247, 333, 321, 307, 316, 346, 346, 267, 316, 318, 316, 344, 309, 313, 321, 313, 331, 308, 328, 220, 206, 339, 334, 323, 184, 342, 332, 319, 327, 317, 274, 201, 330, 346, 323, 307, 340, 321, 358, 328, 148, 343, 331, 313, 321, 343, 327, 329, 321, 143, 321, 330, 146, 315, 341, 299, 306, 294, 264, 325, 340, 298, 310, 318, 327, 314, 233, 337, 341, 311, 300, 313, 308, 328, 262, 323, 202, 306, 320, 228, 314, 163, 350, 146, 327, 246, 331, 318, 323, 345, 314, 327, 328, 321, 155, 300, 262, 306, 312, 251, 330, 327, 327, 273, 324, 300, 279, 334, 326, 325, 319, 330, 117, 323, 340, 231, 301, 332, 341, 261, 314, 307, 215, 319, 301, 310, 221, 318, 333, 200, 354, 334, 336, 318, 317, 346, 289, 321, 258, 331, 321, 332, 239, 316, 302, 314, 148, 326, 303, 309, 330, 300, 306, 326, 328, 356, 334, 328, 324, 314, 346, 293, 324, 159, 326, 346, 337, 319, 316, 317, 294, 310, 308, 325, 318, 342, 344, 328, 269, 313, 338, 337, 342, 340, 321, 189, 314, 199, 329, 314, 188, 330, 319, 338, 315, 314, 324, 317, 263, 336, 312, 326, 302, 334, 288, 319, 334, 353, 357, 316, 314, 316, 309, 333, 330, 345, 317, 264, 321, 342, 315, 334, 223, 318, 209, 311, 229, 340, 335, 323, 329, 291, 328, 330, 318, 339, 336, 334, 325, 315, 320, 319, 145, 343, 337, 319, 318, 319, 308, 319, 318, 359, 317, 333, 331, 315, 329, 345, 163, 316, 335, 332, 338, 316, 334, 350, 318, 317, 319, 330, 322, 289, 308, 311, 315, 323, 230, 191, 311, 316, 281, 320, 309, 352, 287, 266, 185, 305, 315, 190, 332, 292, 303, 316, 151, 248, 318, 322, 312, 207, 162, 319, 352, 323, 311, 337, 344, 241, 137, 317, 307, 324, 234, 333, 285, 323, 302, 313, 308, 329, 331, 325, 335, 257, 144, 266, 330, 345, 330, 340, 320, 326, 309, 162, 330, 318, 321, 287, 329, 329, 330, 325, 318, 336, 318, 325, 336, 333, 321, 325, 274, 336, 348, 173, 325, 313, 331, 313, 328, 340, 314, 318, 332, 273, 318, 330, 341, 309, 308, 308, 307, 327, 329, 309, 335, 320, 320, 328, 148, 265, 238, 315, 316, 327, 201, 320, 317, 312, 317, 330, 331, 269, 332, 326, 321, 327, 347, 117, 252, 334, 320, 328, 315, 308, 320, 341, 313, 190, 347, 186, 315, 325, 181, 304, 319, 332, 324, 294, 292, 275, 316, 331, 279, 285, 314, 338, 175, 275, 324, 331, 335, 297, 311, 329, 318, 316, 320, 298, 341, 211, 189, 310, 345, 336, 325, 324, 340, 230, 342, 303, 342, 283, 314, 337, 355, 261, 315, 327, 331, 315, 326, 320, 317, 325, 314, 328, 267, 307, 332, 306, 319, 335, 305, 268, 327, 320, 321, 328, 320, 333, 324, 310, 170, 344, 300, 333, 289, 313, 299, 154, 323, 157, 329, 325, 338, 205, 301, 319, 329, 312, 331, 323, 315, 318, 343, 324, 321, 306, 163, 329, 316, 279, 328, 346, 333, 323, 325, 312, 342, 312, 327, 335, 305, 308, 317, 315, 312, 308, 318, 327, 332, 318, 331, 330, 321, 323, 148, 289, 280, 251, 325, 315, 308, 341, 336, 174, 219, 172, 318, 297, 329, 317, 324, 225, 328, 329, 294, 132, 160, 315, 145, 171, 309, 200, 313, 310, 318, 310, 315, 317, 355, 327, 330, 317, 331, 326, 336, 310, 287, 334, 327, 321, 163, 340, 354, 328, 322, 272, 315, 330, 321, 322, 309, 337, 316, 315, 183, 345, 300, 324, 324, 329, 334, 307, 144, 325, 319, 318, 322, 342, 307, 331, 335, 325, 330, 336, 315, 311, 336, 330, 327, 347, 315, 337, 310, 324, 334, 276, 330, 329, 309, 348, 173, 268, 330, 320, 322, 339, 343, 339, 316, 324, 335, 292, 126, 323, 286, 313, 341, 266, 336, 315, 335, 211, 307, 301, 341, 297, 305, 135, 322, 325, 349, 315, 322, 242, 330, 339, 333, 332, 334, 340, 333, 180, 326, 318, 326, 349, 319, 333, 314, 325, 320, 309, 328, 313, 316, 321, 326, 317, 329, 325, 317, 266, 321, 331, 135, 337, 208, 328, 318, 325, 314, 320, 325, 263, 318, 287, 311, 315, 317, 296, 315, 356, 291, 319, 347, 328, 325, 337, 326, 315, 105, 306, 306, 321, 324, 314, 330, 338, 120, 331, 335, 331, 318, 258, 319, 329, 314, 305, 131, 333, 210, 224, 333, 335, 328, 248, 296, 326, 276, 328, 262, 326, 326, 326, 266, 323, 335, 334, 300, 312, 287, 308, 111, 325, 322, 285, 335, 109, 325, 128, 321, 314, 314, 310, 273, 270), bio06 = c(184, 213, 102, 216, 215, 149, 145, 176, 176, 186, 144, 184, 207, 208, 221, 206, 200, 115, 98, 190, 193, 165, 115, 194, 104, 188, 223, 199, 151, 186, 74, 195, 176, 194, 163, 216, 180, 182, 136, 190, 212, 215, 216, 168, 168, 172, 156, 205, 206, 174, 108, 125, 205, 205, 214, 215, 196, 171, 174, 202, 70, 204, 203, -3, 218, 189, 195, 224, 197, 199, 222, 188, 214, 210, 212, 173, 190, 182, 201, 219, 137, 29, 196, 206, 190, 198, 133, 198, 183, 195, 185, 212, 207, 162, 219, 187, 190, 217, 189, 206, 153, 201, 130, 195, 214, 213, 211, 211, 159, 218, 218, 177, 150, 84, 224, 134, 203, 212, 132, 222, 206, 213, 39, 165, 209, 216, 21, 217, 226, 211, 188, 208, 210, 208, 205, 166, 207, -51, 108, 150, 180, 217, 166, -10, 187, 165, 109, 179, 220, 117, 183, 207, 203, 180, 133, 200, 207, 211, 166, 138, 190, 175, 179, 209, 203, 117, 106, 209, 191, 178, 202, 199, 150, 214, 210, -4, 204, 219, 219, 166, 196, 26, 140, 217, -57, 58, 205, 218, 211, 181, 208, 217, 219, 186, 168, 187, 135, 210, 197, 191, 192, 176, 145, 203, 217, 210, 205, 109, 89, 21, 197, 162, 222, 212, 211, 214, 151, 216, 220, 205, 182, 147, 184, 184, 214, 211, 211, 210, 208, 200, 178, 187, 205, 65, 178, 168, 211, 126, 187, 217, 195, 203, 26, 217, 200, 219, 168, 192, 137, 158, 180, 212, 208, 222, 180, 138, -70, 94, 202, 204, 203, 192, 174, 222, 146, 213, 187, 209, 215, 203, 189, 215, 204, 201, 225, 220, 107, 90, 179, 176, 215, -35, 216, 153, 207, 205, 163, 142, -8, 208, 216, 185, 207, 179, 210, 219, 125, -109, 181, 216, 193, 217, 215, 150, 158, 207, -43, 211, 202, 42, 201, 229, 141, 177, 163, 122, 212, 156, 216, 204, 164, 206, 199, 107, 216, 213, 207, 187, 200, 121, 203, 132, 215, 31, 204, 204, 92, 191, -53, 198, -116, 147, 133, 138, 128, 151, 216, 201, 209, 192, 179, -104, 184, 136, 204, 216, 121, 209, 219, 224, 133, 205, 145, 91, 155, 223, 221, 209, 211, -64, 217, 216, 65, 223, 211, 209, 80, 201, 151, 103, 206, 193, 186, 128, 171, 150, 88, 214, 196, 204, 205, 183, 214, 172, 214, 105, 223, 216, 221, 73, 186, 170, 199, -77, 152, 162, 203, 213, 151, 203, 221, 189, 212, 202, 214, 198, 190, 214, 173, 202, -123, 194, 175, 173, 204, 201, 215, 194, 213, 205, 222, 163, 196, 201, 138, 126, 203, 180, 180, 216, 207, 137, -26, 207, 85, 208, 204, 74, 185, 207, 154, 195, 212, 218, 201, 142, 187, 219, 218, 203, 196, 173, 155, 177, 205, 218, 177, 193, 207, 204, 190, 201, 175, 187, 101, 206, 214, 196, 207, 93, 205, 6, 204, 21, 213, 179, 211, 210, 130, 226, 219, 197, 169, 160, 173, 222, 204, 161, 203, -38, 221, 203, 214, 207, 169, 207, 181, 166, 225, 166, 211, 209, 189, 197, 214, -62, 212, 179, 173, 151, 210, 154, 205, 204, 205, 209, 146, 172, 180, 187, 123, 204, 219, 60, -62, 209, 208, 102, 173, 176, 202, 153, 152, -46, 221, 208, 3, 146, 138, 182, 186, -89, 112, 179, 217, 203, 117, -38, 215, 216, 184, 204, 147, 227, 119, -111, 207, 193, 215, 47, 166, 173, 218, 123, 205, 164, 183, 207, 216, 177, 114, -80, 121, 216, 215, 149, 212, 186, 220, 121, 70, 135, 202, 209, 131, 188, 190, 189, 183, 180, 178, 204, 214, 207, 152, 178, 201, 155, 208, 217, 63, 199, 203, 210, 124, 219, 208, 206, 213, 220, 163, 205, 178, 153, 204, 205, 193, 216, 224, 192, 201, 213, 204, 177, 218, -71, 98, 127, 199, 205, 188, 78, 209, 163, 206, 205, 149, 213, 113, 166, 135, 217, 220, 218, 16, 127, 156, 214, 134, 196, 208, 189, 216, 120, -31, 219, -64, 189, 146, 72, 133, 177, 193, 211, 178, 133, 130, 205, 178, 140, 157, 189, 219, -41, 151, 221, 176, 190, 225, 199, 152, 209, 192, 214, 181, 217, 88, -69, 198, 183, 192, 182, 218, 211, 19, 214, 189, 153, 157, 194, 163, 217, 113, 210, 185, 202, 188, 221, 214, 193, 222, 207, 210, 125, 171, 214, 206, 212, 178, 131, 100, 219, 202, 215, 206, 206, 190, 206, 208, -39, 216, 148, 212, 138, 206, 223, -25, 193, -28, 203, 150, 167, 98, 220, 214, 192, 195, 189, 212, 186, 184, 215, 206, 131, 204, -59, 207, 182, 80, 206, 179, 212, 176, 144, 207, 218, 197, 177, 156, 204, 205, 159, 231, 175, 219, 195, 183, 221, 185, 190, 208, 189, 142, -46, 154, 165, 128, 221, 207, 199, 218, 167, -55, 3, -37, 172, 190, 187, 217, 199, 49, 211, 184, 209, -42, -12, 217, -94, -116, 204, 12, 174, 206, 214, 204, 203, 208, 214, 191, 216, 203, 220, 217, 224, 196, 119, 189, 220, 218, 51, 173, 217, 217, 220, 142, 176, 183, 218, 215, 205, 205, 187, 207, -90, 214, 186, 137, 222, 188, 216, 172, 47, 224, 189, 188, 219, 218, 187, 187, 163, 135, 212, 142, 198, 227, 213, 228, 220, 211, 210, 190, 196, 220, 197, 150, 210, 217, 205, 218, -45, 77, 138, 166, 216, 212, 217, 177, 210, 216, 192, 212, -63, 198, 165, 208, 215, 86, 221, 208, 167, -19, 182, 221, 215, 148, 213, -39, 210, 196, 217, 176, 183, 129, 180, 180, 162, 146, 158, 170, 181, -33, 223, 200, 177, 223, 137, 155, 213, 145, 170, 204, 226, 205, 167, 191, 162, 211, 188, 215, 214, 121, 149, 174, -65, 215, -1, 217, 203, 217, 203, 205, 192, 136, 136, 156, 209, 212, 213, 169, 205, 222, 172, 165, 217, 136, 135, 196, 145, 200, -78, 202, 206, 212, 215, 213, 217, 174, -104, 214, 209, 212, 172, 76, 133, 167, 203, 194, 13, 141, 2, 88, 187, 161, 184, 120, 187, 205, 133, 214, 142, 213, 184, 212, 120, 214, 193, 205, 185, 208, 173, 205, -75, 207, 173, 177, 144, -79, 218, -63, 199, 203, 201, 220, 55, 148), bio13 = c(263, 307, 304, 397, 393, 494, 365, 379, 387, 320, 399, 273, 301, 378, 411, 285, 268, 459, 238, 254, 224, 469, 319, 331, 189, 375, 366, 520, 495, 368, 182, 182, 445, 347, 314, 315, 259, 273, 241, 298, 347, 345, 401, 400, 268, 264, 387, 353, 459, 194, 195, 182, 405, 208, 385, 329, 338, 236, 340, 472, 204, 200, 352, 164, 321, 243, 273, 320, 305, 175, 352, 303, 316, 371, 267, 369, 257, 254, 216, 336, 322, 90, 271, 333, 327, 306, 261, 325, 244, 242, 282, 278, 350, 288, 234, 362, 284, 966, 296, 407, 263, 282, 190, 269, 235, 330, 367, 328, 231, 327, 278, 254, 308, 6, 337, 283, 308, 329, 336, 371, 458, 301, 145, 209, 333, 330, 123, 306, 406, 275, 308, 224, 328, 334, 373, 283, 343, 149, 10, 93, 327, 345, 242, 120, 434, 255, 310, 337, 254, 329, 378, 218, 335, 354, 339, 359, 337, 272, 268, 435, 372, 370, 391, 435, 295, 282, 230, 330, 348, 268, 324, 509, 159, 365, 362, 158, 214, 288, 324, 260, 324, 114, 280, 271, 188, 146, 316, 328, 346, 268, 414, 297, 325, 270, 257, 279, 2, 289, 245, 305, 305, 421, 235, 350, 347, 334, 337, 2, 232, 155, 314, 177, 405, 322, 342, 317, 380, 360, 345, 297, 354, 401, 294, 287, 284, 224, 377, 356, 336, 457, 251, 382, 356, 114, 309, 257, 243, 387, 349, 351, 435, 357, 138, 326, 250, 340, 250, 282, 297, 324, 279, 241, 358, 364, 269, 323, 154, 140, 321, 249, 386, 481, 239, 434, 253, 331, 170, 350, 366, 343, 141, 334, 294, 343, 301, 387, 148, 257, 251, 349, 373, 145, 301, 264, 222, 322, 279, 332, 165, 373, 355, 299, 344, 343, 220, 343, 189, 169, 267, 410, 260, 262, 283, 341, 250, 295, 138, 305, 335, 216, 321, 420, 356, 579, 337, 1, 297, 355, 189, 333, 261, 174, 323, 164, 256, 368, 344, 339, 280, 289, 449, 343, 363, 94, 374, 328, 125, 272, 150, 217, 162, 496, 188, 255, 181, 202, 335, 318, 315, 289, 335, 133, 396, 404, 348, 315, 131, 400, 348, 337, 251, 324, 241, 224, 257, 279, 392, 344, 372, 143, 336, 414, 140, 737, 345, 453, 4, 286, 223, 210, 312, 586, 568, 217, 321, 321, 191, 316, 343, 483, 218, 268, 304, 213, 323, 9, 375, 311, 199, 38, 263, 214, 254, 208, 307, 310, 296, 299, 292, 365, 346, 248, 249, 479, 310, 410, 286, 289, 378, 377, 173, 439, 242, 358, 229, 277, 350, 311, 346, 311, 276, 296, 176, 207, 258, 4, 400, 282, 258, 244, 445, 288, 156, 339, 233, 329, 300, 134, 480, 334, 325, 357, 334, 308, 260, 438, 269, 305, 301, 336, 313, 198, 31, 283, 481, 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89, 16, 51, 188, 5, 11, 171, 92, 1, 1, 58, 161, 45, 20, 131, 3, 158, 210, 4, 453, 176, 9, 14, 63, 47, 47, 5, 43, 38, 176, 157, 138, 3, 133, 7, 32, 217, 3, 10, 27, 5, 237, 9, 109, 0, 17, 199, 101, 43, 195, 30, 26, 139, 170, 39, 20, 0, 0, 21, 5, 9, 10, 56, 78, 9, 62, 15, 195, 51, 77, 16, 18, 53, 20, 62, 37, 181, 75, 35, 37, 29, 19, 179, 139, 32, 95, 62, 189, 70, 23, 86, 107, 132, 198, 24, 273, 89, 17, 20, 155, 219, 48, 311, 95, 18, 136, 62, 124, 30, 71, 1, 57, 67, 49, 87, 20, 22, 116, 33, 181, 176, 9, 26, 43, 18, 32, 93, 93, 11, 78, 65, 19, 153, 14, 193, 181, 7, 36, 9, 4, 51, 1, 68, 44, 32, 54, 84, 60, 50, 60, 1, 0, 164, 54, 48, 64, 75, 67, 8, 45, 116, 12, 94, 217, 7, 109, 116, 82, 157, 61, 36, 30, 2, 159, 8, 7, 33, 82, 4, 10, 12, 155, 5, 88, 97, 7, 2, 0, 223, 19, 198, 45, 99, 93, 87, 103, 213, 71, 0, 119, 25, 188, 82, 18, 49, 0, 80, 64, 86, 55, 73, 23, 59, 194, 3, 16, 61, 25, 74, 235, 287, 7, 43, 17, 46, 69, 10, 40, 362, 154, 19, 118, 71, 67, 64, 49, 17, 165, 5, 194, 4, 115, 46, 11, 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0, 138, 10, 112, 35, 55, 74, 227, 2, 34, 46, 102, 3, 5, 94, 3, 25, 116, 219, 321, 0, 111)), p = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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4: (new("standardGeneric", .Data = function (x, p, ...) standardGeneric("maxent"), generic = "maxent", package = "dismo", group = list(), valueClass = character(0), signature = c("x", "p"), default = NULL, skeleton = (function (x, p, ...) stop(gettextf("invalid call in method dispatch to '%s' (no default method)", "maxent"), domain = NA))(x, p, ...)))(x = list(bio05 = c(316, 319, 217, 325, 323, 327, 274, 321, 322, 323, 273, 306, 339, 325, 355, 321, 316, 243, 265, 333, 335, 276, 240, 307, 274, 300, 349, 325, 269, 298, 250, 315, 312, 306, 323, 327, 333, 324, 327, 318, 334, 349, 356, 318, 319, 329, 302, 326, 338, 293, 295, 323, 316, 319, 327, 321, 332, 315, 336, 336, 269, 317, 327, 182, 322, 332, 317, 313, 316, 333, 333, 323, 327, 328, 355, 286, 340, 325, 352, 323, 319, 141, 314, 327, 335, 311, 261, 331, 324, 314, 316, 316, 319, 328, 334, 335, 330, 311, 315, 307, 320, 313, 245, 315, 326, 329, 330, 317, 338, 327, 325, 345, 317, 256, 326, 323, 316, 319, 319, 358, 342, 350, 202, 290, 329, 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0, 138, 10, 112, 35, 55, 74, 227, 2, 34, 46, 102, 3, 5, 94, 3, 25, 116, 219, 321, 0, 111)), p = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), args = c("noremoveDuplicates", "noautofeature", "noquadratic", "nohinge", "noproduct", "nothreshold", "betamultiplier=1"))
5: do.call(enm@fun, mod.full.args)
6: cv.enm(d, envs, enm, partitions, tune.tbl.i, doClamp, other.settings, partition.settings, user.val.grps, occs.testing.z, user.eval, algorithm, quiet)
7: tune.regular(d, envs, enm, partitions, tune.tbl, doClamp, other.settings, partition.settings, user.val.grps, occs.testing.z, updateProgress, user.eval, algorithm, quiet)
8: 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)
9: model_maxent(occs = occs, bg = bg, user.grp = partblock, bgMsk = envs, rms, rmsStep, fcs, clampSel = TRUE, algMaxent = i, parallel = FALSE)
10: eval(code, test_env)
11: eval(code, test_env)
12: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
20: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
21: source_file(path, env = env(env), desc = desc, error_call = error_call)
22: FUN(X[[i]], ...)
23: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
28: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
29: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
30: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
31: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
32: test_check("wallace")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-macos-arm64
Version: 2.1.3
Check: tests
Result: ERROR
Running 'testthat.R' [160s]
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 191 ]
══ 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 191 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [143s/204s]
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
`/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 191 ]
══ 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 191 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [139s/199s]
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
`/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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 191 ]
══ 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 191 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [42s/60s]
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
|
| | 0%
|
| | 0%
|
|================== | 25%
*** caught illegal operation ***
address 0x126a2ef78, cause 'illegal trap'
Traceback:
1: rJava::.jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o", dirout, "-s", pfn, args))
2: .local(x, p, ...)
3: (new("standardGeneric", .Data = function (x, p, ...) standardGeneric("maxent"), generic = "maxent", package = "dismo", group = list(), valueClass = character(0), signature = c("x", "p"), default = NULL, skeleton = (function (x, p, ...) stop(gettextf("invalid call in method dispatch to '%s' (no default method)", "maxent"), domain = NA))(x, p, ...)))(x = list(bio05 = c(316, 319, 217, 325, 323, 327, 274, 321, 322, 323, 273, 306, 339, 325, 355, 321, 316, 243, 265, 333, 335, 276, 240, 307, 274, 300, 349, 325, 269, 298, 250, 315, 312, 306, 323, 327, 333, 324, 327, 318, 334, 349, 356, 318, 319, 329, 302, 326, 338, 293, 295, 323, 316, 319, 327, 321, 332, 315, 336, 336, 269, 317, 327, 182, 322, 332, 317, 313, 316, 333, 333, 323, 327, 328, 355, 286, 340, 325, 352, 323, 319, 141, 314, 327, 335, 311, 261, 331, 324, 314, 316, 316, 319, 328, 334, 335, 330, 311, 315, 307, 320, 313, 245, 315, 326, 329, 330, 317, 338, 327, 325, 345, 317, 256, 326, 323, 316, 319, 319, 358, 342, 350, 202, 290, 329, 325, 229, 313, 354, 341, 318, 321, 314, 314, 306, 292, 312, 172, 268, 284, 318, 315, 339, 197, 315, 318, 254, 294, 342, 308, 334, 328, 327, 332, 321, 329, 312, 331, 318, 234, 320, 339, 331, 331, 318, 304, 222, 314, 319, 337, 328, 316, 285, 323, 331, 209, 337, 344, 321, 319, 321, 204, 325, 329, 151, 219, 331, 350, 327, 343, 328, 314, 322, 332, 320, 330, 280, 353, 337, 318, 332, 287, 251, 312, 330, 330, 319, 281, 265, 231, 313, 272, 342, 316, 325, 317, 322, 319, 325, 311, 307, 269, 332, 321, 342, 321, 337, 317, 311, 357, 320, 299, 319, 175, 330, 341, 352, 252, 312, 354, 313, 322, 126, 342, 335, 322, 326, 328, 322, 335, 338, 322, 329, 325, 343, 324, 142, 247, 333, 321, 307, 316, 346, 346, 267, 316, 318, 316, 344, 309, 313, 321, 313, 331, 308, 328, 220, 206, 339, 334, 323, 184, 342, 332, 319, 327, 317, 274, 201, 330, 346, 323, 307, 340, 321, 358, 328, 148, 343, 331, 313, 321, 343, 327, 329, 321, 143, 321, 330, 146, 315, 341, 299, 306, 294, 264, 325, 340, 298, 310, 318, 327, 314, 233, 337, 341, 311, 300, 313, 308, 328, 262, 323, 202, 306, 320, 228, 314, 163, 350, 146, 327, 246, 331, 318, 323, 345, 314, 327, 328, 321, 155, 300, 262, 306, 312, 251, 330, 327, 327, 273, 324, 300, 279, 334, 326, 325, 319, 330, 117, 323, 340, 231, 301, 332, 341, 261, 314, 307, 215, 319, 301, 310, 221, 318, 333, 200, 354, 334, 336, 318, 317, 346, 289, 321, 258, 331, 321, 332, 239, 316, 302, 314, 148, 326, 303, 309, 330, 300, 306, 326, 328, 356, 334, 328, 324, 314, 346, 293, 324, 159, 326, 346, 337, 319, 316, 317, 294, 310, 308, 325, 318, 342, 344, 328, 269, 313, 338, 337, 342, 340, 321, 189, 314, 199, 329, 314, 188, 330, 319, 338, 315, 314, 324, 317, 263, 336, 312, 326, 302, 334, 288, 319, 334, 353, 357, 316, 314, 316, 309, 333, 330, 345, 317, 264, 321, 342, 315, 334, 223, 318, 209, 311, 229, 340, 335, 323, 329, 291, 328, 330, 318, 339, 336, 334, 325, 315, 320, 319, 145, 343, 337, 319, 318, 319, 308, 319, 318, 359, 317, 333, 331, 315, 329, 345, 163, 316, 335, 332, 338, 316, 334, 350, 318, 317, 319, 330, 322, 289, 308, 311, 315, 323, 230, 191, 311, 316, 281, 320, 309, 352, 287, 266, 185, 305, 315, 190, 332, 292, 303, 316, 151, 248, 318, 322, 312, 207, 162, 319, 352, 323, 311, 337, 344, 241, 137, 317, 307, 324, 234, 333, 285, 323, 302, 313, 308, 329, 331, 325, 335, 257, 144, 266, 330, 345, 330, 340, 320, 326, 309, 162, 330, 318, 321, 287, 329, 329, 330, 325, 318, 336, 318, 325, 336, 333, 321, 325, 274, 336, 348, 173, 325, 313, 331, 313, 328, 340, 314, 318, 332, 273, 318, 330, 341, 309, 308, 308, 307, 327, 329, 309, 335, 320, 320, 328, 148, 265, 238, 315, 316, 327, 201, 320, 317, 312, 317, 330, 331, 269, 332, 326, 321, 327, 347, 117, 252, 334, 320, 328, 315, 308, 320, 341, 313, 190, 347, 186, 315, 325, 181, 304, 319, 332, 324, 294, 292, 275, 316, 331, 279, 285, 314, 338, 175, 275, 324, 331, 335, 297, 311, 329, 318, 316, 320, 298, 341, 211, 189, 310, 345, 336, 325, 324, 340, 230, 342, 303, 342, 283, 314, 337, 355, 261, 315, 327, 331, 315, 326, 320, 317, 325, 314, 328, 267, 307, 332, 306, 319, 335, 305, 268, 327, 320, 321, 328, 320, 333, 324, 310, 170, 344, 300, 333, 289, 313, 299, 154, 323, 157, 329, 325, 338, 205, 301, 319, 329, 312, 331, 323, 315, 318, 343, 324, 321, 306, 163, 329, 316, 279, 328, 346, 333, 323, 325, 312, 342, 312, 327, 335, 305, 308, 317, 315, 312, 308, 318, 327, 332, 318, 331, 330, 321, 323, 148, 289, 280, 251, 325, 315, 308, 341, 336, 174, 219, 172, 318, 297, 329, 317, 324, 225, 328, 329, 294, 132, 160, 315, 145, 171, 309, 200, 313, 310, 318, 310, 315, 317, 355, 327, 330, 317, 331, 326, 336, 310, 287, 334, 327, 321, 163, 340, 354, 328, 322, 272, 315, 330, 321, 322, 309, 337, 316, 315, 183, 345, 300, 324, 324, 329, 334, 307, 144, 325, 319, 318, 322, 342, 307, 331, 335, 325, 330, 336, 315, 311, 336, 330, 327, 347, 315, 337, 310, 324, 334, 276, 330, 329, 309, 348, 173, 268, 330, 320, 322, 339, 343, 339, 316, 324, 335, 292, 126, 323, 286, 313, 341, 266, 336, 315, 335, 211, 307, 301, 341, 297, 305, 135, 322, 325, 349, 315, 322, 242, 330, 339, 333, 332, 334, 340, 333, 180, 326, 318, 326, 349, 319, 333, 314, 325, 320, 309, 328, 313, 316, 321, 326, 317, 329, 325, 317, 266, 321, 331, 135, 337, 208, 328, 318, 325, 314, 320, 325, 263, 318, 287, 311, 315, 317, 296, 315, 356, 291, 319, 347, 328, 325, 337, 326, 315, 105, 306, 306, 321, 324, 314, 330, 338, 120, 331, 335, 331, 318, 258, 319, 329, 314, 305, 131, 333, 210, 224, 333, 335, 328, 248, 296, 326, 276, 328, 262, 326, 326, 326, 266, 323, 335, 334, 300, 312, 287, 308, 111, 325, 322, 285, 335, 109, 325, 128, 321, 314, 314, 310, 273, 270), bio06 = c(184, 213, 102, 216, 215, 149, 145, 176, 176, 186, 144, 184, 207, 208, 221, 206, 200, 115, 98, 190, 193, 165, 115, 194, 104, 188, 223, 199, 151, 186, 74, 195, 176, 194, 163, 216, 180, 182, 136, 190, 212, 215, 216, 168, 168, 172, 156, 205, 206, 174, 108, 125, 205, 205, 214, 215, 196, 171, 174, 202, 70, 204, 203, -3, 218, 189, 195, 224, 197, 199, 222, 188, 214, 210, 212, 173, 190, 182, 201, 219, 137, 29, 196, 206, 190, 198, 133, 198, 183, 195, 185, 212, 207, 162, 219, 187, 190, 217, 189, 206, 153, 201, 130, 195, 214, 213, 211, 211, 159, 218, 218, 177, 150, 84, 224, 134, 203, 212, 132, 222, 206, 213, 39, 165, 209, 216, 21, 217, 226, 211, 188, 208, 210, 208, 205, 166, 207, -51, 108, 150, 180, 217, 166, -10, 187, 165, 109, 179, 220, 117, 183, 207, 203, 180, 133, 200, 207, 211, 166, 138, 190, 175, 179, 209, 203, 117, 106, 209, 191, 178, 202, 199, 150, 214, 210, -4, 204, 219, 219, 166, 196, 26, 140, 217, -57, 58, 205, 218, 211, 181, 208, 217, 219, 186, 168, 187, 135, 210, 197, 191, 192, 176, 145, 203, 217, 210, 205, 109, 89, 21, 197, 162, 222, 212, 211, 214, 151, 216, 220, 205, 182, 147, 184, 184, 214, 211, 211, 210, 208, 200, 178, 187, 205, 65, 178, 168, 211, 126, 187, 217, 195, 203, 26, 217, 200, 219, 168, 192, 137, 158, 180, 212, 208, 222, 180, 138, -70, 94, 202, 204, 203, 192, 174, 222, 146, 213, 187, 209, 215, 203, 189, 215, 204, 201, 225, 220, 107, 90, 179, 176, 215, -35, 216, 153, 207, 205, 163, 142, -8, 208, 216, 185, 207, 179, 210, 219, 125, -109, 181, 216, 193, 217, 215, 150, 158, 207, -43, 211, 202, 42, 201, 229, 141, 177, 163, 122, 212, 156, 216, 204, 164, 206, 199, 107, 216, 213, 207, 187, 200, 121, 203, 132, 215, 31, 204, 204, 92, 191, -53, 198, -116, 147, 133, 138, 128, 151, 216, 201, 209, 192, 179, -104, 184, 136, 204, 216, 121, 209, 219, 224, 133, 205, 145, 91, 155, 223, 221, 209, 211, -64, 217, 216, 65, 223, 211, 209, 80, 201, 151, 103, 206, 193, 186, 128, 171, 150, 88, 214, 196, 204, 205, 183, 214, 172, 214, 105, 223, 216, 221, 73, 186, 170, 199, -77, 152, 162, 203, 213, 151, 203, 221, 189, 212, 202, 214, 198, 190, 214, 173, 202, -123, 194, 175, 173, 204, 201, 215, 194, 213, 205, 222, 163, 196, 201, 138, 126, 203, 180, 180, 216, 207, 137, -26, 207, 85, 208, 204, 74, 185, 207, 154, 195, 212, 218, 201, 142, 187, 219, 218, 203, 196, 173, 155, 177, 205, 218, 177, 193, 207, 204, 190, 201, 175, 187, 101, 206, 214, 196, 207, 93, 205, 6, 204, 21, 213, 179, 211, 210, 130, 226, 219, 197, 169, 160, 173, 222, 204, 161, 203, -38, 221, 203, 214, 207, 169, 207, 181, 166, 225, 166, 211, 209, 189, 197, 214, -62, 212, 179, 173, 151, 210, 154, 205, 204, 205, 209, 146, 172, 180, 187, 123, 204, 219, 60, -62, 209, 208, 102, 173, 176, 202, 153, 152, -46, 221, 208, 3, 146, 138, 182, 186, -89, 112, 179, 217, 203, 117, -38, 215, 216, 184, 204, 147, 227, 119, -111, 207, 193, 215, 47, 166, 173, 218, 123, 205, 164, 183, 207, 216, 177, 114, -80, 121, 216, 215, 149, 212, 186, 220, 121, 70, 135, 202, 209, 131, 188, 190, 189, 183, 180, 178, 204, 214, 207, 152, 178, 201, 155, 208, 217, 63, 199, 203, 210, 124, 219, 208, 206, 213, 220, 163, 205, 178, 153, 204, 205, 193, 216, 224, 192, 201, 213, 204, 177, 218, -71, 98, 127, 199, 205, 188, 78, 209, 163, 206, 205, 149, 213, 113, 166, 135, 217, 220, 218, 16, 127, 156, 214, 134, 196, 208, 189, 216, 120, -31, 219, -64, 189, 146, 72, 133, 177, 193, 211, 178, 133, 130, 205, 178, 140, 157, 189, 219, -41, 151, 221, 176, 190, 225, 199, 152, 209, 192, 214, 181, 217, 88, -69, 198, 183, 192, 182, 218, 211, 19, 214, 189, 153, 157, 194, 163, 217, 113, 210, 185, 202, 188, 221, 214, 193, 222, 207, 210, 125, 171, 214, 206, 212, 178, 131, 100, 219, 202, 215, 206, 206, 190, 206, 208, -39, 216, 148, 212, 138, 206, 223, -25, 193, -28, 203, 150, 167, 98, 220, 214, 192, 195, 189, 212, 186, 184, 215, 206, 131, 204, -59, 207, 182, 80, 206, 179, 212, 176, 144, 207, 218, 197, 177, 156, 204, 205, 159, 231, 175, 219, 195, 183, 221, 185, 190, 208, 189, 142, -46, 154, 165, 128, 221, 207, 199, 218, 167, -55, 3, -37, 172, 190, 187, 217, 199, 49, 211, 184, 209, -42, -12, 217, -94, -116, 204, 12, 174, 206, 214, 204, 203, 208, 214, 191, 216, 203, 220, 217, 224, 196, 119, 189, 220, 218, 51, 173, 217, 217, 220, 142, 176, 183, 218, 215, 205, 205, 187, 207, -90, 214, 186, 137, 222, 188, 216, 172, 47, 224, 189, 188, 219, 218, 187, 187, 163, 135, 212, 142, 198, 227, 213, 228, 220, 211, 210, 190, 196, 220, 197, 150, 210, 217, 205, 218, -45, 77, 138, 166, 216, 212, 217, 177, 210, 216, 192, 212, -63, 198, 165, 208, 215, 86, 221, 208, 167, -19, 182, 221, 215, 148, 213, -39, 210, 196, 217, 176, 183, 129, 180, 180, 162, 146, 158, 170, 181, -33, 223, 200, 177, 223, 137, 155, 213, 145, 170, 204, 226, 205, 167, 191, 162, 211, 188, 215, 214, 121, 149, 174, -65, 215, -1, 217, 203, 217, 203, 205, 192, 136, 136, 156, 209, 212, 213, 169, 205, 222, 172, 165, 217, 136, 135, 196, 145, 200, -78, 202, 206, 212, 215, 213, 217, 174, -104, 214, 209, 212, 172, 76, 133, 167, 203, 194, 13, 141, 2, 88, 187, 161, 184, 120, 187, 205, 133, 214, 142, 213, 184, 212, 120, 214, 193, 205, 185, 208, 173, 205, -75, 207, 173, 177, 144, -79, 218, -63, 199, 203, 201, 220, 55, 148), bio13 = c(263, 307, 304, 397, 393, 494, 365, 379, 387, 320, 399, 273, 301, 378, 411, 285, 268, 459, 238, 254, 224, 469, 319, 331, 189, 375, 366, 520, 495, 368, 182, 182, 445, 347, 314, 315, 259, 273, 241, 298, 347, 345, 401, 400, 268, 264, 387, 353, 459, 194, 195, 182, 405, 208, 385, 329, 338, 236, 340, 472, 204, 200, 352, 164, 321, 243, 273, 320, 305, 175, 352, 303, 316, 371, 267, 369, 257, 254, 216, 336, 322, 90, 271, 333, 327, 306, 261, 325, 244, 242, 282, 278, 350, 288, 234, 362, 284, 966, 296, 407, 263, 282, 190, 269, 235, 330, 367, 328, 231, 327, 278, 254, 308, 6, 337, 283, 308, 329, 336, 371, 458, 301, 145, 209, 333, 330, 123, 306, 406, 275, 308, 224, 328, 334, 373, 283, 343, 149, 10, 93, 327, 345, 242, 120, 434, 255, 310, 337, 254, 329, 378, 218, 335, 354, 339, 359, 337, 272, 268, 435, 372, 370, 391, 435, 295, 282, 230, 330, 348, 268, 324, 509, 159, 365, 362, 158, 214, 288, 324, 260, 324, 114, 280, 271, 188, 146, 316, 328, 346, 268, 414, 297, 325, 270, 257, 279, 2, 289, 245, 305, 305, 421, 235, 350, 347, 334, 337, 2, 232, 155, 314, 177, 405, 322, 342, 317, 380, 360, 345, 297, 354, 401, 294, 287, 284, 224, 377, 356, 336, 457, 251, 382, 356, 114, 309, 257, 243, 387, 349, 351, 435, 357, 138, 326, 250, 340, 250, 282, 297, 324, 279, 241, 358, 364, 269, 323, 154, 140, 321, 249, 386, 481, 239, 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393, 475, 476, 221, 324, 337, 428, 363, 342, 1, 285, 279, 266, 433, 278, 198, 54, 301, 79, 310, 260, 225, 316, 305, 302, 258, 381, 238, 108, 367, 319, 308, 272, 295, 143, 250, 180, 291, 236, 286, 328, 168, 261, 405, 276, 431, 291, 282, 343, 264, 146, 322, 381, 362, 335, 702, 289, 483, 206, 336, 347, 222, 259, 370, 227, 303, 329, 260, 86, 114, 279, 291, 239, 274, 481, 210, 237, 427, 112, 750, 279, 127, 284, 267, 509, 428, 138, 121, 272, 359, 310, 348, 179, 318, 273, 242, 407, 327, 243, 306, 175, 400, 255, 319, 46, 348, 349, 261, 247, 304, 488, 336, 439, 355, 276, 101, 95, 5, 341, 334, 270, 265, 357, 327, 287, 165, 239, 265, 219, 327, 275, 310, 243, 309, 413, 273, 313, 292, 332, 159, 266, 264, 323, 463, 365, 179, 313, 289, 279, 181, 383, 463, 328, 380, 341, 405, 387, 275, 251, 293, 373, 209, 540, 345, 273, 290, 377, 447, 254, 312, 138, 238, 211, 588, 351, 264, 119, 211, 346, 338, 250, 265, 319, 158, 369, 242, 275, 393, 344, 130, 483, 229, 331, 248, 452, 329, 162, 422, 337, 126, 234, 118, 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42, 15, 64, 55, 1, 7, 82, 20, 31, 91, 48, 118, 27, 22, 22, 178, 117, 67, 157, 39, 100, 20, 124, 18, 125, 52, 14, 93, 74, 92, 101, 91, 6, 79, 85, 73, 102, 4, 71, 13, 60, 2, 129, 14, 21, 112, 54, 36, 158, 130, 35, 37, 71, 65, 109, 83, 53, 0, 23, 29, 492, 69, 164, 35, 151, 89, 101, 11, 37, 207, 141, 32, 89, 120, 22, 54, 0, 72, 11, 147, 115, 8, 2, 34, 7, 29, 85, 43, 75, 10, 111, 34, 9, 58, 152, 166, 182, 186, 177, 180, 4, 0, 20, 49, 131, 17, 0, 57, 30, 48, 58, 11, 9, 20, 66, 54, 27, 7, 47, 180, 75, 20, 158, 62, 16, 17, 122, 55, 10, 59, 191, 110, 33, 47, 248, 70, 106, 111, 7, 7, 6, 103, 39, 61, 4, 9, 13, 2, 25, 60, 2, 66, 25, 122, 48, 108, 21, 25, 66, 0, 9, 80, 63, 38, 237, 45, 147, 19, 72, 73, 0, 47, 10, 107, 39, 34, 160, 61, 158, 66, 161, 128, 153, 111, 191, 21, 43, 3, 126, 37, 120, 192, 21, 29, 202, 116, 35, 52, 8, 3, 30, 81, 3, 127, 73, 84, 11, 3, 91, 23, 23, 10, 1, 40, 148, 110, 119, 21, 8, 2, 30, 52, 125, 245, 33, 9, 54, 61, 180, 8, 178, 13, 199, 57, 153, 189, 41, 98, 88, 36, 37, 23, 17, 142, 7, 13, 40, 109, 46, 36, 66, 8, 179, 19, 26, 183, 21, 113, 2, 20, 3, 28, 77, 64, 80, 3, 55, 46, 57, 6, 80, 48, 107, 140, 58, 87, 166, 79, 0, 55, 8, 23, 187, 20, 25, 92, 34, 15, 13, 185, 109, 144, 13, 30, 60, 126, 0, 225, 73, 45, 83, 8, 2, 2, 91, 33, 19, 22, 46, 11, 96, 48, 22, 87, 5, 48, 58, 175, 112, 68, 134, 85, 88, 4, 47, 99, 37, 37, 78, 118, 152, 170, 5, 77, 45, 16, 326, 49, 76, 0, 179, 49, 38, 75, 59, 73, 62, 41, 3, 99, 3, 34, 137, 148, 48, 8, 40, 132, 0, 87, 142, 15, 0, 58, 95, 192, 8, 48, 72, 157, 26, 76, 211, 82, 62, 6, 69, 86, 90, 80, 2, 108, 79, 4, 33, 15, 17, 78, 213, 168, 35, 92, 167, 84, 23, 4, 5, 12, 0, 152, 39, 30, 7, 109, 9, 3, 220, 91, 57, 195, 28, 149, 79, 8, 90, 173, 85, 198, 57, 16, 102, 77, 151, 43, 51, 0, 42, 28, 7, 112, 123, 55, 185, 35, 203, 16, 55, 0, 171, 13, 107, 149, 53, 127, 0, 151, 0, 14, 31, 151, 64, 72, 75, 25, 66, 11, 0, 14, 115, 148, 62, 125, 9, 11, 7, 79, 114, 25, 182, 61, 41, 30, 52, 106, 65, 73, 36, 2, 5, 157, 18, 7, 6, 390, 12, 33, 118, 85, 89, 16, 51, 188, 5, 11, 171, 92, 1, 1, 58, 161, 45, 20, 131, 3, 158, 210, 4, 453, 176, 9, 14, 63, 47, 47, 5, 43, 38, 176, 157, 138, 3, 133, 7, 32, 217, 3, 10, 27, 5, 237, 9, 109, 0, 17, 199, 101, 43, 195, 30, 26, 139, 170, 39, 20, 0, 0, 21, 5, 9, 10, 56, 78, 9, 62, 15, 195, 51, 77, 16, 18, 53, 20, 62, 37, 181, 75, 35, 37, 29, 19, 179, 139, 32, 95, 62, 189, 70, 23, 86, 107, 132, 198, 24, 273, 89, 17, 20, 155, 219, 48, 311, 95, 18, 136, 62, 124, 30, 71, 1, 57, 67, 49, 87, 20, 22, 116, 33, 181, 176, 9, 26, 43, 18, 32, 93, 93, 11, 78, 65, 19, 153, 14, 193, 181, 7, 36, 9, 4, 51, 1, 68, 44, 32, 54, 84, 60, 50, 60, 1, 0, 164, 54, 48, 64, 75, 67, 8, 45, 116, 12, 94, 217, 7, 109, 116, 82, 157, 61, 36, 30, 2, 159, 8, 7, 33, 82, 4, 10, 12, 155, 5, 88, 97, 7, 2, 0, 223, 19, 198, 45, 99, 93, 87, 103, 213, 71, 0, 119, 25, 188, 82, 18, 49, 0, 80, 64, 86, 55, 73, 23, 59, 194, 3, 16, 61, 25, 74, 235, 287, 7, 43, 17, 46, 69, 10, 40, 362, 154, 19, 118, 71, 67, 64, 49, 17, 165, 5, 194, 4, 115, 46, 11, 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0, 138, 10, 112, 35, 55, 74, 227, 2, 34, 46, 102, 3, 5, 94, 3, 25, 116, 219, 321, 0, 111)), p = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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4: (new("standardGeneric", .Data = function (x, p, ...) standardGeneric("maxent"), generic = "maxent", package = "dismo", group = list(), valueClass = character(0), signature = c("x", "p"), default = NULL, skeleton = (function (x, p, ...) stop(gettextf("invalid call in method dispatch to '%s' (no default method)", "maxent"), domain = NA))(x, p, ...)))(x = list(bio05 = c(316, 319, 217, 325, 323, 327, 274, 321, 322, 323, 273, 306, 339, 325, 355, 321, 316, 243, 265, 333, 335, 276, 240, 307, 274, 300, 349, 325, 269, 298, 250, 315, 312, 306, 323, 327, 333, 324, 327, 318, 334, 349, 356, 318, 319, 329, 302, 326, 338, 293, 295, 323, 316, 319, 327, 321, 332, 315, 336, 336, 269, 317, 327, 182, 322, 332, 317, 313, 316, 333, 333, 323, 327, 328, 355, 286, 340, 325, 352, 323, 319, 141, 314, 327, 335, 311, 261, 331, 324, 314, 316, 316, 319, 328, 334, 335, 330, 311, 315, 307, 320, 313, 245, 315, 326, 329, 330, 317, 338, 327, 325, 345, 317, 256, 326, 323, 316, 319, 319, 358, 342, 350, 202, 290, 329, 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0, 138, 10, 112, 35, 55, 74, 227, 2, 34, 46, 102, 3, 5, 94, 3, 25, 116, 219, 321, 0, 111)), p = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), args = c("noremoveDuplicates", "noautofeature", "noquadratic", "nohinge", "noproduct", "nothreshold", "betamultiplier=1"))
5: do.call(enm@fun, mod.full.args)
6: cv.enm(d, envs, enm, partitions, tune.tbl.i, doClamp, other.settings, partition.settings, user.val.grps, occs.testing.z, user.eval, algorithm, quiet)
7: tune.regular(d, envs, enm, partitions, tune.tbl, doClamp, other.settings, partition.settings, user.val.grps, occs.testing.z, updateProgress, user.eval, algorithm, quiet)
8: 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)
9: model_maxent(occs = occs, bg = bg, user.grp = partblock, bgMsk = envs, rms, rmsStep, fcs, clampSel = TRUE, algMaxent = i, parallel = FALSE)
10: eval(code, test_env)
11: eval(code, test_env)
12: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
20: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
21: source_file(path, env = env(env), desc = desc, error_call = error_call)
22: FUN(X[[i]], ...)
23: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
28: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
29: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
30: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
31: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
32: test_check("wallace")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-macos-arm64
Version: 2.1.3
Check: tests
Result: ERROR
Running 'testthat.R' [163s]
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\4.4\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\4.4\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\4.4\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\4.4\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\4.4\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\4.4\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 191 ]
══ 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 191 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [44s/63s]
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
|
| | 0%
|
| | 0%
|
|================== | 25%
*** caught illegal operation ***
address 0x14dbaaf78, cause 'illegal trap'
Traceback:
1: rJava::.jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o", dirout, "-s", pfn, args))
2: .local(x, p, ...)
3: (new("standardGeneric", .Data = function (x, p, ...) standardGeneric("maxent"), generic = "maxent", package = "dismo", group = list(), valueClass = character(0), signature = c("x", "p"), default = NULL, skeleton = (function (x, p, ...) stop(gettextf("invalid call in method dispatch to '%s' (no default method)", "maxent"), domain = NA))(x, p, ...)))(x = list(bio05 = c(316, 319, 217, 325, 323, 327, 274, 321, 322, 323, 273, 306, 339, 325, 355, 321, 316, 243, 265, 333, 335, 276, 240, 307, 274, 300, 349, 325, 269, 298, 250, 315, 312, 306, 323, 327, 333, 324, 327, 318, 334, 349, 356, 318, 319, 329, 302, 326, 338, 293, 295, 323, 316, 319, 327, 321, 332, 315, 336, 336, 269, 317, 327, 182, 322, 332, 317, 313, 316, 333, 333, 323, 327, 328, 355, 286, 340, 325, 352, 323, 319, 141, 314, 327, 335, 311, 261, 331, 324, 314, 316, 316, 319, 328, 334, 335, 330, 311, 315, 307, 320, 313, 245, 315, 326, 329, 330, 317, 338, 327, 325, 345, 317, 256, 326, 323, 316, 319, 319, 358, 342, 350, 202, 290, 329, 325, 229, 313, 354, 341, 318, 321, 314, 314, 306, 292, 312, 172, 268, 284, 318, 315, 339, 197, 315, 318, 254, 294, 342, 308, 334, 328, 327, 332, 321, 329, 312, 331, 318, 234, 320, 339, 331, 331, 318, 304, 222, 314, 319, 337, 328, 316, 285, 323, 331, 209, 337, 344, 321, 319, 321, 204, 325, 329, 151, 219, 331, 350, 327, 343, 328, 314, 322, 332, 320, 330, 280, 353, 337, 318, 332, 287, 251, 312, 330, 330, 319, 281, 265, 231, 313, 272, 342, 316, 325, 317, 322, 319, 325, 311, 307, 269, 332, 321, 342, 321, 337, 317, 311, 357, 320, 299, 319, 175, 330, 341, 352, 252, 312, 354, 313, 322, 126, 342, 335, 322, 326, 328, 322, 335, 338, 322, 329, 325, 343, 324, 142, 247, 333, 321, 307, 316, 346, 346, 267, 316, 318, 316, 344, 309, 313, 321, 313, 331, 308, 328, 220, 206, 339, 334, 323, 184, 342, 332, 319, 327, 317, 274, 201, 330, 346, 323, 307, 340, 321, 358, 328, 148, 343, 331, 313, 321, 343, 327, 329, 321, 143, 321, 330, 146, 315, 341, 299, 306, 294, 264, 325, 340, 298, 310, 318, 327, 314, 233, 337, 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0, 138, 10, 112, 35, 55, 74, 227, 2, 34, 46, 102, 3, 5, 94, 3, 25, 116, 219, 321, 0, 111)), p = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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4: (new("standardGeneric", .Data = function (x, p, ...) standardGeneric("maxent"), generic = "maxent", package = "dismo", group = list(), valueClass = character(0), signature = c("x", "p"), default = NULL, skeleton = (function (x, p, ...) stop(gettextf("invalid call in method dispatch to '%s' (no default method)", "maxent"), domain = NA))(x, p, ...)))(x = list(bio05 = c(316, 319, 217, 325, 323, 327, 274, 321, 322, 323, 273, 306, 339, 325, 355, 321, 316, 243, 265, 333, 335, 276, 240, 307, 274, 300, 349, 325, 269, 298, 250, 315, 312, 306, 323, 327, 333, 324, 327, 318, 334, 349, 356, 318, 319, 329, 302, 326, 338, 293, 295, 323, 316, 319, 327, 321, 332, 315, 336, 336, 269, 317, 327, 182, 322, 332, 317, 313, 316, 333, 333, 323, 327, 328, 355, 286, 340, 325, 352, 323, 319, 141, 314, 327, 335, 311, 261, 331, 324, 314, 316, 316, 319, 328, 334, 335, 330, 311, 315, 307, 320, 313, 245, 315, 326, 329, 330, 317, 338, 327, 325, 345, 317, 256, 326, 323, 316, 319, 319, 358, 342, 350, 202, 290, 329, 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210, 216, 192, 212, -63, 198, 165, 208, 215, 86, 221, 208, 167, -19, 182, 221, 215, 148, 213, -39, 210, 196, 217, 176, 183, 129, 180, 180, 162, 146, 158, 170, 181, -33, 223, 200, 177, 223, 137, 155, 213, 145, 170, 204, 226, 205, 167, 191, 162, 211, 188, 215, 214, 121, 149, 174, -65, 215, -1, 217, 203, 217, 203, 205, 192, 136, 136, 156, 209, 212, 213, 169, 205, 222, 172, 165, 217, 136, 135, 196, 145, 200, -78, 202, 206, 212, 215, 213, 217, 174, -104, 214, 209, 212, 172, 76, 133, 167, 203, 194, 13, 141, 2, 88, 187, 161, 184, 120, 187, 205, 133, 214, 142, 213, 184, 212, 120, 214, 193, 205, 185, 208, 173, 205, -75, 207, 173, 177, 144, -79, 218, -63, 199, 203, 201, 220, 55, 148), bio13 = c(263, 307, 304, 397, 393, 494, 365, 379, 387, 320, 399, 273, 301, 378, 411, 285, 268, 459, 238, 254, 224, 469, 319, 331, 189, 375, 366, 520, 495, 368, 182, 182, 445, 347, 314, 315, 259, 273, 241, 298, 347, 345, 401, 400, 268, 264, 387, 353, 459, 194, 195, 182, 405, 208, 385, 329, 338, 236, 340, 472, 204, 200, 352, 164, 321, 243, 273, 320, 305, 175, 352, 303, 316, 371, 267, 369, 257, 254, 216, 336, 322, 90, 271, 333, 327, 306, 261, 325, 244, 242, 282, 278, 350, 288, 234, 362, 284, 966, 296, 407, 263, 282, 190, 269, 235, 330, 367, 328, 231, 327, 278, 254, 308, 6, 337, 283, 308, 329, 336, 371, 458, 301, 145, 209, 333, 330, 123, 306, 406, 275, 308, 224, 328, 334, 373, 283, 343, 149, 10, 93, 327, 345, 242, 120, 434, 255, 310, 337, 254, 329, 378, 218, 335, 354, 339, 359, 337, 272, 268, 435, 372, 370, 391, 435, 295, 282, 230, 330, 348, 268, 324, 509, 159, 365, 362, 158, 214, 288, 324, 260, 324, 114, 280, 271, 188, 146, 316, 328, 346, 268, 414, 297, 325, 270, 257, 279, 2, 289, 245, 305, 305, 421, 235, 350, 347, 334, 337, 2, 232, 155, 314, 177, 405, 322, 342, 317, 380, 360, 345, 297, 354, 401, 294, 287, 284, 224, 377, 356, 336, 457, 251, 382, 356, 114, 309, 257, 243, 387, 349, 351, 435, 357, 138, 326, 250, 340, 250, 282, 297, 324, 279, 241, 358, 364, 269, 323, 154, 140, 321, 249, 386, 481, 239, 434, 253, 331, 170, 350, 366, 343, 141, 334, 294, 343, 301, 387, 148, 257, 251, 349, 373, 145, 301, 264, 222, 322, 279, 332, 165, 373, 355, 299, 344, 343, 220, 343, 189, 169, 267, 410, 260, 262, 283, 341, 250, 295, 138, 305, 335, 216, 321, 420, 356, 579, 337, 1, 297, 355, 189, 333, 261, 174, 323, 164, 256, 368, 344, 339, 280, 289, 449, 343, 363, 94, 374, 328, 125, 272, 150, 217, 162, 496, 188, 255, 181, 202, 335, 318, 315, 289, 335, 133, 396, 404, 348, 315, 131, 400, 348, 337, 251, 324, 241, 224, 257, 279, 392, 344, 372, 143, 336, 414, 140, 737, 345, 453, 4, 286, 223, 210, 312, 586, 568, 217, 321, 321, 191, 316, 343, 483, 218, 268, 304, 213, 323, 9, 375, 311, 199, 38, 263, 214, 254, 208, 307, 310, 296, 299, 292, 365, 346, 248, 249, 479, 310, 410, 286, 289, 378, 377, 173, 439, 242, 358, 229, 277, 350, 311, 346, 311, 276, 296, 176, 207, 258, 4, 400, 282, 258, 244, 445, 288, 156, 339, 233, 329, 300, 134, 480, 334, 325, 357, 334, 308, 260, 438, 269, 305, 301, 336, 313, 198, 31, 283, 481, 393, 475, 476, 221, 324, 337, 428, 363, 342, 1, 285, 279, 266, 433, 278, 198, 54, 301, 79, 310, 260, 225, 316, 305, 302, 258, 381, 238, 108, 367, 319, 308, 272, 295, 143, 250, 180, 291, 236, 286, 328, 168, 261, 405, 276, 431, 291, 282, 343, 264, 146, 322, 381, 362, 335, 702, 289, 483, 206, 336, 347, 222, 259, 370, 227, 303, 329, 260, 86, 114, 279, 291, 239, 274, 481, 210, 237, 427, 112, 750, 279, 127, 284, 267, 509, 428, 138, 121, 272, 359, 310, 348, 179, 318, 273, 242, 407, 327, 243, 306, 175, 400, 255, 319, 46, 348, 349, 261, 247, 304, 488, 336, 439, 355, 276, 101, 95, 5, 341, 334, 270, 265, 357, 327, 287, 165, 239, 265, 219, 327, 275, 310, 243, 309, 413, 273, 313, 292, 332, 159, 266, 264, 323, 463, 365, 179, 313, 289, 279, 181, 383, 463, 328, 380, 341, 405, 387, 275, 251, 293, 373, 209, 540, 345, 273, 290, 377, 447, 254, 312, 138, 238, 211, 588, 351, 264, 119, 211, 346, 338, 250, 265, 319, 158, 369, 242, 275, 393, 344, 130, 483, 229, 331, 248, 452, 329, 162, 422, 337, 126, 234, 118, 313, 273, 129, 277, 388, 252, 294, 211, 98, 4, 323, 302, 252, 275, 294, 336, 154, 233, 320, 378, 296, 481, 102, 549, 349, 271, 339, 264, 424, 124, 97, 303, 258, 265, 327, 306, 253, 161, 372, 385, 351, 443, 287, 255, 337, 4, 365, 290, 396, 550, 331, 311, 271, 290, 336, 345, 2, 342, 329, 333, 296, 389, 263, 1, 293, 334, 325, 332, 347, 280, 340, 328, 176, 376, 252, 329, 325, 396, 817, 154, 330, 152, 334, 390, 365, 221, 708, 311, 272, 341, 264, 350, 277, 321, 277, 413, 357, 376, 187, 250, 279, 152, 256, 254, 337, 241, 280, 328, 332, 268, 273, 323, 399, 361, 260, 360, 453, 609, 272, 287, 344, 400, 220, 302, 326, 288, 151, 503, 370, 463, 278, 290, 458, 164, 368, 143, 210, 169, 425, 498, 274, 363, 329, 149, 326, 356, 284, 144, 166, 318, 92, 150, 294, 131, 383, 358, 311, 267, 308, 307, 263, 276, 322, 479, 385, 345, 368, 178, 259, 295, 390, 280, 138, 354, 240, 313, 321, 275, 444, 361, 288, 315, 362, 201, 144, 351, 180, 338, 299, 332, 306, 268, 365, 497, 205, 277, 310, 295, 360, 420, 368, 333, 340, 346, 351, 158, 319, 316, 194, 291, 375, 258, 325, 339, 313, 284, 190, 409, 332, 356, 397, 371, 194, 214, 255, 265, 355, 345, 363, 259, 291, 348, 236, 181, 136, 265, 366, 340, 334, 186, 238, 285, 275, 182, 546, 763, 413, 250, 332, 150, 345, 515, 375, 369, 311, 263, 269, 279, 283, 326, 234, 261, 324, 84, 279, 287, 240, 330, 183, 227, 335, 268, 282, 374, 288, 299, 404, 335, 281, 366, 235, 350, 304, 2, 236, 266, 170, 250, 47, 318, 299, 327, 302, 330, 476, 344, 325, 308, 349, 324, 318, 258, 404, 394, 537, 279, 365, 340, 340, 185, 273, 292, 154, 362, 380, 343, 382, 301, 364, 271, 140, 324, 296, 328, 319, 112, 340, 282, 311, 375, 296, 348, 147, 133, 331, 333, 286, 262, 389, 328, 448, 406, 239, 394, 300, 351, 4, 356, 274, 473, 425, 261, 284, 377, 139, 203, 246, 445, 332, 158, 400, 163, 484, 329, 298, 831, 10, 387), bio14 = c(50, 78, 64, 72, 70, 100, 166, 77, 76, 82, 171, 189, 146, 109, 32, 171, 207, 204, 57, 69, 53, 243, 140, 211, 35, 180, 27, 45, 241, 212, 30, 0, 116, 201, 50, 84, 31, 42, 15, 64, 55, 1, 7, 82, 20, 31, 91, 48, 118, 27, 22, 22, 178, 117, 67, 157, 39, 100, 20, 124, 18, 125, 52, 14, 93, 74, 92, 101, 91, 6, 79, 85, 73, 102, 4, 71, 13, 60, 2, 129, 14, 21, 112, 54, 36, 158, 130, 35, 37, 71, 65, 109, 83, 53, 0, 23, 29, 492, 69, 164, 35, 151, 89, 101, 11, 37, 207, 141, 32, 89, 120, 22, 54, 0, 72, 11, 147, 115, 8, 2, 34, 7, 29, 85, 43, 75, 10, 111, 34, 9, 58, 152, 166, 182, 186, 177, 180, 4, 0, 20, 49, 131, 17, 0, 57, 30, 48, 58, 11, 9, 20, 66, 54, 27, 7, 47, 180, 75, 20, 158, 62, 16, 17, 122, 55, 10, 59, 191, 110, 33, 47, 248, 70, 106, 111, 7, 7, 6, 103, 39, 61, 4, 9, 13, 2, 25, 60, 2, 66, 25, 122, 48, 108, 21, 25, 66, 0, 9, 80, 63, 38, 237, 45, 147, 19, 72, 73, 0, 47, 10, 107, 39, 34, 160, 61, 158, 66, 161, 128, 153, 111, 191, 21, 43, 3, 126, 37, 120, 192, 21, 29, 202, 116, 35, 52, 8, 3, 30, 81, 3, 127, 73, 84, 11, 3, 91, 23, 23, 10, 1, 40, 148, 110, 119, 21, 8, 2, 30, 52, 125, 245, 33, 9, 54, 61, 180, 8, 178, 13, 199, 57, 153, 189, 41, 98, 88, 36, 37, 23, 17, 142, 7, 13, 40, 109, 46, 36, 66, 8, 179, 19, 26, 183, 21, 113, 2, 20, 3, 28, 77, 64, 80, 3, 55, 46, 57, 6, 80, 48, 107, 140, 58, 87, 166, 79, 0, 55, 8, 23, 187, 20, 25, 92, 34, 15, 13, 185, 109, 144, 13, 30, 60, 126, 0, 225, 73, 45, 83, 8, 2, 2, 91, 33, 19, 22, 46, 11, 96, 48, 22, 87, 5, 48, 58, 175, 112, 68, 134, 85, 88, 4, 47, 99, 37, 37, 78, 118, 152, 170, 5, 77, 45, 16, 326, 49, 76, 0, 179, 49, 38, 75, 59, 73, 62, 41, 3, 99, 3, 34, 137, 148, 48, 8, 40, 132, 0, 87, 142, 15, 0, 58, 95, 192, 8, 48, 72, 157, 26, 76, 211, 82, 62, 6, 69, 86, 90, 80, 2, 108, 79, 4, 33, 15, 17, 78, 213, 168, 35, 92, 167, 84, 23, 4, 5, 12, 0, 152, 39, 30, 7, 109, 9, 3, 220, 91, 57, 195, 28, 149, 79, 8, 90, 173, 85, 198, 57, 16, 102, 77, 151, 43, 51, 0, 42, 28, 7, 112, 123, 55, 185, 35, 203, 16, 55, 0, 171, 13, 107, 149, 53, 127, 0, 151, 0, 14, 31, 151, 64, 72, 75, 25, 66, 11, 0, 14, 115, 148, 62, 125, 9, 11, 7, 79, 114, 25, 182, 61, 41, 30, 52, 106, 65, 73, 36, 2, 5, 157, 18, 7, 6, 390, 12, 33, 118, 85, 89, 16, 51, 188, 5, 11, 171, 92, 1, 1, 58, 161, 45, 20, 131, 3, 158, 210, 4, 453, 176, 9, 14, 63, 47, 47, 5, 43, 38, 176, 157, 138, 3, 133, 7, 32, 217, 3, 10, 27, 5, 237, 9, 109, 0, 17, 199, 101, 43, 195, 30, 26, 139, 170, 39, 20, 0, 0, 21, 5, 9, 10, 56, 78, 9, 62, 15, 195, 51, 77, 16, 18, 53, 20, 62, 37, 181, 75, 35, 37, 29, 19, 179, 139, 32, 95, 62, 189, 70, 23, 86, 107, 132, 198, 24, 273, 89, 17, 20, 155, 219, 48, 311, 95, 18, 136, 62, 124, 30, 71, 1, 57, 67, 49, 87, 20, 22, 116, 33, 181, 176, 9, 26, 43, 18, 32, 93, 93, 11, 78, 65, 19, 153, 14, 193, 181, 7, 36, 9, 4, 51, 1, 68, 44, 32, 54, 84, 60, 50, 60, 1, 0, 164, 54, 48, 64, 75, 67, 8, 45, 116, 12, 94, 217, 7, 109, 116, 82, 157, 61, 36, 30, 2, 159, 8, 7, 33, 82, 4, 10, 12, 155, 5, 88, 97, 7, 2, 0, 223, 19, 198, 45, 99, 93, 87, 103, 213, 71, 0, 119, 25, 188, 82, 18, 49, 0, 80, 64, 86, 55, 73, 23, 59, 194, 3, 16, 61, 25, 74, 235, 287, 7, 43, 17, 46, 69, 10, 40, 362, 154, 19, 118, 71, 67, 64, 49, 17, 165, 5, 194, 4, 115, 46, 11, 100, 20, 30, 37, 10, 169, 23, 171, 28, 2, 170, 226, 34, 108, 115, 286, 90, 33, 40, 66, 51, 68, 53, 12, 7, 40, 157, 79, 85, 196, 14, 8, 10, 3, 14, 4, 91, 104, 12, 122, 57, 23, 51, 19, 27, 4, 25, 107, 1, 3, 161, 18, 102, 203, 157, 128, 224, 175, 7, 88, 57, 31, 92, 103, 50, 16, 38, 7, 91, 96, 14, 16, 6, 68, 104, 171, 103, 18, 98, 112, 230, 9, 5, 144, 3, 11, 95, 8, 102, 76, 25, 124, 76, 90, 52, 55, 86, 36, 138, 22, 4, 5, 197, 18, 79, 87, 7, 61, 85, 4, 160, 35, 203, 88, 3, 65, 35, 77, 227, 15, 17, 21, 15, 21, 171, 40, 34, 24, 183, 128, 70, 19, 1, 100, 116, 180, 8, 18, 0, 198, 38, 11, 272, 361, 33, 47, 7, 16, 81, 45, 14, 85, 82, 40, 34, 38, 40, 7, 28, 9, 27, 0, 80, 109, 96, 23, 22, 18, 177, 12, 34, 218, 63, 186, 88, 56, 54, 188, 48, 75, 99, 0, 45, 32, 2, 16, 0, 67, 132, 131, 201, 67, 63, 99, 14, 5, 194, 163, 158, 182, 189, 1, 110, 23, 14, 2, 4, 3, 10, 56, 4, 231, 187, 76, 119, 102, 29, 36, 2, 47, 10, 44, 74, 19, 8, 52, 154, 218, 22, 2, 9, 45, 23, 5, 29, 57, 100, 64, 100, 84, 26, 78, 19, 47, 0, 138, 10, 112, 35, 55, 74, 227, 2, 34, 46, 102, 3, 5, 94, 3, 25, 116, 219, 321, 0, 111)), p = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), args = c("noremoveDuplicates", "noautofeature", "noquadratic", "nohinge", "noproduct", "nothreshold", "betamultiplier=1"))
5: do.call(enm@fun, mod.full.args)
6: cv.enm(d, envs, enm, partitions, tune.tbl.i, doClamp, other.settings, partition.settings, user.val.grps, occs.testing.z, user.eval, algorithm, quiet)
7: tune.regular(d, envs, enm, partitions, tune.tbl, doClamp, other.settings, partition.settings, user.val.grps, occs.testing.z, updateProgress, user.eval, algorithm, quiet)
8: 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)
9: model_maxent(occs = occs, bg = bg, user.grp = partblock, bgMsk = envs, rms, rmsStep, fcs, clampSel = TRUE, algMaxent = i, parallel = FALSE)
10: eval(code, test_env)
11: eval(code, test_env)
12: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
20: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
21: source_file(path, env = env(env), desc = desc, error_call = error_call)
22: FUN(X[[i]], ...)
23: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
28: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
29: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
30: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
31: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
32: test_check("wallace")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-oldrel-macos-arm64
Version: 2.1.3
Check: tests
Result: ERROR
Running 'testthat.R' [212s]
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\4.3\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\4.3\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\4.3\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\4.3\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\4.3\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\4.3\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 191 ]
══ 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 191 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64