Last updated on 2023-07-07 06:51:23 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6.5 | 46.46 | 262.43 | 308.89 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.6.5 | 36.48 | 214.22 | 250.70 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.6.5 | 346.27 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.6.5 | 463.03 | ERROR | |||
| r-devel-windows-x86_64 | 0.6.5 | 35.00 | 305.00 | 340.00 | ERROR | |
| r-patched-linux-x86_64 | 0.6.5 | 36.70 | 251.01 | 287.71 | ERROR | |
| r-release-linux-x86_64 | 0.6.5 | 31.85 | 245.99 | 277.84 | ERROR | |
| r-release-macos-arm64 | 0.6.5 | 174.00 | NOTE | |||
| r-release-macos-x86_64 | 0.6.5 | 360.00 | NOTE | |||
| r-release-windows-x86_64 | 0.6.5 | 53.00 | 425.00 | 478.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.6.5 | 133.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.6.5 | 256.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.6.5 | 51.00 | 379.00 | 430.00 | ERROR |
Version: 0.6.5
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘SDMTools’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.6.5
Check: tests
Result: ERROR
Running ‘test-all.R’ [22s/29s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("zoon")
Loading required package: zoon
Loading required package: raster
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Please note that rgdal will be retired during October 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
rgdal: version: 1.6-7, (SVN revision 1203)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.7.0, released 2023/05/02
Path to GDAL shared files: /usr/share/gdal
GDAL does not use iconv for recoding strings.
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 9.2.1, June 1st, 2023, [PJ_VERSION: 921]
Path to PROJ shared files: /home/hornik/.local/share/proj:/usr/share/proj
PROJ CDN enabled: TRUE
Linking to sp version:2.0-0
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Please note that 'maptools' will be retired during October 2023,
plan transition at your earliest convenience (see
https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
for guidance);some functionality will be moved to 'sp'.
Checking rgeos availability: FALSE
[ FAIL 4 | WARN 72 | SKIP 31 | PASS 192 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• On CRAN (31): 'testChangeWorkflow.R:4:3', 'testChangeWorkflow.R:32:3',
'testChangeWorkflow.R:153:3', 'testChangeWorkflow.R:230:3',
'testChangeWorkflow.R:298:3', 'testGetMaxEnt.R:6:3',
'testModuleArguments.R:4:3', 'testRerunWorkflow.R:9:3',
'testRerunWorkflow.R:29:3', 'testRerunWorkflow.R:52:3',
'testRerunWorkflow.R:99:3', 'testRerunWorkflow.R:131:3',
'testRerunWorkflow.R:163:3', 'testWholeWorkflows.R:14:3',
'testWholeWorkflows.R:47:3', 'testWholeWorkflows.R:78:3',
'testWholeWorkflows.R:109:3', 'testWholeWorkflows.R:218:3',
'testWholeWorkflows.R:260:3', 'testWholeWorkflows.R:290:3',
'testWholeWorkflows.R:426:3', 'testWholeWorkflows.R:458:3',
'testWholeWorkflows.R:525:3', 'testZoonCitation.R:4:3',
'testcall_path.R:4:3', 'testplot.zoonCitation.R:4:3',
'testplot.zoonWorkflow.r:6:3', 'testplot.zoonWorkflow.r:66:3',
'testprint.zoonWorkflow.R:4:3', 'testsummary.zoonWorkflow.R:4:3',
'testtestModule.R:4:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testTransformCRS.R:25:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")` threw an error with unexpected message.
Expected match: "CRS provided in occurrence data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:25:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Failure ('testTransformCRS.R:29:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data, "tom")` threw an error with unexpected message.
Expected match: "CRS provided in covariate data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:29:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data, "tom")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:62:3'): occurrence data is handled as expected when CRSs vary ──
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:62:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:191:3'): Handles NA values and blanks ────────────
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:191:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
[ FAIL 4 | WARN 72 | SKIP 31 | PASS 192 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.6.5
Check: tests
Result: ERROR
Running ‘test-all.R’ [18s/24s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("zoon")
Loading required package: zoon
Loading required package: raster
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Please note that rgdal will be retired during October 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
rgdal: version: 1.6-7, (SVN revision 1203)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.7.0, released 2023/05/02
Path to GDAL shared files: /usr/share/gdal
GDAL does not use iconv for recoding strings.
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 9.2.1, June 1st, 2023, [PJ_VERSION: 921]
Path to PROJ shared files: /home/hornik/.local/share/proj:/usr/share/proj
PROJ CDN enabled: TRUE
Linking to sp version:2.0-0
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Please note that 'maptools' will be retired during October 2023,
plan transition at your earliest convenience (see
https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
for guidance);some functionality will be moved to 'sp'.
Checking rgeos availability: FALSE
[ FAIL 4 | WARN 73 | SKIP 31 | PASS 192 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• On CRAN (31): 'testChangeWorkflow.R:4:3', 'testChangeWorkflow.R:32:3',
'testChangeWorkflow.R:153:3', 'testChangeWorkflow.R:230:3',
'testChangeWorkflow.R:298:3', 'testGetMaxEnt.R:6:3',
'testModuleArguments.R:4:3', 'testRerunWorkflow.R:9:3',
'testRerunWorkflow.R:29:3', 'testRerunWorkflow.R:52:3',
'testRerunWorkflow.R:99:3', 'testRerunWorkflow.R:131:3',
'testRerunWorkflow.R:163:3', 'testWholeWorkflows.R:14:3',
'testWholeWorkflows.R:47:3', 'testWholeWorkflows.R:78:3',
'testWholeWorkflows.R:109:3', 'testWholeWorkflows.R:218:3',
'testWholeWorkflows.R:260:3', 'testWholeWorkflows.R:290:3',
'testWholeWorkflows.R:426:3', 'testWholeWorkflows.R:458:3',
'testWholeWorkflows.R:525:3', 'testZoonCitation.R:4:3',
'testcall_path.R:4:3', 'testplot.zoonCitation.R:4:3',
'testplot.zoonWorkflow.r:6:3', 'testplot.zoonWorkflow.r:66:3',
'testprint.zoonWorkflow.R:4:3', 'testsummary.zoonWorkflow.R:4:3',
'testtestModule.R:4:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testTransformCRS.R:25:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")` threw an error with unexpected message.
Expected match: "CRS provided in occurrence data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:25:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Failure ('testTransformCRS.R:29:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data, "tom")` threw an error with unexpected message.
Expected match: "CRS provided in covariate data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:29:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data, "tom")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:62:3'): occurrence data is handled as expected when CRSs vary ──
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:62:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:191:3'): Handles NA values and blanks ────────────
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:191:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
[ FAIL 4 | WARN 73 | SKIP 31 | PASS 192 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.5
Check: tests
Result: ERROR
Running ‘test-all.R’ [23s/33s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("zoon")
Loading required package: zoon
Loading required package: raster
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Please note that rgdal will be retired during October 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
rgdal: version: 1.6-7, (SVN revision 1203)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.4.3, released 2022/04/22
Path to GDAL shared files: /usr/local/clang/share/gdal
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 8.2.1, January 1st, 2022, [PJ_VERSION: 821]
Path to PROJ shared files: /data/gannet/ripley/.local/share/proj:/usr/local/share/proj:/usr/local/share/proj
PROJ CDN enabled: TRUE
Linking to sp version:2.0-0
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Please note that 'maptools' will be retired during October 2023,
plan transition at your earliest convenience (see
https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
for guidance);some functionality will be moved to 'sp'.
Checking rgeos availability: FALSE
[ FAIL 4 | WARN 72 | SKIP 31 | PASS 192 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• On CRAN (31): 'testChangeWorkflow.R:4:3', 'testChangeWorkflow.R:32:3',
'testChangeWorkflow.R:153:3', 'testChangeWorkflow.R:230:3',
'testChangeWorkflow.R:298:3', 'testGetMaxEnt.R:6:3',
'testModuleArguments.R:4:3', 'testRerunWorkflow.R:9:3',
'testRerunWorkflow.R:29:3', 'testRerunWorkflow.R:52:3',
'testRerunWorkflow.R:99:3', 'testRerunWorkflow.R:131:3',
'testRerunWorkflow.R:163:3', 'testWholeWorkflows.R:14:3',
'testWholeWorkflows.R:47:3', 'testWholeWorkflows.R:78:3',
'testWholeWorkflows.R:109:3', 'testWholeWorkflows.R:218:3',
'testWholeWorkflows.R:260:3', 'testWholeWorkflows.R:290:3',
'testWholeWorkflows.R:426:3', 'testWholeWorkflows.R:458:3',
'testWholeWorkflows.R:525:3', 'testZoonCitation.R:4:3',
'testcall_path.R:4:3', 'testplot.zoonCitation.R:4:3',
'testplot.zoonWorkflow.r:6:3', 'testplot.zoonWorkflow.r:66:3',
'testprint.zoonWorkflow.R:4:3', 'testsummary.zoonWorkflow.R:4:3',
'testtestModule.R:4:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testTransformCRS.R:25:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")` threw an error with unexpected message.
Expected match: "CRS provided in occurrence data"
Actual message: "source crs creation failed: Unknown error (code 4096)"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:25:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Failure ('testTransformCRS.R:29:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data, "tom")` threw an error with unexpected message.
Expected match: "CRS provided in covariate data"
Actual message: "source crs creation failed: Unknown error (code 4096)"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:29:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data, "tom")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:62:3'): occurrence data is handled as expected when CRSs vary ──
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Unknown error (code 4096)
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:62:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:191:3'): Handles NA values and blanks ────────────
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Unknown error (code 4096)
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:191:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
[ FAIL 4 | WARN 72 | SKIP 31 | PASS 192 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.6.5
Check: tests
Result: ERROR
Running ‘test-all.R’ [37s/46s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("zoon")
Loading required package: zoon
Loading required package: raster
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Please note that rgdal will be retired during October 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
rgdal: version: 1.6-7, (SVN revision 1203)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.4.3, released 2022/04/22
Path to GDAL shared files: /usr/local/share/gdal
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 8.2.1, January 1st, 2022, [PJ_VERSION: 821]
Path to PROJ shared files: /data/gannet/ripley/.local/share/proj:/usr/local/share/proj:/usr/local/share/proj
PROJ CDN enabled: TRUE
Linking to sp version:2.0-0
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Please note that 'maptools' will be retired during October 2023,
plan transition at your earliest convenience (see
https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
for guidance);some functionality will be moved to 'sp'.
Checking rgeos availability: TRUE
non finite transformation detected:
X Y
2 788305.1 593866.933 Inf Inf
4 883017.4 853430.239 Inf Inf
5 940467.3 847739.158 Inf Inf
8 892419.0 295400.081 Inf Inf
11 956833.3 462098.858 Inf Inf
16 899825.0 773686.039 Inf Inf
20 954503.6 279223.811 Inf Inf
21 889539.3 461216.570 Inf Inf
22 692803.4 792738.342 Inf Inf
24 994269.8 394758.986 Inf Inf
25 655705.8 811237.350 Inf Inf
26 708530.5 318563.094 Inf Inf
31 963024.2 231230.884 Inf Inf
32 902299.0 543232.898 Inf Inf
33 690705.3 447570.141 Inf Inf
34 795467.4 130288.137 Inf Inf
37 758459.5 149244.214 Inf Inf
50 857827.7 992615.674 Inf Inf
53 798924.8 891896.270 Inf Inf
58 753307.9 243435.242 Inf Inf
59 895045.4 288266.205 Inf Inf
61 665115.2 727533.633 Inf Inf
65 814640.0 77721.554 Inf Inf
67 810064.4 550922.729 Inf Inf
68 812389.5 135865.396 Inf Inf
69 794342.3 974163.694 Inf Inf
71 754475.2 788409.382 Inf Inf
73 710182.4 878041.775 Inf Inf
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734 924479.0 937016.558 Inf Inf
737 804256.3 299015.456 Inf Inf
738 988963.4 809346.275 Inf Inf
741 992170.6 127309.736 Inf Inf
747 795422.0 816874.062 Inf Inf
749 695020.7 931066.286 Inf Inf
750 948631.5 368689.882 Inf Inf
758 888371.6 401043.247 Inf Inf
769 683010.3 705844.125 Inf Inf
770 653427.8 908724.687 Inf Inf
771 915986.3 676292.887 Inf Inf
772 813113.1 639100.271 Inf Inf
774 807499.1 601125.390 Inf Inf
780 808612.0 471993.161 Inf Inf
782 819467.1 272080.335 Inf Inf
784 654400.8 613353.652 Inf Inf
785 811719.6 132121.966 Inf Inf
790 915272.6 845951.730 Inf Inf
791 933696.5 241650.385 Inf Inf
795 801148.7 362249.210 Inf Inf
806 968641.2 49999.777 Inf Inf
809 748792.9 860954.337 Inf Inf
810 667640.2 518467.249 Inf Inf
812 695105.2 597377.663 Inf Inf
814 884133.6 689286.038 Inf Inf
815 775297.2 480631.645 Inf Inf
821 688721.1 994994.513 Inf Inf
824 991034.3 869539.095 Inf Inf
825 743204.9 540192.957 Inf Inf
830 733952.1 769810.297 Inf Inf
832 771909.5 500742.103 Inf Inf
834 720840.4 208074.670 Inf Inf
837 703813.0 660112.250 Inf Inf
841 962421.3 339431.246 Inf Inf
842 736334.0 481646.265 Inf Inf
847 898360.8 642451.295 Inf Inf
852 726398.9 853324.018 Inf Inf
853 991745.2 461963.777 Inf Inf
854 715133.5 71348.248 Inf Inf
857 948825.3 993576.777 Inf Inf
860 889021.5 938556.002 Inf Inf
873 761985.3 246099.455 Inf Inf
875 860989.4 235524.395 Inf Inf
876 673555.0 935756.926 Inf Inf
878 693198.9 137449.405 Inf Inf
879 891713.7 914364.723 Inf Inf
882 921065.2 142635.179 Inf Inf
883 675362.4 359432.871 Inf Inf
885 745341.8 45905.947 Inf Inf
886 942598.9 784547.902 Inf Inf
892 756650.1 990823.733 Inf Inf
895 811463.7 977608.161 Inf Inf
896 759166.8 558046.242 Inf Inf
900 797902.9 535777.904 Inf Inf
901 923699.2 443831.585 Inf Inf
903 852364.6 157357.536 Inf Inf
905 668323.6 562044.856 Inf Inf
907 762750.6 592365.286 Inf Inf
908 903362.3 727812.863 Inf Inf
909 820474.5 638925.285 Inf Inf
913 866560.2 587341.380 Inf Inf
916 959465.8 82270.042 Inf Inf
921 808386.3 783530.072 Inf Inf
924 856597.0 499104.955 Inf Inf
925 697946.6 562260.535 Inf Inf
926 684486.5 378257.021 Inf Inf
930 784931.6 961061.001 Inf Inf
931 886862.6 527810.140 Inf Inf
933 770623.0 32266.997 Inf Inf
935 957669.7 47348.294 Inf Inf
938 873151.4 805923.975 Inf Inf
939 869706.1 280597.516 Inf Inf
941 975889.7 521825.815 Inf Inf
953 956579.8 211996.233 Inf Inf
956 962615.3 474116.867 Inf Inf
965 907946.4 380004.248 Inf Inf
969 762028.3 934783.353 Inf Inf
971 781968.9 220802.745 Inf Inf
973 819844.7 467288.806 Inf Inf
977 948118.8 144893.147 Inf Inf
982 711692.6 459158.475 Inf Inf
983 919848.1 141365.049 Inf Inf
985 902181.8 675293.500 Inf Inf
986 757329.2 138030.211 Inf Inf
996 829623.9 893417.772 Inf Inf
999 709579.9 401606.648 Inf Inf
[ FAIL 2 | WARN 8 | SKIP 31 | PASS 194 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• On CRAN (31): 'testChangeWorkflow.R:4:3', 'testChangeWorkflow.R:32:3',
'testChangeWorkflow.R:153:3', 'testChangeWorkflow.R:230:3',
'testChangeWorkflow.R:298:3', 'testGetMaxEnt.R:6:3',
'testModuleArguments.R:4:3', 'testRerunWorkflow.R:9:3',
'testRerunWorkflow.R:29:3', 'testRerunWorkflow.R:52:3',
'testRerunWorkflow.R:99:3', 'testRerunWorkflow.R:131:3',
'testRerunWorkflow.R:163:3', 'testWholeWorkflows.R:14:3',
'testWholeWorkflows.R:47:3', 'testWholeWorkflows.R:78:3',
'testWholeWorkflows.R:109:3', 'testWholeWorkflows.R:218:3',
'testWholeWorkflows.R:260:3', 'testWholeWorkflows.R:290:3',
'testWholeWorkflows.R:426:3', 'testWholeWorkflows.R:458:3',
'testWholeWorkflows.R:525:3', 'testZoonCitation.R:4:3',
'testcall_path.R:4:3', 'testplot.zoonCitation.R:4:3',
'testplot.zoonWorkflow.r:6:3', 'testplot.zoonWorkflow.r:66:3',
'testprint.zoonWorkflow.R:4:3', 'testsummary.zoonWorkflow.R:4:3',
'testtestModule.R:4:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testTransformCRS.R:62:3'): occurrence data is handled as expected when CRSs vary ──
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: failure in points 2:4:5:8:11:16:20:21:22:24:25:26:31:32:33:34:37:50:53:58:59:61:65:67:68:69:71:73:84:87:88:89:97:104:106:107:111:114:115:118:126:130:132:133:134:136:137:138:139:145:150:151:167:173:174:179:181:183:189:190:193:195:202:206:214:216:219:220:222:223:224:229:230:238:240:246:248:249:250:256:260:261:262:264:271:275:276:277:281:290:294:295:296:297:300:301:303:304:313:316:317:320:321:324:327:330:333:334:337:339:340:347:352:356:360:363:366:373:376:377:380:382:384:386:391:393:394:400:401:403:407:410:412:417:425:430:431:434:443:445:446:447:450:456:457:458:461:468:470:472:474:475:480:482:484:485:488:490:491:494:496:499:500:509:513:515:518:520:527:529:531:532:534:536:538:541:543:545:546:548:549:554:557:562:563:568:570:572:575:576:581:582:583:585:588:589:593:596:599:602:606:608:614:616:617:618:619:621:622:623:628:631:632:634:637:638:639:642:643:647:651:652:655:656:657:661:662:664:667:677:681:682:683:684:685:701:704:714:719:722:723:724:726:727:729:732:734:737:738:741:747:749:750:758:769:770:771:772:774:780:782:784:785:790:791:795:806:809:810:812:814:815:821:824:825:830:832:834:837:841:842:847:852:853:854:857:860:873:875:876:878:879:882:883:885:886:892:895:896:900:901:903:905:907:908:909:913:916:921:924:925:926:930:931:933:935:938:939:941:953:956:965:969:971:973:977:982:983:985:986:996:999
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:62:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:191:3'): Handles NA values and blanks ────────────
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: failure in points 1:2:3:6:9:14:18:19:20:22:23:24:29:30:31:32:35:48:51:56:57:59:63:65:66:67:69:71:82:85:86:87:95:102:104:105:109:112:113:116:124:128:130:131:132:134:135:136:137:143:148:149:165:171:172:177:179:181:187:188:191:193:200:204:212:214:217:218:220:221:222:227:228:236:238:244:246:247:248:254:258:259:260:262:269:273:274:275:279:288:292:293:294:295:298:299:301:302:311:314:315:318:319:322:325:328:331:332:335:337:338:345:350:354:358:361:364:371:374:375:378:380:382:384:389:391:392:398:399:401:405:408:410:415:423:428:429:432:441:443:444:445:448:454:455:456:459:466:468:470:472:473:478:480:482:483:486:488:489:492:494:497:498:507:511:513:516:518:525:527:529:530:532:534:536:539:541:543:544:546:547:552:555:560:561:566:568:570:573:574:579:580:581:583:586:587:591:594:597:600:604:606:612:614:615:616:617:619:620:621:626:629:630:632:635:636:637:640:641:645:649:650:653:654:655:659:660:662:665:675:679:680:681:682:683:699:702:712:717:720:721:722:724:725:727:730:732:735:736:739:745:747:748:756:767:768:769:770:772:778:780:782:783:788:789:793:804:807:808:810:812:813:819:822:823:828:830:832:835:839:840:845:850:851:852:855:858:871:873:874:876:877:880:881:883:884:890:893:894:898:899:901:903:905:906:907:911:914:919:922:923:924:928:929:931:933:936:937:939:951:954:963:967:969:971:975:980:981:983:984:994:997
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:191:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
[ FAIL 2 | WARN 8 | SKIP 31 | PASS 194 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.6.5
Check: tests
Result: ERROR
Running 'test-all.R' [31s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("zoon")
Loading required package: zoon
Loading required package: raster
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Please note that rgdal will be retired during October 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
rgdal: version: 1.6-7, (SVN revision 1203)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.6.2, released 2023/01/02
Path to GDAL shared files: D:/RCompile/CRANpkg/lib/4.4/rgdal/gdal
GDAL does not use iconv for recoding strings.
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 9.2.0, March 1st, 2023, [PJ_VERSION: 920]
Path to PROJ shared files: D:/RCompile/CRANpkg/lib/4.4/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:2.0-0
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Please note that 'maptools' will be retired during October 2023,
plan transition at your earliest convenience (see
https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
for guidance);some functionality will be moved to 'sp'.
Checking rgeos availability: FALSE
[ FAIL 4 | WARN 73 | SKIP 31 | PASS 192 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• On CRAN (31): 'testChangeWorkflow.R:4:3', 'testChangeWorkflow.R:32:3',
'testChangeWorkflow.R:153:3', 'testChangeWorkflow.R:230:3',
'testChangeWorkflow.R:298:3', 'testGetMaxEnt.R:6:3',
'testModuleArguments.R:4:3', 'testRerunWorkflow.R:9:3',
'testRerunWorkflow.R:29:3', 'testRerunWorkflow.R:52:3',
'testRerunWorkflow.R:99:3', 'testRerunWorkflow.R:131:3',
'testRerunWorkflow.R:163:3', 'testWholeWorkflows.R:14:3',
'testWholeWorkflows.R:47:3', 'testWholeWorkflows.R:78:3',
'testWholeWorkflows.R:109:3', 'testWholeWorkflows.R:218:3',
'testWholeWorkflows.R:260:3', 'testWholeWorkflows.R:290:3',
'testWholeWorkflows.R:426:3', 'testWholeWorkflows.R:458:3',
'testWholeWorkflows.R:525:3', 'testZoonCitation.R:4:3',
'testcall_path.R:4:3', 'testplot.zoonCitation.R:4:3',
'testplot.zoonWorkflow.r:6:3', 'testplot.zoonWorkflow.r:66:3',
'testprint.zoonWorkflow.R:4:3', 'testsummary.zoonWorkflow.R:4:3',
'testtestModule.R:4:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testTransformCRS.R:25:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")` threw an error with unexpected message.
Expected match: "CRS provided in occurrence data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:25:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Failure ('testTransformCRS.R:29:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data, "tom")` threw an error with unexpected message.
Expected match: "CRS provided in covariate data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:29:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data, "tom")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:62:3'): occurrence data is handled as expected when CRSs vary ──
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:62:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:191:3'): Handles NA values and blanks ────────────
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:191:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
[ FAIL 4 | WARN 73 | SKIP 31 | PASS 192 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.6.5
Check: tests
Result: ERROR
Running ‘test-all.R’ [21s/28s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("zoon")
Loading required package: zoon
Loading required package: raster
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Please note that rgdal will be retired during October 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
rgdal: version: 1.6-7, (SVN revision 1203)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.7.0, released 2023/05/02
Path to GDAL shared files: /usr/share/gdal
GDAL does not use iconv for recoding strings.
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 9.2.1, June 1st, 2023, [PJ_VERSION: 921]
Path to PROJ shared files: /home/hornik/.local/share/proj:/usr/share/proj
PROJ CDN enabled: TRUE
Linking to sp version:2.0-0
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Please note that 'maptools' will be retired during October 2023,
plan transition at your earliest convenience (see
https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
for guidance);some functionality will be moved to 'sp'.
Checking rgeos availability: FALSE
[ FAIL 4 | WARN 73 | SKIP 31 | PASS 192 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• On CRAN (31): 'testChangeWorkflow.R:4:3', 'testChangeWorkflow.R:32:3',
'testChangeWorkflow.R:153:3', 'testChangeWorkflow.R:230:3',
'testChangeWorkflow.R:298:3', 'testGetMaxEnt.R:6:3',
'testModuleArguments.R:4:3', 'testRerunWorkflow.R:9:3',
'testRerunWorkflow.R:29:3', 'testRerunWorkflow.R:52:3',
'testRerunWorkflow.R:99:3', 'testRerunWorkflow.R:131:3',
'testRerunWorkflow.R:163:3', 'testWholeWorkflows.R:14:3',
'testWholeWorkflows.R:47:3', 'testWholeWorkflows.R:78:3',
'testWholeWorkflows.R:109:3', 'testWholeWorkflows.R:218:3',
'testWholeWorkflows.R:260:3', 'testWholeWorkflows.R:290:3',
'testWholeWorkflows.R:426:3', 'testWholeWorkflows.R:458:3',
'testWholeWorkflows.R:525:3', 'testZoonCitation.R:4:3',
'testcall_path.R:4:3', 'testplot.zoonCitation.R:4:3',
'testplot.zoonWorkflow.r:6:3', 'testplot.zoonWorkflow.r:66:3',
'testprint.zoonWorkflow.R:4:3', 'testsummary.zoonWorkflow.R:4:3',
'testtestModule.R:4:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testTransformCRS.R:25:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")` threw an error with unexpected message.
Expected match: "CRS provided in occurrence data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:25:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Failure ('testTransformCRS.R:29:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data, "tom")` threw an error with unexpected message.
Expected match: "CRS provided in covariate data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:29:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data, "tom")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:62:3'): occurrence data is handled as expected when CRSs vary ──
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:62:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:191:3'): Handles NA values and blanks ────────────
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:191:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
[ FAIL 4 | WARN 73 | SKIP 31 | PASS 192 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.6.5
Check: tests
Result: ERROR
Running ‘test-all.R’ [20s/27s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("zoon")
Loading required package: zoon
Loading required package: raster
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Please note that rgdal will be retired during October 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
rgdal: version: 1.6-7, (SVN revision 1203)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.7.0, released 2023/05/02
Path to GDAL shared files: /usr/share/gdal
GDAL does not use iconv for recoding strings.
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 9.2.1, June 1st, 2023, [PJ_VERSION: 921]
Path to PROJ shared files: /home/hornik/.local/share/proj:/usr/share/proj
PROJ CDN enabled: TRUE
Linking to sp version:2.0-0
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Please note that 'maptools' will be retired during October 2023,
plan transition at your earliest convenience (see
https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
for guidance);some functionality will be moved to 'sp'.
Checking rgeos availability: FALSE
[ FAIL 4 | WARN 73 | SKIP 31 | PASS 192 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• On CRAN (31): 'testChangeWorkflow.R:4:3', 'testChangeWorkflow.R:32:3',
'testChangeWorkflow.R:153:3', 'testChangeWorkflow.R:230:3',
'testChangeWorkflow.R:298:3', 'testGetMaxEnt.R:6:3',
'testModuleArguments.R:4:3', 'testRerunWorkflow.R:9:3',
'testRerunWorkflow.R:29:3', 'testRerunWorkflow.R:52:3',
'testRerunWorkflow.R:99:3', 'testRerunWorkflow.R:131:3',
'testRerunWorkflow.R:163:3', 'testWholeWorkflows.R:14:3',
'testWholeWorkflows.R:47:3', 'testWholeWorkflows.R:78:3',
'testWholeWorkflows.R:109:3', 'testWholeWorkflows.R:218:3',
'testWholeWorkflows.R:260:3', 'testWholeWorkflows.R:290:3',
'testWholeWorkflows.R:426:3', 'testWholeWorkflows.R:458:3',
'testWholeWorkflows.R:525:3', 'testZoonCitation.R:4:3',
'testcall_path.R:4:3', 'testplot.zoonCitation.R:4:3',
'testplot.zoonWorkflow.r:6:3', 'testplot.zoonWorkflow.r:66:3',
'testprint.zoonWorkflow.R:4:3', 'testsummary.zoonWorkflow.R:4:3',
'testtestModule.R:4:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testTransformCRS.R:25:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")` threw an error with unexpected message.
Expected match: "CRS provided in occurrence data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:25:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Failure ('testTransformCRS.R:29:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data, "tom")` threw an error with unexpected message.
Expected match: "CRS provided in covariate data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:29:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data, "tom")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:62:3'): occurrence data is handled as expected when CRSs vary ──
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:62:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:191:3'): Handles NA values and blanks ────────────
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:191:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
[ FAIL 4 | WARN 73 | SKIP 31 | PASS 192 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.6.5
Check: tests
Result: ERROR
Running 'test-all.R' [41s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("zoon")
Loading required package: zoon
Loading required package: raster
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Please note that rgdal will be retired during October 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
rgdal: version: 1.6-7, (SVN revision 1203)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.6.2, released 2023/01/02
Path to GDAL shared files: D:/RCompile/CRANpkg/lib/4.3/rgdal/gdal
GDAL does not use iconv for recoding strings.
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 9.2.0, March 1st, 2023, [PJ_VERSION: 920]
Path to PROJ shared files: D:/RCompile/CRANpkg/lib/4.3/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:2.0-0
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Please note that 'maptools' will be retired during October 2023,
plan transition at your earliest convenience (see
https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
for guidance);some functionality will be moved to 'sp'.
Checking rgeos availability: FALSE
[ FAIL 4 | WARN 72 | SKIP 31 | PASS 192 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• On CRAN (31): 'testChangeWorkflow.R:4:3', 'testChangeWorkflow.R:32:3',
'testChangeWorkflow.R:153:3', 'testChangeWorkflow.R:230:3',
'testChangeWorkflow.R:298:3', 'testGetMaxEnt.R:6:3',
'testModuleArguments.R:4:3', 'testRerunWorkflow.R:9:3',
'testRerunWorkflow.R:29:3', 'testRerunWorkflow.R:52:3',
'testRerunWorkflow.R:99:3', 'testRerunWorkflow.R:131:3',
'testRerunWorkflow.R:163:3', 'testWholeWorkflows.R:14:3',
'testWholeWorkflows.R:47:3', 'testWholeWorkflows.R:78:3',
'testWholeWorkflows.R:109:3', 'testWholeWorkflows.R:218:3',
'testWholeWorkflows.R:260:3', 'testWholeWorkflows.R:290:3',
'testWholeWorkflows.R:426:3', 'testWholeWorkflows.R:458:3',
'testWholeWorkflows.R:525:3', 'testZoonCitation.R:4:3',
'testcall_path.R:4:3', 'testplot.zoonCitation.R:4:3',
'testplot.zoonWorkflow.r:6:3', 'testplot.zoonWorkflow.r:66:3',
'testprint.zoonWorkflow.R:4:3', 'testsummary.zoonWorkflow.R:4:3',
'testtestModule.R:4:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testTransformCRS.R:25:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")` threw an error with unexpected message.
Expected match: "CRS provided in occurrence data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:25:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Failure ('testTransformCRS.R:29:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data, "tom")` threw an error with unexpected message.
Expected match: "CRS provided in covariate data"
Actual message: "source crs creation failed: Invalid PROJ string syntax"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:29:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data, "tom")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:62:3'): occurrence data is handled as expected when CRSs vary ──
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:62:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:191:3'): Handles NA values and blanks ────────────
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Invalid PROJ string syntax
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:191:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
[ FAIL 4 | WARN 72 | SKIP 31 | PASS 192 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.6.5
Check: tests
Result: ERROR
Running 'test-all.R' [40s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("zoon")
Loading required package: zoon
Loading required package: raster
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Please note that rgdal will be retired during October 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
rgdal: version: 1.6-7, (SVN revision 1203)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.5.2, released 2022/09/02
Path to GDAL shared files: D:/RCompile/CRANpkg/lib/4.2/rgdal/gdal
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 8.2.1, January 1st, 2022, [PJ_VERSION: 821]
Path to PROJ shared files: D:/RCompile/CRANpkg/lib/4.2/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:2.0-0
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Please note that 'maptools' will be retired during October 2023,
plan transition at your earliest convenience (see
https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
for guidance);some functionality will be moved to 'sp'.
Checking rgeos availability: FALSE
[ FAIL 4 | WARN 72 | SKIP 31 | PASS 192 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• On CRAN (31): 'testChangeWorkflow.R:4:3', 'testChangeWorkflow.R:32:3',
'testChangeWorkflow.R:153:3', 'testChangeWorkflow.R:230:3',
'testChangeWorkflow.R:298:3', 'testGetMaxEnt.R:6:3',
'testModuleArguments.R:4:3', 'testRerunWorkflow.R:9:3',
'testRerunWorkflow.R:29:3', 'testRerunWorkflow.R:52:3',
'testRerunWorkflow.R:99:3', 'testRerunWorkflow.R:131:3',
'testRerunWorkflow.R:163:3', 'testWholeWorkflows.R:14:3',
'testWholeWorkflows.R:47:3', 'testWholeWorkflows.R:78:3',
'testWholeWorkflows.R:109:3', 'testWholeWorkflows.R:218:3',
'testWholeWorkflows.R:260:3', 'testWholeWorkflows.R:290:3',
'testWholeWorkflows.R:426:3', 'testWholeWorkflows.R:458:3',
'testWholeWorkflows.R:525:3', 'testZoonCitation.R:4:3',
'testcall_path.R:4:3', 'testplot.zoonCitation.R:4:3',
'testplot.zoonWorkflow.r:6:3', 'testplot.zoonWorkflow.r:66:3',
'testprint.zoonWorkflow.R:4:3', 'testsummary.zoonWorkflow.R:4:3',
'testtestModule.R:4:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testTransformCRS.R:25:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")` threw an error with unexpected message.
Expected match: "CRS provided in occurrence data"
Actual message: "source crs creation failed: Unknown error (code 4096)"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:25:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data_error, "+init=epsg:27700")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Failure ('testTransformCRS.R:29:3'): Expected errors ────────────────────────
`zoon:::TransformCRS(occ_data, "tom")` threw an error with unexpected message.
Expected match: "CRS provided in covariate data"
Actual message: "source crs creation failed: Unknown error (code 4096)"
Backtrace:
▆
1. ├─testthat::expect_error(...) at testTransformCRS.R:29:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─zoon:::TransformCRS(occ_data, "tom")
7. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
8. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:62:3'): occurrence data is handled as expected when CRSs vary ──
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Unknown error (code 4096)
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:62:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
── Error ('testTransformCRS.R:191:3'): Handles NA values and blanks ────────────
Error in `spTransform(x = LL_points, CRSobj = CRS(ras_projection))`: source crs creation failed: Unknown error (code 4096)
Backtrace:
▆
1. └─zoon:::TransformCRS(occ_data, "+init=epsg:4326") at testTransformCRS.R:191:2
2. ├─sp::spTransform(x = LL_points, CRSobj = CRS(ras_projection))
3. └─rgdal (local) spTransform(x = LL_points, CRSobj = CRS(ras_projection))
[ FAIL 4 | WARN 72 | SKIP 31 | PASS 192 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64