Last updated on 2024-12-23 12:49:49 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| gdm | 4 | 6 | 3 |
Current CRAN status: ERROR: 4, NOTE: 6, OK: 3
Version: 1.6.0-4
Check: tests
Result: ERROR
Running ‘tinytest.R’ [12s/13s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
>
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("gdm")
+ }
test_gdm.R.................... 0 tests terra 1.8.5
test_gdm.R.................... 0 tests
test_gdm.R.................... 0 tests
test_gdm.R.................... 0 tests
test_gdm.R.................... 0 tests
test_gdm.R.................... 1 tests <1b>[0;32mOK<1b>[0m
test_gdm.R.................... 1 tests <1b>[0;32mOK<1b>[0m
test_gdm.R.................... 2 tests <1b>[0;31m1 fails<1b>[0m
test_gdm.R.................... 3 tests <1b>[0;31m2 fails<1b>[0m
test_gdm.R.................... 3 tests <1b>[0;31m2 fails<1b>[0m Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'global': object 'trans_raster' not found
Calls: <Anonymous> ... eval -> eval -> <Anonymous> -> .handleSimpleError -> h
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.6.0-4
Check: examples
Result: ERROR
Running examples in ‘gdm-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gdm
> ### Title: Fit a Generalized Dissimilarity Model to Tabular Site-Pair Data
> ### Aliases: gdm
> ### Keywords: gdm
>
> ### ** Examples
>
> ##fit table environmental data
> # format site-pair table using the southwest data table
> head(southwest)
species site awcA phTotal sandA shcA solumDepth bio5 bio6
1 spp1 1066 14.4725 546.1800 71.3250 178.8650 875.1725 31.43824 5.058823
2 spp1 1026 16.2575 470.9950 68.8975 105.8400 928.4925 33.14412 4.852941
3 spp1 1025 23.1375 459.7425 71.4700 88.3550 892.2275 32.84000 4.817143
4 spp1 1026 16.2575 470.9950 68.8975 105.8400 928.4925 33.14412 4.852941
5 spp1 1027 17.0175 489.3950 74.6775 147.2125 951.9050 33.17813 4.590625
6 spp1 1047 17.3625 515.0825 75.7525 164.1875 981.4750 32.61579 4.676316
bio15 bio18 bio19 Lat Long
1 40.38235 0 132.6471 -32.99425 118.7573
2 48.20588 0 140.2941 -32.04285 118.3495
3 53.88571 43 145.0571 -31.99067 117.8260
4 48.20588 0 140.2941 -32.04285 118.3495
5 44.00000 0 135.6875 -32.09326 118.8736
6 42.00000 0 134.0263 -32.54354 118.8157
> sppData <- southwest[c(1,2,13,14)]
> envTab <- southwest[c(2:ncol(southwest))]
>
> sitePairTab <- formatsitepair(sppData, 2, XColumn="Long", YColumn="Lat", sppColumn="species",
+ siteColumn="site", predData=envTab)
Warning in formatsitepair(sppData, 2, XColumn = "Long", YColumn = "Lat", :
No abundance column was specified, so the biological data are assumed to be presences.
Aggregation function missing: defaulting to length
>
> ##fit table GDM
> gdmTabMod <- gdm(sitePairTab, geo=TRUE)
> summary(gdmTabMod)
[1]
[1]
[1] GDM Modelling Summary
[1] Creation Date: Sun Dec 22 15:13:51 2024
[1]
[1] Name: gdmTabMod
[1]
[1] Data: sitePairTab
[1]
[1] Samples: 4371
[1]
[1] Geographical distance used in model fitting? TRUE
[1]
[1] NULL Deviance: 651.914
[1] GDM Deviance: 129.025
[1] Percent Deviance Explained: 80.208
[1]
[1] Intercept: 0.277
[1]
[1] PREDICTOR ORDER BY SUM OF I-SPLINE COEFFICIENTS:
[1]
[1] Predictor 1: bio19
[1] Splines: 3
[1] Min Knot: 114.394
[1] 50% Knot: 172.416
[1] Max Knot: 554.771
[1] Coefficient[1]: 0.941
[1] Coefficient[2]: 0.868
[1] Coefficient[3]: 0
[1] Sum of coefficients for bio19: 1.809
[1]
[1] Predictor 2: phTotal
[1] Splines: 3
[1] Min Knot: 277.978
[1] 50% Knot: 584.609
[1] Max Knot: 1860.37
[1] Coefficient[1]: 1.127
[1] Coefficient[2]: 0.23
[1] Coefficient[3]: 0
[1] Sum of coefficients for phTotal: 1.357
[1]
[1] Predictor 3: bio5
[1] Splines: 3
[1] Min Knot: 25.571
[1] 50% Knot: 32.16
[1] Max Knot: 36.188
[1] Coefficient[1]: 0.127
[1] Coefficient[2]: 0.453
[1] Coefficient[3]: 0.114
[1] Sum of coefficients for bio5: 0.694
[1]
[1] Predictor 4: solumDepth
[1] Splines: 3
[1] Min Knot: 705.02
[1] 50% Knot: 1017.628
[1] Max Knot: 1247.705
[1] Coefficient[1]: 0.682
[1] Coefficient[2]: 0
[1] Coefficient[3]: 0
[1] Sum of coefficients for solumDepth: 0.682
[1]
[1] Predictor 5: awcA
[1] Splines: 3
[1] Min Knot: 12.975
[1] 50% Knot: 22.186
[1] Max Knot: 50.7
[1] Coefficient[1]: 0
[1] Coefficient[2]: 0
[1] Coefficient[3]: 0.523
[1] Sum of coefficients for awcA: 0.523
[1]
[1] Predictor 6: Geographic
[1] Splines: 3
[1] Min Knot: 0.452
[1] 50% Knot: 2.46
[1] Max Knot: 6.532
[1] Coefficient[1]: 0.014
[1] Coefficient[2]: 0.372
[1] Coefficient[3]: 0
[1] Sum of coefficients for Geographic: 0.386
[1]
[1] Predictor 7: sandA
[1] Splines: 3
[1] Min Knot: 56.697
[1] 50% Knot: 72.951
[1] Max Knot: 83.993
[1] Coefficient[1]: 0.092
[1] Coefficient[2]: 0
[1] Coefficient[3]: 0.139
[1] Sum of coefficients for sandA: 0.231
[1]
[1] Predictor 8: shcA
[1] Splines: 3
[1] Min Knot: 78.762
[1] 50% Knot: 179.351
[1] Max Knot: 521.985
[1] Coefficient[1]: 0
[1] Coefficient[2]: 0.156
[1] Coefficient[3]: 0
[1] Sum of coefficients for shcA: 0.156
[1]
[1] Predictor 9: bio6
[1] Splines: 3
[1] Min Knot: 4.373
[1] 50% Knot: 5.509
[1] Max Knot: 9.224
[1] Coefficient[1]: 0.121
[1] Coefficient[2]: 0
[1] Coefficient[3]: 0
[1] Sum of coefficients for bio6: 0.121
[1]
[1] Predictor 10: bio15
[1] Splines: 3
[1] Min Knot: 29.167
[1] 50% Knot: 55.008
[1] Max Knot: 87.143
[1] Coefficient[1]: 0.027
[1] Coefficient[2]: 0
[1] Coefficient[3]: 0
[1] Sum of coefficients for bio15: 0.027
[1]
[1] Predictor 11: bio18
[1] Splines: 3
[1] Min Knot: 0
[1] 50% Knot: 0
[1] Max Knot: 52
[1] Coefficient[1]: 0
[1] Coefficient[2]: 0
[1] Coefficient[3]: 0
[1] Sum of coefficients for bio18: 0
>
> ##fit raster environmental data
> ##sets up site-pair table
> rastFile <- system.file("./extdata/swBioclims.grd", package="gdm")
> envRast <- terra::rast(rastFile)
Error in loadNamespace(x) : there is no package called ‘terra’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.6.0-4
Check: tests
Result: ERROR
Running ‘tinytest.R’ [2s/2s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
>
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("gdm")
+ }
test_gdm.R.................... 0 tests Error in library(terra) : there is no package called 'terra'
Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> library
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.6.0-4
Check: tests
Result: ERROR
Running ‘tinytest.R’ [11s/15s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
>
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("gdm")
+ }
test_gdm.R.................... 0 tests terra 1.8.5
test_gdm.R.................... 0 tests
test_gdm.R.................... 0 tests
test_gdm.R.................... 0 tests
test_gdm.R.................... 0 tests
test_gdm.R.................... 1 tests <1b>[0;32mOK<1b>[0m
test_gdm.R.................... 1 tests <1b>[0;32mOK<1b>[0m
test_gdm.R.................... 2 tests <1b>[0;31m1 fails<1b>[0m
test_gdm.R.................... 3 tests <1b>[0;31m2 fails<1b>[0m
test_gdm.R.................... 3 tests <1b>[0;31m2 fails<1b>[0m Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'global': object 'trans_raster' not found
Calls: <Anonymous> ... eval -> eval -> <Anonymous> -> .handleSimpleError -> h
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.6.0-4
Check: tests
Result: ERROR
Running ‘tinytest.R’ [11s/16s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
>
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("gdm")
+ }
test_gdm.R.................... 0 tests terra 1.8.5
test_gdm.R.................... 0 tests
test_gdm.R.................... 0 tests
test_gdm.R.................... 0 tests
test_gdm.R.................... 0 tests
test_gdm.R.................... 1 tests <1b>[0;32mOK<1b>[0m
test_gdm.R.................... 1 tests <1b>[0;32mOK<1b>[0m
test_gdm.R.................... 2 tests <1b>[0;31m1 fails<1b>[0m
test_gdm.R.................... 3 tests <1b>[0;31m2 fails<1b>[0m
test_gdm.R.................... 3 tests <1b>[0;31m2 fails<1b>[0m Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'global': object 'trans_raster' not found
Calls: <Anonymous> ... eval -> eval -> <Anonymous> -> .handleSimpleError -> h
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.6.0-4
Check: installed package size
Result: NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
extdata 3.8Mb
Flavors: 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