Last updated on 2024-03-29 07:54:38 CET.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 4.2-4 | 58.46 | 494.54 | 553.00 | NOTE | |
r-devel-linux-x86_64-debian-gcc | 4.2-4 | 40.04 | 356.47 | 396.51 | NOTE | |
r-devel-linux-x86_64-fedora-clang | 4.2-4 | 660.30 | NOTE | |||
r-devel-linux-x86_64-fedora-gcc | 4.2-4 | 657.08 | NOTE | |||
r-devel-windows-x86_64 | 4.2-4 | 43.00 | 262.00 | 305.00 | ERROR | |
r-patched-linux-x86_64 | 4.2-4 | 59.69 | 472.47 | 532.16 | NOTE | |
r-release-linux-x86_64 | 4.2-4 | 50.48 | 464.00 | 514.48 | OK | |
r-release-macos-arm64 | 4.2-4 | 145.00 | OK | |||
r-release-macos-x86_64 | 4.2-4 | 492.00 | OK | |||
r-release-windows-x86_64 | 4.2-4 | 58.00 | 440.00 | 498.00 | OK | |
r-oldrel-macos-arm64 | 4.2-4 | 148.00 | OK | |||
r-oldrel-windows-x86_64 | 4.2-4 | 63.00 | 405.00 | 468.00 | OK |
Version: 4.2-4
Check: Rd files
Result: NOTE
checkRd: (-1) BIOMOD.stored.data.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD.stored.data.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD.stored.data.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD.stored.data.Rd:29-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD.stored.data.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD.stored.data.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleForecasting.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleForecasting.Rd:116-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleForecasting.Rd:119-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleForecasting.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:167-168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:169-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:171-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:173-174: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:190-202: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:203-206: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:207-214: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:215-220: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:221-222: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:229: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:231-234: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:236-243: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:245-259: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:261-276: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_EnsembleModeling.Rd:278-282: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_Modeling.Rd:321: Lost braces
321 | \code{\link[rpart]{rpart}}, code{\link[nnet]{nnet}},
| ^
checkRd: (-1) BIOMOD_ModelingOptions.Rd:70-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:77-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:79-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:91-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:96-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:127-142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:135-137: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) BIOMOD_ModelingOptions.Rd:150-151: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) BIOMOD_ModelingOptions.Rd:170-171: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) BIOMOD_ModelingOptions.Rd:240-242: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:253-254: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:266-267: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) BIOMOD_ModelingOptions.Rd:282-287: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:289-294: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) BIOMOD_ModelingOptions.Rd:300-301: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) BIOMOD_ModelingOptions.Rd:310-311: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) BIOMOD_ModelingOptions.Rd:316-317: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) BIOMOD_ModelingOptions.Rd:321-323: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:325-327: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:329-332: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:334-336: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) BIOMOD_ModelingOptions.Rd:342-344: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:346-348: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_ModelingOptions.Rd:350-352: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_Projection.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_Projection.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_Projection.Rd:114-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_Projection.Rd:118-119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_Projection.Rd:120-122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BIOMOD_RangeSize.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BIOMOD_RangeSize.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BIOMOD_RangeSize.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BIOMOD_RangeSize.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BIOMOD_RangeSize.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BIOMOD_RangeSize.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BIOMOD_RangeSize.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BIOMOD_RangeSize.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BIOMOD_RangeSize.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BIOMOD_RangeSize.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) biomod2_ensemble_model.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_ensemble_model.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_ensemble_model.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_ensemble_model.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_ensemble_model.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_ensemble_model.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_ensemble_model.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_model.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_model.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_model.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_model.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_model.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_model.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_model.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_model.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_model.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) biomod2_model.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bm_CVnnet.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_CVnnet.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_CVnnet.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_FindOptimStat.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_FindOptimStat.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_FindOptimStat.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_FindOptimStat.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_FindOptimStat.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_PlotEvalBoxplot.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bm_PlotEvalBoxplot.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bm_PlotEvalMean.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bm_PlotEvalMean.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bm_PlotEvalMean.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bm_PlotEvalMean.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bm_PlotResponseCurves.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bm_PlotVarImpBoxplot.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bm_PseudoAbsences.Rd:114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_PseudoAbsences.Rd:115: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_PseudoAbsences.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_PseudoAbsences.Rd:117-118: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_RunModelsLoop.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_RunModelsLoop.Rd:117: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_RunModelsLoop.Rd:118: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_RunModelsLoop.Rd:119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_RunModelsLoop.Rd:120-121: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_RunModelsLoop.Rd:122-123: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_VariablesImportance.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_VariablesImportance.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bm_VariablesImportance.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
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
Version: 4.2-4
Check: Rd \usage sections
Result: NOTE
Documented arguments not in \usage in Rd file 'predict2.em.Rd':
‘na.rm’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Version: 4.2-4
Check: examples
Result: ERROR
Running examples in 'biomod2-Ex.R' failed
The error most likely occurred in:
> ### Name: BIOMOD.ensemble.models.out
> ### Title: 'BIOMOD_EnsembleModeling()' output object class
> ### Aliases: BIOMOD.ensemble.models.out BIOMOD.ensemble.models.out-class
> ### show,BIOMOD.ensemble.models.out-method
>
> ### ** Examples
>
>
> showClass("BIOMOD.ensemble.models.out")
Class "BIOMOD.ensemble.models.out" [package "biomod2"]
Slots:
Name: modeling.id dir.name
Class: character character
Name: sp.name expl.var.names
Class: character character
Name: models.out em.by
Class: BIOMOD.stored.models.out character
Name: em.computed em.failed
Class: character character
Name: em.models_kept models.evaluation
Class: ANY BIOMOD.stored.data.frame
Name: variables.importance models.prediction
Class: BIOMOD.stored.data.frame BIOMOD.stored.data.frame
Name: models.prediction.eval link
Class: BIOMOD.stored.data.frame character
>
> ## ----------------------------------------------------------------------- #
> library(terra)
terra 1.7.71
>
> # Load species occurrences (6 species available)
> data(DataSpecies)
> head(DataSpecies)
X_WGS84 Y_WGS84 ConnochaetesGnou GuloGulo PantheraOnca PteropusGiganteus
1 -94.5 82.00001 0 0 0 0
2 -91.5 82.00001 0 1 0 0
3 -88.5 82.00001 0 1 0 0
4 -85.5 82.00001 0 1 0 0
5 -82.5 82.00001 0 1 0 0
6 -79.5 82.00001 0 1 0 0
TenrecEcaudatus VulpesVulpes
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
>
> # Select the name of the studied species
> myRespName <- 'GuloGulo'
>
> # Get corresponding presence/absence data
> myResp <- as.numeric(DataSpecies[, myRespName])
>
> # Get corresponding XY coordinates
> myRespXY <- DataSpecies[, c('X_WGS84', 'Y_WGS84')]
>
> # Load environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
> data(bioclim_current)
> myExpl <- terra::rast(bioclim_current)
>
> ## Don't show:
> myExtent <- terra::ext(0,30,45,70)
> myExpl <- terra::crop(myExpl, myExtent)
> ## End(Don't show)
>
> ## ----------------------------------------------------------------------- #
> file.out <- paste0(myRespName, "/", myRespName, ".AllModels.models.out")
> if (file.exists(file.out)) {
+ myBiomodModelOut <- get(load(file.out))
+ } else {
+
+ # Format Data with true absences
+ myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
+ expl.var = myExpl,
+ resp.xy = myRespXY,
+ resp.name = myRespName)
+
+ # Create default modeling options
+ myBiomodOptions <- BIOMOD_ModelingOptions()
+
+ # Model single models
+ myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,
+ modeling.id = 'AllModels',
+ models = c('RF', 'GLM'),
+ bm.options = myBiomodOptions,
+ CV.strategy = 'random',
+ CV.nb.rep = 2,
+ CV.perc = 0.8,
+ metric.eval = c('TSS','ROC'),
+ var.import = 3,
+ seed.val = 42)
+ }
-=-=-=-=-=-=-=-=-=-=-=-=-=-= GuloGulo Data Formating -=-=-=-=-=-=-=-=-=-=-=-=-=-=
! No data has been set aside for modeling evaluation
! No data has been set aside for modeling evaluation
!!! Some data are located in the same raster cell.
Please set `filter.raster = TRUE` if you want an automatic filtering.
! No data has been set aside for modeling evaluation
! Some NAs have been automatically removed from your data
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Done -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Build Single Models -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Checking Models arguments...
> Automatic weights creation to rise a 0.5 prevalence
Creating suitable Workdir...
Checking Cross-Validation arguments...
> Random cross-validation selection
-=-=-=-=-=-=-=-=-=-=-=-=-= GuloGulo Modeling Summary -=-=-=-=-=-=-=-=-=-=-=-=-=
5 environmental variables ( bio3 bio4 bio7 bio11 bio12 )
Number of evaluation repetitions : 2
Models selected : RF GLM
Total number of model runs: 4
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Warning: executing %dopar% sequentially: no parallel backend registered
-=-=-=--=-=-=- GuloGulo_allData_RUN1_RF
Model=Breiman and Cutler's random forests for classification and regression
> RF modeling...
Evaluating Model stuff...
Evaluating Predictor Contributions...
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Flavor: r-devel-windows-x86_64