CRAN Package Check Results for Package biomod2

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

Check Details

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 ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:143-144: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:145-149: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:150-151: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:152-160: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:170-171: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:173: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:180-181: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:182-186: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:187-191: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:192-193: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:194-195: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:202-203: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:213-214: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:223-239: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:230-231: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:232-234: Lost braces in \itemize; meant \describe ? 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 ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:269-273: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:275-280: Lost braces in \itemize; meant \describe ? 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 ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:296-298: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:300-301: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:303-304: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:306-307: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:307-308: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:310-311: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:313-314: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:316-317: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:317-319: Lost braces in \itemize; meant \describe ? 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 ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:338-340: Lost braces in \itemize; meant \describe ? 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... | | | 0% Flavor: r-devel-windows-x86_64