Last updated on 2025-12-07 03:50:23 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.2-6-2 | 48.46 | 439.35 | 487.81 | OK | |
| r-devel-linux-x86_64-debian-gcc | 4.2-6-2 | 29.21 | 252.74 | 281.95 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 4.2-6-2 | 75.00 | 499.95 | 574.95 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 4.2-6-2 | 70.00 | 447.00 | 517.00 | OK | |
| r-devel-windows-x86_64 | 4.2-6-2 | 45.00 | 377.00 | 422.00 | OK | |
| r-patched-linux-x86_64 | 4.2-6-2 | 49.73 | 413.61 | 463.34 | OK | |
| r-release-linux-x86_64 | 4.2-6-2 | 42.98 | 416.50 | 459.48 | OK | |
| r-release-macos-arm64 | 4.2-6-2 | OK | ||||
| r-release-macos-x86_64 | 4.2-6-2 | 39.00 | 311.00 | 350.00 | OK | |
| r-release-windows-x86_64 | 4.2-6-2 | 46.00 | 363.00 | 409.00 | OK | |
| r-oldrel-macos-arm64 | 4.2-6-2 | OK | ||||
| r-oldrel-macos-x86_64 | 4.2-6-2 | 38.00 | 294.00 | 332.00 | OK | |
| r-oldrel-windows-x86_64 | 4.2-6-2 | 63.00 | 520.00 | 583.00 | OK |
Version: 4.2-6-2
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'Hmisc', 'gam', 'ENMeval', 'knitr'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.2-6-2
Check: examples
Result: ERROR
Running examples in ‘biomod2-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bm_CrossValidation
> ### Title: Build cross-validation table
> ### Aliases: bm_CrossValidation bm_CrossValidation_user.defined
> ### bm_CrossValidation_user.defined,BIOMOD.formated.data-method
> ### bm_CrossValidation_user.defined,BIOMOD.formated.data.PA-method
> ### bm_CrossValidation_random
> ### bm_CrossValidation_random,BIOMOD.formated.data-method
> ### bm_CrossValidation_random,BIOMOD.formated.data.PA-method
> ### bm_CrossValidation_kfold
> ### bm_CrossValidation_kfold,BIOMOD.formated.data-method
> ### bm_CrossValidation_kfold,BIOMOD.formated.data.PA-method
> ### bm_CrossValidation_block
> ### bm_CrossValidation_block,BIOMOD.formated.data-method
> ### bm_CrossValidation_block,BIOMOD.formated.data.PA-method
> ### bm_CrossValidation_strat
> ### bm_CrossValidation_strat,BIOMOD.formated.data-method
> ### bm_CrossValidation_strat,BIOMOD.formated.data.PA-method
> ### bm_CrossValidation_env
> ### bm_CrossValidation_env,BIOMOD.formated.data-method
> ### bm_CrossValidation_env,BIOMOD.formated.data.PA-method
>
> ### ** Examples
>
>
> library(terra)
terra 1.8.86
Attaching package: ‘terra’
The following object is masked from ‘package:plotrix’:
rescale
> # 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)
>
> # --------------------------------------------------------------- #
> # Format Data with true absences
> myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
+ expl.var = myExpl,
+ resp.xy = myRespXY,
+ resp.name = myRespName)
-=-=-=-=-=-=-=-=-=-=-=-=-=-= GuloGulo Data Formating -=-=-=-=-=-=-=-=-=-=-=-=-=-=
!!! 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 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>
> # --------------------------------------------------------------- #
> # Create the different validation datasets
>
> # random selection
> cv.r <- bm_CrossValidation(bm.format = myBiomodData,
+ strategy = "random",
+ nb.rep = 3,
+ k = 0.8)
Checking Cross-Validation arguments...
> Random cross-validation selection
>
> # k-fold selection
> cv.k <- bm_CrossValidation(bm.format = myBiomodData,
+ strategy = "kfold",
+ nb.rep = 2,
+ k = 3)
Checking Cross-Validation arguments...
> k-fold cross-validation selection
>
> # block selection
> cv.b <- bm_CrossValidation(bm.format = myBiomodData,
+ strategy = "block")
Checking Cross-Validation arguments...
> Block cross-validation selectionError in .local(bm.format, ...) : Package 'ENMeval' not found
Calls: bm_CrossValidation ... bm_CrossValidation_block -> bm_CrossValidation_block -> .local
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BIOMOD_RangeSize 5.575 0.008 6.282
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.2-6-2
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.2-6-2
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘GuloGulo’
Flavor: r-devel-linux-x86_64-debian-gcc