Check results for 'biomod2'

using R Under development (unstable) (2026-03-01 r89506)
using platform: aarch64-apple-darwin23
R was compiled by Apple clang version 17.0.0 (clang-1700.3.19.1) GNU Fortran (GCC) 14.2.0
running under: macOS Sequoia 15.7.1
using session charset: UTF-8 * current time: 2026-03-12 17:02:44 UTC
checking for file ‘biomod2/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘biomod2’ version ‘4.3-4-5’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... INFO Package suggested but not available for checking: ‘ENMeval’
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘biomod2’ can be installed ... [15s/19s] OK See the install log for details.
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [3s/3s] OK
checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
checking whether the package can be unloaded cleanly ... [3s/3s] OK
checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
checking loading without being on the library search path ... [2s/2s] OK
checking whether startup messages can be suppressed ... [3s/3s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [9s/9s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... INFO Package unavailable to check Rd xrefs: ‘ENMeval’
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... [2s/2s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking R/sysdata.rda ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [13s/14s] ERROR Running examples in ‘biomod2-Ex.R’ failed The error most likely occurred in: > ### 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 1.9.1 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.name = myRespName, + resp.var = myResp, + resp.xy = myRespXY, + expl.var = myExpl) -=-=-=-=-=-=-=-=-=-=-=-=-=-= GuloGulo Data Formating -=-=-=-=-=-=-=-=-=-=-=-=-=-= !!! Some data are located in the same raster cell. Please set `filter.raster = TRUE` if you want an automatic filtering. ! 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
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [6s/7s] OK
checking PDF version of manual ... [5s/5s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '