* using log directory ‘/srv/hornik/tmp/CRAN_pretest/caretSDM.Rcheck’
* using R Under development (unstable) (2025-08-27 r88724)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘caretSDM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘caretSDM’ version ‘1.1.4’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/7s] OK
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘caretSDM’ can be installed ... [24s/24s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘assert_numeric_cli’ ‘assert_subset_cli’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [33s/33s] NOTE
plot_background: no visible binding for global variable ‘var1’
plot_background: no visible binding for global variable ‘var2’
plot_background: no visible binding for global variable ‘density’
plot_niche: no visible binding for global variable ‘var1’
plot_niche: no visible binding for global variable ‘var2’
Undefined global functions or variables:
  density var1 var2
Consider adding
  importFrom("stats", "density")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘summary_sdm_presence_only’ ‘validate_on_independent_data’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'plot_occurrences.Rd'
  ‘raster’

Documented arguments not in \usage in Rd file 'summary_sdm.Rd':
  ‘data_independent’ ‘obs_col_name’ ‘threshold’

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.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [22s/22s] ERROR
Running examples in ‘caretSDM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pdp_sdm
> ### Title: Model Response to Variables
> ### Aliases: pdp_sdm get_pdp_sdm
> 
> ### ** Examples
> 
> # Create sdm_area object:
> sa <- sdm_area(parana, cell_size = 100000, crs = 6933)
! Making grid over study area is an expensive task. Please, be patient!
ℹ Using GDAL to make the grid and resample the variables.
> 
> # Include predictors:
> sa <- add_predictors(sa, bioc) |> select_predictors(c("bio1", "bio12"))
! Making grid over the study area is an expensive task. Please, be patient!
ℹ Using GDAL to make the grid and resample the variables.
> 
> # Include scenarios:
> sa <- add_scenarios(sa)
> 
> # Create occurrences:
> oc <- occurrences_sdm(occ, crs = 6933) |> join_area(sa)
> 
> # Create input_sdm:
> i <- input_sdm(oc, sa)
> 
> # Pseudoabsence generation:
> i <- pseudoabsences(i, method="bioclim", n_set=3)
Error in `FUN()`:
! bioclim envelope for
Araucaria angustifolia
covered all the study area. Change th argument or change the method.
Backtrace:
    ▆
 1. └─caretSDM::pseudoabsences(i, method = "bioclim", n_set = 3)
 2.   └─base::sapply(...)
 3.     └─base::lapply(X = X, FUN = FUN, ...)
 4.       └─caretSDM (local) FUN(X[[i]], ...)
 5.         └─cli::cli_abort(c("bioclim envelope for ", sp, " covered all the study area. Change th argument or change the method."))
 6.           └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [187s/187s] OK
  Running ‘testthat.R’ [187s/187s]
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 2 NOTEs