- using R Under development (unstable) (2026-05-09 r90031)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
* current time: 2026-05-10 11:14:18 UTC
- using option ‘--no-stop-on-test-error’
- checking for file ‘S4DM/DESCRIPTION’ ... OK
- this is package ‘S4DM’ version ‘0.0.1’
- package encoding: UTF-8
- 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 ‘S4DM’ can be installed ... [66s/143s] OK
See the install log for details.
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘fit_density_ratio.R’ ‘fit_plug_and_play.R’
- 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 ... [20s/46s] OK
- checking whether the package can be loaded with stated dependencies ... [20s/45s] OK
- checking whether the package can be unloaded cleanly ... [21s/59s] OK
- checking whether the namespace can be loaded with stated dependencies ... [20s/39s] OK
- checking whether the namespace can be unloaded cleanly ... [21s/44s] OK
- checking loading without being on the library search path ... [21s/54s] OK
- checking use of S3 registration ... 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 ... [90s/182s] NOTE
evaluate_range_map: no visible global function definition for ‘%>%’
get_env_bg: no visible global function definition for ‘%>%’
get_env_pres: no visible global function definition for ‘%>%’
get_response_curves: no visible global function definition for ‘%>%’
stratify_spatial: no visible global function definition for ‘%>%’
Undefined global functions or variables:
%>%
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- 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 ... OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [20s/22s] ERROR
Running examples in ‘S4DM-Ex.R’ failed
The error most likely occurred in:
> ### Name: evaluate_range_map
> ### Title: Evaluate S4DM range map quality
> ### Aliases: evaluate_range_map
>
> ### ** Examples
>
> {
+
+ # load in sample data
+
+ library(S4DM)
+ library(terra)
+
+ # occurrence points
+ data("sample_points")
+ occurrences <- sample_points
+
+ # environmental data
+ env <- rast(system.file('ex/sample_env.tif', package="S4DM"))
+
+ # rescale the environmental data
+
+ env <- scale(env)
+
+ # Evaluate a gaussian/gaussian model calculated with the numbag approach
+ # using 10 bootstrap replicates.
+
+ evaluate_range_map(occurrences = occurrences,
+ env = env,
+ method = NULL,
+ presence_method = "gaussian",
+ background_method = "gaussian",
+ bootstrap = "numbag",
+ bootstrap_reps = 10,
+ quantile = 0.05,
+ constraint_regions = NULL,
+ background_buffer_width = 100000)
+
+
+
+ }
terra 1.9.27
Error in coords %>% st_transform(crs = st_crs(env)) :
could not find function "%>%"
Calls: evaluate_range_map -> get_env_bg
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [293s/301s] OK
Running ‘testthat.R’ [292s/301s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [118s/120s] OK
- checking PDF version of manual ... [7s/11s] OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR, 2 NOTEs