* using log directory ‘/data/gannet/ripley/R/packages/tests-OpenBLAS/EcoCleanR.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘EcoCleanR/DESCRIPTION’ ... OK
* this is package ‘EcoCleanR’ version ‘1.0.1’
* 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 ‘EcoCleanR’ can be installed ... [57s/74s] 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 ... [18s/25s] OK
* checking whether the package can be loaded with stated dependencies ... [17s/26s] OK
* checking whether the package can be unloaded cleanly ... [17s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/20s] OK
* checking whether the namespace can be unloaded cleanly ... [18s/20s] OK
* checking loading without being on the library search path ... [19s/26s] 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 ... [80s/162s] OK
* 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 ... [27s/96s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [282s/385s]
 [282s/386s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [70s/522s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘data_cleaning.Rmd’ using rmarkdown

Quitting from data_cleaning.Rmd:68-73 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
---
Backtrace:
    ▆
 1. └─EcoCleanR::ec_geographic_map(...)
 2.   └─terra::crop(x = world_map, y = geographic_extent)
 3.     └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'data_cleaning.Rmd' failed with diagnostics:
unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
--- failed re-building ‘data_cleaning.Rmd’

--- re-building ‘data_merging.Rmd’ using rmarkdown
trying URL 'https://geodata.ucdavis.edu/gadm/gadm3.6/gadm36_adm0_r3_pk.rds'
Content type 'unknown' length 2438344 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘data_merging.Rmd’

SUMMARY: processing the following file failed:
  ‘data_cleaning.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [8s/13s] 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
See
  ‘/data/gannet/ripley/R/packages/tests-OpenBLAS/EcoCleanR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 29:24.29, 792.82 + 62.34