* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ecospat.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (Debian 13.2.0-24) 13.2.0
    GNU Fortran (Debian 13.2.0-24) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘ecospat/DESCRIPTION’ ... OK
* this is package ‘ecospat’ version ‘4.0.0’
* 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 ‘ecospat’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/ecospat-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [0s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
* checking loading without being on the library search path ... [0s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
Missing or unexported object: ‘biomod2::BIOMOD_ModelingOptions’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [35s/41s] OK
* checking Rd files ... [1s/2s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'ecospat.CCV.modeling.Rd':
  ‘[biomod2]{BIOMOD_ModelingOptions}’

Missing link or links in Rd file 'ecospat.ESM.Modeling.Rd':
  ‘[biomod2]{BIOMOD_ModelingOptions}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/40s] OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
ecospat.Epred 11.602  0.467  13.174
ecospat.cv.rf  4.301  0.198   5.345
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [61s/77s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_ecospat_package.Rmd’ using rmarkdown

Quitting from lines 387-397 [unnamed-chunk-31] (vignette_ecospat_package.Rmd)
Error: processing vignette 'vignette_ecospat_package.Rmd' failed with diagnostics:
'bm_DefaultModelingOptions' is not an exported object from 'namespace:biomod2'
--- failed re-building ‘vignette_ecospat_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [10s/13s] OK
* checking HTML version of manual ... [4s/7s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs