* using log directory 'd:/RCompile/CRANincoming/R-devel/phylospatial.Rcheck'
* using R Under development (unstable) (2024-12-17 r87446 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'phylospatial/DESCRIPTION' ... OK
* this is package 'phylospatial' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [10s] NOTE
Maintainer: 'Matthew Kling <mattkling@berkeley.edu>'

New submission

Possibly misspelled words in DESCRIPTION:
  Phylogenetic (2:16)
  biotic (7:235)
  endemism (7:204)
  phylogenetic (7:38, 7:86)
  randomizations (7:279)
  regionalization (7:242)
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'phylospatial' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... 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 ... [69s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
           user system elapsed
ps_rand   13.60   0.21   13.83
moss_data 11.33   0.57   11.92
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [163s] OK
  Running 'testthat.R' [163s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [424s] ERROR
Error(s) in re-building vignettes:
--- re-building 'alpha-diversity.Rmd' using rmarkdown

Quitting from lines 64-68 [rand] (alpha-diversity.Rmd)
Error: processing vignette 'alpha-diversity.Rmd' failed with diagnostics:
there is no package called 'vegan'
--- failed re-building 'alpha-diversity.Rmd'

--- re-building 'beta-diversity.Rmd' using rmarkdown

Quitting from lines 38-40 [beta] (beta-diversity.Rmd)
Error: processing vignette 'beta-diversity.Rmd' failed with diagnostics:
there is no package called 'vegan'
--- failed re-building 'beta-diversity.Rmd'

--- re-building 'phylospatial-data.Rmd' using rmarkdown
--- finished re-building 'phylospatial-data.Rmd'

--- re-building 'prioritization.Rmd' using rmarkdown
--- finished re-building 'prioritization.Rmd'

SUMMARY: processing the following files failed:
  'alpha-diversity.Rmd' 'beta-diversity.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [30s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs