* using log directory 'd:/RCompile/CRANincoming/R-devel/neonPlantEcology.Rcheck'
* using R Under development (unstable) (2024-01-10 r85799 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'neonPlantEcology/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'neonPlantEcology' version '1.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Adam Mahood <admahood@gmail.com>'

New submission

Unknown, possibly misspelled, fields in DESCRIPTION:
  'DOI'

Size of tarball: 7549049 bytes
* 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 'neonPlantEcology' 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 R 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 ... NOTE
npe_change_native_status: no visible binding for global variable
  'nativeStatusCode'
npe_change_native_status: no visible binding for global variable
  'taxonID'
npe_cm_metadata: no visible binding for global variable 'rowname'
npe_cm_metadata: no visible binding for global variable 'site'
npe_cm_metadata: no visible binding for global variable 'eventID'
npe_cm_metadata: no visible binding for global variable 'plotID'
npe_community_matrix: no visible binding for global variable 'plotID'
npe_community_matrix: no visible binding for global variable
  'subplotID'
npe_community_matrix: no visible binding for global variable 'eventID'
npe_community_matrix: no visible binding for global variable 'taxonID'
npe_community_matrix: no visible binding for global variable
  'targetTaxaPresent'
npe_community_matrix: no visible binding for global variable 'present'
npe_community_matrix: no visible global function definition for
  'na.omit'
npe_community_matrix: no visible binding for global variable 'p_sp_y'
npe_community_matrix: no visible binding for global variable 'cover'
npe_diversity_info: no visible binding for global variable 'site'
npe_diversity_info: no visible binding for global variable 'plotID'
npe_diversity_info: no visible binding for global variable 'subplotID'
npe_diversity_info: no visible binding for global variable 'eventID'
npe_diversity_info: no visible binding for global variable 'taxonID'
npe_diversity_info: no visible binding for global variable 'cover'
npe_diversity_info: no visible binding for global variable
  'nativeStatusCode'
npe_diversity_info: no visible binding for global variable
  'total_cover'
npe_diversity_info: no visible binding for global variable 'rel_cover'
npe_diversity_info: no visible global function definition for
  'contains'
npe_diversity_info: no visible binding for global variable 'family'
npe_diversity_info: no visible binding for global variable
  'scientificName'
npe_diversity_info: no visible binding for global variable 'nspp'
npe_diversity_info: no visible binding for global variable
  'shannon_exotic'
npe_diversity_info: no visible binding for global variable
  'shannon_native'
npe_diversity_info: no visible binding for global variable
  'shannon_unknown'
npe_diversity_info: no visible binding for global variable
  'shannon_notexotic'
npe_diversity_info: no visible binding for global variable
  'shannon_total'
npe_diversity_info: no visible binding for global variable
  'shannon_family'
npe_diversity_info: no visible binding for global variable
  'cover_exotic'
npe_groundcover: no visible binding for global variable 'eventID'
npe_groundcover: no visible binding for global variable 'endDate'
npe_groundcover: no visible binding for global variable 'divDataType'
npe_groundcover: no visible binding for global variable
  'otherVariables'
npe_groundcover: no visible binding for global variable 'plotID'
npe_groundcover: no visible binding for global variable 'percentCover'
npe_groundcover: no visible binding for global variable 'site'
npe_groundcover: no visible binding for global variable 'subplotID'
npe_heights: no visible binding for global variable 'eventID'
npe_heights: no visible binding for global variable 'endDate'
npe_heights: no visible binding for global variable 'divDataType'
npe_heights: no visible binding for global variable 'taxonID'
npe_heights: no visible binding for global variable 'plotID'
npe_heights: no visible binding for global variable
  'heightPlantSpecies'
npe_heights: no visible binding for global variable 'all_na'
npe_heights: no visible binding for global variable 'height'
npe_heights: no visible binding for global variable 'site'
npe_heights: no visible binding for global variable 'subplotID'
npe_longform: no visible binding for global variable 'eventID'
npe_longform: no visible binding for global variable 'divDataType'
npe_longform: no visible binding for global variable 'taxonID'
npe_longform: no visible binding for global variable 'plotID'
npe_longform: no visible binding for global variable 'percentCover'
npe_longform: no visible binding for global variable 'nativeStatusCode'
npe_longform: no visible binding for global variable 'scientificName'
npe_longform: no visible binding for global variable 'family'
npe_longform: no visible binding for global variable 'endDate'
npe_longform: no visible binding for global variable
  'targetTaxaPresent'
npe_longform: no visible binding for global variable 'subplotID'
npe_longform: no visible binding for global variable 'site'
npe_longform: no visible global function definition for 'str_detect'
npe_plot_centroids: no visible global function definition for
  'download.file'
npe_plot_centroids: no visible global function definition for 'unzip'
npe_plot_centroids: no visible binding for global variable 'plot_info'
npe_plot_centroids: no visible binding for global variable 'plotID'
npe_plot_centroids: no visible binding for global variable 'latitude'
npe_plot_centroids: no visible binding for global variable 'longitude'
npe_site_ids: no visible global function definition for 'data'
npe_site_ids: no visible binding for global variable 'domainName'
npe_site_ids: no visible binding for global variable 'siteID'
npe_site_ids: no visible binding for global variable 'domainNumb'
npe_site_ids: no visible binding for global variable 'siteType'
npe_site_ids: no visible binding for global variable 'ai_class'
npe_site_ids: no visible binding for global variable 'koppen_coarse'
npe_site_ids: no visible binding for global variable 'koppen_fine'
Undefined global functions or variables:
  ai_class all_na contains cover cover_exotic data divDataType
  domainName domainNumb download.file endDate eventID family height
  heightPlantSpecies koppen_coarse koppen_fine latitude longitude
  na.omit nativeStatusCode nspp otherVariables p_sp_y percentCover
  plotID plot_info present rel_cover rowname scientificName
  shannon_exotic shannon_family shannon_native shannon_notexotic
  shannon_total shannon_unknown site siteID siteType str_detect
  subplotID targetTaxaPresent taxonID total_cover unzip
Consider adding
  importFrom("stats", "family", "na.omit")
  importFrom("utils", "data", "download.file", "unzip")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File 'neonPlantEcology/R/diversity_data_prep.R':
  data("sites")
See section 'Good practice' in '?data'.
* 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 ... WARNING
  LazyData DB of 7.3 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [12s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [29s] OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs