* using log directory 'd:/RCompile/CRANincoming/R-devel/BIOMASS.Rcheck'
* using R Under development (unstable) (2025-02-18 r87748 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 'BIOMASS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BIOMASS' version '2.2.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [13s] NOTE
Maintainer: 'Dominique Lamonica <dominique.lamonica@ird.fr>'

Found the following (possibly) invalid URLs:
  URL: (https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.12629)
    From: inst/doc/Vignette_BIOMASS.html
    Message: Invalid URI scheme
  URL: https://umr-amap.github.io/BIOMASS (moved to https://umr-amap.github.io/BIOMASS/)
    From: DESCRIPTION
          man/BIOMASS-package.Rd
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.

The Date field is over a month old.

Found the following URLs which should use \doi (with the DOI name only):
  File 'NouraguesCoords.Rd':
    https://doi.org/10.18167/DVN1/HXKS4E
  File 'NouraguesPlot201.Rd':
    https://doi.org/10.18167/DVN1/HXKS4E
* 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 'BIOMASS' 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 whether startup messages can be suppressed ... 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 ... [36s] NOTE
attributeTree: no visible binding for global variable '.I'
attributeTreeCoord: no visible binding for global variable '.I'
attributeTreeCoord : <anonymous>: no visible global function definition
  for '.'
attributeTreeCoord: no visible global function definition for '.'
check_plot_coord: no visible binding for global variable '..rel_coord'
check_plot_coord: no visible binding for global variable '..proj_coord'
check_plot_coord: no visible binding for global variable '..longlat'
check_plot_coord: no visible binding for global variable 'x_rel'
check_plot_coord: no visible binding for global variable 'y_rel'
check_plot_coord : check_corner_fct: no visible binding for global
  variable 'x_proj'
check_plot_coord : check_corner_fct: no visible binding for global
  variable 'y_proj'
check_plot_coord : check_corner_fct: no visible binding for global
  variable '.I'
check_plot_coord : check_corner_fct: no visible binding for global
  variable 'x_rel'
check_plot_coord : check_corner_fct: no visible binding for global
  variable 'y_rel'
check_plot_coord : check_corner_fct: no visible binding for global
  variable 'outlier'
check_plot_coord : check_corner_fct: no visible binding for global
  variable 'x_proj_mean'
check_plot_coord : check_corner_fct: no visible binding for global
  variable 'y_proj_mean'
check_plot_coord : check_corner_fct: no visible binding for global
  variable 'is_in_plot'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'x'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'y'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable '.data'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'whatpoint'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'x_proj'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'y_proj'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'x_rel'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'y_rel'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'x_end'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'y_end'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'tree_shape'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'is_in_plot'
check_plot_coord : draw_plot_fct: no visible binding for global
  variable 'tree_label'
computeE: no visible binding for global variable 'RASTval'
computeE: no visible binding for global variable 'i.RASTval'
correctTaxo: no visible binding for global variable 'query'
correctTaxo: no visible binding for global variable 'from'
correctTaxo: no visible global function definition for '.'
correctTaxo: no visible binding for global variable 'submittedName'
correctTaxo: no visible binding for global variable 'slice'
correctTaxo: no visible binding for global variable '.I'
correctTaxo : <anonymous>: no visible global function definition for
  '.'
correctTaxo : <anonymous>: no visible binding for global variable
  'Name_submitted'
correctTaxo : <anonymous>: no visible binding for global variable
  'Overall_score'
correctTaxo : <anonymous>: no visible binding for global variable
  'Name_matched'
correctTaxo : <anonymous>: no visible binding for global variable
  'Accepted_name'
correctTaxo: no visible binding for global variable '..score'
correctTaxo: no visible binding for global variable 'acceptedName'
correctTaxo: no visible binding for global variable 'matchedName'
correctTaxo: no visible binding for global variable 'outName'
correctTaxo: no visible binding for global variable 'nameModified'
correctTaxo: no visible binding for global variable 'genusCorrected'
correctTaxo: no visible binding for global variable 'speciesCorrected'
correctTaxo: no visible binding for global variable '.N'
cutPlot : gridFunction: no visible global function definition for '.'
cutPlot : numberingCorner : <anonymous>: no visible global function
  definition for '.'
divide_plot : divide_plot_fct: no visible binding for global variable
  'x_rel'
divide_plot : divide_plot_fct: no visible binding for global variable
  'y_rel'
divide_plot : divide_plot_fct : <anonymous>: no visible binding for
  global variable 'x_rel'
divide_plot : divide_plot_fct : <anonymous>: no visible binding for
  global variable 'y_rel'
divide_plot : divide_plot_fct : <anonymous>: no visible global function
  definition for '.'
divide_plot : divide_plot_fct: no visible binding for global variable
  'subplot_ID'
divide_plot: no visible binding for global variable 'plot_ID'
divide_plot : <anonymous>: no visible binding for global variable
  'plot_ID'
divide_plot : <anonymous>: no visible binding for global variable
  'x_rel'
divide_plot : <anonymous>: no visible binding for global variable
  'y_rel'
divide_plot : <anonymous>: no visible binding for global variable
  'subplot_ID'
divide_plot: no visible binding for global variable 'subplot_ID'
getTaxonomy: no visible global function definition for '.'
getTaxonomy: no visible binding for global variable 'id'
getTaxonomy: no visible binding for global variable 'family'
getWoodDensity: no visible binding for global variable 'regionId'
getWoodDensity: no visible binding for global variable 'i.family'
getWoodDensity: no visible binding for global variable 'wd'
getWoodDensity: no visible binding for global variable 'wd.x'
getWoodDensity: no visible binding for global variable 'wd.y'
getWoodDensity: no visible binding for global variable '.N'
getWoodDensity: no visible global function definition for '.'
getWoodDensity: no visible binding for global variable 'taxo'
getWoodDensity: no visible binding for global variable '.EACHI'
getWoodDensity: no visible binding for global variable 'meanWDsp'
getWoodDensity: no visible binding for global variable 'nIndsp'
getWoodDensity: no visible binding for global variable 'sdWDsp'
getWoodDensity: no visible binding for global variable 'meanWD'
getWoodDensity: no visible binding for global variable 'meanWDgn'
getWoodDensity: no visible binding for global variable 'nInd'
getWoodDensity: no visible binding for global variable 'nIndgn'
getWoodDensity: no visible binding for global variable 'sdWD'
getWoodDensity: no visible binding for global variable 'sdWDgn'
getWoodDensity: no visible binding for global variable 'levelWD'
getWoodDensity: no visible binding for global variable 'meanWDfm'
getWoodDensity: no visible binding for global variable 'nIndfm'
getWoodDensity: no visible binding for global variable 'sdWDfm'
getWoodDensity: no visible binding for global variable 'meanWDst'
getWoodDensity: no visible binding for global variable 'nIndst'
getWoodDensity: no visible binding for global variable 'sdWDst'
latlong2UTM: no visible global function definition for '.'
modelHD: no visible binding for global variable 'x'
modelHD: no visible binding for global variable 'y'
numberCorner : cornerFun: no visible global function definition for '.'
numberCorner: no visible global function definition for '.'
predictHeight: no visible binding for global variable 'H'
subplot_summary: no visible binding for global variable 'subplot_ID'
subplot_summary: no visible binding for global variable 'plot_id'
subplot_summary : <anonymous>: no visible global function definition
  for '.'
subplot_summary : <anonymous>: no visible binding for global variable
  'x_proj'
subplot_summary : <anonymous>: no visible binding for global variable
  'y_proj'
subplot_summary : <anonymous>: no visible binding for global variable
  'subplot_ID'
subplot_summary : <anonymous>: no visible binding for global variable
  'V1'
subplot_summary : <anonymous>: no visible binding for global variable
  '.data'
summaryByPlot: no visible binding for global variable '.I'
summaryByPlot: no visible global function definition for '.'
summaryByPlot : mySample: no visible binding for global variable
  'indice_line'
summaryByPlot : mySummary: no visible binding for global variable
  'indice_line'
summaryByPlot : mySummary: no visible binding for global variable
  'indice_col'
summaryByPlot : mySummary: no visible binding for global variable 'V1'
summaryByPlot: no visible binding for global variable 'i'
summaryByPlot: no visible binding for global variable 'Cred_2.5'
summaryByPlot: no visible binding for global variable 'Cred_97.5'
Undefined global functions or variables:
  . ..longlat ..proj_coord ..rel_coord ..score .EACHI .I .N .data
  Accepted_name Cred_2.5 Cred_97.5 H Name_matched Name_submitted
  Overall_score RASTval V1 acceptedName family from genusCorrected i
  i.RASTval i.family id indice_col indice_line is_in_plot levelWD
  matchedName meanWD meanWDfm meanWDgn meanWDsp meanWDst nInd nIndfm
  nIndgn nIndsp nIndst nameModified outName outlier plot_ID plot_id
  query regionId sdWD sdWDfm sdWDgn sdWDsp sdWDst slice
  speciesCorrected submittedName subplot_ID taxo tree_label tree_shape
  wd wd.x wd.y whatpoint x x_end x_proj x_proj_mean x_rel y y_end
  y_proj y_proj_mean y_rel
Consider adding
  importFrom("stats", "family")
to your NAMESPACE file.
* 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 ... [18s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [91s] ERROR
  Running 'testthat.R' [91s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BIOMASS)
  For more information on using BIOMASS, visit https://umr-amap.github.io/BIOMASS
  
  Using temporary cache
    It is recommended to use a permanent cache to avoid to re-download files on each session.
    See function createCache() or BIOMASS.cache option.
  > 
  > test_check("BIOMASS")
  pj_obj_create: Cannot find proj.db
  trying URL 'https://github.com/umr-amap/BIOMASS/raw/master/data-raw/climate_variable/E.zip'
  Content type 'application/zip' length 31208287 bytes (29.8 MB)
  ================================
  downloaded 19.5 MB
  
  trying URL 'https://github.com/umr-amap/BIOMASS/raw/master/data-raw/climate_variable/wc2-5.zip'
  Content type 'application/zip' length 19531044 bytes (18.6 MB)
  ==================================================
  downloaded 18.6 MB
  
  trying URL 'https://github.com/umr-amap/BIOMASS/raw/master/data-raw/climate_variable/CWD.zip'
  Content type 'application/zip' length 15777909 bytes (15.0 MB)
  ==================================================
  downloaded 15.0 MB
  
  trying URL 'https://github.com/umr-amap/BIOMASS/raw/master/data-raw/climate_variable/E.zip'
  Content type 'application/zip' length 31208287 bytes (29.8 MB)
  ==================================================
  downloaded 29.8 MB
  
  pj_obj_create: Cannot find proj.db
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 446 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-AGBmonteCarlo.R:153:3', 'test-check_coord_plot.R:106:3',
    'test-check_coord_plot.R:131:3', 'test-computeAGB.R:44:3',
    'test-correctTaxo.R:5:3', 'test-retrieveH.R:36:3',
    'test-small_function.R:49:3', 'test-subplot_summary.R:31:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-small_function.R:26:3'): Compute E ─────────────────────────────
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'rast': download from 'https://github.com/umr-amap/BIOMASS/raw/master/data-raw/climate_variable/E.zip' failed
  Backtrace:
      ▆
   1. ├─BIOMASS::computeE(coord) at test-small_function.R:26:3
   2. │ ├─terra::rast(cacheManager("E.bil"))
   3. │ └─BIOMASS::cacheManager("E.bil")
   4. │   └─utils::download.file(url, dest)
   5. └─base::.handleSimpleError(...)
   6.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 446 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [41s] OK
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs