* using log directory ‘/srv/hornik/tmp/CRAN_pretest/BIOMASS.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * 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 ... [5s/6s] NOTE Maintainer: ‘Dominique Lamonica ’ 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 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 ‘BIOMASS’ can be installed ... [12s/12s] 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 ... [4s/4s] OK * checking whether the package can be loaded with stated dependencies ... [3s/3s] OK * checking whether the package can be unloaded cleanly ... [3s/3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK * checking whether the namespace can be unloaded cleanly ... [4s/4s] OK * checking loading without being on the library search path ... [4s/4s] OK * checking whether startup messages can be suppressed ... [4s/4s] 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 ... [19s/19s] NOTE attributeTree: no visible binding for global variable ‘.I’ attributeTreeCoord: no visible binding for global variable ‘.I’ attributeTreeCoord : : 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 : : no visible global function definition for ‘.’ correctTaxo : : no visible binding for global variable ‘Name_submitted’ correctTaxo : : no visible binding for global variable ‘Overall_score’ correctTaxo : : no visible binding for global variable ‘Name_matched’ correctTaxo : : 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 : : 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 : : 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 : : 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 : : no visible binding for global variable ‘plot_ID’ divide_plot : : no visible binding for global variable ‘x_rel’ divide_plot : : no visible binding for global variable ‘y_rel’ divide_plot : : 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 : : no visible global function definition for ‘.’ subplot_summary : : no visible binding for global variable ‘x_proj’ subplot_summary : : no visible binding for global variable ‘y_proj’ subplot_summary : : no visible binding for global variable ‘subplot_ID’ subplot_summary : : no visible binding for global variable ‘V1’ subplot_summary : : 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 ... [0s/0s] 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 ... [0s/0s] 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 ... [16s/10s] NOTE Examples with CPU time > 2.5 times elapsed time user system elapsed ratio subplot_summary 1.025 0.02 0.286 3.654 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [47s/20s] OK Running ‘testthat.R’ [47s/20s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [39s/31s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 NOTEs