* using log directory 'd:/RCompile/CRANincoming/R-devel/MF.beta4.Rcheck' * using R Under development (unstable) (2023-11-26 r85638 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 'MF.beta4/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MF.beta4' version '1.0.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Anne Chao ' New submission Possibly misspelled words in DESCRIPTION: BEF (3:61, 15:57) multifunctionality (3:28, 9:65, 11:7, 12:7, 12:66) Found the following (possibly) invalid URLs: URL: https://www.rstudio.com/products/RStudio/#Desktop (moved to https://posit.co/products/open-source/rstudio/#Desktop) From: inst/doc/Vignette-MFbeta4.html 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 Title field should be in title case. Current version is: 'Measuring ecosystem multifunctionality and assessing BEF relationships' In title case that is: 'Measuring Ecosystem Multifunctionality and Assessing BEF Relationships' * 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 'MF.beta4' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'lme4::lmer' by 'lmerTest::lmer' when loading 'MF.beta4' See 'd:/RCompile/CRANincoming/R-devel/MF.beta4.Rcheck/00install.out' for details. * 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 ... [15s] NOTE Lmm_fit: no visible global function definition for 'coef' Lmm_fit : johnson_r2: no visible global function definition for 'model.matrix' Lmm_fit : johnson_r2: no visible global function definition for 'var' MF1_single : : no visible binding for global variable '.' MF1_single: no visible binding for global variable 'Order.q' MF1_single : : no visible binding for global variable 'plotID' MF1_single : : no visible binding for global variable 'species' MF1_single : : no visible binding for global variable 'abundance' MF1_single: no visible binding for global variable '.' MF2_multiple: no visible global function definition for 'combn' MF2_multiple : : no visible binding for global variable '.' MF2_multiple : : no visible binding for global variable 'Order.q' MF2_multiple : : no visible binding for global variable 'MF_g' MF2_multiple : : no visible binding for global variable 'Tau' MF2_multiple : : no visible binding for global variable 'MF_a' MF2_multiple : : no visible binding for global variable 'MF_b' MF2_multiple : : no visible binding for global variable 'L_g' MF2_multiple : : no visible binding for global variable 'R_g' MF2_multiple : : no visible binding for global variable 'L_a' MF2_multiple : : no visible binding for global variable 'R_a' MF2_multiple : : no visible binding for global variable 'L_b' MF2_multiple : : no visible binding for global variable 'R_b' MF2_multiple : : no visible binding for global variable 'corr_corrected_Gamma' MF2_multiple : : no visible binding for global variable 'corr_corrected_Beta' MF2_multiple : : no visible binding for global variable 'plotID' MF2_multiple : : no visible binding for global variable 'species' MF2_multiple : : no visible binding for global variable 'abundance' MF2_multiple : : no visible binding for global variable 'x1' MF2_multiple : : no visible binding for global variable 'x2' MF2_multiple: no visible binding for global variable '.' MF2_multiple : : no visible global function definition for 'combn' MF2_multiple : : : no visible binding for global variable '.' MF2_multiple : : : no visible binding for global variable 'Order.q' MF2_multiple : : : no visible binding for global variable 'MF_g' MF2_multiple : : : no visible binding for global variable 'Tau' MF2_multiple : : : no visible binding for global variable 'MF_a' MF2_multiple : : : no visible binding for global variable 'MF_b' MF2_multiple : : : no visible binding for global variable 'L_g' MF2_multiple : : : no visible binding for global variable 'R_g' MF2_multiple : : : no visible binding for global variable 'L_a' MF2_multiple : : : no visible binding for global variable 'R_a' MF2_multiple : : : no visible binding for global variable 'L_b' MF2_multiple : : : no visible binding for global variable 'R_b' MF2_multiple : : : no visible binding for global variable 'corr_corrected_Gamma' MF2_multiple : : : no visible binding for global variable 'corr_corrected_Beta' MF2_multiple : : : no visible binding for global variable 'plotID' MF2_multiple : : : no visible binding for global variable 'species' MF2_multiple : : : no visible binding for global variable 'abundance' MF2_multiple : : : no visible binding for global variable 'x1' MF2_multiple : : : no visible binding for global variable 'x2' MF2_multiple: no visible binding for global variable 'Species_Gamma' MF2_multiple: no visible binding for global variable 'Species_Alpha' MF2_multiple: no visible binding for global variable 'Species_Beta' MFggplot: no visible binding for global variable '.' MFggplot: no visible binding for global variable 'Type' MFggplot: no visible binding for global variable 'Order.q' MFggplot: no visible global function definition for 'lm' MFggplot: no visible binding for global variable 'r.squared' MFggplot: no visible binding for global variable 'p.value' MFggplot: no visible binding for global variable 'term' MFggplot: no visible binding for global variable 'std.error' MFggplot: no visible binding for global variable 'statistic' MFggplot: no visible binding for global variable 'Species.diversity' MFggplot: no visible binding for global variable 'Significance' MFggplot: no visible binding for global variable 'group' MFggplot: no visible binding for global variable 'estimate' MFggplot: no visible binding for global variable 'Label' MFggplot: no visible binding for global variable 'h' MFggplot: no visible binding for global variable 'v' MFggplot: no visible binding for global variable '(Intercept)' MFggplot: no visible binding for global variable 'Intercept' MFggplot: no visible binding for global variable 'Slope' MFggplot: no visible binding for global variable 'x0' MFggplot: no visible binding for global variable 'x1' MFggplot: no visible binding for global variable 'R2_C' MFggplot: no visible binding for global variable 'R2_M' MFggplot: no visible binding for global variable 'R2_type' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'Order.q' MFggplot : multiple_plots : scale_plot: no visible global function definition for 'lm' MFggplot : multiple_plots : scale_plot: no visible binding for global variable '.' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'r.squared' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'p.value' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'term' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'std.error' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'statistic' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'Species.diversity' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'Significance' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'group' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'estimate' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'Label' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'h' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'v' MFggplot : multiple_plots : scale_plot: no visible binding for global variable '(Intercept)' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'Intercept' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'Slope' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'x0' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'x1' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'R2_C' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'R2_M' MFggplot : multiple_plots : scale_plot: no visible binding for global variable 'R2_type' MFggplot : multiple_plots: no visible binding for global variable 'Order.q' MFggplot : : no visible binding for global variable 'Type' function_normalization: no visible binding for global variable '.' function_normalization : : no visible binding for global variable '.' Undefined global functions or variables: (Intercept) . Intercept L_a L_b L_g Label MF_a MF_b MF_g Order.q R2_C R2_M R2_type R_a R_b R_g Significance Slope Species.diversity Species_Alpha Species_Beta Species_Gamma Tau Type abundance coef combn corr_corrected_Beta corr_corrected_Gamma estimate group h lm model.matrix p.value plotID r.squared species statistic std.error term v var x0 x1 x2 Consider adding importFrom("stats", "coef", "lm", "model.matrix", "var") importFrom("utils", "combn") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) function_normalization.Rd:32: Lost braces; missing escapes or markup? 32 | e.g., 10^{(-5)}. In a similar manner, for negative functionality, if the highest raw value is not 0, the transformed 0 will also be replaced by a very small number, e.g., 10^{(-5)}. | ^ checkRd: (-1) function_normalization.Rd:32: Lost braces; missing escapes or markup? 32 | e.g., 10^{(-5)}. In a similar manner, for negative functionality, if the highest raw value is not 0, the transformed 0 will also be replaced by a very small number, e.g., 10^{(-5)}. | ^ * 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 ... [77s] NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed MFggplot 39.62 1.53 41.16 MF2_multiple 29.67 0.99 30.65 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [424s] OK * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs