* using log directory 'd:/RCompile/CRANincoming/R-devel/LipidomicsR.Rcheck' * using R Under development (unstable) (2024-03-08 r86072 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 'LipidomicsR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'LipidomicsR' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Hengyu Zhu ' New submission Possibly misspelled words in DESCRIPTION: Lipidomics (3:58) PCA (19:123) boxplot (19:140) cahnnels (13:114) heatmap (19:114, 20:48) lipidomic (15:109, 17:57) lipidomics (9:58) unsaturation (11:101) The Description field should not start with the package name, 'This package' or similar. * 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 serialization versions ... OK * checking whether package 'LipidomicsR' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Maintainer field differs from that derived from Authors@R Maintainer: 'Hengyu Zhu ' Authors@R: 'Mingshi Li ' * 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 ... NOTE Package in Depends field not imported from: 'tidyverse' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE FC_P: no visible global function definition for 't.test' FC_P: no visible global function definition for 'p.adjust' QCplot: no visible global function definition for '%>%' QCplot: no visible global function definition for 'pivot_longer' QCplot: no visible global function definition for 'everything' QCplot: no visible global function definition for 'aes' QCplot: no visible binding for global variable 'name' QCplot: no visible binding for global variable 'value' QCplot: no visible binding for global variable 'color' QCplot: no visible global function definition for 'geom_boxplot' QCplot: no visible global function definition for 'stat_boxplot' QCplot: no visible binding for global variable '..lower..' QCplot: no visible binding for global variable '..upper..' QCplot: no visible binding for global variable '..ymax..' QCplot: no visible binding for global variable '..ymin..' QCplot: no visible global function definition for 'theme_classic' QCplot: no visible global function definition for 'theme' QCplot: no visible global function definition for 'element_text' QCplot: no visible global function definition for 'dist' QCplot: no visible global function definition for 'colorRampPalette' QCplot: no visible global function definition for 'prcomp' QCplot: no visible binding for global variable 'PC1' QCplot: no visible binding for global variable 'PC2' QCplot: no visible global function definition for 'stat_ellipse' QCplot: no visible global function definition for 'guides' QCplot: no visible global function definition for 'scale_colour_manual' QCplot: no visible global function definition for 'scale_shape_manual' QCplot: no visible global function definition for 'geom_point_interactive' QCplot: no visible global function definition for 'girafe' QCplot: no visible global function definition for 'opts_hover_inv' QCplot: no visible global function definition for 'opts_hover' abundance.lineplot : two_way_test: no visible global function definition for 'shapiro.test' abundance.lineplot : two_way_test: no visible global function definition for 'leveneTest' abundance.lineplot : two_way_test: no visible binding for global variable 'median' abundance.lineplot : two_way_test: no visible global function definition for 'scheirerRayHare' abundance.lineplot : .summary: no visible global function definition for 'median' abundance.lineplot : .error: no visible global function definition for 'sd' abundance.lineplot: no visible global function definition for 'right_join' abundance.lineplot: no visible global function definition for '%>%' abundance.lineplot: no visible binding for global variable 'species' abundance.lineplot: no visible global function definition for 'p_to_stars' abundance.lineplot: no visible global function definition for 'aes' abundance.lineplot: no visible binding for global variable 'variable.2' abundance.lineplot: no visible binding for global variable 'variable.1' abundance.lineplot: no visible global function definition for 'position_dodge' abundance.lineplot: no visible global function definition for 'xlab' abundance.lineplot: no visible global function definition for 'ylab' abundance.lineplot: no visible global function definition for 'ylim' abundance.lineplot: no visible global function definition for 'theme' abundance.lineplot: no visible global function definition for 'element_text' abundance.lineplot: no visible global function definition for 'element_line' abundance.lineplot: no visible global function definition for 'unit' abundance.lineplot: no visible global function definition for 'element_blank' abundance.lineplot: no visible global function definition for 'annotate' abundance.plot: no visible global function definition for 'right_join' abundance.plot: no visible global function definition for '%>%' abundance.plot: no visible binding for global variable 'species' abundance.plot: no visible global function definition for 'aes' abundance.plot: no visible binding for global variable 'variable.1' abundance.plot: no visible binding for global variable 'variable.2' abundance.plot: no visible global function definition for 'position_dodge' abundance.plot: no visible binding for global variable 'error' abundance.plot: no visible global function definition for 'xlab' abundance.plot: no visible global function definition for 'ylab' abundance.plot: no visible global function definition for 'theme' abundance.plot: no visible global function definition for 'element_text' abundance.plot: no visible global function definition for 'element_line' abundance.plot: no visible global function definition for 'unit' abundance.plot: no visible global function definition for 'element_blank' abundance.signif: no visible global function definition for 'right_join' abundance.signif: no visible global function definition for '%>%' abundance.signif: no visible binding for global variable 'species' abundance.signif: no visible global function definition for 'tidy' abundance.summary : : no visible global function definition for 'sd' abundance.summary: no visible global function definition for '%>%' abundance.summary: no visible binding for global variable 'species' abundance.summary: no visible binding for global variable 'lipid_type' abundance.summary: no visible binding for global variable 'carbon_number' abundance.summary: no visible binding for global variable 'unsaturation' abundance.summary: no visible binding for global variable 'abundance' channel.delete: no visible global function definition for 'na.omit' channel.delete: no visible binding for global variable 'Sample.NAme' cleanXpert: no visible global function definition for 'menu' cleanXpert: no visible binding for global variable 'parameter.path' cleanXpert: no visible global function definition for 'normalization.calculator' cleanXpert: no visible global function definition for 'write.csv' delRep: no visible global function definition for 'combn' delRep : : : no visible global function definition for 'sd' heatmap: no visible global function definition for 'colorRampPalette' heatmap: no visible global function definition for '%>%' importer: no visible global function definition for 'read.csv' paramWizard: no visible global function definition for 'read.table' paramWizard: no visible binding for global variable 'V2' paramWizard: no visible global function definition for 'menu' paramWizard: no visible global function definition for 'fix' percent.calculator: no visible global function definition for 'na.omit' plotRadar : pat: no visible global function definition for '%>%' plotRadar : pat: no visible global function definition for 'pivot_longer' plotRadar : pat: no visible binding for global variable 'lipid_type' plotRadar : pat: no visible global function definition for 'median' plotRadar : pat: no visible binding for global variable 'value' plotRadar : pat: no visible global function definition for 'pdf' plotRadar : pat: no visible global function definition for 'legend' plotRadar : pat: no visible global function definition for 'title' plotRadar : pat: no visible global function definition for 'dev.off' plotRadar : pat: no visible binding for global variable 'carbon_number' plotRadar : pat: no visible binding for global variable 'unsaturation' replicate.delete: no visible global function definition for 'na.omit' replicate.delete: no visible binding for global variable 'Sample.NAme' volcano: no visible global function definition for '%>%' volcano: no visible binding for global variable 'Log2FC' volcano: no visible binding for global variable '-log10Pvalue' volcano: no visible global function definition for 'aes' volcano: no visible binding for global variable 'Change' volcano: no visible global function definition for 'xlab' volcano: no visible global function definition for 'ylab' volcano: no visible global function definition for 'scale_color_manual' volcano: no visible global function definition for 'theme' volcano: no visible global function definition for 'element_line' volcano: no visible global function definition for 'element_rect' volcano: no visible global function definition for 'element_blank' volcano: no visible global function definition for 'geom_point_interactive' volcano: no visible global function definition for 'girafe' volcano: no visible global function definition for 'opts_hover_inv' volcano: no visible global function definition for 'opts_hover' Undefined global functions or variables: %>% -log10Pvalue ..lower.. ..upper.. ..ymax.. ..ymin.. Change Log2FC PC1 PC2 Sample.NAme V2 abundance aes annotate carbon_number color colorRampPalette combn dev.off dist element_blank element_line element_rect element_text error everything fix geom_boxplot geom_point_interactive girafe guides legend leveneTest lipid_type median menu na.omit name normalization.calculator opts_hover opts_hover_inv p.adjust p_to_stars parameter.path pdf pivot_longer position_dodge prcomp read.csv read.table right_join scale_color_manual scale_colour_manual scale_shape_manual scheirerRayHare sd shapiro.test species stat_boxplot stat_ellipse t.test theme theme_classic tidy title unit unsaturation value variable.1 variable.2 write.csv xlab ylab ylim Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "pdf") importFrom("graphics", "legend", "title") importFrom("stats", "dist", "median", "na.omit", "p.adjust", "prcomp", "sd", "shapiro.test", "t.test") importFrom("utils", "combn", "fix", "menu", "read.csv", "read.table", "write.csv") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'normalization_calculator.Rd': \usage lines wider than 90 characters: normalization_calculator(data, normalization.mode=c('relative','absolute','percent'), normalization.index, qc=1:5) These lines will be truncated in the PDF manual. * 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 examples ... OK * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 5 NOTEs