* using log directory ‘/srv/hornik/tmp/CRAN/LipidomicsR.Rcheck’ * using R Under development (unstable) (2024-03-09 r86073) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * 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 ... [3s/3s] WARNING Maintainer: ‘Zhu, Hengyu ’ The display-name part of the maintainer field should be enclosed in "" New submission Possibly misspelled words in DESCRIPTION: LipidomicsR (9:15) cahnnels (13:115) lipidomic (15:110, 17:58) lipidomics (3:58, 9:59) unsaturation (11:102) The Title field should be in title case. Current version is: ‘Elegant tools for processing and visualization of lipidomics data’ In title case that is: ‘Elegant Tools for Processing and Visualization of Lipidomics Data’ 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘LipidomicsR’ can be installed ... [5s/5s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT Maintainer field differs from that derived from Authors@R Maintainer: ‘Zhu, Hengyu ’ 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘cowplot’ ‘fmsb’ ‘ggplotify’ ‘pheatmap’ ‘scales’ ‘stringr’ 'library' or 'require' calls not declared from: ‘RColorBrewer’ ‘ggiraph’ 'library' or 'require' call to ‘tidyverse’ which was already attached by Depends. Please remove these calls from your code. 'library' or 'require' calls in package code: ‘RColorBrewer’ ‘ggiraph’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. 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 ... [5s/5s] NOTE FC_P: no visible global function definition for ‘t.test’ FC_P: no visible global function definition for ‘p.adjust’ QCplot: no visible binding for global variable ‘brewer.pal.info’ 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 ‘brewer.pal’ 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 : .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 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 global function definition for ‘fix’ paramWizard: no visible binding for global variable ‘V2’ paramWizard: no visible global function definition for ‘menu’ 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 binding for global variable ‘brewer.pal.info’ 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’ two_way_test: no visible global function definition for ‘shapiro.test’ two_way_test: no visible global function definition for ‘leveneTest’ two_way_test: no visible binding for global variable ‘median’ two_way_test: no visible global function definition for ‘scheirerRayHare’ 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 brewer.pal brewer.pal.info 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 opts_hover opts_hover_inv p.adjust p_to_stars 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. Found the following calls to attach(): File ‘LipidomicsR/R/data_cleaner.R’: attach(input_data) See section ‘Good practice’ in ‘?attach’. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'QCplot.Rd': \examples lines wider than 100 characters: QCplot(data,"all",group,qcdt,box.sample.name=c("wt_1","wt_2","wt_3","wt_4","ko_1","ko_2","ko_3","ko_4"), errorbar.lty="solid",heat.sample.name=c("wt_1","wt_2","wt_3","wt_4","ko_1","ko_2","ko_3","ko_4"), heat.col="Oranges",group.show=FALSE, range.show=TRUE,range.alpha=0.4,shape=FALSE,point.size=2,marked=FALSE,combine=TRUE, 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 ... WARNING Functions or methods with usage in Rd file 'noridx.output.Rd' but not in code: ‘nordix’ Functions or methods with usage in Rd file 'normalization.calculator.Rd' but not in code: ‘normalization_calculator’ Codoc mismatches from Rd file 'cleanXpert.Rd': cleanXpert Code: function(parameter_input_external = F, parameter.path = "parameters.txt", dir = NULL) Docs: function(parameter_input_external = F, data.path = "parameters.txt", dir = NULL) Argument names in code not in docs: parameter.path Argument names in docs not in code: data.path Mismatches in argument names: Position: 2 Code: parameter.path Docs: data.path * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'abundance.lineplot.Rd' ‘data’ Documented arguments not in \usage in Rd file 'abundance.lineplot.Rd': ‘data.summary’ ‘errorbar.type’ Undocumented arguments in Rd file 'cleanXpert.Rd' ‘data.path’ Documented arguments not in \usage in Rd file 'cleanXpert.Rd': ‘parameter.path’ Undocumented arguments in Rd file 'importer.Rd' ‘header’ ‘sep’ Undocumented arguments in Rd file 'nor.relative.Rd' ‘qc’ Objects in \usage without \alias in Rd file 'noridx.output.Rd': ‘nordix’ Objects in \usage without \alias in Rd file 'normalization.calculator.Rd': ‘normalization_calculator’ Undocumented arguments in Rd file 'volcano.Rd' ‘interact’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... [1s/1s] ERROR Running examples in ‘LipidomicsR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: QCplot > ### Title: QCplot() > ### Aliases: QCplot > > ### ** Examples > > WT_1=rnorm(n=5,mean=0.2,sd=0.1) > WT_2=rnorm(n=5,mean=0.2,sd=0.1) > WT_3=rnorm(n=5,mean=0.2,sd=0.1) > WT_4=rnorm(n=5,mean=0.2,sd=0.1) > KO_1=rnorm(n=5,mean=0.8,sd=0.1) > KO_2=rnorm(n=5,mean=0.8,sd=0.1) > KO_3=rnorm(n=5,mean=0.8,sd=0.1) > KO_4=rnorm(n=5,mean=0.8,sd=0.1) > data=data.frame(WT_1,WT_2,WT_3,WT_4,KO_1,KO_2,KO_3,KO_4) > rownames(data)=c("LPC(16:0)","PC(14:0/16:1)","PC(18:1/18:1)","PE(18:0/20:1)","PS(20:1/20:1)") > group=rep(c("WT","KO"),each=4) > ptype="all" > wt_1=rnorm(n=5,mean=0.5,sd=0.1) > wt_2=rnorm(n=5,mean=0.5,sd=0.1) > wt_3=rnorm(n=5,mean=0.5,sd=0.1) > wt_4=rnorm(n=5,mean=0.5,sd=0.1) > ko_1=rnorm(n=5,mean=0.5,sd=0.1) > ko_2=rnorm(n=5,mean=0.5,sd=0.1) > ko_3=rnorm(n=5,mean=0.5,sd=0.1) > ko_4=rnorm(n=5,mean=0.5,sd=0.1) > qcdt=data.frame(wt_1,wt_2,wt_3,wt_4,ko_1,ko_2,ko_3,ko_4) > rownames(qcdt)=c("inter_label 1","inter_label 2","inter_label 3","inter_label 4","inter_label 5") > QCplot(data,"all",group,qcdt,box.sample.name=c("wt_1","wt_2","wt_3","wt_4","ko_1","ko_2","ko_3","ko_4"), + errorbar.lty="solid",heat.sample.name=c("wt_1","wt_2","wt_3","wt_4","ko_1","ko_2","ko_3","ko_4"), + heat.col="Oranges",group.show=FALSE, range.show=TRUE,range.alpha=0.4,shape=FALSE,point.size=2,marked=FALSE,combine=TRUE, + title.hjust=0,title.vjust=0.5,title.size=15,a.title.size=13,a.text.size=11, + a.text.angle=30) Error in loadNamespace(x) : there is no package called ‘ggplotify’ Calls: QCplot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 4 WARNINGs, 3 NOTEs